class BioInterchange::SO

Public Class Methods

AACCCT_box() click to toggle source

A conserved 17-bp sequence (5’-ATCA(C/A)AACCCTAACCCT-3’) commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site. (purl.obolibrary.org/obo/SO_0001901)

# File lib/biointerchange/so.rb, line 11611
def self.AACCCT_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001901')
end
AFLP_fragment() click to toggle source

A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments. (purl.obolibrary.org/obo/SO_0001830)

# File lib/biointerchange/so.rb, line 11185
def self.AFLP_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001830')
end
AP_1_binding_site() click to toggle source

A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors. (purl.obolibrary.org/obo/SO_0001842)

# File lib/biointerchange/so.rb, line 11257
def self.AP_1_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001842')
end
ARIA() click to toggle source

A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts consist of C rich repeats. (purl.obolibrary.org/obo/SO_0001925)

# File lib/biointerchange/so.rb, line 11755
def self.ARIA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001925')
end
ARRET() click to toggle source

A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats. (purl.obolibrary.org/obo/SO_0001924)

# File lib/biointerchange/so.rb, line 11749
def self.ARRET
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001924')
end
ARS() click to toggle source

A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host. (purl.obolibrary.org/obo/SO_0000436)

# File lib/biointerchange/so.rb, line 2931
def self.ARS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000436')
end
ARS_consensus_sequence() click to toggle source

The ACS is an 11-bp sequence of the form 5’-WTTTAYRTTTW-3’ which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5’ (C domain) and 3’ (B domain) flanking sequences of the ACS. (purl.obolibrary.org/obo/SO_0002004)

# File lib/biointerchange/so.rb, line 12227
def self.ARS_consensus_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002004')
end
ASPE_primer() click to toggle source

"A primer containing an SNV at the 3’ end for accurate genotyping. (www.ncbi.nlm.nih.gov/pubmed/11252801) (purl.obolibrary.org/obo/SO_0001698)

# File lib/biointerchange/so.rb, line 10399
def self.ASPE_primer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001698')
end
AU_rich_element() click to toggle source

A cis-acting element found in the 3’ UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable. (purl.obolibrary.org/obo/SO_0001180)

# File lib/biointerchange/so.rb, line 7351
def self.AU_rich_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001180')
end
A_box() click to toggle source

A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG. (purl.obolibrary.org/obo/SO_0000619)

# File lib/biointerchange/so.rb, line 4037
def self.A_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000619')
end
A_box_type_1() click to toggle source

An A box within an RNA polymerase III type 1 promoter. (purl.obolibrary.org/obo/SO_0001675)

# File lib/biointerchange/so.rb, line 10261
def self.A_box_type_1
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001675')
end
A_box_type_2() click to toggle source

An A box within an RNA polymerase III type 2 promoter. (purl.obolibrary.org/obo/SO_0001676)

# File lib/biointerchange/so.rb, line 10267
def self.A_box_type_2
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001676')
end
A_minor_RNA_motif() click to toggle source

A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix. (purl.obolibrary.org/obo/SO_0000022)

# File lib/biointerchange/so.rb, line 441
def self.A_minor_RNA_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000022')
end
A_to_C_transversion() click to toggle source

A transversion from adenine to cytidine. (purl.obolibrary.org/obo/SO_1000024)

# File lib/biointerchange/so.rb, line 12587
def self.A_to_C_transversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000024')
end
A_to_G_transition() click to toggle source

A transition of an adenine to a guanine. (purl.obolibrary.org/obo/SO_1000015)

# File lib/biointerchange/so.rb, line 12533
def self.A_to_G_transition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000015')
end
A_to_T_transversion() click to toggle source

A transversion from adenine to thymine. (purl.obolibrary.org/obo/SO_1000025)

# File lib/biointerchange/so.rb, line 12593
def self.A_to_T_transversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000025')
end
Ace2_UAS() click to toggle source

A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2. (purl.obolibrary.org/obo/SO_0001857)

# File lib/biointerchange/so.rb, line 11347
def self.Ace2_UAS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001857')
end
BAC() click to toggle source

Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host. (purl.obolibrary.org/obo/SO_0000153)

# File lib/biointerchange/so.rb, line 1235
def self.BAC
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000153')
end
BAC_clone() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000764)

# File lib/biointerchange/so.rb, line 4907
def self.BAC_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000764')
end
BAC_cloned_genomic_insert() click to toggle source

Requested by Andy Schroder - Flybase Harvard, Nov 2006. (purl.obolibrary.org/obo/SO_0000992)

# File lib/biointerchange/so.rb, line 6227
def self.BAC_cloned_genomic_insert
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000992')
end
BAC_end() click to toggle source

A region of sequence from the end of a BAC clone that may provide a highly specific marker. (purl.obolibrary.org/obo/SO_0000999)

# File lib/biointerchange/so.rb, line 6269
def self.BAC_end
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000999')
end
BAC_read_contig() click to toggle source

A contig of BAC reads. (purl.obolibrary.org/obo/SO_0001866)

# File lib/biointerchange/so.rb, line 11401
def self.BAC_read_contig
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001866')
end
BREd_motif() click to toggle source

A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G). (purl.obolibrary.org/obo/SO_0001663)

# File lib/biointerchange/so.rb, line 10189
def self.BREd_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001663')
end
BREu_motif() click to toggle source

A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB. (purl.obolibrary.org/obo/SO_0000016)

# File lib/biointerchange/so.rb, line 411
def self.BREu_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000016')
end
B_box() click to toggle source

A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC. (purl.obolibrary.org/obo/SO_0000620)

# File lib/biointerchange/so.rb, line 4043
def self.B_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000620')
end
Bruno_response_element() click to toggle source

A cis-acting element found in the 3’ UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs. (purl.obolibrary.org/obo/SO_0001181)

# File lib/biointerchange/so.rb, line 7357
def self.Bruno_response_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001181')
end
CAAT_signal() click to toggle source

Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT. (purl.obolibrary.org/obo/SO_0000172)

# File lib/biointerchange/so.rb, line 1349
def self.CAAT_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000172')
end
CAGE_cluster() click to toggle source

A kind of transcription_initiation_cluster defined by the clustering of CAGE tags on a sequence region. (purl.obolibrary.org/obo/SO_0001917)

# File lib/biointerchange/so.rb, line 11707
def self.CAGE_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001917')
end
CAGE_tag() click to toggle source

A CAGE tag is a sequence tag hat corresponds to 5’ ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites. (purl.obolibrary.org/obo/SO_0001916)

# File lib/biointerchange/so.rb, line 11701
def self.CAGE_tag
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001916')
end
CCAAT_motif() click to toggle source

A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels. (purl.obolibrary.org/obo/SO_0001856)

# File lib/biointerchange/so.rb, line 11341
def self.CCAAT_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001856')
end
CCA_tail() click to toggle source

Base sequence at the 3’ end of a tRNA. The 3’-hydroxyl group on the terminal adenosine is the attachment point for the amino acid. (purl.obolibrary.org/obo/SO_0001175)

# File lib/biointerchange/so.rb, line 7321
def self.CCA_tail
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001175')
end
CDRE_motif() click to toggle source

An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA. (purl.obolibrary.org/obo/SO_0001865)

# File lib/biointerchange/so.rb, line 11395
def self.CDRE_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001865')
end
CDS() click to toggle source

A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon. (purl.obolibrary.org/obo/SO_0000316)

# File lib/biointerchange/so.rb, line 2217
def self.CDS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000316')
end
CDS_fragment() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001384)

# File lib/biointerchange/so.rb, line 8569
def self.CDS_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001384')
end
CDS_independently_known() click to toggle source

A CDS with the evidence status of being independently known. (purl.obolibrary.org/obo/SO_1001246)

# File lib/biointerchange/so.rb, line 13463
def self.CDS_independently_known
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001246')
end
CDS_predicted() click to toggle source

A CDS that is predicted. (purl.obolibrary.org/obo/SO_1001254)

# File lib/biointerchange/so.rb, line 13487
def self.CDS_predicted
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001254')
end
CDS_region() click to toggle source

A region of a CDS. (purl.obolibrary.org/obo/SO_0000851)

# File lib/biointerchange/so.rb, line 5387
def self.CDS_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000851')
end
CDS_supported_by_EST_or_cDNA_data() click to toggle source

A CDS that is supported by similarity to EST or cDNA data. (purl.obolibrary.org/obo/SO_1001259)

# File lib/biointerchange/so.rb, line 13499
def self.CDS_supported_by_EST_or_cDNA_data
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001259')
end
CDS_supported_by_domain_match_data() click to toggle source

A CDS that is supported by domain similarity. (purl.obolibrary.org/obo/SO_1001249)

# File lib/biointerchange/so.rb, line 13475
def self.CDS_supported_by_domain_match_data
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001249')
end
CDS_supported_by_sequence_similarity_data() click to toggle source

A CDS that is supported by sequence similarity data. (purl.obolibrary.org/obo/SO_1001251)

# File lib/biointerchange/so.rb, line 13481
def self.CDS_supported_by_sequence_similarity_data
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001251')
end
CRE() click to toggle source

A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors. (purl.obolibrary.org/obo/SO_0001843)

# File lib/biointerchange/so.rb, line 11263
def self.CRE
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001843')
end
CRISPR() click to toggle source

Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences. (purl.obolibrary.org/obo/SO_0001459)

# File lib/biointerchange/so.rb, line 9013
def self.CRISPR
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001459')
end
CRM() click to toggle source

A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3’UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. (purl.obolibrary.org/obo/SO_0000727)

# File lib/biointerchange/so.rb, line 4685
def self.CRM
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000727')
end
CSL_response_element() click to toggle source

A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors. (purl.obolibrary.org/obo/SO_0001839)

# File lib/biointerchange/so.rb, line 11239
def self.CSL_response_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001839')
end
CTCF_binding_site() click to toggle source

A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor. (purl.obolibrary.org/obo/SO_0001974)

# File lib/biointerchange/so.rb, line 12053
def self.CTCF_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001974')
end
CTG_start_codon() click to toggle source

A non-canonical start codon of sequence CTG. (purl.obolibrary.org/obo/SO_1001273)

# File lib/biointerchange/so.rb, line 13583
def self.CTG_start_codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001273')
end
C_D_box_snoRNA() click to toggle source

Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C’ and D’, are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D’. (purl.obolibrary.org/obo/SO_0000593)

# File lib/biointerchange/so.rb, line 3881
def self.C_D_box_snoRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000593')
end
C_D_box_snoRNA_encoding() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000585)

# File lib/biointerchange/so.rb, line 3833
def self.C_D_box_snoRNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000585')
end
C_D_box_snoRNA_primary_transcript() click to toggle source

A primary transcript encoding a small nucleolar RNA of the box C/D family. (purl.obolibrary.org/obo/SO_0000595)

# File lib/biointerchange/so.rb, line 3893
def self.C_D_box_snoRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000595')
end
C_box() click to toggle source

An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn. (purl.obolibrary.org/obo/SO_0000622)

# File lib/biointerchange/so.rb, line 4055
def self.C_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000622')
end
C_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene. (purl.obolibrary.org/obo/SO_0000558)

# File lib/biointerchange/so.rb, line 3671
def self.C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000558')
end
C_gene_segment() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5’ UTR (SO:0000204) and 3’ UTR (SO:0000205). (purl.obolibrary.org/obo/SO_0000478)

# File lib/biointerchange/so.rb, line 3187
def self.C_gene_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000478')
end
C_region() click to toggle source

The constant region of an immunoglobulin polypeptide sequence. (purl.obolibrary.org/obo/SO_0001834)

# File lib/biointerchange/so.rb, line 11209
def self.C_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001834')
end
C_to_A_transversion() click to toggle source

A transversion from cytidine to adenine. (purl.obolibrary.org/obo/SO_1000019)

# File lib/biointerchange/so.rb, line 12557
def self.C_to_A_transversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000019')
end
C_to_G_transversion() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_1000020)

# File lib/biointerchange/so.rb, line 12563
def self.C_to_G_transversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000020')
end
C_to_T_transition() click to toggle source

A transition of a cytidine to a thymine. (purl.obolibrary.org/obo/SO_1000011)

# File lib/biointerchange/so.rb, line 12509
def self.C_to_T_transition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000011')
end
C_to_T_transition_at_pCpG_site() click to toggle source

The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5’-methylcytidine. (purl.obolibrary.org/obo/SO_1000012)

# File lib/biointerchange/so.rb, line 12515
def self.C_to_T_transition_at_pCpG_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000012')
end
ChIP_seq_region() click to toggle source

A region of sequence identified by CHiP seq technology to contain a protein binding site. (purl.obolibrary.org/obo/SO_0001697)

# File lib/biointerchange/so.rb, line 10393
def self.ChIP_seq_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001697')
end
CpG_island() click to toggle source

Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5’ ends of genes. (purl.obolibrary.org/obo/SO_0000307)

# File lib/biointerchange/so.rb, line 2163
def self.CpG_island
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000307')
end
CsrB_RsmB_RNA() click to toggle source

An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family. (purl.obolibrary.org/obo/SO_0000377)

# File lib/biointerchange/so.rb, line 2577
def self.CsrB_RsmB_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000377')
end
CuRE() click to toggle source

A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast). (purl.obolibrary.org/obo/SO_0001844)

# File lib/biointerchange/so.rb, line 11269
def self.CuRE
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001844')
end
DArT_marker() click to toggle source

A genetic marker, discovered using Diversity Arrays Technology (DArT) technology. (purl.obolibrary.org/obo/SO_0001646)

# File lib/biointerchange/so.rb, line 10111
def self.DArT_marker
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001646')
end
DCE() click to toggle source

A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII. (purl.obolibrary.org/obo/SO_0001664)

# File lib/biointerchange/so.rb, line 10195
def self.DCE
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001664')
end
DCE_SI() click to toggle source

A sub element of the DCE core promoter element, with consensus sequence CTTC. (purl.obolibrary.org/obo/SO_0001665)

# File lib/biointerchange/so.rb, line 10201
def self.DCE_SI
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001665')
end
DCE_SII() click to toggle source

A sub element of the DCE core promoter element with consensus sequence CTGT. (purl.obolibrary.org/obo/SO_0001666)

# File lib/biointerchange/so.rb, line 10207
def self.DCE_SII
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001666')
end
DCE_SIII() click to toggle source

A sub element of the DCE core promoter element with consensus sequence AGC. (purl.obolibrary.org/obo/SO_0001667)

# File lib/biointerchange/so.rb, line 10213
def self.DCE_SIII
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001667')
end
DDB_box() click to toggle source

A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases. (purl.obolibrary.org/obo/SO_0001804)

# File lib/biointerchange/so.rb, line 11029
def self.DDB_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001804')
end
DHU_loop() click to toggle source

Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues. (purl.obolibrary.org/obo/SO_0001176)

# File lib/biointerchange/so.rb, line 7327
def self.DHU_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001176')
end
DJ_C_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene. (purl.obolibrary.org/obo/SO_0000539)

# File lib/biointerchange/so.rb, line 3553
def self.DJ_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000539')
end
DJ_J_C_cluster() click to toggle source

Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE. (purl.obolibrary.org/obo/SO_0000540)

# File lib/biointerchange/so.rb, line 3559
def self.DJ_J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000540')
end
DJ_J_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene. (purl.obolibrary.org/obo/SO_0000485)

# File lib/biointerchange/so.rb, line 3229
def self.DJ_J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000485')
end
DJ_gene_segment() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5’ UTR and 3’ UTR, also designated as D-J-segment. (purl.obolibrary.org/obo/SO_0000572)

# File lib/biointerchange/so.rb, line 3755
def self.DJ_gene_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000572')
end
DMv1_motif() click to toggle source

A promoter motif with consensus sequence CARCCCT. (purl.obolibrary.org/obo/SO_0001165)

# File lib/biointerchange/so.rb, line 7261
def self.DMv1_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001165')
end
DMv2_motif() click to toggle source

A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162). (purl.obolibrary.org/obo/SO_0001161)

# File lib/biointerchange/so.rb, line 7237
def self.DMv2_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001161')
end
DMv3_motif() click to toggle source

A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162). (purl.obolibrary.org/obo/SO_0001160)

# File lib/biointerchange/so.rb, line 7231
def self.DMv3_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001160')
end
DMv4_motif() click to toggle source

A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014). (purl.obolibrary.org/obo/SO_0001157)

# File lib/biointerchange/so.rb, line 7213
def self.DMv4_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001157')
end
DMv5_motif() click to toggle source

A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162). (purl.obolibrary.org/obo/SO_0001159)

# File lib/biointerchange/so.rb, line 7225
def self.DMv5_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001159')
end
DNA() click to toggle source

An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone. (purl.obolibrary.org/obo/SO_0000352)

# File lib/biointerchange/so.rb, line 2433
def self.DNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000352')
end
DNA_aptamer() click to toggle source

DNA molecules that have been selected from random pools based on their ability to bind other molecules. (purl.obolibrary.org/obo/SO_0000032)

# File lib/biointerchange/so.rb, line 501
def self.DNA_aptamer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000032')
end
DNA_binding_site() click to toggle source

A binding site that, in the molecule, interacts selectively and non-covalently with DNA. (purl.obolibrary.org/obo/SO_0001429)

# File lib/biointerchange/so.rb, line 8839
def self.DNA_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001429')
end
DNA_chromosome() click to toggle source

Structural unit composed of a self-replicating, DNA molecule. (purl.obolibrary.org/obo/SO_0000954)

# File lib/biointerchange/so.rb, line 6005
def self.DNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000954')
end
DNA_constraint_sequence() click to toggle source

A double-stranded DNA used to control macromolecular structure and function. (www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au]&dispmax=50) (purl.obolibrary.org/obo/SO_0001009)

# File lib/biointerchange/so.rb, line 6329
def self.DNA_constraint_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001009')
end
DNA_invertase_target_sequence() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000660)

# File lib/biointerchange/so.rb, line 4283
def self.DNA_invertase_target_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000660')
end
DNA_motif() click to toggle source

A motif that is active in the DNA form of the sequence. (purl.obolibrary.org/obo/SO_0000713)

# File lib/biointerchange/so.rb, line 4601
def self.DNA_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000713')
end
DNA_replication_mode() click to toggle source

This has been obsoleted as it represents a process. replaced_by: GO:0006260. (purl.obolibrary.org/obo/SO_0000971)

# File lib/biointerchange/so.rb, line 6107
def self.DNA_replication_mode
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000971')
end
DNA_sequence_secondary_structure() click to toggle source

A folded DNA sequence. (purl.obolibrary.org/obo/SO_0000142)

# File lib/biointerchange/so.rb, line 1169
def self.DNA_sequence_secondary_structure
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000142')
end
DNA_transposon() click to toggle source

A transposon where the mechanism of transposition is via a DNA intermediate. (purl.obolibrary.org/obo/SO_0000182)

# File lib/biointerchange/so.rb, line 1413
def self.DNA_transposon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000182')
end
DNAseI_hypersensitive_site() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000685)

# File lib/biointerchange/so.rb, line 4433
def self.DNAseI_hypersensitive_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000685')
end
DNAzyme() click to toggle source

A DNA sequence with catalytic activity. (purl.obolibrary.org/obo/SO_0001012)

# File lib/biointerchange/so.rb, line 6347
def self.DNAzyme
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001012')
end
DPE1_motif() click to toggle source

A promoter motif with consensus sequence CGGACGT. (purl.obolibrary.org/obo/SO_0001164)

# File lib/biointerchange/so.rb, line 7255
def self.DPE1_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001164')
end
DPE_motif() click to toggle source

A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C). (purl.obolibrary.org/obo/SO_0000015)

# File lib/biointerchange/so.rb, line 405
def self.DPE_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000015')
end
DRE() click to toggle source

A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis. (purl.obolibrary.org/obo/SO_0001845)

# File lib/biointerchange/so.rb, line 11275
def self.DRE
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001845')
end
DRE_motif() click to toggle source

A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW. (purl.obolibrary.org/obo/SO_0001156)

# File lib/biointerchange/so.rb, line 7207
def self.DRE_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001156')
end
DSR_motif() click to toggle source

The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC. The motif targets meiotic transcripts for removal during mitosis via the exosome. (purl.obolibrary.org/obo/SO_0002005)

# File lib/biointerchange/so.rb, line 12233
def self.DSR_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002005')
end
D_DJ_C_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene. (purl.obolibrary.org/obo/SO_0000504)

# File lib/biointerchange/so.rb, line 3343
def self.D_DJ_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000504')
end
D_DJ_J_C_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene. (purl.obolibrary.org/obo/SO_0000506)

# File lib/biointerchange/so.rb, line 3355
def self.D_DJ_J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000506')
end
D_DJ_J_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene. (purl.obolibrary.org/obo/SO_0000508)

# File lib/biointerchange/so.rb, line 3367
def self.D_DJ_J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000508')
end
D_DJ_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene. (purl.obolibrary.org/obo/SO_0000505)

# File lib/biointerchange/so.rb, line 3349
def self.D_DJ_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000505')
end
D_J_C_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene. (purl.obolibrary.org/obo/SO_0000509)

# File lib/biointerchange/so.rb, line 3373
def self.D_J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000509')
end
D_J_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene. (purl.obolibrary.org/obo/SO_0000560)

# File lib/biointerchange/so.rb, line 3683
def self.D_J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000560')
end
D_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene. (purl.obolibrary.org/obo/SO_0000559)

# File lib/biointerchange/so.rb, line 3677
def self.D_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000559')
end
D_gene_recombination_feature() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000492)

# File lib/biointerchange/so.rb, line 3271
def self.D_gene_recombination_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000492')
end
D_gene_segment() click to toggle source

Germline genomic DNA including D-region with 5’ UTR and 3’ UTR, also designated as D-segment. (purl.obolibrary.org/obo/SO_0000458)

# File lib/biointerchange/so.rb, line 3067
def self.D_gene_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000458')
end
D_loop() click to toggle source

Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein. (purl.obolibrary.org/obo/SO_0000297)

# File lib/biointerchange/so.rb, line 2103
def self.D_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000297')
end
DsrA_RNA() click to toggle source

DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation. (purl.obolibrary.org/obo/SO_0000378)

# File lib/biointerchange/so.rb, line 2583
def self.DsrA_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000378')
end
ER_retention_signal() click to toggle source

A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL. (purl.obolibrary.org/obo/SO_0001806)

# File lib/biointerchange/so.rb, line 11041
def self.ER_retention_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001806')
end
EST() click to toggle source

A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long. (purl.obolibrary.org/obo/SO_0000345)

# File lib/biointerchange/so.rb, line 2391
def self.EST
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000345')
end
EST_match() click to toggle source

A match against an EST sequence. (purl.obolibrary.org/obo/SO_0000668)

# File lib/biointerchange/so.rb, line 4331
def self.EST_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000668')
end
E_box_motif() click to toggle source

A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015). (purl.obolibrary.org/obo/SO_0001158)

# File lib/biointerchange/so.rb, line 7219
def self.E_box_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001158')
end
FLEX_element() click to toggle source

A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain. (purl.obolibrary.org/obo/SO_0001846)

# File lib/biointerchange/so.rb, line 11281
def self.FLEX_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001846')
end
FRT_flanked() click to toggle source

An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT. (purl.obolibrary.org/obo/SO_0000361)

# File lib/biointerchange/so.rb, line 2481
def self.FRT_flanked
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000361')
end
FRT_site() click to toggle source

An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid. (purl.obolibrary.org/obo/SO_0000350)

# File lib/biointerchange/so.rb, line 2421
def self.FRT_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000350')
end
GAGA_motif() click to toggle source

A non directional promoter motif with consensus sequence GAGAGCG. (purl.obolibrary.org/obo/SO_0001166)

# File lib/biointerchange/so.rb, line 7267
def self.GAGA_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001166')
end
GATA_box() click to toggle source

A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G). (purl.obolibrary.org/obo/SO_0001840)

# File lib/biointerchange/so.rb, line 11245
def self.GATA_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001840')
end
GC_rich_promoter_region() click to toggle source

A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG. (purl.obolibrary.org/obo/SO_0000173)

# File lib/biointerchange/so.rb, line 1355
def self.GC_rich_promoter_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000173')
end
GNA() click to toggle source

An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, ®-GNA and (S)-GNA. (purl.obolibrary.org/obo/SO_0001192)

# File lib/biointerchange/so.rb, line 7423
def self.GNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001192')
end
GNA_oligo() click to toggle source

An oligo composed of GNA residues. (purl.obolibrary.org/obo/SO_0001193)

# File lib/biointerchange/so.rb, line 7429
def self.GNA_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001193')
end
GTT_trinucleotide_repeat() click to toggle source

A trinucleotide repeat region composed of GTT repeating elements. (purl.obolibrary.org/obo/SO_0001863)

# File lib/biointerchange/so.rb, line 11383
def self.GTT_trinucleotide_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001863')
end
GT_dinucleotide_repeat() click to toggle source

A dinucleotide repeat region composed of GT repeating elements. (purl.obolibrary.org/obo/SO_0001862)

# File lib/biointerchange/so.rb, line 11377
def self.GT_dinucleotide_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001862')
end
G_box() click to toggle source

A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a. (purl.obolibrary.org/obo/SO_0001980)

# File lib/biointerchange/so.rb, line 12083
def self.G_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001980')
end
G_quartet() click to toggle source

G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet. (purl.obolibrary.org/obo/SO_0000003)

# File lib/biointerchange/so.rb, line 333
def self.G_quartet
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000003')
end
G_to_A_transition() click to toggle source

A transition of a guanine to an adenine. (purl.obolibrary.org/obo/SO_1000016)

# File lib/biointerchange/so.rb, line 12539
def self.G_to_A_transition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000016')
end
G_to_C_transversion() click to toggle source

A transversion from guanine to cytidine. (purl.obolibrary.org/obo/SO_1000026)

# File lib/biointerchange/so.rb, line 12599
def self.G_to_C_transversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000026')
end
G_to_T_transversion() click to toggle source

A transversion from guanine to thymine. (purl.obolibrary.org/obo/SO_1000027)

# File lib/biointerchange/so.rb, line 12605
def self.G_to_T_transversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000027')
end
GcvB_RNA() click to toggle source

A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli. (purl.obolibrary.org/obo/SO_0000379)

# File lib/biointerchange/so.rb, line 2589
def self.GcvB_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000379')
end
H2AK5_acetylation_site() click to toggle source

A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated. (purl.obolibrary.org/obo/SO_0001938)

# File lib/biointerchange/so.rb, line 11833
def self.H2AK5_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001938')
end
H2AK9_acetylation_site() click to toggle source

A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated. (purl.obolibrary.org/obo/SO_0001944)

# File lib/biointerchange/so.rb, line 11869
def self.H2AK9_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001944')
end
H2BK120_acetylation_site() click to toggle source

A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated. (purl.obolibrary.org/obo/SO_0001940)

# File lib/biointerchange/so.rb, line 11845
def self.H2BK120_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001940')
end
H2BK12_acetylation_site() click to toggle source

A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated. (purl.obolibrary.org/obo/SO_0001937)

# File lib/biointerchange/so.rb, line 11827
def self.H2BK12_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001937')
end
H2BK15_acetylation_site() click to toggle source

A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated. (purl.obolibrary.org/obo/SO_0001946)

# File lib/biointerchange/so.rb, line 11881
def self.H2BK15_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001946')
end
H2BK20_acetylation_site() click to toggle source

A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated. (purl.obolibrary.org/obo/SO_0001942)

# File lib/biointerchange/so.rb, line 11857
def self.H2BK20_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001942')
end
H2BK5_monomethylation_site() click to toggle source

A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated. (purl.obolibrary.org/obo/SO_0001714)

# File lib/biointerchange/so.rb, line 10495
def self.H2BK5_monomethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001714')
end
H2B_ubiquitination_site() click to toggle source

A histone modification site on H2B where ubiquitin may be added. (purl.obolibrary.org/obo/SO_0001717)

# File lib/biointerchange/so.rb, line 10513
def self.H2B_ubiquitination_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001717')
end
H3K14_acetylation_site() click to toggle source

A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated. (purl.obolibrary.org/obo/SO_0001704)

# File lib/biointerchange/so.rb, line 10435
def self.H3K14_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001704')
end
H3K18_acetylation_site() click to toggle source

A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated. (purl.obolibrary.org/obo/SO_0001718)

# File lib/biointerchange/so.rb, line 10519
def self.H3K18_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001718')
end
H3K20_trimethylation_site() click to toggle source

A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated. (purl.obolibrary.org/obo/SO_0001935)

# File lib/biointerchange/so.rb, line 11815
def self.H3K20_trimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001935')
end
H3K23_acylation_site() click to toggle source

A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated. (purl.obolibrary.org/obo/SO_0001719)

# File lib/biointerchange/so.rb, line 10525
def self.H3K23_acylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001719')
end
H3K23_dimethylation_site() click to toggle source

A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated. (purl.obolibrary.org/obo/SO_0001951)

# File lib/biointerchange/so.rb, line 11911
def self.H3K23_dimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001951')
end
H3K27_acylation_site() click to toggle source

A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated. (purl.obolibrary.org/obo/SO_0001721)

# File lib/biointerchange/so.rb, line 10537
def self.H3K27_acylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001721')
end
H3K27_dimethylation_site() click to toggle source

A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated. (purl.obolibrary.org/obo/SO_0001726)

# File lib/biointerchange/so.rb, line 10567
def self.H3K27_dimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001726')
end
H3K27_methylation_site() click to toggle source

A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated. (purl.obolibrary.org/obo/SO_0001732)

# File lib/biointerchange/so.rb, line 10603
def self.H3K27_methylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001732')
end
H3K27_monomethylation_site() click to toggle source

A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated. (purl.obolibrary.org/obo/SO_0001708)

# File lib/biointerchange/so.rb, line 10459
def self.H3K27_monomethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001708')
end
H3K27_trimethylation_site() click to toggle source

A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated. (purl.obolibrary.org/obo/SO_0001709)

# File lib/biointerchange/so.rb, line 10465
def self.H3K27_trimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001709')
end
H3K36_acetylation_site() click to toggle source

A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated. (purl.obolibrary.org/obo/SO_0001936)

# File lib/biointerchange/so.rb, line 11821
def self.H3K36_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001936')
end
H3K36_dimethylation_site() click to toggle source

A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated. (purl.obolibrary.org/obo/SO_0001723)

# File lib/biointerchange/so.rb, line 10549
def self.H3K36_dimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001723')
end
H3K36_methylation_site() click to toggle source

A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated. (purl.obolibrary.org/obo/SO_0001733)

# File lib/biointerchange/so.rb, line 10609
def self.H3K36_methylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001733')
end
H3K36_monomethylation_site() click to toggle source

A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated. (purl.obolibrary.org/obo/SO_0001722)

# File lib/biointerchange/so.rb, line 10543
def self.H3K36_monomethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001722')
end
H3K36_trimethylation_site() click to toggle source

A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated. (purl.obolibrary.org/obo/SO_0001724)

# File lib/biointerchange/so.rb, line 10555
def self.H3K36_trimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001724')
end
H3K4_dimethylation_site() click to toggle source

A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated. (purl.obolibrary.org/obo/SO_0001725)

# File lib/biointerchange/so.rb, line 10561
def self.H3K4_dimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001725')
end
H3K4_methylation_site() click to toggle source

A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated. (purl.obolibrary.org/obo/SO_0001734)

# File lib/biointerchange/so.rb, line 10615
def self.H3K4_methylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001734')
end
H3K4_monomethylation_site() click to toggle source

A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated. (purl.obolibrary.org/obo/SO_0001705)

# File lib/biointerchange/so.rb, line 10441
def self.H3K4_monomethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001705')
end
H3K4_trimethylation() click to toggle source

A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated. (purl.obolibrary.org/obo/SO_0001706)

# File lib/biointerchange/so.rb, line 10447
def self.H3K4_trimethylation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001706')
end
H3K4ac_acetylation_site() click to toggle source

A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated. (purl.obolibrary.org/obo/SO_0001943)

# File lib/biointerchange/so.rb, line 11863
def self.H3K4ac_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001943')
end
H3K56_acetylation_site() click to toggle source

A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated. (purl.obolibrary.org/obo/SO_0001945)

# File lib/biointerchange/so.rb, line 11875
def self.H3K56_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001945')
end
H3K79_dimethylation_site() click to toggle source

A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated. (purl.obolibrary.org/obo/SO_0001711)

# File lib/biointerchange/so.rb, line 10477
def self.H3K79_dimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001711')
end
H3K79_methylation_site() click to toggle source

A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated. (purl.obolibrary.org/obo/SO_0001735)

# File lib/biointerchange/so.rb, line 10621
def self.H3K79_methylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001735')
end
H3K79_monomethylation_site() click to toggle source

A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated. (purl.obolibrary.org/obo/SO_0001710)

# File lib/biointerchange/so.rb, line 10471
def self.H3K79_monomethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001710')
end
H3K79_trimethylation_site() click to toggle source

A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated. (purl.obolibrary.org/obo/SO_0001712)

# File lib/biointerchange/so.rb, line 10483
def self.H3K79_trimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001712')
end
H3K9_acetylation_site() click to toggle source

A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated. (purl.obolibrary.org/obo/SO_0001703)

# File lib/biointerchange/so.rb, line 10429
def self.H3K9_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001703')
end
H3K9_dimethylation_site() click to toggle source

A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated. (purl.obolibrary.org/obo/SO_0001728)

# File lib/biointerchange/so.rb, line 10579
def self.H3K9_dimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001728')
end
H3K9_methylation_site() click to toggle source

A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated. (purl.obolibrary.org/obo/SO_0001736)

# File lib/biointerchange/so.rb, line 10627
def self.H3K9_methylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001736')
end
H3K9_monomethylation_site() click to toggle source

A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated. (purl.obolibrary.org/obo/SO_0001727)

# File lib/biointerchange/so.rb, line 10573
def self.H3K9_monomethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001727')
end
H3K9_trimethylation_site() click to toggle source

A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated. (purl.obolibrary.org/obo/SO_0001707)

# File lib/biointerchange/so.rb, line 10453
def self.H3K9_trimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001707')
end
H3R2_dimethylation_site() click to toggle source

A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated. (purl.obolibrary.org/obo/SO_0001948)

# File lib/biointerchange/so.rb, line 11893
def self.H3R2_dimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001948')
end
H3R2_monomethylation_site() click to toggle source

A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated. (purl.obolibrary.org/obo/SO_0001947)

# File lib/biointerchange/so.rb, line 11887
def self.H3R2_monomethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001947')
end
H4K12_acetylation_site() click to toggle source

A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated. (purl.obolibrary.org/obo/SO_0001939)

# File lib/biointerchange/so.rb, line 11839
def self.H4K12_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001939')
end
H4K16_acylation_site() click to toggle source

A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated. (purl.obolibrary.org/obo/SO_0001729)

# File lib/biointerchange/so.rb, line 10585
def self.H4K16_acylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001729')
end
H4K20_monomethylation_site() click to toggle source

A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated. (purl.obolibrary.org/obo/SO_0001713)

# File lib/biointerchange/so.rb, line 10489
def self.H4K20_monomethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001713')
end
H4K4_trimethylation_site() click to toggle source

A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated. (purl.obolibrary.org/obo/SO_0001950)

# File lib/biointerchange/so.rb, line 11905
def self.H4K4_trimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001950')
end
H4K5_acylation_site() click to toggle source

A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated. (purl.obolibrary.org/obo/SO_0001730)

# File lib/biointerchange/so.rb, line 10591
def self.H4K5_acylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001730')
end
H4K8_acylation_site() click to toggle source

A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated. (purl.obolibrary.org/obo/SO_0001731)

# File lib/biointerchange/so.rb, line 10597
def self.H4K8_acylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001731')
end
H4K91_acetylation_site() click to toggle source

A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated. (purl.obolibrary.org/obo/SO_0001941)

# File lib/biointerchange/so.rb, line 11851
def self.H4K91_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001941')
end
H4K_acylation_region() click to toggle source

A region of the H4 histone whereby multiple lysines are acylated. (purl.obolibrary.org/obo/SO_0001738)

# File lib/biointerchange/so.rb, line 10639
def self.H4K_acylation_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001738')
end
H4R3_dimethylation_site() click to toggle source

A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated. (purl.obolibrary.org/obo/SO_0001949)

# File lib/biointerchange/so.rb, line 11899
def self.H4R3_dimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001949')
end
HSE() click to toggle source

A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF. (purl.obolibrary.org/obo/SO_0001850)

# File lib/biointerchange/so.rb, line 11305
def self.HSE
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001850')
end
H_ACA_box_snoRNA() click to toggle source

Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3’ end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains. (purl.obolibrary.org/obo/SO_0000594)

# File lib/biointerchange/so.rb, line 3887
def self.H_ACA_box_snoRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000594')
end
H_ACA_box_snoRNA_encoding() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000608)

# File lib/biointerchange/so.rb, line 3971
def self.H_ACA_box_snoRNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000608')
end
H_ACA_box_snoRNA_primary_transcript() click to toggle source

A primary transcript encoding a small nucleolar RNA of the box H/ACA family. (purl.obolibrary.org/obo/SO_0000596)

# File lib/biointerchange/so.rb, line 3899
def self.H_ACA_box_snoRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000596')
end
H_pseudoknot() click to toggle source

A pseudoknot which contains two stems and at least two loops. (purl.obolibrary.org/obo/SO_0000592)

# File lib/biointerchange/so.rb, line 3875
def self.H_pseudoknot
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000592')
end
Hoogsteen_base_pair() click to toggle source

A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds. (purl.obolibrary.org/obo/SO_0000500)

# File lib/biointerchange/so.rb, line 3319
def self.Hoogsteen_base_pair
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000500')
end
INR1_motif() click to toggle source

A promoter motif with consensus sequence TCATTCG. (purl.obolibrary.org/obo/SO_0001163)

# File lib/biointerchange/so.rb, line 7249
def self.INR1_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001163')
end
INR_motif() click to toggle source

A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element. (purl.obolibrary.org/obo/SO_0000014)

# File lib/biointerchange/so.rb, line 399
def self.INR_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000014')
end
IRLinv_site() click to toggle source

Component of the inversion site located at the left of a region susceptible to site-specific inversion. (purl.obolibrary.org/obo/SO_0001046)

# File lib/biointerchange/so.rb, line 6551
def self.IRLinv_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001046')
end
IRRinv_site() click to toggle source

Component of the inversion site located at the right of a region susceptible to site-specific inversion. (purl.obolibrary.org/obo/SO_0001047)

# File lib/biointerchange/so.rb, line 6557
def self.IRRinv_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001047')
end
ISRE() click to toggle source

An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding. (purl.obolibrary.org/obo/SO_0001715)

# File lib/biointerchange/so.rb, line 10501
def self.ISRE
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001715')
end
I_box() click to toggle source

A plant regulatory promoter motif, composed of a highly conserved hexamer GATAAG (I-box core). (purl.obolibrary.org/obo/SO_0001982)

# File lib/biointerchange/so.rb, line 12095
def self.I_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001982')
end
J_C_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene. (purl.obolibrary.org/obo/SO_0000511)

# File lib/biointerchange/so.rb, line 3385
def self.J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000511')
end
J_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene. (purl.obolibrary.org/obo/SO_0000513)

# File lib/biointerchange/so.rb, line 3397
def self.J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000513')
end
J_gene_recombination_feature() click to toggle source

Recombination signal including J-heptamer, J-spacer and J-nonamer in 5’ of J-region of a J-gene or J-sequence. (purl.obolibrary.org/obo/SO_0000302)

# File lib/biointerchange/so.rb, line 2133
def self.J_gene_recombination_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000302')
end
J_gene_segment() click to toggle source

Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5’ UTR (SO:0000204) and 3’ UTR (SO:0000205), also designated as J-segment. (purl.obolibrary.org/obo/SO_0000470)

# File lib/biointerchange/so.rb, line 3139
def self.J_gene_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000470')
end
J_heptamer() click to toggle source

7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene. (purl.obolibrary.org/obo/SO_0000515)

# File lib/biointerchange/so.rb, line 3409
def self.J_heptamer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000515')
end
J_nonamer() click to toggle source

9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene. (purl.obolibrary.org/obo/SO_0000514)

# File lib/biointerchange/so.rb, line 3403
def self.J_nonamer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000514')
end
J_spacer() click to toggle source

12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene. (purl.obolibrary.org/obo/SO_0000517)

# File lib/biointerchange/so.rb, line 3421
def self.J_spacer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000517')
end
KEN_box() click to toggle source

A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN. (purl.obolibrary.org/obo/SO_0001807)

# File lib/biointerchange/so.rb, line 11047
def self.KEN_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001807')
end
K_turn_RNA_motif() click to toggle source

The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices. (purl.obolibrary.org/obo/SO_0000023)

# File lib/biointerchange/so.rb, line 447
def self.K_turn_RNA_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000023')
end
LINE_element() click to toggle source

A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF’s one of which is reverse transcriptase, and 3’and 5’ direct repeats. (purl.obolibrary.org/obo/SO_0000194)

# File lib/biointerchange/so.rb, line 1485
def self.LINE_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000194')
end
LNA() click to toggle source

An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of ‘locked’ deoxyribose rings connected to a phosphate backbone. The deoxyribose unit’s conformation is ‘locked’ by a 2’-C,4’-C-oxymethylene link. (purl.obolibrary.org/obo/SO_0001188)

# File lib/biointerchange/so.rb, line 7399
def self.LNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001188')
end
LNA_oligo() click to toggle source

An oligo composed of LNA residues. (purl.obolibrary.org/obo/SO_0001189)

# File lib/biointerchange/so.rb, line 7405
def self.LNA_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001189')
end
LTR_component() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000848)

# File lib/biointerchange/so.rb, line 5369
def self.LTR_component
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000848')
end
LTR_retrotransposon() click to toggle source

A retrotransposon flanked by long terminal repeat sequences. (purl.obolibrary.org/obo/SO_0000186)

# File lib/biointerchange/so.rb, line 1437
def self.LTR_retrotransposon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000186')
end
L_box() click to toggle source

An orientation dependent regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants. (purl.obolibrary.org/obo/SO_0001981)

# File lib/biointerchange/so.rb, line 12089
def self.L_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001981')
end
M26_binding_site() click to toggle source

A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components. (purl.obolibrary.org/obo/SO_0001900)

# File lib/biointerchange/so.rb, line 11605
def self.M26_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001900')
end
MCB() click to toggle source

A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle. (purl.obolibrary.org/obo/SO_0001855)

# File lib/biointerchange/so.rb, line 11335
def self.MCB
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001855')
end
MITE() click to toggle source

A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins. (purl.obolibrary.org/obo/SO_0000338)

# File lib/biointerchange/so.rb, line 2349
def self.MITE
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000338')
end
MNP() click to toggle source

A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT. (purl.obolibrary.org/obo/SO_0001013)

# File lib/biointerchange/so.rb, line 6353
def self.MNP
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001013')
end
MNV() click to toggle source

A multiple nucleotide substitution in which the inserted sequence is the same length as the replaced sequence. (purl.obolibrary.org/obo/SO_0002007)

# File lib/biointerchange/so.rb, line 12245
def self.MNV
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002007')
end
MTE() click to toggle source

A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159). (purl.obolibrary.org/obo/SO_0001162)

# File lib/biointerchange/so.rb, line 7243
def self.MTE
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001162')
end
MicF_RNA() click to toggle source

A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message. (purl.obolibrary.org/obo/SO_0000383)

# File lib/biointerchange/so.rb, line 2613
def self.MicF_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000383')
end
N2_2_prime_O_dimethylguanosine() click to toggle source

N2_2prime_O_dimethylguanosine is a modified guanosine base feature. (purl.obolibrary.org/obo/SO_0001329)

# File lib/biointerchange/so.rb, line 8239
def self.N2_2_prime_O_dimethylguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001329')
end
N2_7_2prirme_O_trimethylguanosine() click to toggle source

N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature. (purl.obolibrary.org/obo/SO_0001343)

# File lib/biointerchange/so.rb, line 8323
def self.N2_7_2prirme_O_trimethylguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001343')
end
N2_7_dimethylguanosine() click to toggle source

N2_7_dimethylguanosine is a modified guanosine base feature. (purl.obolibrary.org/obo/SO_0001338)

# File lib/biointerchange/so.rb, line 8293
def self.N2_7_dimethylguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001338')
end
N2_N2_2_prime_O_trimethylguanosine() click to toggle source

N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature. (purl.obolibrary.org/obo/SO_0001330)

# File lib/biointerchange/so.rb, line 8245
def self.N2_N2_2_prime_O_trimethylguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001330')
end
N2_N2_7_trimethylguanosine() click to toggle source

N2_N2_7_trimethylguanosine is a modified guanosine base feature. (purl.obolibrary.org/obo/SO_0001339)

# File lib/biointerchange/so.rb, line 8299
def self.N2_N2_7_trimethylguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001339')
end
N2_N2_dimethylguanosine() click to toggle source

N2_N2_dimethylguanosine is a modified guanosine base feature. (purl.obolibrary.org/obo/SO_0001328)

# File lib/biointerchange/so.rb, line 8233
def self.N2_N2_dimethylguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001328')
end
N2_methylguanosine() click to toggle source

N2_methylguanosine is a modified guanosine base feature. (purl.obolibrary.org/obo/SO_0001325)

# File lib/biointerchange/so.rb, line 8215
def self.N2_methylguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001325')
end
N4_2_prime_O_dimethylcytidine() click to toggle source

N4,2’-O-dimethylcytidine is a modified cytidine. (purl.obolibrary.org/obo/SO_0001291)

# File lib/biointerchange/so.rb, line 8011
def self.N4_2_prime_O_dimethylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001291')
end
N4_N4_2_prime_O_trimethylcytidine() click to toggle source

N4_N4_2_prime_O_trimethylcytidine is a modified cytidine. (purl.obolibrary.org/obo/SO_0001294)

# File lib/biointerchange/so.rb, line 8029
def self.N4_N4_2_prime_O_trimethylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001294')
end
N4_acetyl_2_prime_O_methylcytidine() click to toggle source

N4-acetyl-2’-O-methylcytidine is a modified cytidine. (purl.obolibrary.org/obo/SO_0001288)

# File lib/biointerchange/so.rb, line 7993
def self.N4_acetyl_2_prime_O_methylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001288')
end
N4_acetylcytidine() click to toggle source

N4-acetylcytidine is a modified cytidine. (purl.obolibrary.org/obo/SO_0001285)

# File lib/biointerchange/so.rb, line 7975
def self.N4_acetylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001285')
end
N4_methylcytidine() click to toggle source

N4-methylcytidine is a modified cytidine. (purl.obolibrary.org/obo/SO_0001290)

# File lib/biointerchange/so.rb, line 8005
def self.N4_methylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001290')
end
N6_2_prime_O_dimethyladenosine() click to toggle source

N6_2prime_O_dimethyladenosine is a modified adenosine. (purl.obolibrary.org/obo/SO_0001312)

# File lib/biointerchange/so.rb, line 8137
def self.N6_2_prime_O_dimethyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001312')
end
N6_N6_2_prime_O_trimethyladenosine() click to toggle source

N6_N6_2prime_O_trimethyladenosine is a modified adenosine. (purl.obolibrary.org/obo/SO_0001313)

# File lib/biointerchange/so.rb, line 8143
def self.N6_N6_2_prime_O_trimethyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001313')
end
N6_N6_dimethyladenosine() click to toggle source

N6_N6_dimethyladenosine is a modified adenosine. (purl.obolibrary.org/obo/SO_0001311)

# File lib/biointerchange/so.rb, line 8131
def self.N6_N6_dimethyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001311')
end
N6_acetyladenosine() click to toggle source

N6_acetyladenosine is a modified adenosine. (purl.obolibrary.org/obo/SO_0001315)

# File lib/biointerchange/so.rb, line 8155
def self.N6_acetyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001315')
end
N6_cis_hydroxyisopentenyl_adenosine() click to toggle source

N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine. (purl.obolibrary.org/obo/SO_0001302)

# File lib/biointerchange/so.rb, line 8077
def self.N6_cis_hydroxyisopentenyl_adenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001302')
end
N6_glycinylcarbamoyladenosine() click to toggle source

N6_glycinylcarbamoyladenosine is a modified adenosine. (purl.obolibrary.org/obo/SO_0001304)

# File lib/biointerchange/so.rb, line 8089
def self.N6_glycinylcarbamoyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001304')
end
N6_hydroxynorvalylcarbamoyladenosine() click to toggle source

N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine. (purl.obolibrary.org/obo/SO_0001308)

# File lib/biointerchange/so.rb, line 8113
def self.N6_hydroxynorvalylcarbamoyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001308')
end
N6_isopentenyladenosine() click to toggle source

N6_isopentenyladenosine is a modified adenosine. (purl.obolibrary.org/obo/SO_0001300)

# File lib/biointerchange/so.rb, line 8065
def self.N6_isopentenyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001300')
end
N6_methyl_N6_threonylcarbamoyladenosine() click to toggle source

N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine. (purl.obolibrary.org/obo/SO_0001307)

# File lib/biointerchange/so.rb, line 8107
def self.N6_methyl_N6_threonylcarbamoyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001307')
end
N6_methyladenine() click to toggle source

An adenine methylated at the 6 nitrogen. (purl.obolibrary.org/obo/SO_0001920)

# File lib/biointerchange/so.rb, line 11725
def self.N6_methyladenine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001920')
end
N6_methyladenosine() click to toggle source

N6_methyladenosine is a modified adenosine. (purl.obolibrary.org/obo/SO_0001297)

# File lib/biointerchange/so.rb, line 8047
def self.N6_methyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001297')
end
N6_threonylcarbamoyladenosine() click to toggle source

N6_threonylcarbamoyladenosine is a modified adenosine. (purl.obolibrary.org/obo/SO_0001305)

# File lib/biointerchange/so.rb, line 8095
def self.N6_threonylcarbamoyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001305')
end
NDM2_motif() click to toggle source

A non directional promoter motif with consensus CGMYGYCR. (purl.obolibrary.org/obo/SO_0001167)

# File lib/biointerchange/so.rb, line 7273
def self.NDM2_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001167')
end
NDM3_motif() click to toggle source

A non directional promoter motif with consensus sequence GAAAGCT. (purl.obolibrary.org/obo/SO_0001168)

# File lib/biointerchange/so.rb, line 7279
def self.NDM3_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001168')
end
NMD_transcript_variant() click to toggle source

A variant in a transcript that is the target of NMD. (purl.obolibrary.org/obo/SO_0001621)

# File lib/biointerchange/so.rb, line 9967
def self.NMD_transcript_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001621')
end
N_region() click to toggle source

Extra nucleotides inserted between rearranged immunoglobulin segments. (purl.obolibrary.org/obo/SO_0001835)

# File lib/biointerchange/so.rb, line 11215
def self.N_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001835')
end
ORF() click to toggle source

The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER. (purl.obolibrary.org/obo/SO_0000236)

# File lib/biointerchange/so.rb, line 1737
def self.ORF
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000236')
end
Okazaki_fragment() click to toggle source

Any of the DNA segments produced by discontinuous synthesis of the lagging strand during DNA replication. (purl.obolibrary.org/obo/SO_0001985)

# File lib/biointerchange/so.rb, line 12113
def self.Okazaki_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001985')
end
OxyS_RNA() click to toggle source

A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages. (purl.obolibrary.org/obo/SO_0000384)

# File lib/biointerchange/so.rb, line 2619
def self.OxyS_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000384')
end
PAC() click to toggle source

The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells. (purl.obolibrary.org/obo/SO_0000154)

# File lib/biointerchange/so.rb, line 1241
def self.PAC
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000154')
end
PAC_clone() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000762)

# File lib/biointerchange/so.rb, line 4895
def self.PAC_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000762')
end
PAC_end() click to toggle source

A region of sequence from the end of a PAC clone that may provide a highly specific marker. (purl.obolibrary.org/obo/SO_0001480)

# File lib/biointerchange/so.rb, line 9139
def self.PAC_end
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001480')
end
PCB() click to toggle source

A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle. (purl.obolibrary.org/obo/SO_0001871)

# File lib/biointerchange/so.rb, line 11431
def self.PCB
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001871')
end
PCR_product() click to toggle source

A region amplified by a PCR reaction. (purl.obolibrary.org/obo/SO_0000006)

# File lib/biointerchange/so.rb, line 351
def self.PCR_product
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000006')
end
PIP_box() click to toggle source

A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains. (purl.obolibrary.org/obo/SO_0001810)

# File lib/biointerchange/so.rb, line 11065
def self.PIP_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001810')
end
PNA() click to toggle source

An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds. (purl.obolibrary.org/obo/SO_0001184)

# File lib/biointerchange/so.rb, line 7375
def self.PNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001184')
end
PNA_oligo() click to toggle source

Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds. (purl.obolibrary.org/obo/SO_0001011)

# File lib/biointerchange/so.rb, line 6341
def self.PNA_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001011')
end
PSE_motif() click to toggle source

A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G). (purl.obolibrary.org/obo/SO_0000017)

# File lib/biointerchange/so.rb, line 417
def self.PSE_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000017')
end
Phage_RNA_Polymerase_Promoter() click to toggle source

A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription. (purl.obolibrary.org/obo/SO_0001204)

# File lib/biointerchange/so.rb, line 7495
def self.Phage_RNA_Polymerase_Promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001204')
end
QTL() click to toggle source

A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. (purl.obolibrary.org/obo/SO_0000771)

# File lib/biointerchange/so.rb, line 4943
def self.QTL
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000771')
end
RAPD() click to toggle source

RAPD is a ‘PCR product’ where a sequence variant is identified through the use of PCR with random primers. (purl.obolibrary.org/obo/SO_0001481)

# File lib/biointerchange/so.rb, line 9145
def self.RAPD
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001481')
end
RFLP_fragment() click to toggle source

A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme. (purl.obolibrary.org/obo/SO_0000193)

# File lib/biointerchange/so.rb, line 1479
def self.RFLP_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000193')
end
RH_map() click to toggle source

A radiation hybrid map is a physical map. (purl.obolibrary.org/obo/SO_0001252)

# File lib/biointerchange/so.rb, line 7777
def self.RH_map
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001252')
end
RNA() click to toggle source

An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone. (purl.obolibrary.org/obo/SO_0000356)

# File lib/biointerchange/so.rb, line 2457
def self.RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000356')
end
RNA_6S() click to toggle source

A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase. (purl.obolibrary.org/obo/SO_0000376)

# File lib/biointerchange/so.rb, line 2571
def self.RNA_6S
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000376')
end
RNA_aptamer() click to toggle source

RNA molecules that have been selected from random pools based on their ability to bind other molecules. (purl.obolibrary.org/obo/SO_0000033)

# File lib/biointerchange/so.rb, line 507
def self.RNA_aptamer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000033')
end
RNA_chromosome() click to toggle source

Structural unit composed of a self-replicating, RNA molecule. (purl.obolibrary.org/obo/SO_0000961)

# File lib/biointerchange/so.rb, line 6047
def self.RNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000961')
end
RNA_hook_turn() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000027)

# File lib/biointerchange/so.rb, line 471
def self.RNA_hook_turn
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000027')
end
RNA_internal_loop() click to toggle source

A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge. (purl.obolibrary.org/obo/SO_0000020)

# File lib/biointerchange/so.rb, line 429
def self.RNA_internal_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000020')
end
RNA_junction_loop() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000026)

# File lib/biointerchange/so.rb, line 465
def self.RNA_junction_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000026')
end
RNA_motif() click to toggle source

A motif that is active in RNA sequence. (purl.obolibrary.org/obo/SO_0000715)

# File lib/biointerchange/so.rb, line 4613
def self.RNA_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000715')
end
RNA_polymerase_III_TATA_box() click to toggle source

A TATA box core promoter of a gene transcribed by RNA polymerase III. (purl.obolibrary.org/obo/SO_0001662)

# File lib/biointerchange/so.rb, line 10183
def self.RNA_polymerase_III_TATA_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001662')
end
RNA_polymerase_II_TATA_box() click to toggle source

A TATA box core promoter of a gene transcribed by RNA polymerase II. (purl.obolibrary.org/obo/SO_0001661)

# File lib/biointerchange/so.rb, line 10177
def self.RNA_polymerase_II_TATA_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001661')
end
RNA_polymerase_promoter() click to toggle source

A region (DNA) to which RNA polymerase binds, to begin transcription. (purl.obolibrary.org/obo/SO_0001203)

# File lib/biointerchange/so.rb, line 7489
def self.RNA_polymerase_promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001203')
end
RNA_replication_mode() click to toggle source

This has been obsoleted as it represents a process. replaced_by: GO:0034961. (purl.obolibrary.org/obo/SO_0000972)

# File lib/biointerchange/so.rb, line 6113
def self.RNA_replication_mode
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000972')
end
RNA_sequence_secondary_structure() click to toggle source

A folded RNA sequence. (purl.obolibrary.org/obo/SO_0000122)

# File lib/biointerchange/so.rb, line 1049
def self.RNA_sequence_secondary_structure
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000122')
end
RNA_stability_element() click to toggle source

Either:

RNA secondary structure that affects the stability of an RNA molecule.
(http://purl.obolibrary.org/obo/SO_0001957)

Or:

A motif that affects the stability of RNA.
(http://purl.obolibrary.org/obo/SO_0001979)
# File lib/biointerchange/so.rb, line 11951
def self.RNA_stability_element
  return [ RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001957'), RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001979') ]
end
RNAi_reagent() click to toggle source

A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference. (purl.obolibrary.org/obo/SO_0000337)

# File lib/biointerchange/so.rb, line 2343
def self.RNAi_reagent
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000337')
end
RNApol_III_promoter() click to toggle source

A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription. (purl.obolibrary.org/obo/SO_0000171)

# File lib/biointerchange/so.rb, line 1343
def self.RNApol_III_promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000171')
end
RNApol_III_promoter_type_1() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000617)

# File lib/biointerchange/so.rb, line 4025
def self.RNApol_III_promoter_type_1
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000617')
end
RNApol_III_promoter_type_1_region() click to toggle source

A region of sequence which is a promoter for RNA polymerase III type 1. (purl.obolibrary.org/obo/SO_0000845)

# File lib/biointerchange/so.rb, line 5351
def self.RNApol_III_promoter_type_1_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000845')
end
RNApol_III_promoter_type_2() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000618)

# File lib/biointerchange/so.rb, line 4031
def self.RNApol_III_promoter_type_2
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000618')
end
RNApol_III_promoter_type_2_region() click to toggle source

A region of sequence which is a promoter for RNA polymerase III type 2. (purl.obolibrary.org/obo/SO_0000846)

# File lib/biointerchange/so.rb, line 5357
def self.RNApol_III_promoter_type_2_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000846')
end
RNApol_III_promoter_type_3() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000621)

# File lib/biointerchange/so.rb, line 4049
def self.RNApol_III_promoter_type_3
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000621')
end
RNApol_II_core_promoter() click to toggle source

The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes. (purl.obolibrary.org/obo/SO_0001669)

# File lib/biointerchange/so.rb, line 10225
def self.RNApol_II_core_promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001669')
end
RNApol_II_promoter() click to toggle source

A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription. (purl.obolibrary.org/obo/SO_0000170)

# File lib/biointerchange/so.rb, line 1337
def self.RNApol_II_promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000170')
end
RNApol_II_promoter_region() click to toggle source

A region of sequence which is a promoter for RNA polymerase II. (purl.obolibrary.org/obo/SO_0000844)

# File lib/biointerchange/so.rb, line 5345
def self.RNApol_II_promoter_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000844')
end
RNApol_I_promoter() click to toggle source

A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription. (purl.obolibrary.org/obo/SO_0000169)

# File lib/biointerchange/so.rb, line 1331
def self.RNApol_I_promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000169')
end
RNase_MRP_RNA() click to toggle source

The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs. (purl.obolibrary.org/obo/SO_0000385)

# File lib/biointerchange/so.rb, line 2625
def self.RNase_MRP_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000385')
end
RNase_MRP_RNA_gene() click to toggle source

A gene that encodes a RNase_MRP_RNA. (purl.obolibrary.org/obo/SO_0001640)

# File lib/biointerchange/so.rb, line 10075
def self.RNase_MRP_RNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001640')
end
RNase_P_RNA() click to toggle source

The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs. (purl.obolibrary.org/obo/SO_0000386)

# File lib/biointerchange/so.rb, line 2631
def self.RNase_P_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000386')
end
RNase_P_RNA_gene() click to toggle source

A gene that encodes an RNase P RNA. (purl.obolibrary.org/obo/SO_0001639)

# File lib/biointerchange/so.rb, line 10069
def self.RNase_P_RNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001639')
end
RRE_RNA() click to toggle source

The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins. (purl.obolibrary.org/obo/SO_0000388)

# File lib/biointerchange/so.rb, line 2643
def self.RRE_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000388')
end
RR_tract() click to toggle source

A polypurine tract within an LTR_retrotransposon. (purl.obolibrary.org/obo/SO_0000435)

# File lib/biointerchange/so.rb, line 2925
def self.RR_tract
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000435')
end
RST() click to toggle source

A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long. (purl.obolibrary.org/obo/SO_0001467)

# File lib/biointerchange/so.rb, line 9061
def self.RST
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001467')
end
RST_match() click to toggle source

A match against an RST sequence. (purl.obolibrary.org/obo/SO_0001471)

# File lib/biointerchange/so.rb, line 9085
def self.RST_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001471')
end
R_GNA() click to toggle source

An attribute describing a GNA sequence in the ®-GNA enantiomer. (purl.obolibrary.org/obo/SO_0001194)

# File lib/biointerchange/so.rb, line 7435
def self.R_GNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001194')
end
R_GNA_oligo() click to toggle source

An oligo composed of ®-GNA residues. (purl.obolibrary.org/obo/SO_0001195)

# File lib/biointerchange/so.rb, line 7441
def self.R_GNA_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001195')
end
R_LTR_region() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000423)

# File lib/biointerchange/so.rb, line 2853
def self.R_LTR_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000423')
end
R_five_prime_LTR_region() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000427)

# File lib/biointerchange/so.rb, line 2877
def self.R_five_prime_LTR_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000427')
end
R_three_prime_LTR_region() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000430)

# File lib/biointerchange/so.rb, line 2895
def self.R_three_prime_LTR_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000430')
end
Robertsonian_fusion() click to toggle source

A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere. (purl.obolibrary.org/obo/SO_1000043)

# File lib/biointerchange/so.rb, line 12689
def self.Robertsonian_fusion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000043')
end
RprA_RNA() click to toggle source

Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential. (purl.obolibrary.org/obo/SO_0000387)

# File lib/biointerchange/so.rb, line 2637
def self.RprA_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000387')
end
SAGE_tag() click to toggle source

A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts. (purl.obolibrary.org/obo/SO_0000326)

# File lib/biointerchange/so.rb, line 2277
def self.SAGE_tag
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000326')
end
SECIS_element() click to toggle source

The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3’ UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes. (purl.obolibrary.org/obo/SO_1001274)

# File lib/biointerchange/so.rb, line 13589
def self.SECIS_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001274')
end
SINE_element() click to toggle source

A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element. (purl.obolibrary.org/obo/SO_0000206)

# File lib/biointerchange/so.rb, line 1557
def self.SINE_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000206')
end
SL10_acceptor_site() click to toggle source

A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5’ end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts. (purl.obolibrary.org/obo/SO_0001755)

# File lib/biointerchange/so.rb, line 10741
def self.SL10_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001755')
end
SL11_acceptor_site() click to toggle source

A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5’ end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts. (purl.obolibrary.org/obo/SO_0001756)

# File lib/biointerchange/so.rb, line 10747
def self.SL11_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001756')
end
SL12_acceptor_site() click to toggle source

A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5’ end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts. (purl.obolibrary.org/obo/SO_0001757)

# File lib/biointerchange/so.rb, line 10753
def self.SL12_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001757')
end
SL1_acceptor_site() click to toggle source

A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5’ end of most mRNAs. (purl.obolibrary.org/obo/SO_0000708)

# File lib/biointerchange/so.rb, line 4571
def self.SL1_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000708')
end
SL2_acceptor_site() click to toggle source

A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5’ end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts. (purl.obolibrary.org/obo/SO_0000709)

# File lib/biointerchange/so.rb, line 4577
def self.SL2_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000709')
end
SL3_acceptor_site() click to toggle source

A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5’ end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts. (purl.obolibrary.org/obo/SO_0001748)

# File lib/biointerchange/so.rb, line 10699
def self.SL3_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001748')
end
SL4_acceptor_site() click to toggle source

A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5’ end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts. (purl.obolibrary.org/obo/SO_0001749)

# File lib/biointerchange/so.rb, line 10705
def self.SL4_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001749')
end
SL5_acceptor_site() click to toggle source

A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5’ end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts. (purl.obolibrary.org/obo/SO_0001750)

# File lib/biointerchange/so.rb, line 10711
def self.SL5_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001750')
end
SL6_acceptor_site() click to toggle source

A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5’ end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts. (purl.obolibrary.org/obo/SO_0001751)

# File lib/biointerchange/so.rb, line 10717
def self.SL6_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001751')
end
SL7_acceptor_site() click to toggle source

A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5’ end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts. (purl.obolibrary.org/obo/SO_0001752)

# File lib/biointerchange/so.rb, line 10723
def self.SL7_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001752')
end
SL8_acceptor_site() click to toggle source

A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5’ end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts. (purl.obolibrary.org/obo/SO_0001753)

# File lib/biointerchange/so.rb, line 10729
def self.SL8_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001753')
end
SL9_acceptor_site() click to toggle source

A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5’ end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts. (purl.obolibrary.org/obo/SO_0001754)

# File lib/biointerchange/so.rb, line 10735
def self.SL9_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001754')
end
SNP() click to toggle source

SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater. (purl.obolibrary.org/obo/SO_0000694)

# File lib/biointerchange/so.rb, line 4487
def self.SNP
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000694')
end
SNV() click to toggle source

SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist. (purl.obolibrary.org/obo/SO_0001483)

# File lib/biointerchange/so.rb, line 9157
def self.SNV
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001483')
end
SP6_RNA_Polymerase_Promoter() click to toggle source

A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription. (purl.obolibrary.org/obo/SO_0001205)

# File lib/biointerchange/so.rb, line 7501
def self.SP6_RNA_Polymerase_Promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001205')
end
SRP_RNA() click to toggle source

The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding. (purl.obolibrary.org/obo/SO_0000590)

# File lib/biointerchange/so.rb, line 3863
def self.SRP_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000590')
end
SRP_RNA_encoding() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000642)

# File lib/biointerchange/so.rb, line 4175
def self.SRP_RNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000642')
end
SRP_RNA_gene() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001269)

# File lib/biointerchange/so.rb, line 7879
def self.SRP_RNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001269')
end
SRP_RNA_primary_transcript() click to toggle source

A primary transcript encoding a signal recognition particle RNA. (purl.obolibrary.org/obo/SO_0000589)

# File lib/biointerchange/so.rb, line 3857
def self.SRP_RNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000589')
end
STREP_motif() click to toggle source

A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2. (purl.obolibrary.org/obo/SO_0001859)

# File lib/biointerchange/so.rb, line 11359
def self.STREP_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001859')
end
STS() click to toggle source

Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known. (purl.obolibrary.org/obo/SO_0000331)

# File lib/biointerchange/so.rb, line 2307
def self.STS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000331')
end
STS_map() click to toggle source

An STS map is a physical map organized by the unique STS landmarks. (purl.obolibrary.org/obo/SO_0001251)

# File lib/biointerchange/so.rb, line 7771
def self.STS_map
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001251')
end
S_GNA() click to toggle source

An attribute describing a GNA sequence in the (S)-GNA enantiomer. (purl.obolibrary.org/obo/SO_0001196)

# File lib/biointerchange/so.rb, line 7447
def self.S_GNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001196')
end
S_GNA_oligo() click to toggle source

An oligo composed of (S)-GNA residues. (purl.obolibrary.org/obo/SO_0001197)

# File lib/biointerchange/so.rb, line 7453
def self.S_GNA_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001197')
end
S_region() click to toggle source

The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell. (purl.obolibrary.org/obo/SO_0001836)

# File lib/biointerchange/so.rb, line 11221
def self.S_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001836')
end
Sap1_recognition_motif() click to toggle source

A DNA motif to which the S. pombe Sap1 protein binds. The consensus sequence is 5’-TARGCAGNTNYAACGMG-3’; it is found at the mating type locus, where it is important for mating type switching, and at replication fork barriers in rDNA repeats. (purl.obolibrary.org/obo/SO_0001864)

# File lib/biointerchange/so.rb, line 11389
def self.Sap1_recognition_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001864')
end
Sequence_Ontology() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000000)

# File lib/biointerchange/so.rb, line 315
def self.Sequence_Ontology
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000000')
end
Shine_Dalgarno_sequence() click to toggle source

A region in the 5’ UTR that pairs with the 16S rRNA during formation of the preinitiation complex. (purl.obolibrary.org/obo/SO_0000552)

# File lib/biointerchange/so.rb, line 3631
def self.Shine_Dalgarno_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000552')
end
T3_RNA_Polymerase_Promoter() click to toggle source

A DNA sequence to which the T3 RNA polymerase binds, to begin transcription. (purl.obolibrary.org/obo/SO_0001206)

# File lib/biointerchange/so.rb, line 7507
def self.T3_RNA_Polymerase_Promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001206')
end
T7_RNA_Polymerase_Promoter() click to toggle source

A region (DNA) to which the T7 RNA polymerase binds, to begin transcription. (purl.obolibrary.org/obo/SO_0001207)

# File lib/biointerchange/so.rb, line 7513
def self.T7_RNA_Polymerase_Promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001207')
end
TATA_box() click to toggle source

A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T). (purl.obolibrary.org/obo/SO_0000174)

# File lib/biointerchange/so.rb, line 1361
def self.TATA_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000174')
end
TCT_motif() click to toggle source

A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator. (purl.obolibrary.org/obo/SO_0001959)

# File lib/biointerchange/so.rb, line 11963
def self.TCT_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001959')
end
TERRA() click to toggle source

A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long. (purl.obolibrary.org/obo/SO_0001923)

# File lib/biointerchange/so.rb, line 11743
def self.TERRA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001923')
end
TFBS_ablation() click to toggle source

A feature ablation whereby the deleted region includes a transcription factor binding site. (purl.obolibrary.org/obo/SO_0001895)

# File lib/biointerchange/so.rb, line 11575
def self.TFBS_ablation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001895')
end
TFBS_amplification() click to toggle source

A feature amplification of a region containing a transcription factor binding site. (purl.obolibrary.org/obo/SO_0001892)

# File lib/biointerchange/so.rb, line 11557
def self.TFBS_amplification
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001892')
end
TFBS_fusion() click to toggle source

A fusion where the deletion brings together transcription factor binding sites. (purl.obolibrary.org/obo/SO_0001888)

# File lib/biointerchange/so.rb, line 11533
def self.TFBS_fusion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001888')
end
TFBS_translocation() click to toggle source

A feature translocation where the region contains a transcription factor binding site. (purl.obolibrary.org/obo/SO_0001885)

# File lib/biointerchange/so.rb, line 11515
def self.TFBS_translocation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001885')
end
TF_binding_site() click to toggle source

A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]. (purl.obolibrary.org/obo/SO_0000235)

# File lib/biointerchange/so.rb, line 1731
def self.TF_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000235')
end
TF_binding_site_variant() click to toggle source

A sequence variant located within a transcription factor binding site. (purl.obolibrary.org/obo/SO_0001782)

# File lib/biointerchange/so.rb, line 10903
def self.TF_binding_site_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001782')
end
TNA() click to toggle source

An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone. (purl.obolibrary.org/obo/SO_0001190)

# File lib/biointerchange/so.rb, line 7411
def self.TNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001190')
end
TNA_oligo() click to toggle source

An oligo composed of TNA residues. (purl.obolibrary.org/obo/SO_0001191)

# File lib/biointerchange/so.rb, line 7417
def self.TNA_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001191')
end
TR_box() click to toggle source

A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis. (purl.obolibrary.org/obo/SO_0001858)

# File lib/biointerchange/so.rb, line 11353
def self.TR_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001858')
end
TSS() click to toggle source

The first base where RNA polymerase begins to synthesize the RNA transcript. (purl.obolibrary.org/obo/SO_0000315)

# File lib/biointerchange/so.rb, line 2211
def self.TSS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000315')
end
TSS_region() click to toggle source

The region of a gene from the 5’ most TSS to the 3’ TSS. (purl.obolibrary.org/obo/SO_0001240)

# File lib/biointerchange/so.rb, line 7711
def self.TSS_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001240')
end
T_loop() click to toggle source

Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C. (purl.obolibrary.org/obo/SO_0001177)

# File lib/biointerchange/so.rb, line 7333
def self.T_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001177')
end
T_to_A_transversion() click to toggle source

A transversion from T to A. (purl.obolibrary.org/obo/SO_1000021)

# File lib/biointerchange/so.rb, line 12569
def self.T_to_A_transversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000021')
end
T_to_C_transition() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_1000013)

# File lib/biointerchange/so.rb, line 12521
def self.T_to_C_transition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000013')
end
T_to_G_transversion() click to toggle source

A transversion from T to G. (purl.obolibrary.org/obo/SO_1000022)

# File lib/biointerchange/so.rb, line 12575
def self.T_to_G_transversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000022')
end
U11_snRNA() click to toggle source

U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5’ splice site sequence. (purl.obolibrary.org/obo/SO_0000398)

# File lib/biointerchange/so.rb, line 2703
def self.U11_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000398')
end
U12_intron() click to toggle source

A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs. (purl.obolibrary.org/obo/SO_0000295)

# File lib/biointerchange/so.rb, line 2091
def self.U12_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000295')
end
U12_snRNA() click to toggle source

The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns. (purl.obolibrary.org/obo/SO_0000399)

# File lib/biointerchange/so.rb, line 2709
def self.U12_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000399')
end
U14_snoRNA() click to toggle source

U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates. (purl.obolibrary.org/obo/SO_0000403)

# File lib/biointerchange/so.rb, line 2733
def self.U14_snoRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000403')
end
U14_snoRNA_primary_transcript() click to toggle source

The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA. (purl.obolibrary.org/obo/SO_0005837)

# File lib/biointerchange/so.rb, line 12257
def self.U14_snoRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005837')
end
U1_snRNA() click to toggle source

U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5’ end forms complementary base pairs with the 5’ splice junction, thus defining the 5’ donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a ‘common core’ consisting of helices I, II, the proximal region of III, and IV. (purl.obolibrary.org/obo/SO_0000391)

# File lib/biointerchange/so.rb, line 2661
def self.U1_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000391')
end
U2_intron() click to toggle source

A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs. (purl.obolibrary.org/obo/SO_0000184)

# File lib/biointerchange/so.rb, line 1425
def self.U2_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000184')
end
U2_snRNA() click to toggle source

U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5’ end but 3’ to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5’ splice site, thus starting the first of two transesterification reactions that mediate splicing. (purl.obolibrary.org/obo/SO_0000392)

# File lib/biointerchange/so.rb, line 2667
def self.U2_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000392')
end
U3_LTR_region() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000424)

# File lib/biointerchange/so.rb, line 2859
def self.U3_LTR_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000424')
end
U3_five_prime_LTR_region() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000429)

# File lib/biointerchange/so.rb, line 2889
def self.U3_five_prime_LTR_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000429')
end
U3_snoRNA() click to toggle source

U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5’ domain (with boxes A and A’), and a larger 3’ domain (with boxes B, C, C’, and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C’ and D form the C’/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5’ domain and the hinge region act as a pre-rRNA-binding domain. The 3’ domain has conserved protein-binding sites. Both the box B/C and box C’/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C’/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C’/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA. (purl.obolibrary.org/obo/SO_0001179)

# File lib/biointerchange/so.rb, line 7345
def self.U3_snoRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001179')
end
U3_three_prime_LTR_region() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000431)

# File lib/biointerchange/so.rb, line 2901
def self.U3_three_prime_LTR_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000431')
end
U4_snRNA() click to toggle source

U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6. (purl.obolibrary.org/obo/SO_0000393)

# File lib/biointerchange/so.rb, line 2673
def self.U4_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000393')
end
U4atac_snRNA() click to toggle source

An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397). (purl.obolibrary.org/obo/SO_0000394)

# File lib/biointerchange/so.rb, line 2679
def self.U4atac_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000394')
end
U5_LTR_region() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000422)

# File lib/biointerchange/so.rb, line 2847
def self.U5_LTR_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000422')
end
U5_five_prime_LTR_region() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000428)

# File lib/biointerchange/so.rb, line 2883
def self.U5_five_prime_LTR_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000428')
end
U5_snRNA() click to toggle source

U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5’ loop is required for splice site selection and p220 binding, and that both the 3’ stem-loop and the Sm site are important for Sm protein binding and cap methylation. (purl.obolibrary.org/obo/SO_0000395)

# File lib/biointerchange/so.rb, line 2685
def self.U5_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000395')
end
U5_three_prime_LTR_region() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000432)

# File lib/biointerchange/so.rb, line 2907
def self.U5_three_prime_LTR_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000432')
end
U6_snRNA() click to toggle source

U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5’ stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA. (purl.obolibrary.org/obo/SO_0000396)

# File lib/biointerchange/so.rb, line 2691
def self.U6_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000396')
end
U6atac_snRNA() click to toggle source

U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394). (purl.obolibrary.org/obo/SO_0000397)

# File lib/biointerchange/so.rb, line 2697
def self.U6atac_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000397')
end
UAA_stop_codon_signal() click to toggle source

A stop codon signal for a UAA stop codon redefinition. (purl.obolibrary.org/obo/SO_1001283)

# File lib/biointerchange/so.rb, line 13631
def self.UAA_stop_codon_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001283')
end
UAG_stop_codon_signal() click to toggle source

A stop codon signal for a UAG stop codon redefinition. (purl.obolibrary.org/obo/SO_1001282)

# File lib/biointerchange/so.rb, line 13625
def self.UAG_stop_codon_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001282')
end
UGA_stop_codon_signal() click to toggle source

A stop codon signal for a UGA stop codon redefinition. (purl.obolibrary.org/obo/SO_1001285)

# File lib/biointerchange/so.rb, line 13643
def self.UGA_stop_codon_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001285')
end
UPD() click to toggle source

Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent. (purl.obolibrary.org/obo/SO_0001744)

# File lib/biointerchange/so.rb, line 10675
def self.UPD
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001744')
end
UST() click to toggle source

An EST spanning part or all of the untranslated regions of a protein-coding transcript. (purl.obolibrary.org/obo/SO_0001464)

# File lib/biointerchange/so.rb, line 9043
def self.UST
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001464')
end
UST_match() click to toggle source

A match against an UST sequence. (purl.obolibrary.org/obo/SO_0001470)

# File lib/biointerchange/so.rb, line 9079
def self.UST_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001470')
end
UTR() click to toggle source

Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated. (purl.obolibrary.org/obo/SO_0000203)

# File lib/biointerchange/so.rb, line 1539
def self.UTR
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000203')
end
UTR_intron() click to toggle source

Intron located in the untranslated region. (purl.obolibrary.org/obo/SO_0000446)

# File lib/biointerchange/so.rb, line 2995
def self.UTR_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000446')
end
UTR_region() click to toggle source

A region of UTR. (purl.obolibrary.org/obo/SO_0000837)

# File lib/biointerchange/so.rb, line 5303
def self.UTR_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000837')
end
UTR_variant() click to toggle source

A transcript variant that is located within the UTR. (purl.obolibrary.org/obo/SO_0001622)

# File lib/biointerchange/so.rb, line 9973
def self.UTR_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001622')
end
U_box() click to toggle source

An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription. (purl.obolibrary.org/obo/SO_0001788)

# File lib/biointerchange/so.rb, line 10933
def self.U_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001788')
end
VDJ_C_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene. (purl.obolibrary.org/obo/SO_0000541)

# File lib/biointerchange/so.rb, line 3565
def self.VDJ_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000541')
end
VDJ_J_C_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene. (purl.obolibrary.org/obo/SO_0000487)

# File lib/biointerchange/so.rb, line 3241
def self.VDJ_J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000487')
end
VDJ_J_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene. (purl.obolibrary.org/obo/SO_0000488)

# File lib/biointerchange/so.rb, line 3247
def self.VDJ_J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000488')
end
VDJ_gene_segment() click to toggle source

Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5’UTR (SO:0000204) and 3’UTR (SO:0000205). (purl.obolibrary.org/obo/SO_0000574)

# File lib/biointerchange/so.rb, line 3767
def self.VDJ_gene_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000574')
end
VD_gene_segment() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5’ UTR (SO:0000204) and 3’ UTR (SO:0000205). (purl.obolibrary.org/obo/SO_0000510)

# File lib/biointerchange/so.rb, line 3379
def self.VD_gene_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000510')
end
VJ_C_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene. (purl.obolibrary.org/obo/SO_0000489)

# File lib/biointerchange/so.rb, line 3253
def self.VJ_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000489')
end
VJ_J_C_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene. (purl.obolibrary.org/obo/SO_0000490)

# File lib/biointerchange/so.rb, line 3259
def self.VJ_J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000490')
end
VJ_J_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene. (purl.obolibrary.org/obo/SO_0000491)

# File lib/biointerchange/so.rb, line 3265
def self.VJ_J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000491')
end
VJ_gene_segment() click to toggle source

Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5’UTR (SO:0000204) and 3’UTR (SO:0000205). (purl.obolibrary.org/obo/SO_0000576)

# File lib/biointerchange/so.rb, line 3779
def self.VJ_gene_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000576')
end
V_DJ_C_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene. (purl.obolibrary.org/obo/SO_0000542)

# File lib/biointerchange/so.rb, line 3571
def self.V_DJ_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000542')
end
V_DJ_J_C_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene. (purl.obolibrary.org/obo/SO_0000564)

# File lib/biointerchange/so.rb, line 3707
def self.V_DJ_J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000564')
end
V_DJ_J_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene. (purl.obolibrary.org/obo/SO_0000519)

# File lib/biointerchange/so.rb, line 3433
def self.V_DJ_J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000519')
end
V_DJ_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene. (purl.obolibrary.org/obo/SO_0000518)

# File lib/biointerchange/so.rb, line 3427
def self.V_DJ_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000518')
end
V_D_DJ_C_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene. (purl.obolibrary.org/obo/SO_0000527)

# File lib/biointerchange/so.rb, line 3481
def self.V_D_DJ_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000527')
end
V_D_DJ_J_C_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene. (purl.obolibrary.org/obo/SO_0000529)

# File lib/biointerchange/so.rb, line 3493
def self.V_D_DJ_J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000529')
end
V_D_DJ_J_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene. (purl.obolibrary.org/obo/SO_0000530)

# File lib/biointerchange/so.rb, line 3499
def self.V_D_DJ_J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000530')
end
V_D_DJ_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene. (purl.obolibrary.org/obo/SO_0000528)

# File lib/biointerchange/so.rb, line 3487
def self.V_D_DJ_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000528')
end
V_D_J_C_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene. (purl.obolibrary.org/obo/SO_0000531)

# File lib/biointerchange/so.rb, line 3505
def self.V_D_J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000531')
end
V_D_J_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene. (purl.obolibrary.org/obo/SO_0000532)

# File lib/biointerchange/so.rb, line 3511
def self.V_D_J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000532')
end
V_J_C_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene. (purl.obolibrary.org/obo/SO_0000535)

# File lib/biointerchange/so.rb, line 3529
def self.V_J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000535')
end
V_J_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene. (purl.obolibrary.org/obo/SO_0000534)

# File lib/biointerchange/so.rb, line 3523
def self.V_J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000534')
end
V_VDJ_C_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene. (purl.obolibrary.org/obo/SO_0000520)

# File lib/biointerchange/so.rb, line 3439
def self.V_VDJ_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000520')
end
V_VDJ_J_C_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene. (purl.obolibrary.org/obo/SO_0000565)

# File lib/biointerchange/so.rb, line 3713
def self.V_VDJ_J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000565')
end
V_VDJ_J_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene. (purl.obolibrary.org/obo/SO_0000522)

# File lib/biointerchange/so.rb, line 3451
def self.V_VDJ_J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000522')
end
V_VDJ_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene. (purl.obolibrary.org/obo/SO_0000521)

# File lib/biointerchange/so.rb, line 3445
def self.V_VDJ_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000521')
end
V_VJ_C_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene. (purl.obolibrary.org/obo/SO_0000523)

# File lib/biointerchange/so.rb, line 3457
def self.V_VJ_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000523')
end
V_VJ_J_C_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene. (purl.obolibrary.org/obo/SO_0000566)

# File lib/biointerchange/so.rb, line 3719
def self.V_VJ_J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000566')
end
V_VJ_J_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene. (purl.obolibrary.org/obo/SO_0000525)

# File lib/biointerchange/so.rb, line 3469
def self.V_VJ_J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000525')
end
V_VJ_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene. (purl.obolibrary.org/obo/SO_0000524)

# File lib/biointerchange/so.rb, line 3463
def self.V_VJ_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000524')
end
V_cluster() click to toggle source

Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene. (purl.obolibrary.org/obo/SO_0000526)

# File lib/biointerchange/so.rb, line 3475
def self.V_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000526')
end
V_gene_recombination_feature() click to toggle source

Recombination signal including V-heptamer, V-spacer and V-nonamer in 3’ of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene. (purl.obolibrary.org/obo/SO_0000538)

# File lib/biointerchange/so.rb, line 3547
def self.V_gene_recombination_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000538')
end
V_gene_segment() click to toggle source

Germline genomic DNA including L-part1, V-intron and V-exon, with the 5’ UTR and 3’ UTR. (purl.obolibrary.org/obo/SO_0000466)

# File lib/biointerchange/so.rb, line 3115
def self.V_gene_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000466')
end
V_heptamer() click to toggle source

7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene. (purl.obolibrary.org/obo/SO_0000533)

# File lib/biointerchange/so.rb, line 3517
def self.V_heptamer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000533')
end
V_nonamer() click to toggle source

9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene. (purl.obolibrary.org/obo/SO_0000536)

# File lib/biointerchange/so.rb, line 3535
def self.V_nonamer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000536')
end
V_region() click to toggle source

The variable region of an immunoglobulin polypeptide sequence. (purl.obolibrary.org/obo/SO_0001833)

# File lib/biointerchange/so.rb, line 11203
def self.V_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001833')
end
V_spacer() click to toggle source

12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene. (purl.obolibrary.org/obo/SO_0000537)

# File lib/biointerchange/so.rb, line 3541
def self.V_spacer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000537')
end
WC_base_pair() click to toggle source

The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation. (purl.obolibrary.org/obo/SO_0000029)

# File lib/biointerchange/so.rb, line 483
def self.WC_base_pair
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000029')
end
W_region() click to toggle source

The leftmost segment of homology in the HML and MAT mating loci, but not present in HMR. (purl.obolibrary.org/obo/SO_0002000)

# File lib/biointerchange/so.rb, line 12203
def self.W_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002000')
end
X_element() click to toggle source

The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site. (purl.obolibrary.org/obo/SO_0001497)

# File lib/biointerchange/so.rb, line 9241
def self.X_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001497')
end
X_element_combinatorial_repeat() click to toggle source

An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y’ element. (purl.obolibrary.org/obo/SO_0001484)

# File lib/biointerchange/so.rb, line 9163
def self.X_element_combinatorial_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001484')
end
YAC() click to toggle source

Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells. (purl.obolibrary.org/obo/SO_0000152)

# File lib/biointerchange/so.rb, line 1229
def self.YAC
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000152')
end
YAC_clone() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000760)

# File lib/biointerchange/so.rb, line 4883
def self.YAC_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000760')
end
YAC_end() click to toggle source

A region of sequence from the end of a YAC clone that may provide a highly specific marker. (purl.obolibrary.org/obo/SO_0001498)

# File lib/biointerchange/so.rb, line 9247
def self.YAC_end
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001498')
end
Y_RNA() click to toggle source

Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin. (purl.obolibrary.org/obo/SO_0000405)

# File lib/biointerchange/so.rb, line 2745
def self.Y_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000405')
end
Y_prime_element() click to toggle source

A Y’ element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies. (purl.obolibrary.org/obo/SO_0001485)

# File lib/biointerchange/so.rb, line 9169
def self.Y_prime_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001485')
end
Y_region() click to toggle source

A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha). (purl.obolibrary.org/obo/SO_0002001)

# File lib/biointerchange/so.rb, line 12209
def self.Y_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002001')
end
Z1_region() click to toggle source

A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR). (purl.obolibrary.org/obo/SO_0002002)

# File lib/biointerchange/so.rb, line 12215
def self.Z1_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002002')
end
Z2_region() click to toggle source

A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR). (purl.obolibrary.org/obo/SO_0002003)

# File lib/biointerchange/so.rb, line 12221
def self.Z2_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002003')
end
a_2KB_upstream_variant() click to toggle source

A sequence variant located within 2KB 5’ of a gene. (purl.obolibrary.org/obo/SO_0001636)

# File lib/biointerchange/so.rb, line 10051
def self.a_2KB_upstream_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001636')
end
a_3D_polypeptide_structure_variant() click to toggle source

A sequence variant that changes the resulting polypeptide structure. (purl.obolibrary.org/obo/SO_0001599)

# File lib/biointerchange/so.rb, line 9835
def self.a_3D_polypeptide_structure_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001599')
end
a_3_prime_UTR_variant() click to toggle source

A UTR variant of the 3’ UTR. (purl.obolibrary.org/obo/SO_0001624)

# File lib/biointerchange/so.rb, line 9985
def self.a_3_prime_UTR_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001624')
end
a_4_methylcytosine() click to toggle source

A cytosine methylated at the 4 nitrogen. (purl.obolibrary.org/obo/SO_0001919)

# File lib/biointerchange/so.rb, line 11719
def self.a_4_methylcytosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001919')
end
a_500B_downstream_variant() click to toggle source

A sequence variant located within a half KB of the end of a gene. (purl.obolibrary.org/obo/SO_0001634)

# File lib/biointerchange/so.rb, line 10039
def self.a_500B_downstream_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001634')
end
a_5KB_downstream_variant() click to toggle source

A sequence variant located within 5 KB of the end of a gene. (purl.obolibrary.org/obo/SO_0001633)

# File lib/biointerchange/so.rb, line 10033
def self.a_5KB_downstream_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001633')
end
a_5KB_upstream_variant() click to toggle source

A sequence variant located within 5KB 5’ of a gene. (purl.obolibrary.org/obo/SO_0001635)

# File lib/biointerchange/so.rb, line 10045
def self.a_5KB_upstream_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001635')
end
a_5_carboxylcytosine() click to toggle source

A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon. (purl.obolibrary.org/obo/SO_0001966)

# File lib/biointerchange/so.rb, line 12005
def self.a_5_carboxylcytosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001966')
end
a_5_formylcytosine() click to toggle source

A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon. (purl.obolibrary.org/obo/SO_0001961)

# File lib/biointerchange/so.rb, line 11975
def self.a_5_formylcytosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001961')
end
a_5_hydroxymethylcytosine() click to toggle source

A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon. (purl.obolibrary.org/obo/SO_0001960)

# File lib/biointerchange/so.rb, line 11969
def self.a_5_hydroxymethylcytosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001960')
end
a_5_methylcytosine() click to toggle source

A cytosine methylated at the 5 carbon. (purl.obolibrary.org/obo/SO_0001918)

# File lib/biointerchange/so.rb, line 11713
def self.a_5_methylcytosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001918')
end
a_5_prime_UTR_premature_start_codon_gain_variant() click to toggle source

A 5’ UTR variant where a premature start codon is gained. (purl.obolibrary.org/obo/SO_0001988)

# File lib/biointerchange/so.rb, line 12131
def self.a_5_prime_UTR_premature_start_codon_gain_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001988')
end
a_5_prime_UTR_premature_start_codon_loss_variant() click to toggle source

A 5’ UTR variant where a premature start codon is lost. (purl.obolibrary.org/obo/SO_0001989)

# File lib/biointerchange/so.rb, line 12137
def self.a_5_prime_UTR_premature_start_codon_loss_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001989')
end
a_5_prime_UTR_premature_start_codon_variant() click to toggle source

A 5’ UTR variant where a premature start codon is introduced, moved or lost. (purl.obolibrary.org/obo/SO_0001983)

# File lib/biointerchange/so.rb, line 12101
def self.a_5_prime_UTR_premature_start_codon_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001983')
end
a_5_prime_UTR_variant() click to toggle source

A UTR variant of the 5’ UTR. (purl.obolibrary.org/obo/SO_0001623)

# File lib/biointerchange/so.rb, line 9979
def self.a_5_prime_UTR_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001623')
end
a_8_oxoadenine() click to toggle source

A modified DNA adenine base,at the 8 carbon, often the product of DNA damage. (purl.obolibrary.org/obo/SO_0001967)

# File lib/biointerchange/so.rb, line 12011
def self.a_8_oxoadenine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001967')
end
a_8_oxoguanine() click to toggle source

A modified DNA guanine base,at the 8 carbon, often the product of DNA damage. (purl.obolibrary.org/obo/SO_0001965)

# File lib/biointerchange/so.rb, line 11999
def self.a_8_oxoguanine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001965')
end
aberrant_processed_transcript() click to toggle source

A transcript that has been processed "incorrectly", for example by the failure of splicing of one or more exons. (SO:ke) (purl.obolibrary.org/obo/SO_0000681)

# File lib/biointerchange/so.rb, line 4409
def self.aberrant_processed_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000681')
end
active_peptide() click to toggle source

Active peptides are proteins which are biologically active, released from a precursor molecule. (purl.obolibrary.org/obo/SO_0001064)

# File lib/biointerchange/so.rb, line 6667
def self.active_peptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001064')
end
adaptive_island() click to toggle source

An adaptive island is a genomic island that provides an adaptive advantage to the host. (purl.obolibrary.org/obo/SO_0000775)

# File lib/biointerchange/so.rb, line 4967
def self.adaptive_island
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000775')
end
adjacent_to() click to toggle source

A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap. (purl.obolibrary.org/obo/so_2_5_2.obo#adjacent_to)

# File lib/biointerchange/so.rb, line 17
def self.adjacent_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#adjacent_to')
end
alanine() click to toggle source

A place holder for a cross product with chebi. (purl.obolibrary.org/obo/SO_0001435)

# File lib/biointerchange/so.rb, line 8869
def self.alanine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001435')
end
alanine_tRNA_primary_transcript() click to toggle source

A primary transcript encoding alanyl tRNA. (purl.obolibrary.org/obo/SO_0000211)

# File lib/biointerchange/so.rb, line 1587
def self.alanine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000211')
end
alanyl_tRNA() click to toggle source

A tRNA sequence that has an alanine anticodon, and a 3’ alanine binding region. (purl.obolibrary.org/obo/SO_0000254)

# File lib/biointerchange/so.rb, line 1845
def self.alanyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000254')
end
allele() click to toggle source

An allele is one of a set of coexisting sequence variants of a gene. (purl.obolibrary.org/obo/SO_0001023)

# File lib/biointerchange/so.rb, line 6413
def self.allele
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001023')
end
allelically_excluded() click to toggle source

Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell. (purl.obolibrary.org/obo/SO_0000137)

# File lib/biointerchange/so.rb, line 1139
def self.allelically_excluded
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000137')
end
allelically_excluded_gene() click to toggle source

A gene that is allelically_excluded. (purl.obolibrary.org/obo/SO_0000897)

# File lib/biointerchange/so.rb, line 5663
def self.allelically_excluded_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000897')
end
allopolyploid() click to toggle source

A polyploid where the multiple chromosome set was derived from a different organism. (purl.obolibrary.org/obo/SO_0001256)

# File lib/biointerchange/so.rb, line 7801
def self.allopolyploid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001256')
end
alpha_beta_motif() click to toggle source

A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative. (purl.obolibrary.org/obo/SO_0100008)

# File lib/biointerchange/so.rb, line 12395
def self.alpha_beta_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100008')
end
alpha_helix() click to toggle source

The helix has 3.6 residues per turn which corersponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier. (purl.obolibrary.org/obo/SO_0001117)

# File lib/biointerchange/so.rb, line 6973
def self.alpha_helix
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001117')
end
alteration_attribute() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001508)

# File lib/biointerchange/so.rb, line 9307
def self.alteration_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001508')
end
alternate_sequence_site() click to toggle source

Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting. (purl.obolibrary.org/obo/SO_0001149)

# File lib/biointerchange/so.rb, line 7165
def self.alternate_sequence_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001149')
end
alternately_spliced_gene_encodeing_one_transcript() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000503)

# File lib/biointerchange/so.rb, line 3337
def self.alternately_spliced_gene_encodeing_one_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000503')
end
alternately_spliced_gene_encoding_greater_than_one_transcript() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000543)

# File lib/biointerchange/so.rb, line 3577
def self.alternately_spliced_gene_encoding_greater_than_one_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000543')
end
alternatively_spliced() click to toggle source

An attribute describing a situation where a gene may encode for more than 1 transcript. (purl.obolibrary.org/obo/SO_0000877)

# File lib/biointerchange/so.rb, line 5543
def self.alternatively_spliced
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000877')
end
alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_1001194)

# File lib/biointerchange/so.rb, line 13427
def self.alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001194')
end
alternatively_spliced_transcript() click to toggle source

A transcript that is alternatively spliced. (purl.obolibrary.org/obo/SO_1001187)

# File lib/biointerchange/so.rb, line 13385
def self.alternatively_spliced_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001187')
end
alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_1001244)

# File lib/biointerchange/so.rb, line 13457
def self.alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001244')
end
ambisense_ssRNA_viral_sequence() click to toggle source

A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity. (purl.obolibrary.org/obo/SO_0001202)

# File lib/biointerchange/so.rb, line 7483
def self.ambisense_ssRNA_viral_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001202')
end
amino_acid() click to toggle source

A sequence feature that corresponds to a single amino acid residue in a polypeptide. (purl.obolibrary.org/obo/SO_0001237)

# File lib/biointerchange/so.rb, line 7693
def self.amino_acid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001237')
end
amino_acid_deletion() click to toggle source

A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide. (purl.obolibrary.org/obo/SO_0001604)

# File lib/biointerchange/so.rb, line 9865
def self.amino_acid_deletion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001604')
end
amino_acid_insertion() click to toggle source

A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide. (purl.obolibrary.org/obo/SO_0001605)

# File lib/biointerchange/so.rb, line 9871
def self.amino_acid_insertion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001605')
end
amino_acid_substitution() click to toggle source

A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide. (purl.obolibrary.org/obo/SO_0001606)

# File lib/biointerchange/so.rb, line 9877
def self.amino_acid_substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001606')
end
amplification_origin() click to toggle source

An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence. (purl.obolibrary.org/obo/SO_0000750)

# File lib/biointerchange/so.rb, line 4823
def self.amplification_origin
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000750')
end
anchor_binding_site() click to toggle source

Part of an edited transcript only. (purl.obolibrary.org/obo/SO_0000977)

# File lib/biointerchange/so.rb, line 6137
def self.anchor_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000977')
end
anchor_region() click to toggle source

A region of a guide_RNA that base-pairs to a target mRNA. (purl.obolibrary.org/obo/SO_0000931)

# File lib/biointerchange/so.rb, line 5867
def self.anchor_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000931')
end
androgen_response_element() click to toggle source

A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen. (purl.obolibrary.org/obo/SO_0001853)

# File lib/biointerchange/so.rb, line 11323
def self.androgen_response_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001853')
end
aneuploid() click to toggle source

A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number. (purl.obolibrary.org/obo/SO_0000054)

# File lib/biointerchange/so.rb, line 637
def self.aneuploid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000054')
end
aneuploid_chromosome() click to toggle source

A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking. (purl.obolibrary.org/obo/SO_0000550)

# File lib/biointerchange/so.rb, line 3619
def self.aneuploid_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000550')
end
annotation_directed_improved_draft() click to toggle source

The status of a whole genome sequence,where annotation, and verification of coding regions has occurred. (purl.obolibrary.org/obo/SO_0001489)

# File lib/biointerchange/so.rb, line 9193
def self.annotation_directed_improved_draft
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001489')
end
anti_ARRET() click to toggle source

A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts are antisense of ARRET transcripts. (purl.obolibrary.org/obo/SO_0001926)

# File lib/biointerchange/so.rb, line 11761
def self.anti_ARRET
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001926')
end
anticodon() click to toggle source

A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA. (purl.obolibrary.org/obo/SO_0001174)

# File lib/biointerchange/so.rb, line 7315
def self.anticodon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001174')
end
anticodon_loop() click to toggle source

A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5’-pyrimidine-purine-anticodon-modified purine-any base-3. (purl.obolibrary.org/obo/SO_0001173)

# File lib/biointerchange/so.rb, line 7309
def self.anticodon_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001173')
end
antiparallel_beta_strand() click to toggle source

A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other’s flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets. (purl.obolibrary.org/obo/SO_0001112)

# File lib/biointerchange/so.rb, line 6943
def self.antiparallel_beta_strand
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001112')
end
antisense() click to toggle source

A region sequence that is complementary to a sequence of messenger RNA. (purl.obolibrary.org/obo/SO_0000077)

# File lib/biointerchange/so.rb, line 779
def self.antisense
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000077')
end
antisense_RNA() click to toggle source

Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA. (purl.obolibrary.org/obo/SO_0000644)

# File lib/biointerchange/so.rb, line 4187
def self.antisense_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000644')
end
antisense_lncRNA() click to toggle source

Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA. (purl.obolibrary.org/obo/SO_0001904)

# File lib/biointerchange/so.rb, line 11629
def self.antisense_lncRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001904')
end
antisense_primary_transcript() click to toggle source

The reverse complement of the primary transcript. (purl.obolibrary.org/obo/SO_0000645)

# File lib/biointerchange/so.rb, line 4193
def self.antisense_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000645')
end
apicoplast_chromosome() click to toggle source

A chromosome originating in an apicoplast. (purl.obolibrary.org/obo/SO_0001259)

# File lib/biointerchange/so.rb, line 7819
def self.apicoplast_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001259')
end
apicoplast_gene() click to toggle source

A gene from apicoplast sequence. (purl.obolibrary.org/obo/SO_0000091)

# File lib/biointerchange/so.rb, line 863
def self.apicoplast_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000091')
end
apicoplast_sequence() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000743)

# File lib/biointerchange/so.rb, line 4781
def self.apicoplast_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000743')
end
aptamer() click to toggle source

DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules. (purl.obolibrary.org/obo/SO_0000031)

# File lib/biointerchange/so.rb, line 495
def self.aptamer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000031')
end
archaeal_intron() click to toggle source

An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease. (purl.obolibrary.org/obo/SO_1001271)

# File lib/biointerchange/so.rb, line 13571
def self.archaeal_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001271')
end
archaeosine() click to toggle source

Archaeosine is a modified 7-deazoguanosine. (purl.obolibrary.org/obo/SO_0001323)

# File lib/biointerchange/so.rb, line 8203
def self.archaeosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001323')
end
arginine() click to toggle source

A place holder for a cross product with chebi. (purl.obolibrary.org/obo/SO_0001451)

# File lib/biointerchange/so.rb, line 8965
def self.arginine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001451')
end
arginine_tRNA_primary_transcript() click to toggle source

A primary transcript encoding arginyl tRNA (SO:0000255). (purl.obolibrary.org/obo/SO_0000212)

# File lib/biointerchange/so.rb, line 1593
def self.arginine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000212')
end
arginyl_tRNA() click to toggle source

A tRNA sequence that has an arginine anticodon, and a 3’ arginine binding region. (purl.obolibrary.org/obo/SO_0001036)

# File lib/biointerchange/so.rb, line 6491
def self.arginyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001036')
end
asparagine() click to toggle source

A place holder for a cross product with chebi. (purl.obolibrary.org/obo/SO_0001449)

# File lib/biointerchange/so.rb, line 8953
def self.asparagine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001449')
end
asparagine_tRNA_primary_transcript() click to toggle source

A primary transcript encoding asparaginyl tRNA (SO:0000256). (purl.obolibrary.org/obo/SO_0000213)

# File lib/biointerchange/so.rb, line 1599
def self.asparagine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000213')
end
asparaginyl_tRNA() click to toggle source

A tRNA sequence that has an asparagine anticodon, and a 3’ asparagine binding region. (purl.obolibrary.org/obo/SO_0000256)

# File lib/biointerchange/so.rb, line 1857
def self.asparaginyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000256')
end
aspartic_acid() click to toggle source

A place holder for a cross product with chebi. (purl.obolibrary.org/obo/SO_0001453)

# File lib/biointerchange/so.rb, line 8977
def self.aspartic_acid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001453')
end
aspartic_acid_tRNA_primary_transcript() click to toggle source

A primary transcript encoding aspartyl tRNA (SO:0000257). (purl.obolibrary.org/obo/SO_0000214)

# File lib/biointerchange/so.rb, line 1605
def self.aspartic_acid_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000214')
end
aspartyl_tRNA() click to toggle source

A tRNA sequence that has an aspartic acid anticodon, and a 3’ aspartic acid binding region. (purl.obolibrary.org/obo/SO_0000257)

# File lib/biointerchange/so.rb, line 1863
def self.aspartyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000257')
end
assembly() click to toggle source

A region of the genome of known length that is composed by ordering and aligning two or more different regions. (purl.obolibrary.org/obo/SO_0001248)

# File lib/biointerchange/so.rb, line 7753
def self.assembly
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001248')
end
assembly_component() click to toggle source

A region of known length which may be used to manufacture a longer region. (purl.obolibrary.org/obo/SO_0000143)

# File lib/biointerchange/so.rb, line 1175
def self.assembly_component
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000143')
end
assembly_error_correction() click to toggle source

A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake. (purl.obolibrary.org/obo/SO_0001525)

# File lib/biointerchange/so.rb, line 9409
def self.assembly_error_correction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001525')
end
associated_with() click to toggle source

This relationship is vague and up for discussion. (purl.obolibrary.org/obo/so_2_5_2.obo#associated_with)

# File lib/biointerchange/so.rb, line 23
def self.associated_with
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#associated_with')
end
assortment_derived_aneuploid() click to toggle source

Either:

-- No comment or description provided. --
(http://purl.obolibrary.org/obo/SO_0000058)

Or:

A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication.
(http://purl.obolibrary.org/obo/SO_0000803)
# File lib/biointerchange/so.rb, line 665
def self.assortment_derived_aneuploid
  return [ RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000058'), RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000803') ]
end
assortment_derived_deficiency() click to toggle source

Either:

-- No comment or description provided. --
(http://purl.obolibrary.org/obo/SO_0000052)

Or:

A multi-chromosome deficiency aberration generated by reassortment of other aberration components.
(http://purl.obolibrary.org/obo/SO_0000802)
# File lib/biointerchange/so.rb, line 625
def self.assortment_derived_deficiency
  return [ RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000052'), RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000802') ]
end
assortment_derived_deficiency_plus_duplication() click to toggle source

Either:

-- No comment or description provided. --
(http://purl.obolibrary.org/obo/SO_0000554)

Or:

A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication.
(http://purl.obolibrary.org/obo/SO_0000801)
# File lib/biointerchange/so.rb, line 3647
def self.assortment_derived_deficiency_plus_duplication
  return [ RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000554'), RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000801') ]
end
assortment_derived_duplication() click to toggle source

Either:

-- No comment or description provided. --
(http://purl.obolibrary.org/obo/SO_0000437)

Or:

A multi-chromosome duplication aberration generated by reassortment of other aberration components.
(http://purl.obolibrary.org/obo/SO_0000800)
# File lib/biointerchange/so.rb, line 2941
def self.assortment_derived_duplication
  return [ RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000437'), RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000800') ]
end
assortment_derived_variation() click to toggle source

A chromosome variation derived from an event during meiosis. (purl.obolibrary.org/obo/SO_0001504)

# File lib/biointerchange/so.rb, line 9283
def self.assortment_derived_variation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001504')
end
asx_motif() click to toggle source

A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4). (purl.obolibrary.org/obo/SO_0001106)

# File lib/biointerchange/so.rb, line 6907
def self.asx_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001106')
end
asx_turn() click to toggle source

A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2). (purl.obolibrary.org/obo/SO_0000912)

# File lib/biointerchange/so.rb, line 5753
def self.asx_turn
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000912')
end
asx_turn_left_handed_type_one() click to toggle source

Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. (purl.obolibrary.org/obo/SO_0001129)

# File lib/biointerchange/so.rb, line 7045
def self.asx_turn_left_handed_type_one
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001129')
end
asx_turn_left_handed_type_two() click to toggle source

Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. (purl.obolibrary.org/obo/SO_0001130)

# File lib/biointerchange/so.rb, line 7051
def self.asx_turn_left_handed_type_two
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001130')
end
asx_turn_right_handed_type_one() click to toggle source

Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. (purl.obolibrary.org/obo/SO_0001132)

# File lib/biointerchange/so.rb, line 7063
def self.asx_turn_right_handed_type_one
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001132')
end
asx_turn_right_handed_type_two() click to toggle source

Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. (purl.obolibrary.org/obo/SO_0001131)

# File lib/biointerchange/so.rb, line 7057
def self.asx_turn_right_handed_type_two
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001131')
end
asymmetric_RNA_internal_loop() click to toggle source

An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand. (purl.obolibrary.org/obo/SO_0000021)

# File lib/biointerchange/so.rb, line 435
def self.asymmetric_RNA_internal_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000021')
end
attB_site() click to toggle source

An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site. (purl.obolibrary.org/obo/SO_0000943)

# File lib/biointerchange/so.rb, line 5939
def self.attB_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000943')
end
attC_site() click to toggle source

An attC site is a sequence required for the integration of a DNA of an integron. (purl.obolibrary.org/obo/SO_0000950)

# File lib/biointerchange/so.rb, line 5981
def self.attC_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000950')
end
attCtn_site() click to toggle source

An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon. (purl.obolibrary.org/obo/SO_0001043)

# File lib/biointerchange/so.rb, line 6533
def self.attCtn_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001043')
end
attI_site() click to toggle source

A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place. (purl.obolibrary.org/obo/SO_0000367)

# File lib/biointerchange/so.rb, line 2517
def self.attI_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000367')
end
attL_site() click to toggle source

A region that results from recombination between attP_site and attB_site, composed of the 5’ portion of attB_site and the 3’ portion of attP_site. (purl.obolibrary.org/obo/SO_0000944)

# File lib/biointerchange/so.rb, line 5945
def self.attL_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000944')
end
attP_site() click to toggle source

An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome. (purl.obolibrary.org/obo/SO_0000942)

# File lib/biointerchange/so.rb, line 5933
def self.attP_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000942')
end
attR_site() click to toggle source

A region that results from recombination between attP_site and attB_site, composed of the 5’ portion of attP_site and the 3’ portion of attB_site. (purl.obolibrary.org/obo/SO_0000945)

# File lib/biointerchange/so.rb, line 5951
def self.attR_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000945')
end
attenuator() click to toggle source

A sequence segment located within the five prime end of an mRNA that causes premature termination of translation. (purl.obolibrary.org/obo/SO_0000140)

# File lib/biointerchange/so.rb, line 1157
def self.attenuator
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000140')
end
autocatalytically_spliced_intron() click to toggle source

A self spliced intron. (purl.obolibrary.org/obo/SO_0000588)

# File lib/biointerchange/so.rb, line 3851
def self.autocatalytically_spliced_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000588')
end
autopolyploid() click to toggle source

A polyploid where the multiple chromosome set was derived from the same organism. (purl.obolibrary.org/obo/SO_0001255)

# File lib/biointerchange/so.rb, line 7795
def self.autopolyploid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001255')
end
autoregulated() click to toggle source

The gene product is involved in its own transcriptional regulation. (purl.obolibrary.org/obo/SO_0000471)

# File lib/biointerchange/so.rb, line 3145
def self.autoregulated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000471')
end
autosynaptic_chromosome() click to toggle source

An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome. (purl.obolibrary.org/obo/SO_1000136)

# File lib/biointerchange/so.rb, line 13163
def self.autosynaptic_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000136')
end
bacterial_RNApol_promoter() click to toggle source

A DNA sequence to which bacterial RNA polymerase binds, to begin transcription. (purl.obolibrary.org/obo/SO_0000613)

# File lib/biointerchange/so.rb, line 4001
def self.bacterial_RNApol_promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000613')
end
bacterial_RNApol_promoter_region() click to toggle source

A region which is part of a bacterial RNA polymerase promoter. (purl.obolibrary.org/obo/SO_0000843)

# File lib/biointerchange/so.rb, line 5339
def self.bacterial_RNApol_promoter_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000843')
end
bacterial_RNApol_promoter_sigma54() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001672)

# File lib/biointerchange/so.rb, line 10243
def self.bacterial_RNApol_promoter_sigma54
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001672')
end
bacterial_RNApol_promoter_sigma_70() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001671)

# File lib/biointerchange/so.rb, line 10237
def self.bacterial_RNApol_promoter_sigma_70
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001671')
end
bacterial_RNApol_promoter_sigma_ecf() click to toggle source

A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation. (purl.obolibrary.org/obo/SO_0001913)

# File lib/biointerchange/so.rb, line 11683
def self.bacterial_RNApol_promoter_sigma_ecf
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001913')
end
bacterial_terminator() click to toggle source

A terminator signal for bacterial transcription. (purl.obolibrary.org/obo/SO_0000614)

# File lib/biointerchange/so.rb, line 4007
def self.bacterial_terminator
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000614')
end
base() click to toggle source

A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. (purl.obolibrary.org/obo/SO_0001236)

# File lib/biointerchange/so.rb, line 7687
def self.base
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001236')
end
base_call_error_correction() click to toggle source

A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake. (purl.obolibrary.org/obo/SO_0001526)

# File lib/biointerchange/so.rb, line 9415
def self.base_call_error_correction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001526')
end
base_pair() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000028)

# File lib/biointerchange/so.rb, line 477
def self.base_pair
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000028')
end
benign_variant() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001770)

# File lib/biointerchange/so.rb, line 10831
def self.benign_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001770')
end
beta_bulge() click to toggle source

A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees. (purl.obolibrary.org/obo/SO_0001107)

# File lib/biointerchange/so.rb, line 6913
def self.beta_bulge
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001107')
end
beta_bulge_loop() click to toggle source

A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins. (purl.obolibrary.org/obo/SO_0001108)

# File lib/biointerchange/so.rb, line 6919
def self.beta_bulge_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001108')
end
beta_bulge_loop_five() click to toggle source

A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3. (purl.obolibrary.org/obo/SO_0001109)

# File lib/biointerchange/so.rb, line 6925
def self.beta_bulge_loop_five
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001109')
end
beta_bulge_loop_six() click to toggle source

A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4. (purl.obolibrary.org/obo/SO_0001110)

# File lib/biointerchange/so.rb, line 6931
def self.beta_bulge_loop_six
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001110')
end
beta_strand() click to toggle source

A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array. (purl.obolibrary.org/obo/SO_0001111)

# File lib/biointerchange/so.rb, line 6937
def self.beta_strand
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001111')
end
beta_turn() click to toggle source

A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization. (purl.obolibrary.org/obo/SO_0001133)

# File lib/biointerchange/so.rb, line 7069
def self.beta_turn
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001133')
end
beta_turn_left_handed_type_one() click to toggle source

Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. (purl.obolibrary.org/obo/SO_0001134)

# File lib/biointerchange/so.rb, line 7075
def self.beta_turn_left_handed_type_one
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001134')
end
beta_turn_left_handed_type_two() click to toggle source

Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees. (purl.obolibrary.org/obo/SO_0001135)

# File lib/biointerchange/so.rb, line 7081
def self.beta_turn_left_handed_type_two
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001135')
end
beta_turn_right_handed_type_one() click to toggle source

Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. (purl.obolibrary.org/obo/SO_0001136)

# File lib/biointerchange/so.rb, line 7087
def self.beta_turn_right_handed_type_one
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001136')
end
beta_turn_right_handed_type_two() click to toggle source

Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. (purl.obolibrary.org/obo/SO_0001137)

# File lib/biointerchange/so.rb, line 7093
def self.beta_turn_right_handed_type_two
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001137')
end
beta_turn_type_eight() click to toggle source

A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees. (purl.obolibrary.org/obo/SO_0001155)

# File lib/biointerchange/so.rb, line 7201
def self.beta_turn_type_eight
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001155')
end
beta_turn_type_six() click to toggle source

A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline. (purl.obolibrary.org/obo/SO_0001150)

# File lib/biointerchange/so.rb, line 7171
def self.beta_turn_type_six
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001150')
end
beta_turn_type_six_a() click to toggle source

A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees. (purl.obolibrary.org/obo/SO_0001151)

# File lib/biointerchange/so.rb, line 7177
def self.beta_turn_type_six_a
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001151')
end
beta_turn_type_six_a_one() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001152)

# File lib/biointerchange/so.rb, line 7183
def self.beta_turn_type_six_a_one
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001152')
end
beta_turn_type_six_a_two() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001153)

# File lib/biointerchange/so.rb, line 7189
def self.beta_turn_type_six_a_two
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001153')
end
beta_turn_type_six_b() click to toggle source

A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees. (purl.obolibrary.org/obo/SO_0001154)

# File lib/biointerchange/so.rb, line 7195
def self.beta_turn_type_six_b
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001154')
end
bidirectional_promoter() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000568)

# File lib/biointerchange/so.rb, line 3731
def self.bidirectional_promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000568')
end
binding_site() click to toggle source

A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. (purl.obolibrary.org/obo/SO_0000409)

# File lib/biointerchange/so.rb, line 2769
def self.binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000409')
end
biochemical_region_of_peptide() click to toggle source

A region of a peptide that is involved in a biochemical function. (purl.obolibrary.org/obo/SO_0100001)

# File lib/biointerchange/so.rb, line 12353
def self.biochemical_region_of_peptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100001')
end
biological_region() click to toggle source

A region defined by its disposition to be involved in a biological process. (purl.obolibrary.org/obo/SO_0001411)

# File lib/biointerchange/so.rb, line 8731
def self.biological_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001411')
end
biomaterial_region() click to toggle source

A region which is intended for use in an experiment. (purl.obolibrary.org/obo/SO_0001409)

# File lib/biointerchange/so.rb, line 8719
def self.biomaterial_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001409')
end
bipartite_duplication() click to toggle source

An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break. (purl.obolibrary.org/obo/SO_1000149)

# File lib/biointerchange/so.rb, line 13229
def self.bipartite_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000149')
end
bipartite_inversion() click to toggle source

A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed). (purl.obolibrary.org/obo/SO_1000151)

# File lib/biointerchange/so.rb, line 13241
def self.bipartite_inversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000151')
end
blocked_reading_frame() click to toggle source

A reading_frame that is interrupted by one or more stop codons; usually identified through intergenomic sequence comparisons. (purl.obolibrary.org/obo/SO_0000718)

# File lib/biointerchange/so.rb, line 4631
def self.blocked_reading_frame
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000718')
end
blunt_end_restriction_enzyme_cleavage_junction() click to toggle source

A restriction enzyme cleavage site where both strands are cut at the same position. (purl.obolibrary.org/obo/SO_0001693)

# File lib/biointerchange/so.rb, line 10369
def self.blunt_end_restriction_enzyme_cleavage_junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001693')
end
blunt_end_restriction_enzyme_cleavage_site() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001691)

# File lib/biointerchange/so.rb, line 10357
def self.blunt_end_restriction_enzyme_cleavage_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001691')
end
bound_by_factor() click to toggle source

An attribute describing a sequence that is bound by another molecule. (purl.obolibrary.org/obo/SO_0000277)

# File lib/biointerchange/so.rb, line 1983
def self.bound_by_factor
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000277')
end
bound_by_nucleic_acid() click to toggle source

An attribute describing a sequence that is bound by a nucleic acid. (purl.obolibrary.org/obo/SO_0000876)

# File lib/biointerchange/so.rb, line 5537
def self.bound_by_nucleic_acid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000876')
end
bound_by_protein() click to toggle source

An attribute describing a sequence that is bound by a protein. (purl.obolibrary.org/obo/SO_0000875)

# File lib/biointerchange/so.rb, line 5531
def self.bound_by_protein
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000875')
end
branch_site() click to toggle source

A pyrimidine rich sequence near the 3’ end of an intron to which the 5’end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat. (purl.obolibrary.org/obo/SO_0000611)

# File lib/biointerchange/so.rb, line 3989
def self.branch_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000611')
end
cDNA() click to toggle source

DNA synthesized by reverse transcriptase using RNA as a template. (purl.obolibrary.org/obo/SO_0000756)

# File lib/biointerchange/so.rb, line 4859
def self.cDNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000756')
end
cDNA_clone() click to toggle source

Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host. (purl.obolibrary.org/obo/SO_0000317)

# File lib/biointerchange/so.rb, line 2223
def self.cDNA_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000317')
end
cDNA_match() click to toggle source

A match against cDNA sequence. (purl.obolibrary.org/obo/SO_0000689)

# File lib/biointerchange/so.rb, line 4457
def self.cDNA_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000689')
end
c_terminal_region() click to toggle source

The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa). (purl.obolibrary.org/obo/SO_0100015)

# File lib/biointerchange/so.rb, line 12437
def self.c_terminal_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100015')
end
candidate_gene() click to toggle source

A gene suspected of being involved in the expression of a trait. (purl.obolibrary.org/obo/SO_0001867)

# File lib/biointerchange/so.rb, line 11407
def self.candidate_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001867')
end
canonical_five_prime_splice_site() click to toggle source

The canonical 5’ splice site has the sequence "GT". (SO:ke) (purl.obolibrary.org/obo/SO_0000677)

# File lib/biointerchange/so.rb, line 4385
def self.canonical_five_prime_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000677')
end
canonical_splice_site() click to toggle source

The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively. (purl.obolibrary.org/obo/SO_0000675)

# File lib/biointerchange/so.rb, line 4373
def self.canonical_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000675')
end
canonical_three_prime_splice_site() click to toggle source

The canonical 3’ splice site has the sequence "AG". (SO:ke) (purl.obolibrary.org/obo/SO_0000676)

# File lib/biointerchange/so.rb, line 4379
def self.canonical_three_prime_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000676')
end
cap() click to toggle source

A structure consisting of a 7-methylguanosine in 5’-5’ triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA. (purl.obolibrary.org/obo/SO_0000581)

# File lib/biointerchange/so.rb, line 3809
def self.cap
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000581')
end
capped() click to toggle source

An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5’ end. (purl.obolibrary.org/obo/SO_0000146)

# File lib/biointerchange/so.rb, line 1193
def self.capped
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000146')
end
capped_mRNA() click to toggle source

An mRNA that is capped. (purl.obolibrary.org/obo/SO_0000862)

# File lib/biointerchange/so.rb, line 5453
def self.capped_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000862')
end
capped_primary_transcript() click to toggle source

A primary transcript that is capped. (purl.obolibrary.org/obo/SO_0000861)

# File lib/biointerchange/so.rb, line 5447
def self.capped_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000861')
end
cassette_array_member() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0005847)

# File lib/biointerchange/so.rb, line 12281
def self.cassette_array_member
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005847')
end
cassette_pseudogene() click to toggle source

A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy. (purl.obolibrary.org/obo/SO_0001434)

# File lib/biointerchange/so.rb, line 8863
def self.cassette_pseudogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001434')
end
catalytic_residue() click to toggle source

Amino acid involved in the activity of an enzyme. (purl.obolibrary.org/obo/SO_0001104)

# File lib/biointerchange/so.rb, line 6895
def self.catalytic_residue
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001104')
end
catmat_left_handed_four() click to toggle source

A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2. (purl.obolibrary.org/obo/SO_0100005)

# File lib/biointerchange/so.rb, line 12377
def self.catmat_left_handed_four
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100005')
end
catmat_left_handed_three() click to toggle source

A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1. (purl.obolibrary.org/obo/SO_0100004)

# File lib/biointerchange/so.rb, line 12371
def self.catmat_left_handed_three
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100004')
end
catmat_right_handed_four() click to toggle source

A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2. (purl.obolibrary.org/obo/SO_0100007)

# File lib/biointerchange/so.rb, line 12389
def self.catmat_right_handed_four
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100007')
end
catmat_right_handed_three() click to toggle source

A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1. (purl.obolibrary.org/obo/SO_0100006)

# File lib/biointerchange/so.rb, line 12383
def self.catmat_right_handed_three
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100006')
end
central_hydrophobic_region_of_signal_peptide() click to toggle source

The central, hydrophobic region of the signal peptide (approx 7-15 aa). (purl.obolibrary.org/obo/SO_0100016)

# File lib/biointerchange/so.rb, line 12443
def self.central_hydrophobic_region_of_signal_peptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100016')
end
centromere() click to toggle source

A region of chromosome where the spindle fibers attach during mitosis and meiosis. (purl.obolibrary.org/obo/SO_0000577)

# File lib/biointerchange/so.rb, line 3785
def self.centromere
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000577')
end
centromere_DNA_Element_I() click to toggle source

A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p). (purl.obolibrary.org/obo/SO_0001493)

# File lib/biointerchange/so.rb, line 9217
def self.centromere_DNA_Element_I
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001493')
end
centromere_DNA_Element_II() click to toggle source

A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length. (purl.obolibrary.org/obo/SO_0001494)

# File lib/biointerchange/so.rb, line 9223
def self.centromere_DNA_Element_II
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001494')
end
centromere_DNA_Element_III() click to toggle source

A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex. (purl.obolibrary.org/obo/SO_0001495)

# File lib/biointerchange/so.rb, line 9229
def self.centromere_DNA_Element_III
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001495')
end
centromeric_repeat() click to toggle source

A repeat region found within the modular centromere. (purl.obolibrary.org/obo/SO_0001797)

# File lib/biointerchange/so.rb, line 10987
def self.centromeric_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001797')
end
chimeric_cDNA_clone() click to toggle source

A cDNA clone invalidated because it is chimeric. (purl.obolibrary.org/obo/SO_0000810)

# File lib/biointerchange/so.rb, line 5153
def self.chimeric_cDNA_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000810')
end
chloroplast_DNA() click to toggle source

This term is used by MO. (purl.obolibrary.org/obo/SO_0001033)

# File lib/biointerchange/so.rb, line 6473
def self.chloroplast_DNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001033')
end
chloroplast_DNA_read() click to toggle source

A sequencer read of a chloroplast DNA sample. (purl.obolibrary.org/obo/SO_0001930)

# File lib/biointerchange/so.rb, line 11785
def self.chloroplast_DNA_read
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001930')
end
chloroplast_chromosome() click to toggle source

A chromosome originating in a chloroplast. (purl.obolibrary.org/obo/SO_0000820)

# File lib/biointerchange/so.rb, line 5213
def self.chloroplast_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000820')
end
chloroplast_sequence() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000745)

# File lib/biointerchange/so.rb, line 4793
def self.chloroplast_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000745')
end
chromoplast_chromosome() click to toggle source

A chromosome originating in a chromoplast. (purl.obolibrary.org/obo/SO_0000821)

# File lib/biointerchange/so.rb, line 5219
def self.chromoplast_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000821')
end
chromoplast_gene() click to toggle source

A gene from chromoplast_sequence. (purl.obolibrary.org/obo/SO_0000093)

# File lib/biointerchange/so.rb, line 875
def self.chromoplast_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000093')
end
chromoplast_sequence() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000744)

# File lib/biointerchange/so.rb, line 4787
def self.chromoplast_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000744')
end
chromosomal_deletion() click to toggle source

An incomplete chromosome. (purl.obolibrary.org/obo/SO_1000029)

# File lib/biointerchange/so.rb, line 12617
def self.chromosomal_deletion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000029')
end
chromosomal_duplication() click to toggle source

An extra chromosome. (purl.obolibrary.org/obo/SO_1000037)

# File lib/biointerchange/so.rb, line 12653
def self.chromosomal_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000037')
end
chromosomal_inversion() click to toggle source

An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type. (purl.obolibrary.org/obo/SO_1000030)

# File lib/biointerchange/so.rb, line 12623
def self.chromosomal_inversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000030')
end
chromosomal_regulatory_element() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000626)

# File lib/biointerchange/so.rb, line 4079
def self.chromosomal_regulatory_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000626')
end
chromosomal_structural_element() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000628)

# File lib/biointerchange/so.rb, line 4091
def self.chromosomal_structural_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000628')
end
chromosomal_translocation() click to toggle source

An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations. (purl.obolibrary.org/obo/SO_1000044)

# File lib/biointerchange/so.rb, line 12695
def self.chromosomal_translocation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000044')
end
chromosomal_transposition() click to toggle source

A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type. (purl.obolibrary.org/obo/SO_0000453)

# File lib/biointerchange/so.rb, line 3037
def self.chromosomal_transposition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000453')
end
chromosomal_variation_attribute() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001509)

# File lib/biointerchange/so.rb, line 9313
def self.chromosomal_variation_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001509')
end
chromosomally_aberrant_genome() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001524)

# File lib/biointerchange/so.rb, line 9403
def self.chromosomally_aberrant_genome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001524')
end
chromosome() click to toggle source

Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication. (purl.obolibrary.org/obo/SO_0000340)

# File lib/biointerchange/so.rb, line 2361
def self.chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000340')
end
chromosome_arm() click to toggle source

A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere. (purl.obolibrary.org/obo/SO_0000105)

# File lib/biointerchange/so.rb, line 947
def self.chromosome_arm
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000105')
end
chromosome_band() click to toggle source

A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark. (purl.obolibrary.org/obo/SO_0000341)

# File lib/biointerchange/so.rb, line 2367
def self.chromosome_band
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000341')
end
chromosome_breakage_sequence() click to toggle source

A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation. (purl.obolibrary.org/obo/SO_0000670)

# File lib/biointerchange/so.rb, line 4343
def self.chromosome_breakage_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000670')
end
chromosome_breakpoint() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001021)

# File lib/biointerchange/so.rb, line 6401
def self.chromosome_breakpoint
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001021')
end
chromosome_fission() click to toggle source

A chromosome that occurred by the division of a larger chromosome. (purl.obolibrary.org/obo/SO_1000141)

# File lib/biointerchange/so.rb, line 13181
def self.chromosome_fission
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000141')
end
chromosome_number_variation() click to toggle source

A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number. (purl.obolibrary.org/obo/SO_1000182)

# File lib/biointerchange/so.rb, line 13349
def self.chromosome_number_variation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000182')
end
chromosome_part() click to toggle source

A region of a chromosome. (purl.obolibrary.org/obo/SO_0000830)

# File lib/biointerchange/so.rb, line 5261
def self.chromosome_part
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000830')
end
chromosome_structure_variation() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_1000183)

# File lib/biointerchange/so.rb, line 13355
def self.chromosome_structure_variation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000183')
end
chromosome_variation() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000240)

# File lib/biointerchange/so.rb, line 1761
def self.chromosome_variation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000240')
end
circular() click to toggle source

A quality of a nucleotide polymer that has no terminal nucleotide residues. (purl.obolibrary.org/obo/SO_0000988)

# File lib/biointerchange/so.rb, line 6203
def self.circular
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000988')
end
circular_double_stranded_DNA_chromosome() click to toggle source

Structural unit composed of a self-replicating, double-stranded, circular DNA molecule. (purl.obolibrary.org/obo/SO_0000958)

# File lib/biointerchange/so.rb, line 6029
def self.circular_double_stranded_DNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000958')
end
circular_double_stranded_RNA_chromosome() click to toggle source

Structural unit composed of a self-replicating, double-stranded, circular RNA molecule. (purl.obolibrary.org/obo/SO_0000967)

# File lib/biointerchange/so.rb, line 6083
def self.circular_double_stranded_RNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000967')
end
circular_single_stranded_DNA_chromosome() click to toggle source

Structural unit composed of a self-replicating, single-stranded, circular DNA molecule. (purl.obolibrary.org/obo/SO_0000960)

# File lib/biointerchange/so.rb, line 6041
def self.circular_single_stranded_DNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000960')
end
circular_single_stranded_RNA_chromosome() click to toggle source

Structural unit composed of a self-replicating, single-stranded, circular DNA molecule. (purl.obolibrary.org/obo/SO_0000966)

# File lib/biointerchange/so.rb, line 6077
def self.circular_single_stranded_RNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000966')
end
cis_regulatory_frameshift_element() click to toggle source

A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence. (purl.obolibrary.org/obo/SO_0001427)

# File lib/biointerchange/so.rb, line 8827
def self.cis_regulatory_frameshift_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001427')
end
cis_splice_site() click to toggle source

Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron. (purl.obolibrary.org/obo/SO_0001419)

# File lib/biointerchange/so.rb, line 8779
def self.cis_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001419')
end
class_II_RNA() click to toggle source

Small non-coding RNA (59-60 nt long) containing 5’ and 3’ ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm. (purl.obolibrary.org/obo/SO_0000989)

# File lib/biointerchange/so.rb, line 6209
def self.class_II_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000989')
end
class_I_RNA() click to toggle source

Small non-coding RNA (55-65 nt long) containing highly conserved 5’ and 3’ ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm. (purl.obolibrary.org/obo/SO_0000990)

# File lib/biointerchange/so.rb, line 6215
def self.class_I_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000990')
end
cleaved_for_gpi_anchor_region() click to toggle source

The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor. (purl.obolibrary.org/obo/SO_0001408)

# File lib/biointerchange/so.rb, line 8713
def self.cleaved_for_gpi_anchor_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001408')
end
cleaved_initiator_methionine() click to toggle source

The initiator methionine that has been cleaved from a mature polypeptide sequence. (purl.obolibrary.org/obo/SO_0000691)

# File lib/biointerchange/so.rb, line 4469
def self.cleaved_initiator_methionine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000691')
end
cleaved_peptide_region() click to toggle source

The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation. (purl.obolibrary.org/obo/SO_0100011)

# File lib/biointerchange/so.rb, line 12413
def self.cleaved_peptide_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100011')
end
clip() click to toggle source

Part of the primary transcript that is clipped off during processing. (purl.obolibrary.org/obo/SO_0000303)

# File lib/biointerchange/so.rb, line 2139
def self.clip
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000303')
end
clone() click to toggle source

A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism. (purl.obolibrary.org/obo/SO_0000151)

# File lib/biointerchange/so.rb, line 1223
def self.clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000151')
end
clone_attribute() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000787)

# File lib/biointerchange/so.rb, line 5039
def self.clone_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000787')
end
clone_end() click to toggle source

A read from an end of the clone sequence. (purl.obolibrary.org/obo/SO_0001793)

# File lib/biointerchange/so.rb, line 10963
def self.clone_end
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001793')
end
clone_insert() click to toggle source

The region of sequence that has been inserted and is being propagated by the clone. (purl.obolibrary.org/obo/SO_0000753)

# File lib/biointerchange/so.rb, line 4841
def self.clone_insert
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000753')
end
clone_insert_end() click to toggle source

The end of the clone insert. (purl.obolibrary.org/obo/SO_0000103)

# File lib/biointerchange/so.rb, line 935
def self.clone_insert_end
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000103')
end
clone_insert_start() click to toggle source

Either:

The start of the clone insert.
(http://purl.obolibrary.org/obo/SO_0000179)

Or:

-- No comment or description provided. --
(http://purl.obolibrary.org/obo/SO_0000767)
# File lib/biointerchange/so.rb, line 1395
def self.clone_insert_start
  return [ RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000179'), RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000767') ]
end
cloned() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000788)

# File lib/biointerchange/so.rb, line 5045
def self.cloned
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000788')
end
cloned_cDNA() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000792)

# File lib/biointerchange/so.rb, line 5069
def self.cloned_cDNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000792')
end
cloned_cDNA_insert() click to toggle source

A clone insert made from cDNA. (purl.obolibrary.org/obo/SO_0000913)

# File lib/biointerchange/so.rb, line 5759
def self.cloned_cDNA_insert
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000913')
end
cloned_genomic() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000791)

# File lib/biointerchange/so.rb, line 5063
def self.cloned_genomic
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000791')
end
cloned_genomic_insert() click to toggle source

A clone insert made from genomic DNA. (purl.obolibrary.org/obo/SO_0000914)

# File lib/biointerchange/so.rb, line 5765
def self.cloned_genomic_insert
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000914')
end
cloned_region() click to toggle source

Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions. (purl.obolibrary.org/obo/SO_0000785)

# File lib/biointerchange/so.rb, line 5027
def self.cloned_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000785')
end
coding_conserved_region() click to toggle source

Coding region of sequence similarity by descent from a common ancestor. (purl.obolibrary.org/obo/SO_0000332)

# File lib/biointerchange/so.rb, line 2313
def self.coding_conserved_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000332')
end
coding_end() click to toggle source

The last base to be translated into protein. It does not include the stop codon. (purl.obolibrary.org/obo/SO_0000327)

# File lib/biointerchange/so.rb, line 2283
def self.coding_end
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000327')
end
coding_exon() click to toggle source

An exon whereby at least one base is part of a codon (here, ‘codon’ is inclusive of the stop_codon). (purl.obolibrary.org/obo/SO_0000195)

# File lib/biointerchange/so.rb, line 1491
def self.coding_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000195')
end
coding_region_of_exon() click to toggle source

The region of an exon that encodes for protein sequence. (purl.obolibrary.org/obo/SO_0001215)

# File lib/biointerchange/so.rb, line 7561
def self.coding_region_of_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001215')
end
coding_sequence_variant() click to toggle source

A sequence variant that changes the coding sequence. (purl.obolibrary.org/obo/SO_0001580)

# File lib/biointerchange/so.rb, line 9739
def self.coding_sequence_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001580')
end
coding_start() click to toggle source

The first base to be translated into protein. (purl.obolibrary.org/obo/SO_0000323)

# File lib/biointerchange/so.rb, line 2259
def self.coding_start
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000323')
end
coding_transcript_intron_variant() click to toggle source

A transcript variant occurring within an intron of a coding transcript. (purl.obolibrary.org/obo/SO_0001969)

# File lib/biointerchange/so.rb, line 12023
def self.coding_transcript_intron_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001969')
end
coding_transcript_variant() click to toggle source

A transcript variant of a protein coding gene. (purl.obolibrary.org/obo/SO_0001968)

# File lib/biointerchange/so.rb, line 12017
def self.coding_transcript_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001968')
end
coding_variant_quality() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001814)

# File lib/biointerchange/so.rb, line 11089
def self.coding_variant_quality
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001814')
end
codon() click to toggle source

A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS. (purl.obolibrary.org/obo/SO_0000360)

# File lib/biointerchange/so.rb, line 2475
def self.codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000360')
end
codon_redefined() click to toggle source

An attribute describing the alteration of codon meaning. (purl.obolibrary.org/obo/SO_0000882)

# File lib/biointerchange/so.rb, line 5573
def self.codon_redefined
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000882')
end
coiled_coil() click to toggle source

A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope. (purl.obolibrary.org/obo/SO_0001080)

# File lib/biointerchange/so.rb, line 6751
def self.coiled_coil
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001080')
end
cointegrated_plasmid() click to toggle source

A MGE region consisting of two fused plasmids resulting from a replicative transposition event. (purl.obolibrary.org/obo/SO_0001045)

# File lib/biointerchange/so.rb, line 6545
def self.cointegrated_plasmid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001045')
end
common_variant() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001767)

# File lib/biointerchange/so.rb, line 10813
def self.common_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001767')
end
compensatory_transcript_secondary_structure_variant() click to toggle source

A secondary structure variant that compensate for the change made by a previous variant. (purl.obolibrary.org/obo/SO_0001597)

# File lib/biointerchange/so.rb, line 9823
def self.compensatory_transcript_secondary_structure_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001597')
end
complete_evidence_for_feature() click to toggle source

B is complete_evidence_for_feature A if the extent (5’ and 3’ boundaries) and internal boundaries of B fully support the extent and internal boundaries of A. (purl.obolibrary.org/obo/so_2_5_2.obo#complete_evidence_for_feature)

# File lib/biointerchange/so.rb, line 29
def self.complete_evidence_for_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#complete_evidence_for_feature')
end
complex_3D_structural_variant() click to toggle source

A sequence variant that changes the resulting polypeptide structure. (purl.obolibrary.org/obo/SO_0001600)

# File lib/biointerchange/so.rb, line 9841
def self.complex_3D_structural_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001600')
end
complex_change_of_translational_product_variant() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001602)

# File lib/biointerchange/so.rb, line 9853
def self.complex_change_of_translational_product_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001602')
end
complex_chromosomal_mutation() click to toggle source

A chromosome structure variant with 4 or more breakpoints. (purl.obolibrary.org/obo/SO_1000146)

# File lib/biointerchange/so.rb, line 13211
def self.complex_chromosomal_mutation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000146')
end
complex_structural_alteration() click to toggle source

A structural sequence alteration or rearrangement encompassing one or more genome fragments. (purl.obolibrary.org/obo/SO_0001784)

# File lib/biointerchange/so.rb, line 10909
def self.complex_structural_alteration
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001784')
end
complex_substitution() click to toggle source

When no simple or well defined DNA mutation event describes the observed DNA change, the keyword "complex" should be used. Usually there are multiple equally plausible explanations for the change. (EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html) (purl.obolibrary.org/obo/SO_1000005)

# File lib/biointerchange/so.rb, line 12485
def self.complex_substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000005')
end
complex_transcript_variant() click to toggle source

A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border. (purl.obolibrary.org/obo/SO_0001577)

# File lib/biointerchange/so.rb, line 9721
def self.complex_transcript_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001577')
end
compositionally_biased_region_of_peptide() click to toggle source

Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length. (purl.obolibrary.org/obo/SO_0001066)

# File lib/biointerchange/so.rb, line 6673
def self.compositionally_biased_region_of_peptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001066')
end
compound_chromosome() click to toggle source

A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms. (purl.obolibrary.org/obo/SO_1000042)

# File lib/biointerchange/so.rb, line 12683
def self.compound_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000042')
end
compound_chromosome_arm() click to toggle source

FLAG - this term is should probably be a part of rather than an is_a. (purl.obolibrary.org/obo/SO_0000060)

# File lib/biointerchange/so.rb, line 677
def self.compound_chromosome_arm
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000060')
end
computed_feature() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000309)

# File lib/biointerchange/so.rb, line 2175
def self.computed_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000309')
end
computed_feature_by_similarity() click to toggle source

. (purl.obolibrary.org/obo/SO_0000311)

# File lib/biointerchange/so.rb, line 2187
def self.computed_feature_by_similarity
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000311')
end
conformational_change_variant() click to toggle source

A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence. (purl.obolibrary.org/obo/SO_0001601)

# File lib/biointerchange/so.rb, line 9847
def self.conformational_change_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001601')
end
conformational_switch() click to toggle source

A region of a polypeptide, involved in the transition from one conformational state to another. (purl.obolibrary.org/obo/SO_0001422)

# File lib/biointerchange/so.rb, line 8797
def self.conformational_switch
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001422')
end
conjugative_transposon() click to toggle source

A transposon that encodes function required for conjugation. (purl.obolibrary.org/obo/SO_0000371)

# File lib/biointerchange/so.rb, line 2541
def self.conjugative_transposon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000371')
end
connects_on() click to toggle source

X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z. (purl.obolibrary.org/obo/so_2_5_2.obo#connects_on)

# File lib/biointerchange/so.rb, line 35
def self.connects_on
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#connects_on')
end
consensus() click to toggle source

Term added Dec 06 to comply with mapping to MGED terms. It should be used to generate consensus regions. The specific cross product terms they require are consensus_region and consensus_mRNA. (purl.obolibrary.org/obo/SO_0000993)

# File lib/biointerchange/so.rb, line 6233
def self.consensus
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000993')
end
consensus_AFLP_fragment() click to toggle source

A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input. (purl.obolibrary.org/obo/SO_0001991)

# File lib/biointerchange/so.rb, line 12149
def self.consensus_AFLP_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001991')
end
consensus_gDNA() click to toggle source

Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input. (purl.obolibrary.org/obo/SO_0001931)

# File lib/biointerchange/so.rb, line 11791
def self.consensus_gDNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001931')
end
consensus_mRNA() click to toggle source

DO not obsolete without considering MGED mapping. (purl.obolibrary.org/obo/SO_0000995)

# File lib/biointerchange/so.rb, line 6245
def self.consensus_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000995')
end
consensus_region() click to toggle source

DO not obsolete without considering MGED mapping. (purl.obolibrary.org/obo/SO_0000994)

# File lib/biointerchange/so.rb, line 6239
def self.consensus_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000994')
end
conservative_amino_acid_substitution() click to toggle source

A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide. (purl.obolibrary.org/obo/SO_0001607)

# File lib/biointerchange/so.rb, line 9883
def self.conservative_amino_acid_substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001607')
end
conservative_inframe_deletion() click to toggle source

An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons. (purl.obolibrary.org/obo/SO_0001825)

# File lib/biointerchange/so.rb, line 11155
def self.conservative_inframe_deletion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001825')
end
conservative_inframe_insertion() click to toggle source

An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons. (purl.obolibrary.org/obo/SO_0001823)

# File lib/biointerchange/so.rb, line 11143
def self.conservative_inframe_insertion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001823')
end
conservative_missense_variant() click to toggle source

A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious. (purl.obolibrary.org/obo/SO_0001585)

# File lib/biointerchange/so.rb, line 9757
def self.conservative_missense_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001585')
end
conserved() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000856)

# File lib/biointerchange/so.rb, line 5417
def self.conserved
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000856')
end
conserved_region() click to toggle source

Region of sequence similarity by descent from a common ancestor. (purl.obolibrary.org/obo/SO_0000330)

# File lib/biointerchange/so.rb, line 2301
def self.conserved_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000330')
end
contained_by() click to toggle source

X contained_by Y iff X starts after start of Y and X ends before end of Y. (purl.obolibrary.org/obo/so_2_5_2.obo#contained_by)

# File lib/biointerchange/so.rb, line 41
def self.contained_by
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#contained_by')
end
contains() click to toggle source

The inverse of contained_by. (purl.obolibrary.org/obo/so_2_5_2.obo#contains)

# File lib/biointerchange/so.rb, line 47
def self.contains
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#contains')
end
contig() click to toggle source

A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N’s from unavailable bases. (purl.obolibrary.org/obo/SO_0000149)

# File lib/biointerchange/so.rb, line 1211
def self.contig
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000149')
end
contig_collection() click to toggle source

A collection of contigs. (purl.obolibrary.org/obo/SO_0001462)

# File lib/biointerchange/so.rb, line 9031
def self.contig_collection
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001462')
end
contig_read() click to toggle source

A DNA sequencer read which is part of a contig. (purl.obolibrary.org/obo/SO_0000476)

# File lib/biointerchange/so.rb, line 3175
def self.contig_read
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000476')
end
copy_number_change() click to toggle source

A sequence variant where copies of a feature (CNV) are either increased or decreased. (purl.obolibrary.org/obo/SO_0001563)

# File lib/biointerchange/so.rb, line 9637
def self.copy_number_change
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001563')
end
copy_number_decrease() click to toggle source

A sequence variant where copies of a feature are decreased relative to the reference. (purl.obolibrary.org/obo/SO_0001912)

# File lib/biointerchange/so.rb, line 11677
def self.copy_number_decrease
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001912')
end
copy_number_gain() click to toggle source

A sequence alteration whereby the copy number of a given regions is greater than the reference sequence. (purl.obolibrary.org/obo/SO_0001742)

# File lib/biointerchange/so.rb, line 10663
def self.copy_number_gain
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001742')
end
copy_number_increase() click to toggle source

A sequence variant where copies of a feature are increased relative to the reference. (purl.obolibrary.org/obo/SO_0001911)

# File lib/biointerchange/so.rb, line 11671
def self.copy_number_increase
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001911')
end
copy_number_loss() click to toggle source

A sequence alteration whereby the copy number of a given region is less than the reference sequence. (purl.obolibrary.org/obo/SO_0001743)

# File lib/biointerchange/so.rb, line 10669
def self.copy_number_loss
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001743')
end
copy_number_variation() click to toggle source

A variation that increases or decreases the copy number of a given region. (purl.obolibrary.org/obo/SO_0001019)

# File lib/biointerchange/so.rb, line 6389
def self.copy_number_variation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001019')
end
core_promoter_element() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001660)

# File lib/biointerchange/so.rb, line 10171
def self.core_promoter_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001660')
end
cosmid() click to toggle source

A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites. (purl.obolibrary.org/obo/SO_0000156)

# File lib/biointerchange/so.rb, line 1253
def self.cosmid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000156')
end
cosmid_clone() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000765)

# File lib/biointerchange/so.rb, line 4913
def self.cosmid_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000765')
end
covalent_binding_site() click to toggle source

Binding involving a covalent bond. (purl.obolibrary.org/obo/SO_0001090)

# File lib/biointerchange/so.rb, line 6811
def self.covalent_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001090')
end
cross_genome_match() click to toggle source

A nucleotide match against a sequence from another organism. (purl.obolibrary.org/obo/SO_0000177)

# File lib/biointerchange/so.rb, line 1379
def self.cross_genome_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000177')
end
cryptic() click to toggle source

A feature_attribute describing a feature that is not manifest under normal conditions. (purl.obolibrary.org/obo/SO_0000976)

# File lib/biointerchange/so.rb, line 6131
def self.cryptic
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000976')
end
cryptic_gene() click to toggle source

A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning. (purl.obolibrary.org/obo/SO_0001431)

# File lib/biointerchange/so.rb, line 8845
def self.cryptic_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001431')
end
cryptic_prophage() click to toggle source

A remnant of an integrated prophage in the host genome or an "island" in the host genome that includes phage like-genes. (GOC:jl) (purl.obolibrary.org/obo/SO_0001007)

# File lib/biointerchange/so.rb, line 6317
def self.cryptic_prophage
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001007')
end
cryptic_splice_acceptor() click to toggle source

A sequence variant whereby a new splice site is created due to the activation of a new acceptor. (purl.obolibrary.org/obo/SO_0001570)

# File lib/biointerchange/so.rb, line 9679
def self.cryptic_splice_acceptor
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001570')
end
cryptic_splice_donor() click to toggle source

A sequence variant whereby a new splice site is created due to the activation of a new donor. (purl.obolibrary.org/obo/SO_0001571)

# File lib/biointerchange/so.rb, line 9685
def self.cryptic_splice_donor
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001571')
end
cryptic_splice_site() click to toggle source

A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error. (purl.obolibrary.org/obo/SO_0001533)

# File lib/biointerchange/so.rb, line 9457
def self.cryptic_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001533')
end
cryptic_splice_site_variant() click to toggle source

A sequence variant causing a new (functional) splice site. (purl.obolibrary.org/obo/SO_0001569)

# File lib/biointerchange/so.rb, line 9673
def self.cryptic_splice_site_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001569')
end
cryptogene() click to toggle source

A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence. (purl.obolibrary.org/obo/SO_1001196)

# File lib/biointerchange/so.rb, line 13439
def self.cryptogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001196')
end
ct_gene() click to toggle source

A gene from chloroplast sequence. (purl.obolibrary.org/obo/SO_0000092)

# File lib/biointerchange/so.rb, line 869
def self.ct_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000092')
end
cyanelle_chromosome() click to toggle source

A chromosome originating in a cyanelle. (purl.obolibrary.org/obo/SO_0000822)

# File lib/biointerchange/so.rb, line 5225
def self.cyanelle_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000822')
end
cyanelle_gene() click to toggle source

A gene from cyanelle sequence. (purl.obolibrary.org/obo/SO_0000094)

# File lib/biointerchange/so.rb, line 881
def self.cyanelle_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000094')
end
cyanelle_sequence() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000746)

# File lib/biointerchange/so.rb, line 4799
def self.cyanelle_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000746')
end
cyclic_translocation() click to toggle source

A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third. (purl.obolibrary.org/obo/SO_1000150)

# File lib/biointerchange/so.rb, line 13235
def self.cyclic_translocation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000150')
end
cysteine() click to toggle source

A place holder for a cross product with chebi. (purl.obolibrary.org/obo/SO_0001447)

# File lib/biointerchange/so.rb, line 8941
def self.cysteine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001447')
end
cysteine_tRNA_primary_transcript() click to toggle source

A primary transcript encoding cysteinyl tRNA (SO:0000258). (purl.obolibrary.org/obo/SO_0000215)

# File lib/biointerchange/so.rb, line 1611
def self.cysteine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000215')
end
cysteinyl_tRNA() click to toggle source

A tRNA sequence that has a cysteine anticodon, and a 3’ cysteine binding region. (purl.obolibrary.org/obo/SO_0000258)

# File lib/biointerchange/so.rb, line 1869
def self.cysteinyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000258')
end
cytoplasmic_polypeptide_region() click to toggle source

Polypeptide region that is localized inside the cytoplasm. (purl.obolibrary.org/obo/SO_0001073)

# File lib/biointerchange/so.rb, line 6709
def self.cytoplasmic_polypeptide_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001073')
end
dCAPS_primer() click to toggle source

A primer with one or more mis-matches to the DNA template corresponding to a position within a restriction enzyme recognition site. (purl.obolibrary.org/obo/SO_0001699)

# File lib/biointerchange/so.rb, line 10405
def self.dCAPS_primer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001699')
end
databank_entry() click to toggle source

The sequence referred to by an entry in a databank such as Genbank or SwissProt. (purl.obolibrary.org/obo/SO_2000061)

# File lib/biointerchange/so.rb, line 13667
def self.databank_entry
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_2000061')
end
de_novo_variant() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001781)

# File lib/biointerchange/so.rb, line 10897
def self.de_novo_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001781')
end
decayed_exon() click to toggle source

A non-functional descendant of an exon. (purl.obolibrary.org/obo/SO_0000464)

# File lib/biointerchange/so.rb, line 3103
def self.decayed_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000464')
end
decreased_polyadenylation_variant() click to toggle source

A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference. (purl.obolibrary.org/obo/SO_0001803)

# File lib/biointerchange/so.rb, line 11023
def self.decreased_polyadenylation_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001803')
end
decreased_transcript_level_variant() click to toggle source

A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001541)

# File lib/biointerchange/so.rb, line 9505
def self.decreased_transcript_level_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001541')
end
decreased_transcript_stability_variant() click to toggle source

A sequence variant that decreases transcript stability with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001547)

# File lib/biointerchange/so.rb, line 9541
def self.decreased_transcript_stability_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001547')
end
decreased_transcription_rate_variant() click to toggle source

A sequence variant that decreases the rate of transcription with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001552)

# File lib/biointerchange/so.rb, line 9571
def self.decreased_transcription_rate_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001552')
end
decreased_translational_product_level() click to toggle source

A sequence variant which decreases the translational product level with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001555)

# File lib/biointerchange/so.rb, line 9589
def self.decreased_translational_product_level
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001555')
end
defective_conjugative_transposon() click to toggle source

An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon. (purl.obolibrary.org/obo/SO_0001049)

# File lib/biointerchange/so.rb, line 6569
def self.defective_conjugative_transposon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001049')
end
deficient_interchromosomal_transposition() click to toggle source

An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining. (purl.obolibrary.org/obo/SO_0000063)

# File lib/biointerchange/so.rb, line 695
def self.deficient_interchromosomal_transposition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000063')
end
deficient_intrachromosomal_transposition() click to toggle source

An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining. (purl.obolibrary.org/obo/SO_0000062)

# File lib/biointerchange/so.rb, line 689
def self.deficient_intrachromosomal_transposition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000062')
end
deficient_inversion() click to toggle source

A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted. (purl.obolibrary.org/obo/SO_1000171)

# File lib/biointerchange/so.rb, line 13319
def self.deficient_inversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000171')
end
deficient_translocation() click to toggle source

A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining. (purl.obolibrary.org/obo/SO_1000147)

# File lib/biointerchange/so.rb, line 13217
def self.deficient_translocation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000147')
end
delete() click to toggle source

To remove a subsection of sequence. (purl.obolibrary.org/obo/SO_0000045)

# File lib/biointerchange/so.rb, line 579
def self.delete
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000045')
end
delete_U() click to toggle source

An edit to delete a uridine. (purl.obolibrary.org/obo/SO_0000918)

# File lib/biointerchange/so.rb, line 5789
def self.delete_U
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000918')
end
deletion() click to toggle source

The point at which one or more contiguous nucleotides were excised. (purl.obolibrary.org/obo/SO_0000159)

# File lib/biointerchange/so.rb, line 1271
def self.deletion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000159')
end
deletion_breakpoint() click to toggle source

The point within a chromosome where a deletion begins or ends. (purl.obolibrary.org/obo/SO_0001415)

# File lib/biointerchange/so.rb, line 8755
def self.deletion_breakpoint
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001415')
end
deletion_junction() click to toggle source

The space between two bases in a sequence which marks the position where a deletion has occurred. (purl.obolibrary.org/obo/SO_0000687)

# File lib/biointerchange/so.rb, line 4445
def self.deletion_junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000687')
end
derives_from() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/so_2_5_2.obo#derives_from)

# File lib/biointerchange/so.rb, line 53
def self.derives_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#derives_from')
end
designed_sequence() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000546)

# File lib/biointerchange/so.rb, line 3595
def self.designed_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000546')
end
destruction_box() click to toggle source

A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN. (purl.obolibrary.org/obo/SO_0001805)

# File lib/biointerchange/so.rb, line 11035
def self.destruction_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001805')
end
dexstrosynaptic_chromosome() click to toggle source

An autosynaptic chromosome carrying the two right (D = dextro) telomeres. (purl.obolibrary.org/obo/SO_1000142)

# File lib/biointerchange/so.rb, line 13187
def self.dexstrosynaptic_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000142')
end
dg_repeat() click to toggle source

A repeat region which is part of the regional centromere outer repeat region. (purl.obolibrary.org/obo/SO_0001898)

# File lib/biointerchange/so.rb, line 11593
def self.dg_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001898')
end
dh_repeat() click to toggle source

A repeat region which is part of the regional centromere outer repeat region. (purl.obolibrary.org/obo/SO_0001899)

# File lib/biointerchange/so.rb, line 11599
def self.dh_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001899')
end
dicistronic() click to toggle source

An attribute describing a sequence that contains the code for two gene products. (purl.obolibrary.org/obo/SO_0000879)

# File lib/biointerchange/so.rb, line 5555
def self.dicistronic
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000879')
end
dicistronic_mRNA() click to toggle source

An mRNA that has the quality dicistronic. (purl.obolibrary.org/obo/SO_0000716)

# File lib/biointerchange/so.rb, line 4619
def self.dicistronic_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000716')
end
dicistronic_primary_transcript() click to toggle source

A primary transcript that has the quality dicistronic. (purl.obolibrary.org/obo/SO_1001197)

# File lib/biointerchange/so.rb, line 13445
def self.dicistronic_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001197')
end
dicistronic_transcript() click to toggle source

A transcript that is dicistronic. (purl.obolibrary.org/obo/SO_0000079)

# File lib/biointerchange/so.rb, line 791
def self.dicistronic_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000079')
end
dif_site() click to toggle source

A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase. (purl.obolibrary.org/obo/SO_0000949)

# File lib/biointerchange/so.rb, line 5975
def self.dif_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000949')
end
dihydrouridine() click to toggle source

A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring. (purl.obolibrary.org/obo/SO_0001228)

# File lib/biointerchange/so.rb, line 7639
def self.dihydrouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001228')
end
dinucleotide_repeat_microsatellite_feature() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000290)

# File lib/biointerchange/so.rb, line 2061
def self.dinucleotide_repeat_microsatellite_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000290')
end
diplotype() click to toggle source

A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known. (purl.obolibrary.org/obo/SO_0001028)

# File lib/biointerchange/so.rb, line 6443
def self.diplotype
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001028')
end
direct() click to toggle source

A quality of an insertion where the insert is not in a cytologically inverted orientation. (purl.obolibrary.org/obo/SO_0001514)

# File lib/biointerchange/so.rb, line 9343
def self.direct
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001514')
end
direct_repeat() click to toggle source

A repeat where the same sequence is repeated in the same direction. Example: GCTGA—–GCTGA. (purl.obolibrary.org/obo/SO_0000314)

# File lib/biointerchange/so.rb, line 2205
def self.direct_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000314')
end
direct_tandem_duplication() click to toggle source

A tandem duplication where the individual regions are in the same orientation. (purl.obolibrary.org/obo/SO_1000039)

# File lib/biointerchange/so.rb, line 12665
def self.direct_tandem_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000039')
end
direction_attribute() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001029)

# File lib/biointerchange/so.rb, line 6449
def self.direction_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001029')
end
disconnected_from() click to toggle source

X is disconnected_from Y iff it is not the case that X overlaps Y. (purl.obolibrary.org/obo/so_2_5_2.obo#disconnected_from)

# File lib/biointerchange/so.rb, line 59
def self.disconnected_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#disconnected_from')
end
disease_associated_variant() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001771)

# File lib/biointerchange/so.rb, line 10837
def self.disease_associated_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001771')
end
disease_causing_variant() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001772)

# File lib/biointerchange/so.rb, line 10843
def self.disease_causing_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001772')
end
dispersed_repeat() click to toggle source

A repeat that is located at dispersed sites in the genome. (purl.obolibrary.org/obo/SO_0000658)

# File lib/biointerchange/so.rb, line 4271
def self.dispersed_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000658')
end
disruptive_inframe_deletion() click to toggle source

An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon. (purl.obolibrary.org/obo/SO_0001826)

# File lib/biointerchange/so.rb, line 11161
def self.disruptive_inframe_deletion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001826')
end
disruptive_inframe_insertion() click to toggle source

An inframe_increase_in_cds_length that inserts one or more codons into the coding sequence within an existing codon. (purl.obolibrary.org/obo/SO_0001824)

# File lib/biointerchange/so.rb, line 11149
def self.disruptive_inframe_insertion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001824')
end
distal_duplication() click to toggle source

A duplication of the distal region of a chromosome. (purl.obolibrary.org/obo/SO_0001928)

# File lib/biointerchange/so.rb, line 11773
def self.distal_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001928')
end
distal_promoter_element() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001670)

# File lib/biointerchange/so.rb, line 10231
def self.distal_promoter_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001670')
end
distant_three_prime_recoding_signal() click to toggle source

A recoding signal that is found many hundreds of nucleotides 3’ of a redefined stop codon. (purl.obolibrary.org/obo/SO_1001287)

# File lib/biointerchange/so.rb, line 13655
def self.distant_three_prime_recoding_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001287')
end
disulfide_bond() click to toggle source

The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules. (purl.obolibrary.org/obo/SO_0001088)

# File lib/biointerchange/so.rb, line 6799
def self.disulfide_bond
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001088')
end
double() click to toggle source

Attributes added to describe the different kinds of replicon. SO workshop, September 2006. (purl.obolibrary.org/obo/SO_0000985)

# File lib/biointerchange/so.rb, line 6185
def self.double
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000985')
end
double_stranded_DNA_chromosome() click to toggle source

Structural unit composed of a self-replicating, double-stranded DNA molecule. (purl.obolibrary.org/obo/SO_0000955)

# File lib/biointerchange/so.rb, line 6011
def self.double_stranded_DNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000955')
end
double_stranded_RNA_chromosome() click to toggle source

Structural unit composed of a self-replicating, double-stranded RNA molecule. (purl.obolibrary.org/obo/SO_0000965)

# File lib/biointerchange/so.rb, line 6071
def self.double_stranded_RNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000965')
end
double_stranded_cDNA() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000758)

# File lib/biointerchange/so.rb, line 4871
def self.double_stranded_cDNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000758')
end
downstream_gene_variant() click to toggle source

A sequence variant located 3’ of a gene. (purl.obolibrary.org/obo/SO_0001632)

# File lib/biointerchange/so.rb, line 10027
def self.downstream_gene_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001632')
end
downstream_transcript_variant() click to toggle source

Requested by Graham Ritchie, EBI/Sanger. (purl.obolibrary.org/obo/SO_0001987)

# File lib/biointerchange/so.rb, line 12125
def self.downstream_transcript_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001987')
end
ds_DNA_viral_sequence() click to toggle source

A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA. (purl.obolibrary.org/obo/SO_0001198)

# File lib/biointerchange/so.rb, line 7459
def self.ds_DNA_viral_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001198')
end
ds_RNA_viral_sequence() click to toggle source

A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA. (purl.obolibrary.org/obo/SO_0001169)

# File lib/biointerchange/so.rb, line 7285
def self.ds_RNA_viral_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001169')
end
ds_oligo() click to toggle source

A double stranded oligonucleotide. (purl.obolibrary.org/obo/SO_0000442)

# File lib/biointerchange/so.rb, line 2971
def self.ds_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000442')
end
duplicated_pseudogene() click to toggle source

A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence. (purl.obolibrary.org/obo/SO_0001758)

# File lib/biointerchange/so.rb, line 10759
def self.duplicated_pseudogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001758')
end
duplication() click to toggle source

An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome. (purl.obolibrary.org/obo/SO_1000035)

# File lib/biointerchange/so.rb, line 12641
def self.duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000035')
end
duplication_attribute() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001523)

# File lib/biointerchange/so.rb, line 9397
def self.duplication_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001523')
end
dye_terminator_read() click to toggle source

A read produced by the dye terminator method of sequencing. (purl.obolibrary.org/obo/SO_0001423)

# File lib/biointerchange/so.rb, line 8803
def self.dye_terminator_read
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001423')
end
edit_operation() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000916)

# File lib/biointerchange/so.rb, line 5777
def self.edit_operation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000916')
end
edited() click to toggle source

An attribute describing a sequence that is modified by editing. (purl.obolibrary.org/obo/SO_0000116)

# File lib/biointerchange/so.rb, line 1013
def self.edited
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000116')
end
edited_CDS() click to toggle source

A CDS that is edited. (purl.obolibrary.org/obo/SO_0000935)

# File lib/biointerchange/so.rb, line 5891
def self.edited_CDS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000935')
end
edited_by_A_to_I_substitution() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000600)

# File lib/biointerchange/so.rb, line 3923
def self.edited_by_A_to_I_substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000600')
end
edited_by_C_insertion_and_dinucleotide_insertion() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000598)

# File lib/biointerchange/so.rb, line 3911
def self.edited_by_C_insertion_and_dinucleotide_insertion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000598')
end
edited_by_C_to_U_substitution() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000599)

# File lib/biointerchange/so.rb, line 3917
def self.edited_by_C_to_U_substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000599')
end
edited_by_G_addition() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000601)

# File lib/biointerchange/so.rb, line 3929
def self.edited_by_G_addition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000601')
end
edited_from() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/so_2_5_2.obo#edited_from)

# File lib/biointerchange/so.rb, line 65
def self.edited_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#edited_from')
end
edited_mRNA() click to toggle source

An mRNA that is edited. (purl.obolibrary.org/obo/SO_0000929)

# File lib/biointerchange/so.rb, line 5855
def self.edited_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000929')
end
edited_to() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/so_2_5_2.obo#edited_to)

# File lib/biointerchange/so.rb, line 71
def self.edited_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#edited_to')
end
edited_transcript() click to toggle source

A transcript that is edited. (purl.obolibrary.org/obo/SO_0000873)

# File lib/biointerchange/so.rb, line 5519
def self.edited_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000873')
end
edited_transcript_by_A_to_I_substitution() click to toggle source

A transcript that has been edited by A to I substitution. (purl.obolibrary.org/obo/SO_0000874)

# File lib/biointerchange/so.rb, line 5525
def self.edited_transcript_by_A_to_I_substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000874')
end
edited_transcript_feature() click to toggle source

A locatable feature on a transcript that is edited. (purl.obolibrary.org/obo/SO_0000579)

# File lib/biointerchange/so.rb, line 3797
def self.edited_transcript_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000579')
end
editing_block() click to toggle source

Edited mRNA sequence mediated by a single guide RNA (SO:0000602). (purl.obolibrary.org/obo/SO_0000604)

# File lib/biointerchange/so.rb, line 3947
def self.editing_block
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000604')
end
editing_domain() click to toggle source

Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602). (purl.obolibrary.org/obo/SO_0000606)

# File lib/biointerchange/so.rb, line 3959
def self.editing_domain
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000606')
end
editing_variant() click to toggle source

A transcript processing variant whereby the process of editing is disrupted with respect to the reference. (purl.obolibrary.org/obo/SO_0001544)

# File lib/biointerchange/so.rb, line 9523
def self.editing_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001544')
end
eight_cutter_restriction_site() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000251)

# File lib/biointerchange/so.rb, line 1827
def self.eight_cutter_restriction_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000251')
end
elongated_in_frame_polypeptide_C_terminal() click to toggle source

A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus. (purl.obolibrary.org/obo/SO_0001612)

# File lib/biointerchange/so.rb, line 9913
def self.elongated_in_frame_polypeptide_C_terminal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001612')
end
elongated_in_frame_polypeptide_N_terminal_elongation() click to toggle source

A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus. (purl.obolibrary.org/obo/SO_0001614)

# File lib/biointerchange/so.rb, line 9925
def self.elongated_in_frame_polypeptide_N_terminal_elongation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001614')
end
elongated_out_of_frame_polypeptide_C_terminal() click to toggle source

A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus. (purl.obolibrary.org/obo/SO_0001613)

# File lib/biointerchange/so.rb, line 9919
def self.elongated_out_of_frame_polypeptide_C_terminal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001613')
end
elongated_out_of_frame_polypeptide_N_terminal() click to toggle source

A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus. (purl.obolibrary.org/obo/SO_0001615)

# File lib/biointerchange/so.rb, line 9931
def self.elongated_out_of_frame_polypeptide_N_terminal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001615')
end
elongated_polypeptide() click to toggle source

A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence. (purl.obolibrary.org/obo/SO_0001609)

# File lib/biointerchange/so.rb, line 9895
def self.elongated_polypeptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001609')
end
elongated_polypeptide_C_terminal() click to toggle source

A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus. (purl.obolibrary.org/obo/SO_0001610)

# File lib/biointerchange/so.rb, line 9901
def self.elongated_polypeptide_C_terminal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001610')
end
elongated_polypeptide_N_terminal() click to toggle source

A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus. (purl.obolibrary.org/obo/SO_0001611)

# File lib/biointerchange/so.rb, line 9907
def self.elongated_polypeptide_N_terminal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001611')
end
encodes_1_polypeptide() click to toggle source

A gene that is alternately spliced, but encodes only one polypeptide. (purl.obolibrary.org/obo/SO_1001188)

# File lib/biointerchange/so.rb, line 13391
def self.encodes_1_polypeptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001188')
end
encodes_alternate_transcription_start_sites() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001241)

# File lib/biointerchange/so.rb, line 7717
def self.encodes_alternate_transcription_start_sites
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001241')
end
encodes_alternately_spliced_transcripts() click to toggle source

A gene that encodes more than one transcript. (purl.obolibrary.org/obo/SO_0000463)

# File lib/biointerchange/so.rb, line 3097
def self.encodes_alternately_spliced_transcripts
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000463')
end
encodes_different_polypeptides_different_stop() click to toggle source

A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons. (purl.obolibrary.org/obo/SO_1001190)

# File lib/biointerchange/so.rb, line 13403
def self.encodes_different_polypeptides_different_stop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001190')
end
encodes_disjoint_polypeptides() click to toggle source

A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences. (purl.obolibrary.org/obo/SO_1001192)

# File lib/biointerchange/so.rb, line 13415
def self.encodes_disjoint_polypeptides
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001192')
end
encodes_greater_than_1_polypeptide() click to toggle source

A gene that is alternately spliced, and encodes more than one polypeptide. (purl.obolibrary.org/obo/SO_1001189)

# File lib/biointerchange/so.rb, line 13397
def self.encodes_greater_than_1_polypeptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001189')
end
encodes_overlapping_peptides() click to toggle source

A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences. (purl.obolibrary.org/obo/SO_1001195)

# File lib/biointerchange/so.rb, line 13433
def self.encodes_overlapping_peptides
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001195')
end
encodes_overlapping_peptides_different_start() click to toggle source

A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons. (purl.obolibrary.org/obo/SO_1001191)

# File lib/biointerchange/so.rb, line 13409
def self.encodes_overlapping_peptides_different_start
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001191')
end
encodes_overlapping_polypeptides_different_start_and_stop() click to toggle source

A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons. (purl.obolibrary.org/obo/SO_1001193)

# File lib/biointerchange/so.rb, line 13421
def self.encodes_overlapping_polypeptides_different_start_and_stop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001193')
end
end_overlapping_gene() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000072)

# File lib/biointerchange/so.rb, line 749
def self.end_overlapping_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000072')
end
endogenous_retroviral_gene() click to toggle source

A proviral gene with origin endogenous retrovirus. (purl.obolibrary.org/obo/SO_0000100)

# File lib/biointerchange/so.rb, line 917
def self.endogenous_retroviral_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000100')
end
endogenous_retroviral_sequence() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000903)

# File lib/biointerchange/so.rb, line 5699
def self.endogenous_retroviral_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000903')
end
endonuclease_spliced_intron() click to toggle source

An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification. (purl.obolibrary.org/obo/SO_0001216)

# File lib/biointerchange/so.rb, line 7567
def self.endonuclease_spliced_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001216')
end
endosomal_localization_signal() click to toggle source

A polypeptide region that targets a polypeptide to the endosome. (purl.obolibrary.org/obo/SO_0001529)

# File lib/biointerchange/so.rb, line 9433
def self.endosomal_localization_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001529')
end
engineered() click to toggle source

An attribute to describe a region that was modified in vitro. (purl.obolibrary.org/obo/SO_0000783)

# File lib/biointerchange/so.rb, line 5015
def self.engineered
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000783')
end
engineered_DNA() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000793)

# File lib/biointerchange/so.rb, line 5075
def self.engineered_DNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000793')
end
engineered_episome() click to toggle source

An episome that is engineered. (purl.obolibrary.org/obo/SO_0000779)

# File lib/biointerchange/so.rb, line 4991
def self.engineered_episome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000779')
end
engineered_foreign_gene() click to toggle source

A gene that is engineered and foreign. (purl.obolibrary.org/obo/SO_0000281)

# File lib/biointerchange/so.rb, line 2007
def self.engineered_foreign_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000281')
end
engineered_foreign_region() click to toggle source

A region that is engineered and foreign. (purl.obolibrary.org/obo/SO_0000805)

# File lib/biointerchange/so.rb, line 5123
def self.engineered_foreign_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000805')
end
engineered_foreign_repetitive_element() click to toggle source

A repetitive element that is engineered and foreign. (purl.obolibrary.org/obo/SO_0000293)

# File lib/biointerchange/so.rb, line 2079
def self.engineered_foreign_repetitive_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000293')
end
engineered_foreign_transposable_element() click to toggle source

A transposable_element that is engineered and foreign. (purl.obolibrary.org/obo/SO_0000799)

# File lib/biointerchange/so.rb, line 5111
def self.engineered_foreign_transposable_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000799')
end
engineered_foreign_transposable_element_gene() click to toggle source

A transposable_element that is engineered and foreign. (purl.obolibrary.org/obo/SO_0000283)

# File lib/biointerchange/so.rb, line 2019
def self.engineered_foreign_transposable_element_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000283')
end
engineered_fusion_gene() click to toggle source

A fusion gene that is engineered. (purl.obolibrary.org/obo/SO_0000288)

# File lib/biointerchange/so.rb, line 2049
def self.engineered_fusion_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000288')
end
engineered_gene() click to toggle source

A gene that is engineered. (purl.obolibrary.org/obo/SO_0000280)

# File lib/biointerchange/so.rb, line 2001
def self.engineered_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000280')
end
engineered_insert() click to toggle source

A clone insert that is engineered. (purl.obolibrary.org/obo/SO_0000915)

# File lib/biointerchange/so.rb, line 5771
def self.engineered_insert
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000915')
end
engineered_plasmid() click to toggle source

A plasmid that is engineered. (purl.obolibrary.org/obo/SO_0000637)

# File lib/biointerchange/so.rb, line 4145
def self.engineered_plasmid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000637')
end
engineered_region() click to toggle source

A region that is engineered. (purl.obolibrary.org/obo/SO_0000804)

# File lib/biointerchange/so.rb, line 5117
def self.engineered_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000804')
end
engineered_rescue_region() click to toggle source

A rescue region that is engineered. (purl.obolibrary.org/obo/SO_0000794)

# File lib/biointerchange/so.rb, line 5081
def self.engineered_rescue_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000794')
end
engineered_tag() click to toggle source

A tag that is engineered. (purl.obolibrary.org/obo/SO_0000807)

# File lib/biointerchange/so.rb, line 5135
def self.engineered_tag
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000807')
end
engineered_transposable_element() click to toggle source

TE that has been modified by manipulations in vitro. (purl.obolibrary.org/obo/SO_0000798)

# File lib/biointerchange/so.rb, line 5105
def self.engineered_transposable_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000798')
end
enhanceosome() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001057)

# File lib/biointerchange/so.rb, line 6625
def self.enhanceosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001057')
end
enhancer() click to toggle source

A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter. (purl.obolibrary.org/obo/SO_0000165)

# File lib/biointerchange/so.rb, line 1307
def self.enhancer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000165')
end
enhancerRNA() click to toggle source

A short ncRNA that is transcribed from an enhancer. May have a regulatory function. (purl.obolibrary.org/obo/SO_0001870)

# File lib/biointerchange/so.rb, line 11425
def self.enhancerRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001870')
end
enhancer_attribute() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000402)

# File lib/biointerchange/so.rb, line 2727
def self.enhancer_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000402')
end
enhancer_binding_site() click to toggle source

A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues. (purl.obolibrary.org/obo/SO_0001461)

# File lib/biointerchange/so.rb, line 9025
def self.enhancer_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001461')
end
enhancer_bound_by_factor() click to toggle source

An enhancer bound by a factor. (purl.obolibrary.org/obo/SO_0000166)

# File lib/biointerchange/so.rb, line 1313
def self.enhancer_bound_by_factor
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000166')
end
enhancer_trap_construct() click to toggle source

An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic. (purl.obolibrary.org/obo/SO_0001479)

# File lib/biointerchange/so.rb, line 9133
def self.enhancer_trap_construct
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001479')
end
enzymatic() click to toggle source

An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein. (purl.obolibrary.org/obo/SO_0001185)

# File lib/biointerchange/so.rb, line 7381
def self.enzymatic
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001185')
end
enzymatic_RNA() click to toggle source

An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein. (purl.obolibrary.org/obo/SO_0000372)

# File lib/biointerchange/so.rb, line 2547
def self.enzymatic_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000372')
end
epigenetically_modified() click to toggle source

This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones. (purl.obolibrary.org/obo/SO_0000133)

# File lib/biointerchange/so.rb, line 1115
def self.epigenetically_modified
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000133')
end
epigenetically_modified_gene() click to toggle source

A gene that is epigenetically modified. (purl.obolibrary.org/obo/SO_0000898)

# File lib/biointerchange/so.rb, line 5669
def self.epigenetically_modified_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000898')
end
epigenetically_modified_region() click to toggle source

A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence. (purl.obolibrary.org/obo/SO_0001720)

# File lib/biointerchange/so.rb, line 10531
def self.epigenetically_modified_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001720')
end
episome() click to toggle source

A plasmid that may integrate with a chromosome. (purl.obolibrary.org/obo/SO_0000768)

# File lib/biointerchange/so.rb, line 4925
def self.episome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000768')
end
epitope() click to toggle source

A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells. (purl.obolibrary.org/obo/SO_0001018)

# File lib/biointerchange/so.rb, line 6383
def self.epitope
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001018')
end
epoxyqueuosine() click to toggle source

Epoxyqueuosine is a modified 7-deazoguanosine. (purl.obolibrary.org/obo/SO_0001318)

# File lib/biointerchange/so.rb, line 8173
def self.epoxyqueuosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001318')
end
eukaryotic_terminator() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000951)

# File lib/biointerchange/so.rb, line 5987
def self.eukaryotic_terminator
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000951')
end
evidence_for_feature() click to toggle source

B is evidence_for_feature A, if an instance of B supports the existence of A. (purl.obolibrary.org/obo/so_2_5_2.obo#evidence_for_feature)

# File lib/biointerchange/so.rb, line 77
def self.evidence_for_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#evidence_for_feature')
end
exemplar() click to toggle source

An attribute describing a sequence is representative of a class of similar sequences. (purl.obolibrary.org/obo/SO_0000864)

# File lib/biointerchange/so.rb, line 5465
def self.exemplar
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000864')
end
exemplar_mRNA() click to toggle source

An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group. (purl.obolibrary.org/obo/SO_0000734)

# File lib/biointerchange/so.rb, line 4727
def self.exemplar_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000734')
end
exemplar_of() click to toggle source

X is exemplar of Y if X is the best evidence for Y. (purl.obolibrary.org/obo/so_2_5_2.obo#exemplar_of)

# File lib/biointerchange/so.rb, line 83
def self.exemplar_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#exemplar_of')
end
exon() click to toggle source

A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing. (purl.obolibrary.org/obo/SO_0000147)

# File lib/biointerchange/so.rb, line 1199
def self.exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000147')
end
exon_junction() click to toggle source

The boundary between two exons in a processed transcript. (purl.obolibrary.org/obo/SO_0000333)

# File lib/biointerchange/so.rb, line 2319
def self.exon_junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000333')
end
exon_loss_variant() click to toggle source

A sequence variant whereby an exon is lost from the transcript. (purl.obolibrary.org/obo/SO_0001572)

# File lib/biointerchange/so.rb, line 9691
def self.exon_loss_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001572')
end
exon_of_single_exon_gene() click to toggle source

An exon that is the only exon in a gene. (purl.obolibrary.org/obo/SO_0005845)

# File lib/biointerchange/so.rb, line 12275
def self.exon_of_single_exon_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005845')
end
exon_region() click to toggle source

A region of an exon. (purl.obolibrary.org/obo/SO_0000852)

# File lib/biointerchange/so.rb, line 5393
def self.exon_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000852')
end
exon_variant() click to toggle source

A sequence variant that changes exon sequence. (purl.obolibrary.org/obo/SO_0001791)

# File lib/biointerchange/so.rb, line 10951
def self.exon_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001791')
end
exonic_splice_enhancer() click to toggle source

Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron. (purl.obolibrary.org/obo/SO_0000683)

# File lib/biointerchange/so.rb, line 4421
def self.exonic_splice_enhancer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000683')
end
experimental_feature() click to toggle source

A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. (purl.obolibrary.org/obo/SO_0001410)

# File lib/biointerchange/so.rb, line 8725
def self.experimental_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001410')
end
experimental_feature_attribute() click to toggle source

An attribute of an experimentally derived feature. (purl.obolibrary.org/obo/SO_0001684)

# File lib/biointerchange/so.rb, line 10315
def self.experimental_feature_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001684')
end
experimental_result_region() click to toggle source

A region of sequence implicated in an experimental result. (purl.obolibrary.org/obo/SO_0000703)

# File lib/biointerchange/so.rb, line 4541
def self.experimental_result_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000703')
end
experimentally_defined_binding_region() click to toggle source

A region that has been implicated in binding although the exact coordinates of binding may be unknown. (purl.obolibrary.org/obo/SO_0001696)

# File lib/biointerchange/so.rb, line 10387
def self.experimentally_defined_binding_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001696')
end
experimentally_determined() click to toggle source

Attribute to describe a feature that has been experimentally verified. (purl.obolibrary.org/obo/SO_0000312)

# File lib/biointerchange/so.rb, line 2193
def self.experimentally_determined
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000312')
end
expressed_sequence_assembly() click to toggle source

A sequence assembly derived from expressed sequences. (purl.obolibrary.org/obo/SO_0001428)

# File lib/biointerchange/so.rb, line 8833
def self.expressed_sequence_assembly
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001428')
end
expressed_sequence_match() click to toggle source

A match to an EST or cDNA sequence. (purl.obolibrary.org/obo/SO_0000102)

# File lib/biointerchange/so.rb, line 929
def self.expressed_sequence_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000102')
end
extended_cis_splice_site() click to toggle source

Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after. (purl.obolibrary.org/obo/SO_0001993)

# File lib/biointerchange/so.rb, line 12161
def self.extended_cis_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001993')
end
extended_intronic_splice_region() click to toggle source

Region of intronic sequence within 10 bases of an exon. (purl.obolibrary.org/obo/SO_0001996)

# File lib/biointerchange/so.rb, line 12179
def self.extended_intronic_splice_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001996')
end
extended_intronic_splice_region_variant() click to toggle source

A sequence variant occurring in the intron, within 10 bases of exon. (purl.obolibrary.org/obo/SO_0001995)

# File lib/biointerchange/so.rb, line 12173
def self.extended_intronic_splice_region_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001995')
end
external_transcribed_spacer_region() click to toggle source

Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA. (purl.obolibrary.org/obo/SO_0000640)

# File lib/biointerchange/so.rb, line 4163
def self.external_transcribed_spacer_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000640')
end
extrachromosomal_mobile_genetic_element() click to toggle source

An MGE that is not integrated into the host chromosome. (purl.obolibrary.org/obo/SO_0001038)

# File lib/biointerchange/so.rb, line 6503
def self.extrachromosomal_mobile_genetic_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001038')
end
extramembrane_polypeptide_region() click to toggle source

Polypeptide region that is localized outside of a lipid bilayer. (purl.obolibrary.org/obo/SO_0001072)

# File lib/biointerchange/so.rb, line 6703
def self.extramembrane_polypeptide_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001072')
end
feature_ablation() click to toggle source

A sequence variant, caused by an alteration of the genomic sequence, where the deletion, is greater than the extent of the underlying genomic features. (purl.obolibrary.org/obo/SO_0001879)

# File lib/biointerchange/so.rb, line 11479
def self.feature_ablation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001879')
end
feature_amplification() click to toggle source

A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features. (purl.obolibrary.org/obo/SO_0001880)

# File lib/biointerchange/so.rb, line 11485
def self.feature_amplification
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001880')
end
feature_attribute() click to toggle source

An attribute describing a located_sequence_feature. (purl.obolibrary.org/obo/SO_0000733)

# File lib/biointerchange/so.rb, line 4721
def self.feature_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000733')
end
feature_elongation() click to toggle source

A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence. (purl.obolibrary.org/obo/SO_0001907)

# File lib/biointerchange/so.rb, line 11647
def self.feature_elongation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001907')
end
feature_fusion() click to toggle source

A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features. (purl.obolibrary.org/obo/SO_0001882)

# File lib/biointerchange/so.rb, line 11497
def self.feature_fusion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001882')
end
feature_translocation() click to toggle source

A sequence variant, caused by an alteration of the genomic sequence, where the structural change, a translocation, is greater than the extent of the underlying genomic features. (purl.obolibrary.org/obo/SO_0001881)

# File lib/biointerchange/so.rb, line 11491
def self.feature_translocation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001881')
end
feature_truncation() click to toggle source

A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence. (purl.obolibrary.org/obo/SO_0001906)

# File lib/biointerchange/so.rb, line 11641
def self.feature_truncation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001906')
end
feature_variant() click to toggle source

A sequence variant that falls entirely or partially within a genomic feature. (purl.obolibrary.org/obo/SO_0001878)

# File lib/biointerchange/so.rb, line 11473
def self.feature_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001878')
end
fingerprint_map() click to toggle source

A fingerprint_map is a physical map composed of restriction fragments. (purl.obolibrary.org/obo/SO_0001250)

# File lib/biointerchange/so.rb, line 7765
def self.fingerprint_map
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001250')
end
finished_by() click to toggle source

Xy is finished_by Y if Y part of X, and X and Y share a 3’ boundary. (purl.obolibrary.org/obo/so_2_5_2.obo#finished_by)

# File lib/biointerchange/so.rb, line 89
def self.finished_by
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#finished_by')
end
finished_genome() click to toggle source

The status of a whole genome sequence, with less than 1 error per 100,000 base pairs. (purl.obolibrary.org/obo/SO_0001491)

# File lib/biointerchange/so.rb, line 9205
def self.finished_genome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001491')
end
finishes() click to toggle source

X finishes Y if X is part_of Y and X and Y share a 3’ or C terminal boundary. (purl.obolibrary.org/obo/so_2_5_2.obo#finishes)

# File lib/biointerchange/so.rb, line 95
def self.finishes
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#finishes')
end
five_aminomethyl_two_thiouridine() click to toggle source

5_aminomethyl_2_thiouridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001363)

# File lib/biointerchange/so.rb, line 8443
def self.five_aminomethyl_two_thiouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001363')
end
five_carbamoylmethyl_two_prime_O_methyluridine() click to toggle source

5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001368)

# File lib/biointerchange/so.rb, line 8473
def self.five_carbamoylmethyl_two_prime_O_methyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001368')
end
five_carbamoylmethyluridine() click to toggle source

5_carbamoylmethyluridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001367)

# File lib/biointerchange/so.rb, line 8467
def self.five_carbamoylmethyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001367')
end
five_carboxyhydroxymethyl_uridine() click to toggle source

5_carboxyhydroxymethyl_uridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001358)

# File lib/biointerchange/so.rb, line 8413
def self.five_carboxyhydroxymethyl_uridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001358')
end
five_carboxyhydroxymethyl_uridine_methyl_ester() click to toggle source

5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001359)

# File lib/biointerchange/so.rb, line 8419
def self.five_carboxyhydroxymethyl_uridine_methyl_ester
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001359')
end
five_carboxymethylaminomethyl_two_prime_O_methyluridine() click to toggle source

5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001370)

# File lib/biointerchange/so.rb, line 8485
def self.five_carboxymethylaminomethyl_two_prime_O_methyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001370')
end
five_carboxymethylaminomethyl_two_thiouridine() click to toggle source

5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001371)

# File lib/biointerchange/so.rb, line 8491
def self.five_carboxymethylaminomethyl_two_thiouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001371')
end
five_carboxymethylaminomethyluridine() click to toggle source

5_carboxymethylaminomethyluridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001369)

# File lib/biointerchange/so.rb, line 8479
def self.five_carboxymethylaminomethyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001369')
end
five_carboxymethyluridine() click to toggle source

5_carboxymethyluridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001374)

# File lib/biointerchange/so.rb, line 8509
def self.five_carboxymethyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001374')
end
five_formyl_two_prime_O_methylcytidine() click to toggle source

5-formyl-2’-O-methylcytidine is a modified cytidine. (purl.obolibrary.org/obo/SO_0001293)

# File lib/biointerchange/so.rb, line 8023
def self.five_formyl_two_prime_O_methylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001293')
end
five_formylcytidine() click to toggle source

5-formylcytidine is a modified cytidine. (purl.obolibrary.org/obo/SO_0001286)

# File lib/biointerchange/so.rb, line 7981
def self.five_formylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001286')
end
five_hydroxymethylcytidine() click to toggle source

5-hydroxymethylcytidine is a modified cytidine. (purl.obolibrary.org/obo/SO_0001292)

# File lib/biointerchange/so.rb, line 8017
def self.five_hydroxymethylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001292')
end
five_hydroxyuridine() click to toggle source

5_hydroxyuridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001354)

# File lib/biointerchange/so.rb, line 8389
def self.five_hydroxyuridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001354')
end
five_isopentenylaminomethyl_two_prime_O_methyluridine() click to toggle source

5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001382)

# File lib/biointerchange/so.rb, line 8557
def self.five_isopentenylaminomethyl_two_prime_O_methyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001382')
end
five_isopentenylaminomethyl_two_thiouridine() click to toggle source

5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001381)

# File lib/biointerchange/so.rb, line 8551
def self.five_isopentenylaminomethyl_two_thiouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001381')
end
five_isopentenylaminomethyl_uridine() click to toggle source

5_isopentenylaminomethyl_uridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001380)

# File lib/biointerchange/so.rb, line 8545
def self.five_isopentenylaminomethyl_uridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001380')
end
five_methoxycarbonylmethyl_two_prime_O_methyluridine() click to toggle source

Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001361)

# File lib/biointerchange/so.rb, line 8431
def self.five_methoxycarbonylmethyl_two_prime_O_methyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001361')
end
five_methoxycarbonylmethyl_two_thiouridine() click to toggle source

5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001362)

# File lib/biointerchange/so.rb, line 8437
def self.five_methoxycarbonylmethyl_two_thiouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001362')
end
five_methoxycarbonylmethyluridine() click to toggle source

Five_methoxycarbonylmethyluridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001360)

# File lib/biointerchange/so.rb, line 8425
def self.five_methoxycarbonylmethyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001360')
end
five_methoxyuridine() click to toggle source

5_methoxyuridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001355)

# File lib/biointerchange/so.rb, line 8395
def self.five_methoxyuridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001355')
end
five_methyl_2_thiouridine() click to toggle source

5_methyl_2_thiouridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001351)

# File lib/biointerchange/so.rb, line 8371
def self.five_methyl_2_thiouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001351')
end
five_methylaminomethyl_two_selenouridine() click to toggle source

5_methylaminomethyl_2_selenouridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001366)

# File lib/biointerchange/so.rb, line 8461
def self.five_methylaminomethyl_two_selenouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001366')
end
five_methylaminomethyl_two_thiouridine() click to toggle source

5_methylaminomethyl_2_thiouridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001365)

# File lib/biointerchange/so.rb, line 8455
def self.five_methylaminomethyl_two_thiouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001365')
end
five_methylaminomethyluridine() click to toggle source

5_methylaminomethyluridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001364)

# File lib/biointerchange/so.rb, line 8449
def self.five_methylaminomethyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001364')
end
five_methylcytidine() click to toggle source

5-methylcytidine is a modified cytidine. (purl.obolibrary.org/obo/SO_0001282)

# File lib/biointerchange/so.rb, line 7957
def self.five_methylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001282')
end
five_methyldihydrouridine() click to toggle source

5_methyldihydrouridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001376)

# File lib/biointerchange/so.rb, line 8521
def self.five_methyldihydrouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001376')
end
five_methyluridine() click to toggle source

5_methyluridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001344)

# File lib/biointerchange/so.rb, line 8329
def self.five_methyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001344')
end
five_prime_D_heptamer() click to toggle source

7 nucleotide recombination site (e.g. CACTGTG), part of a 5’ D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene. (purl.obolibrary.org/obo/SO_0000496)

# File lib/biointerchange/so.rb, line 3295
def self.five_prime_D_heptamer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000496')
end
five_prime_D_nonamer() click to toggle source

9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene. (purl.obolibrary.org/obo/SO_0000497)

# File lib/biointerchange/so.rb, line 3301
def self.five_prime_D_nonamer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000497')
end
five_prime_D_recombination_signal_sequence() click to toggle source

Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5’ D-nonamer (SO:0000497), 5’ D-spacer (SO:0000498), and 5’ D-heptamer (SO:0000396) in 5’ of the D-region of a D-gene, or in 5’ of the D-region of DJ-gene. (purl.obolibrary.org/obo/SO_0000556)

# File lib/biointerchange/so.rb, line 3659
def self.five_prime_D_recombination_signal_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000556')
end
five_prime_D_spacer() click to toggle source

12 or 23 nucleotide spacer between the 5’ D-heptamer (SO:0000496) and 5’ D-nonamer (SO:0000497) of a 5’ D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene. (purl.obolibrary.org/obo/SO_0000498)

# File lib/biointerchange/so.rb, line 3307
def self.five_prime_D_spacer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000498')
end
five_prime_EST() click to toggle source

An EST read from the 5’ end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family. (purl.obolibrary.org/obo/SO_0001208)

# File lib/biointerchange/so.rb, line 7519
def self.five_prime_EST
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001208')
end
five_prime_LTR() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000425)

# File lib/biointerchange/so.rb, line 2865
def self.five_prime_LTR
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000425')
end
five_prime_LTR_component() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000850)

# File lib/biointerchange/so.rb, line 5381
def self.five_prime_LTR_component
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000850')
end
five_prime_RST() click to toggle source

A tag produced from a single sequencing read from a 5’-RACE product; typically a few hundred base pairs long. (purl.obolibrary.org/obo/SO_0001469)

# File lib/biointerchange/so.rb, line 9073
def self.five_prime_RST
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001469')
end
five_prime_UST() click to toggle source

An UST located in the 5’UTR of a protein-coding transcript. (purl.obolibrary.org/obo/SO_0001466)

# File lib/biointerchange/so.rb, line 9055
def self.five_prime_UST
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001466')
end
five_prime_UTR() click to toggle source

A region at the 5’ end of a mature transcript (preceding the initiation codon) that is not translated into a protein. (purl.obolibrary.org/obo/SO_0000204)

# File lib/biointerchange/so.rb, line 1545
def self.five_prime_UTR
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000204')
end
five_prime_UTR_intron() click to toggle source

An intron located in the 5’ UTR. (purl.obolibrary.org/obo/SO_0000447)

# File lib/biointerchange/so.rb, line 3001
def self.five_prime_UTR_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000447')
end
five_prime_UTR_premature_start_codon_location_variant() click to toggle source

A 5’ UTR variant where a premature start codon is moved. (purl.obolibrary.org/obo/SO_0001990)

# File lib/biointerchange/so.rb, line 12143
def self.five_prime_UTR_premature_start_codon_location_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001990')
end
five_prime_cis_splice_site() click to toggle source

Intronic 2 bp region bordering the exon, at the 5’ edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron. (purl.obolibrary.org/obo/SO_0000163)

# File lib/biointerchange/so.rb, line 1295
def self.five_prime_cis_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000163')
end
five_prime_clip() click to toggle source

5’ most region of a precursor transcript that is clipped off during processing. (purl.obolibrary.org/obo/SO_0000555)

# File lib/biointerchange/so.rb, line 3653
def self.five_prime_clip
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000555')
end
five_prime_coding_exon() click to toggle source

The 5’ most coding exon. (purl.obolibrary.org/obo/SO_0000200)

# File lib/biointerchange/so.rb, line 1521
def self.five_prime_coding_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000200')
end
five_prime_coding_exon_coding_region() click to toggle source

The sequence of the five_prime_coding_exon that codes for protein. (purl.obolibrary.org/obo/SO_0000196)

# File lib/biointerchange/so.rb, line 1497
def self.five_prime_coding_exon_coding_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000196')
end
five_prime_coding_exon_noncoding_region() click to toggle source

The sequence of the 5’ exon preceding the start codon. (purl.obolibrary.org/obo/SO_0000486)

# File lib/biointerchange/so.rb, line 3235
def self.five_prime_coding_exon_noncoding_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000486')
end
five_prime_five_prime_overlap() click to toggle source

An attribute to describe a gene when the five prime region overlaps with another gene’s five prime region. (purl.obolibrary.org/obo/SO_0000074)

# File lib/biointerchange/so.rb, line 761
def self.five_prime_five_prime_overlap
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000074')
end
five_prime_flanking_region() click to toggle source

A flanking region located five prime of a specific region. (purl.obolibrary.org/obo/SO_0001416)

# File lib/biointerchange/so.rb, line 8761
def self.five_prime_flanking_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001416')
end
five_prime_intron() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000190)

# File lib/biointerchange/so.rb, line 1461
def self.five_prime_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000190')
end
five_prime_noncoding_exon() click to toggle source

Non-coding exon in the 5’ UTR. (purl.obolibrary.org/obo/SO_0000445)

# File lib/biointerchange/so.rb, line 2989
def self.five_prime_noncoding_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000445')
end
five_prime_open_reading_frame() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000629)

# File lib/biointerchange/so.rb, line 4097
def self.five_prime_open_reading_frame
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000629')
end
five_prime_recoding_site() click to toggle source

The recoding stimulatory signal located upstream of the recoding site. (purl.obolibrary.org/obo/SO_1001280)

# File lib/biointerchange/so.rb, line 13613
def self.five_prime_recoding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001280')
end
five_prime_restriction_enzyme_junction() click to toggle source

The restriction enzyme cleavage junction on the 5’ strand of the nucleotide sequence. (purl.obolibrary.org/obo/SO_0001689)

# File lib/biointerchange/so.rb, line 10345
def self.five_prime_restriction_enzyme_junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001689')
end
five_prime_sticky_end_restriction_enzyme_cleavage_site() click to toggle source

A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs. (purl.obolibrary.org/obo/SO_0001975)

# File lib/biointerchange/so.rb, line 12059
def self.five_prime_sticky_end_restriction_enzyme_cleavage_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001975')
end
five_prime_terminal_inverted_repeat() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000420)

# File lib/biointerchange/so.rb, line 2835
def self.five_prime_terminal_inverted_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000420')
end
five_prime_three_prime_overlap() click to toggle source

An attribute to describe a gene when the five prime region overlaps with another gene’s 3’ region. (purl.obolibrary.org/obo/SO_0000073)

# File lib/biointerchange/so.rb, line 755
def self.five_prime_three_prime_overlap
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000073')
end
five_taurinomethyl_two_thiouridine() click to toggle source

5_taurinomethyl_2_thiouridineis a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001379)

# File lib/biointerchange/so.rb, line 8539
def self.five_taurinomethyl_two_thiouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001379')
end
five_taurinomethyluridine() click to toggle source

5_taurinomethyluridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001378)

# File lib/biointerchange/so.rb, line 8533
def self.five_taurinomethyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001378')
end
five_two_prime_O_dimethylcytidine() click to toggle source

5,2’-O-dimethylcytidine is a modified cytidine. (purl.obolibrary.org/obo/SO_0001287)

# File lib/biointerchange/so.rb, line 7987
def self.five_two_prime_O_dimethylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001287')
end
five_two_prime_O_dimethyluridine() click to toggle source

5_2_prime_O_dimethyluridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001346)

# File lib/biointerchange/so.rb, line 8341
def self.five_two_prime_O_dimethyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001346')
end
fixed_variant() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001768)

# File lib/biointerchange/so.rb, line 10819
def self.fixed_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001768')
end
flanked() click to toggle source

An attribute describing a region that is bounded either side by a particular kind of region. (purl.obolibrary.org/obo/SO_0000357)

# File lib/biointerchange/so.rb, line 2463
def self.flanked
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000357')
end
flanking_region() click to toggle source

The sequences extending on either side of a specific region. (purl.obolibrary.org/obo/SO_0000239)

# File lib/biointerchange/so.rb, line 1755
def self.flanking_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000239')
end
flanking_three_prime_quadruplet_recoding_signal() click to toggle source

Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons. (purl.obolibrary.org/obo/SO_1001281)

# File lib/biointerchange/so.rb, line 13619
def self.flanking_three_prime_quadruplet_recoding_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001281')
end
floxed() click to toggle source

An attribute describing sequence that is flanked by Lox-P sites. (purl.obolibrary.org/obo/SO_0000359)

# File lib/biointerchange/so.rb, line 2469
def self.floxed
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000359')
end
floxed_gene() click to toggle source

A transgene that is floxed. (purl.obolibrary.org/obo/SO_0000363)

# File lib/biointerchange/so.rb, line 2493
def self.floxed_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000363')
end
foldback_element() click to toggle source

A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats. (purl.obolibrary.org/obo/SO_0000238)

# File lib/biointerchange/so.rb, line 1749
def self.foldback_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000238')
end
foreign() click to toggle source

An attribute to describe a region from another species. (purl.obolibrary.org/obo/SO_0000784)

# File lib/biointerchange/so.rb, line 5021
def self.foreign
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000784')
end
foreign_gene() click to toggle source

A gene that is foreign. (purl.obolibrary.org/obo/SO_0000285)

# File lib/biointerchange/so.rb, line 2031
def self.foreign_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000285')
end
foreign_transposable_element() click to toggle source

A transposable element that is foreign. (purl.obolibrary.org/obo/SO_0000720)

# File lib/biointerchange/so.rb, line 4643
def self.foreign_transposable_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000720')
end
forkhead_motif() click to toggle source

A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain. (purl.obolibrary.org/obo/SO_0001847)

# File lib/biointerchange/so.rb, line 11287
def self.forkhead_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001847')
end
forward() click to toggle source

Forward is an attribute of the feature, where the feature is in the 5’ to 3’ direction. (purl.obolibrary.org/obo/SO_0001030)

# File lib/biointerchange/so.rb, line 6455
def self.forward
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001030')
end
forward_primer() click to toggle source

A single stranded oligo used for polymerase chain reaction. (purl.obolibrary.org/obo/SO_0000121)

# File lib/biointerchange/so.rb, line 1043
def self.forward_primer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000121')
end
fosmid() click to toggle source

A cloning vector that utilizes the E. coli F factor. (purl.obolibrary.org/obo/SO_0000158)

# File lib/biointerchange/so.rb, line 1265
def self.fosmid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000158')
end
fosmid_clone() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000763)

# File lib/biointerchange/so.rb, line 4901
def self.fosmid_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000763')
end
four_bp_start_codon() click to toggle source

A non-canonical start codon with 4 base pairs. (purl.obolibrary.org/obo/SO_1001269)

# File lib/biointerchange/so.rb, line 13559
def self.four_bp_start_codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001269')
end
four_cutter_restriction_site() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000244)

# File lib/biointerchange/so.rb, line 1785
def self.four_cutter_restriction_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000244')
end
four_demethylwyosine() click to toggle source

4_demethylwyosine is a modified guanosine base feature. (purl.obolibrary.org/obo/SO_0001341)

# File lib/biointerchange/so.rb, line 8311
def self.four_demethylwyosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001341')
end
four_thiouridine() click to toggle source

4_thiouridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001350)

# File lib/biointerchange/so.rb, line 8365
def self.four_thiouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001350')
end
fragment_assembly() click to toggle source

A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths. (purl.obolibrary.org/obo/SO_0001249)

# File lib/biointerchange/so.rb, line 7759
def self.fragment_assembly
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001249')
end
fragmentary() click to toggle source

An attribute to describe a feature that is incomplete. (purl.obolibrary.org/obo/SO_0000731)

# File lib/biointerchange/so.rb, line 4709
def self.fragmentary
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000731')
end
frame_restoring_sequence_variant() click to toggle source

A mutation that reverts the sequence of a previous frameshift mutation back to the initial frame. (purl.obolibrary.org/obo/SO_1000110)

# File lib/biointerchange/so.rb, line 13055
def self.frame_restoring_sequence_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000110')
end
frame_restoring_variant() click to toggle source

A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame. (purl.obolibrary.org/obo/SO_0001591)

# File lib/biointerchange/so.rb, line 9787
def self.frame_restoring_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001591')
end
frameshift() click to toggle source

An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3. (purl.obolibrary.org/obo/SO_0000865)

# File lib/biointerchange/so.rb, line 5471
def self.frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000865')
end
frameshift_elongation() click to toggle source

A frameshift variant that causes the translational reading frame to be extended relative to the reference feature. (purl.obolibrary.org/obo/SO_0001909)

# File lib/biointerchange/so.rb, line 11659
def self.frameshift_elongation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001909')
end
frameshift_sequence_variation() click to toggle source

A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three. (purl.obolibrary.org/obo/SO_1000065)

# File lib/biointerchange/so.rb, line 12803
def self.frameshift_sequence_variation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000065')
end
frameshift_truncation() click to toggle source

A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature. (purl.obolibrary.org/obo/SO_0001910)

# File lib/biointerchange/so.rb, line 11665
def self.frameshift_truncation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001910')
end
frameshift_variant() click to toggle source

A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three. (purl.obolibrary.org/obo/SO_0001589)

# File lib/biointerchange/so.rb, line 9775
def self.frameshift_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001589')
end
free() click to toggle source

The quality of a duplication where the new region exists independently of the original. (purl.obolibrary.org/obo/SO_0001516)

# File lib/biointerchange/so.rb, line 9355
def self.free
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001516')
end
free_chromosome_arm() click to toggle source

A chromosome structure variation whereby an arm exists as an individual chromosome element. (purl.obolibrary.org/obo/SO_0000065)

# File lib/biointerchange/so.rb, line 707
def self.free_chromosome_arm
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000065')
end
free_duplication() click to toggle source

A chromosome structure variation whereby the duplicated sequences are carried as a free centric element. (purl.obolibrary.org/obo/SO_1000144)

# File lib/biointerchange/so.rb, line 13199
def self.free_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000144')
end
free_ring_duplication() click to toggle source

A ring chromosome which is a copy of another chromosome. (purl.obolibrary.org/obo/SO_1000145)

# File lib/biointerchange/so.rb, line 13205
def self.free_ring_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000145')
end
functional_candidate_gene() click to toggle source

A candidate gene whose function has something in common biologically with the trait under investigation. (purl.obolibrary.org/obo/SO_0001869)

# File lib/biointerchange/so.rb, line 11419
def self.functional_candidate_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001869')
end
functional_variant() click to toggle source

A sequence variant in which the function of a gene product is altered with respect to a reference. (purl.obolibrary.org/obo/SO_0001536)

# File lib/biointerchange/so.rb, line 9475
def self.functional_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001536')
end
fusion() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000806)

# File lib/biointerchange/so.rb, line 5129
def self.fusion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000806')
end
fusion_gene() click to toggle source

A gene that is a fusion. (purl.obolibrary.org/obo/SO_0000287)

# File lib/biointerchange/so.rb, line 2043
def self.fusion_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000287')
end
gRNA_encoding() click to toggle source

A non-protein_coding gene that encodes a guide_RNA. (purl.obolibrary.org/obo/SO_0000979)

# File lib/biointerchange/so.rb, line 6149
def self.gRNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000979')
end
gRNA_gene() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001264)

# File lib/biointerchange/so.rb, line 7849
def self.gRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001264')
end
gained() click to toggle source

X gained Y if X is a variant_of X’ and Y part of X but not X’. (purl.obolibrary.org/obo/so_2_5_2.obo#gained)

# File lib/biointerchange/so.rb, line 101
def self.gained
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#gained')
end
galactosyl_queuosine() click to toggle source

Galactosyl_queuosine is a modified 7-deazoguanosine. (purl.obolibrary.org/obo/SO_0001319)

# File lib/biointerchange/so.rb, line 8179
def self.galactosyl_queuosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001319')
end
gamma_turn() click to toggle source

Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees. (purl.obolibrary.org/obo/SO_0001138)

# File lib/biointerchange/so.rb, line 7099
def self.gamma_turn
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001138')
end
gamma_turn_classic() click to toggle source

Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0. (purl.obolibrary.org/obo/SO_0001139)

# File lib/biointerchange/so.rb, line 7105
def self.gamma_turn_classic
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001139')
end
gamma_turn_inverse() click to toggle source

Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0. (purl.obolibrary.org/obo/SO_0001140)

# File lib/biointerchange/so.rb, line 7111
def self.gamma_turn_inverse
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001140')
end
gap() click to toggle source

A gap in the sequence of known length. The unknown bases are filled in with N’s. (purl.obolibrary.org/obo/SO_0000730)

# File lib/biointerchange/so.rb, line 4703
def self.gap
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000730')
end
gene() click to toggle source

A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. (purl.obolibrary.org/obo/SO_0000704)

# File lib/biointerchange/so.rb, line 4547
def self.gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000704')
end
gene_array() click to toggle source

An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so. (purl.obolibrary.org/obo/SO_0005851)

# File lib/biointerchange/so.rb, line 12305
def self.gene_array
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005851')
end
gene_array_member() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000081)

# File lib/biointerchange/so.rb, line 803
def self.gene_array_member
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000081')
end
gene_attribute() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000401)

# File lib/biointerchange/so.rb, line 2721
def self.gene_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000401')
end
gene_by_genome_location() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000085)

# File lib/biointerchange/so.rb, line 827
def self.gene_by_genome_location
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000085')
end
gene_by_organelle_of_genome() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000086)

# File lib/biointerchange/so.rb, line 833
def self.gene_by_organelle_of_genome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000086')
end
gene_by_polyadenylation_attribute() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000066)

# File lib/biointerchange/so.rb, line 713
def self.gene_by_polyadenylation_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000066')
end
gene_by_transcript_attribute() click to toggle source

This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s). A product of SO meeting 2004. (purl.obolibrary.org/obo/SO_0000064)

# File lib/biointerchange/so.rb, line 701
def self.gene_by_transcript_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000064')
end
gene_cassette() click to toggle source

A gene that can be substituted for a related gene at a different site in the genome. (purl.obolibrary.org/obo/SO_0005853)

# File lib/biointerchange/so.rb, line 12317
def self.gene_cassette
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005853')
end
gene_cassette_array() click to toggle source

An array of non-functional genes whose members, when captured by recombination form functional genes. (purl.obolibrary.org/obo/SO_0005854)

# File lib/biointerchange/so.rb, line 12323
def self.gene_cassette_array
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005854')
end
gene_cassette_member() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0005848)

# File lib/biointerchange/so.rb, line 12287
def self.gene_cassette_member
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005848')
end
gene_class() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000009)

# File lib/biointerchange/so.rb, line 369
def self.gene_class
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000009')
end
gene_component_region() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000842)

# File lib/biointerchange/so.rb, line 5333
def self.gene_component_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000842')
end
gene_fragment() click to toggle source

This term is mapped to MGED. Do not obsolete without consulting MGED ontology. (purl.obolibrary.org/obo/SO_0000997)

# File lib/biointerchange/so.rb, line 6257
def self.gene_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000997')
end
gene_fusion() click to toggle source

A sequence variant whereby a two genes have become joined. (purl.obolibrary.org/obo/SO_0001565)

# File lib/biointerchange/so.rb, line 9649
def self.gene_fusion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001565')
end
gene_group() click to toggle source

A collection of related genes. (purl.obolibrary.org/obo/SO_0005855)

# File lib/biointerchange/so.rb, line 12329
def self.gene_group
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005855')
end
gene_group_regulatory_region() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000752)

# File lib/biointerchange/so.rb, line 4835
def self.gene_group_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000752')
end
gene_member_region() click to toggle source

A region of a gene. (purl.obolibrary.org/obo/SO_0000831)

# File lib/biointerchange/so.rb, line 5267
def self.gene_member_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000831')
end
gene_not_polyadenylated() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000438)

# File lib/biointerchange/so.rb, line 2947
def self.gene_not_polyadenylated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000438')
end
gene_part() click to toggle source

A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene. (purl.obolibrary.org/obo/SO_0000050)

# File lib/biointerchange/so.rb, line 609
def self.gene_part
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000050')
end
gene_rearranged_at_DNA_level() click to toggle source

An epigenetically modified gene, rearranged at the DNA level. (purl.obolibrary.org/obo/SO_0000138)

# File lib/biointerchange/so.rb, line 1145
def self.gene_rearranged_at_DNA_level
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000138')
end
gene_segment() click to toggle source

A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination. (purl.obolibrary.org/obo/SO_3000000)

# File lib/biointerchange/so.rb, line 13673
def self.gene_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_3000000')
end
gene_sensu_your_favorite_organism() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000008)

# File lib/biointerchange/so.rb, line 363
def self.gene_sensu_your_favorite_organism
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000008')
end
gene_silenced_by_DNA_methylation() click to toggle source

A gene that is silenced by DNA methylation. (purl.obolibrary.org/obo/SO_0000129)

# File lib/biointerchange/so.rb, line 1091
def self.gene_silenced_by_DNA_methylation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000129')
end
gene_silenced_by_DNA_modification() click to toggle source

A gene that is silenced by DNA modification. (purl.obolibrary.org/obo/SO_0000128)

# File lib/biointerchange/so.rb, line 1085
def self.gene_silenced_by_DNA_modification
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000128')
end
gene_silenced_by_RNA_interference() click to toggle source

A gene that is silenced by RNA interference. (purl.obolibrary.org/obo/SO_0001224)

# File lib/biointerchange/so.rb, line 7615
def self.gene_silenced_by_RNA_interference
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001224')
end
gene_silenced_by_histone_deacetylation() click to toggle source

A gene that is silenced by histone deacetylation. (purl.obolibrary.org/obo/SO_0001227)

# File lib/biointerchange/so.rb, line 7633
def self.gene_silenced_by_histone_deacetylation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001227')
end
gene_silenced_by_histone_methylation() click to toggle source

A gene that is silenced by histone methylation. (purl.obolibrary.org/obo/SO_0001226)

# File lib/biointerchange/so.rb, line 7627
def self.gene_silenced_by_histone_methylation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001226')
end
gene_silenced_by_histone_modification() click to toggle source

A gene that is silenced by histone modification. (purl.obolibrary.org/obo/SO_0001225)

# File lib/biointerchange/so.rb, line 7621
def self.gene_silenced_by_histone_modification
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001225')
end
gene_subarray() click to toggle source

A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function. (purl.obolibrary.org/obo/SO_0005852)

# File lib/biointerchange/so.rb, line 12311
def self.gene_subarray
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005852')
end
gene_subarray_member() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0005849)

# File lib/biointerchange/so.rb, line 12293
def self.gene_subarray_member
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005849')
end
gene_to_gene_feature() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000067)

# File lib/biointerchange/so.rb, line 719
def self.gene_to_gene_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000067')
end
gene_trap_construct() click to toggle source

A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker. (purl.obolibrary.org/obo/SO_0001477)

# File lib/biointerchange/so.rb, line 9121
def self.gene_trap_construct
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001477')
end
gene_variant() click to toggle source

A sequence variant where the structure of the gene is changed. (purl.obolibrary.org/obo/SO_0001564)

# File lib/biointerchange/so.rb, line 9643
def self.gene_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001564')
end
gene_with_dicistronic_mRNA() click to toggle source

A gene that encodes a polycistronic mRNA. (purl.obolibrary.org/obo/SO_0000722)

# File lib/biointerchange/so.rb, line 4655
def self.gene_with_dicistronic_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000722')
end
gene_with_dicistronic_primary_transcript() click to toggle source

A gene that encodes a dicistronic primary transcript. (purl.obolibrary.org/obo/SO_0000721)

# File lib/biointerchange/so.rb, line 4649
def self.gene_with_dicistronic_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000721')
end
gene_with_dicistronic_transcript() click to toggle source

A gene that encodes a dicistronic transcript. (purl.obolibrary.org/obo/SO_0000692)

# File lib/biointerchange/so.rb, line 4475
def self.gene_with_dicistronic_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000692')
end
gene_with_edited_transcript() click to toggle source

A gene that encodes a transcript that is edited. (purl.obolibrary.org/obo/SO_0000548)

# File lib/biointerchange/so.rb, line 3607
def self.gene_with_edited_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000548')
end
gene_with_mRNA_recoded_by_translational_bypass() click to toggle source

A gene with mRNA recoded by translational bypass. (purl.obolibrary.org/obo/SO_0000711)

# File lib/biointerchange/so.rb, line 4589
def self.gene_with_mRNA_recoded_by_translational_bypass
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000711')
end
gene_with_mRNA_with_frameshift() click to toggle source

A gene that encodes an mRNA with a frameshift. (purl.obolibrary.org/obo/SO_0000455)

# File lib/biointerchange/so.rb, line 3049
def self.gene_with_mRNA_with_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000455')
end
gene_with_non_canonical_start_codon() click to toggle source

A gene with a start codon other than AUG. (purl.obolibrary.org/obo/SO_0001739)

# File lib/biointerchange/so.rb, line 10645
def self.gene_with_non_canonical_start_codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001739')
end
gene_with_polyadenylated_mRNA() click to toggle source

A gene that encodes a polyadenylated mRNA. (purl.obolibrary.org/obo/SO_0000451)

# File lib/biointerchange/so.rb, line 3025
def self.gene_with_polyadenylated_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000451')
end
gene_with_polycistronic_transcript() click to toggle source

A gene that encodes a polycistronic transcript. (purl.obolibrary.org/obo/SO_0000690)

# File lib/biointerchange/so.rb, line 4463
def self.gene_with_polycistronic_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000690')
end
gene_with_recoded_mRNA() click to toggle source

A gene that encodes an mRNA that is recoded. (purl.obolibrary.org/obo/SO_0000693)

# File lib/biointerchange/so.rb, line 4481
def self.gene_with_recoded_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000693')
end
gene_with_start_codon_CUG() click to toggle source

A gene with a translational start codon of CUG. (purl.obolibrary.org/obo/SO_0001740)

# File lib/biointerchange/so.rb, line 10651
def self.gene_with_start_codon_CUG
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001740')
end
gene_with_stop_codon_read_through() click to toggle source

A gene that encodes a transcript with stop codon readthrough. (purl.obolibrary.org/obo/SO_0000697)

# File lib/biointerchange/so.rb, line 4505
def self.gene_with_stop_codon_read_through
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000697')
end
gene_with_stop_codon_redefined_as_pyrrolysine() click to toggle source

A gene encoding an mRNA that has the stop codon redefined as pyrrolysine. (purl.obolibrary.org/obo/SO_0000698)

# File lib/biointerchange/so.rb, line 4511
def self.gene_with_stop_codon_redefined_as_pyrrolysine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000698')
end
gene_with_stop_codon_redefined_as_selenocysteine() click to toggle source

A gene encoding an mRNA that has the stop codon redefined as selenocysteine. (purl.obolibrary.org/obo/SO_0000710)

# File lib/biointerchange/so.rb, line 4583
def self.gene_with_stop_codon_redefined_as_selenocysteine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000710')
end
gene_with_trans_spliced_transcript() click to toggle source

A gene with a transcript that is trans-spliced. (purl.obolibrary.org/obo/SO_0000459)

# File lib/biointerchange/so.rb, line 3073
def self.gene_with_trans_spliced_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000459')
end
gene_with_transcript_with_translational_frameshift() click to toggle source

A gene encoding a transcript that has a translational frameshift. (purl.obolibrary.org/obo/SO_0000712)

# File lib/biointerchange/so.rb, line 4595
def self.gene_with_transcript_with_translational_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000712')
end
genetic_marker() click to toggle source

A measurable sequence feature that varies within a population. (purl.obolibrary.org/obo/SO_0001645)

# File lib/biointerchange/so.rb, line 10105
def self.genetic_marker
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001645')
end
genome() click to toggle source

A genome is the sum of genetic material within a cell or virion. (purl.obolibrary.org/obo/SO_0001026)

# File lib/biointerchange/so.rb, line 6431
def self.genome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001026')
end
genome_of() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/so_2_5_2.obo#genome_of)

# File lib/biointerchange/so.rb, line 107
def self.genome_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#genome_of')
end
genomic_DNA() click to toggle source

This term is mapped to MGED. Do not obsolete without consulting MGED ontology. (purl.obolibrary.org/obo/SO_0000991)

# File lib/biointerchange/so.rb, line 6221
def self.genomic_DNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000991')
end
genomic_DNA_read() click to toggle source

A sequencer read of a genomic DNA substrate. (purl.obolibrary.org/obo/SO_0001828)

# File lib/biointerchange/so.rb, line 11173
def self.genomic_DNA_read
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001828')
end
genomic_clone() click to toggle source

A clone of a DNA region of a genome. (purl.obolibrary.org/obo/SO_0000040)

# File lib/biointerchange/so.rb, line 549
def self.genomic_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000040')
end
genomic_island() click to toggle source

A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility. (purl.obolibrary.org/obo/SO_0000772)

# File lib/biointerchange/so.rb, line 4949
def self.genomic_island
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000772')
end
genomically_contaminated_cDNA_clone() click to toggle source

A cDNA clone invalidated by genomic contamination. (purl.obolibrary.org/obo/SO_0000811)

# File lib/biointerchange/so.rb, line 5159
def self.genomically_contaminated_cDNA_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000811')
end
genomically_imprinted() click to toggle source

Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin. (purl.obolibrary.org/obo/SO_0000134)

# File lib/biointerchange/so.rb, line 1121
def self.genomically_imprinted
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000134')
end
genotype() click to toggle source

A genotype is a variant genome, complete or incomplete. (purl.obolibrary.org/obo/SO_0001027)

# File lib/biointerchange/so.rb, line 6437
def self.genotype
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001027')
end
germline_variant() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001778)

# File lib/biointerchange/so.rb, line 10879
def self.germline_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001778')
end
glutamic_acid() click to toggle source

A place holder for a cross product with chebi. (purl.obolibrary.org/obo/SO_0001454)

# File lib/biointerchange/so.rb, line 8983
def self.glutamic_acid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001454')
end
glutamic_acid_tRNA_primary_transcript() click to toggle source

A primary transcript encoding glutaminyl tRNA (SO:0000260). (purl.obolibrary.org/obo/SO_0000216)

# File lib/biointerchange/so.rb, line 1617
def self.glutamic_acid_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000216')
end
glutamine() click to toggle source

A place holder for a cross product with chebi. (purl.obolibrary.org/obo/SO_0001448)

# File lib/biointerchange/so.rb, line 8947
def self.glutamine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001448')
end
glutamine_tRNA_primary_transcript() click to toggle source

A primary transcript encoding glutamyl tRNA (SO:0000260). (purl.obolibrary.org/obo/SO_0000217)

# File lib/biointerchange/so.rb, line 1623
def self.glutamine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000217')
end
glutaminyl_tRNA() click to toggle source

A tRNA sequence that has a glutamine anticodon, and a 3’ glutamine binding region. (purl.obolibrary.org/obo/SO_0000259)

# File lib/biointerchange/so.rb, line 1875
def self.glutaminyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000259')
end
glutamyl_tRNA() click to toggle source

A tRNA sequence that has a glutamic acid anticodon, and a 3’ glutamic acid binding region. (purl.obolibrary.org/obo/SO_0000260)

# File lib/biointerchange/so.rb, line 1881
def self.glutamyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000260')
end
glycine() click to toggle source

A place holder for a cross product with chebi. (purl.obolibrary.org/obo/SO_0001443)

# File lib/biointerchange/so.rb, line 8917
def self.glycine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001443')
end
glycine_tRNA_primary_transcript() click to toggle source

A primary transcript encoding glycyl tRNA (SO:0000263). (purl.obolibrary.org/obo/SO_0000218)

# File lib/biointerchange/so.rb, line 1629
def self.glycine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000218')
end
glycyl_tRNA() click to toggle source

A tRNA sequence that has a glycine anticodon, and a 3’ glycine binding region. (purl.obolibrary.org/obo/SO_0000261)

# File lib/biointerchange/so.rb, line 1887
def self.glycyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000261')
end
golden_path() click to toggle source

A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence. (purl.obolibrary.org/obo/SO_0000688)

# File lib/biointerchange/so.rb, line 4451
def self.golden_path
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000688')
end
golden_path_fragment() click to toggle source

One of the pieces of sequence that make up a golden path. (purl.obolibrary.org/obo/SO_0000468)

# File lib/biointerchange/so.rb, line 3127
def self.golden_path_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000468')
end
group_1_intron_homing_endonuclease_target_region() click to toggle source

A region of intronic nucleotide sequence targeted by a nuclease enzyme. (purl.obolibrary.org/obo/SO_0000354)

# File lib/biointerchange/so.rb, line 2445
def self.group_1_intron_homing_endonuclease_target_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000354')
end
group_IIA_intron() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000381)

# File lib/biointerchange/so.rb, line 2601
def self.group_IIA_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000381')
end
group_IIB_intron() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000382)

# File lib/biointerchange/so.rb, line 2607
def self.group_IIB_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000382')
end
group_III_intron() click to toggle source

Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile. (purl.obolibrary.org/obo/SO_0001213)

# File lib/biointerchange/so.rb, line 7549
def self.group_III_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001213')
end
group_II_intron() click to toggle source

Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2’ hydroxyl of a bulged adenosine in domain VI attacks the 5’ splice site, followed by nucleophilic attack on the 3’ splice site by the 3’ OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3’ splice site, some tertiary interactions, and intronic ORF phylogeny. (purl.obolibrary.org/obo/SO_0000603)

# File lib/biointerchange/so.rb, line 3941
def self.group_II_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000603')
end
group_I_intron() click to toggle source

Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions. (purl.obolibrary.org/obo/SO_0000587)

# File lib/biointerchange/so.rb, line 3845
def self.group_I_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000587')
end
guide_RNA() click to toggle source

A short 3’-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA. (purl.obolibrary.org/obo/SO_0000602)

# File lib/biointerchange/so.rb, line 3935
def self.guide_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000602')
end
guide_RNA_region() click to toggle source

A region of guide RNA. (purl.obolibrary.org/obo/SO_0000930)

# File lib/biointerchange/so.rb, line 5861
def self.guide_RNA_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000930')
end
guided_by() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/so_2_5_2.obo#guided_by)

# File lib/biointerchange/so.rb, line 113
def self.guided_by
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#guided_by')
end
guides() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/so_2_5_2.obo#guides)

# File lib/biointerchange/so.rb, line 119
def self.guides
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#guides')
end
hammerhead_ribozyme() click to toggle source

A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter’s hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs. (purl.obolibrary.org/obo/SO_0000380)

# File lib/biointerchange/so.rb, line 2595
def self.hammerhead_ribozyme
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000380')
end
haplotype() click to toggle source

A haplotype is one of a set of coexisting sequence variants of a haplotype block. (purl.obolibrary.org/obo/SO_0001024)

# File lib/biointerchange/so.rb, line 6419
def self.haplotype
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001024')
end
haplotype_block() click to toggle source

A region of the genome which is co-inherited as the result of the lack of historic recombination within it. (purl.obolibrary.org/obo/SO_0000355)

# File lib/biointerchange/so.rb, line 2451
def self.haplotype_block
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000355')
end
has_integral_part() click to toggle source

X has_integral_part Y if and only if: X has_part Y and Y part_of X. (purl.obolibrary.org/obo/so_2_5_2.obo#has_integral_part)

# File lib/biointerchange/so.rb, line 125
def self.has_integral_part
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#has_integral_part')
end
has_origin() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/so_2_5_2.obo#has_origin)

# File lib/biointerchange/so.rb, line 131
def self.has_origin
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#has_origin')
end
has_parent?(uri, parent) click to toggle source

Recursively tries to determine the parent for a given URI.

uri

URI that is tested for whether it has the given parent URI.

parent

Parent URI.

# File lib/biointerchange/so.rb, line 20563
def self.has_parent?(uri, parent)
  if @@parent_properties.has_key?(uri) then
    if @@parent_properties[uri] == parent then
      return true
    end
    return has_parent?(@@parent_properties[uri], parent)
  end
  return false
end
has_part() click to toggle source

Inverse of part_of. (purl.obolibrary.org/obo/so_2_5_2.obo#has_part)

# File lib/biointerchange/so.rb, line 137
def self.has_part
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#has_part')
end
has_quality() click to toggle source

The relationship between a feature and an attribute. (purl.obolibrary.org/obo/so_2_5_2.obo#has_quality)

# File lib/biointerchange/so.rb, line 143
def self.has_quality
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#has_quality')
end
helitron() click to toggle source

A rolling circle transposon. Autonomous helitrons encode a 5’-to-3’ DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons. (purl.obolibrary.org/obo/SO_0000544)

# File lib/biointerchange/so.rb, line 3583
def self.helitron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000544')
end
helix_turn_helix() click to toggle source

A motif comprising two helices separated by a turn. (purl.obolibrary.org/obo/SO_0001081)

# File lib/biointerchange/so.rb, line 6757
def self.helix_turn_helix
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001081')
end
heptamer_of_recombination_feature_of_vertebrate_immune_system_gene() click to toggle source

Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene. (purl.obolibrary.org/obo/SO_0000561)

# File lib/biointerchange/so.rb, line 3689
def self.heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000561')
end
heritable_phenotypic_marker() click to toggle source

A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus. (purl.obolibrary.org/obo/SO_0001500)

# File lib/biointerchange/so.rb, line 9259
def self.heritable_phenotypic_marker
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001500')
end
hetero_compound_chromosome() click to toggle source

A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them. (purl.obolibrary.org/obo/SO_1000140)

# File lib/biointerchange/so.rb, line 13175
def self.hetero_compound_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000140')
end
high_identity_region() click to toggle source

An experimental feature with high sequence identity to another sequence. (purl.obolibrary.org/obo/SO_0001502)

# File lib/biointerchange/so.rb, line 9271
def self.high_identity_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001502')
end
high_quality_draft() click to toggle source

The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome. (purl.obolibrary.org/obo/SO_0001487)

# File lib/biointerchange/so.rb, line 9181
def self.high_quality_draft
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001487')
end
histidine() click to toggle source

A place holder for a cross product with chebi. (purl.obolibrary.org/obo/SO_0001452)

# File lib/biointerchange/so.rb, line 8971
def self.histidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001452')
end
histidine_tRNA_primary_transcript() click to toggle source

A primary transcript encoding histidyl tRNA (SO:0000262). (purl.obolibrary.org/obo/SO_0000219)

# File lib/biointerchange/so.rb, line 1635
def self.histidine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000219')
end
histidyl_tRNA() click to toggle source

A tRNA sequence that has a histidine anticodon, and a 3’ histidine binding region. (purl.obolibrary.org/obo/SO_0000262)

# File lib/biointerchange/so.rb, line 1893
def self.histidyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000262')
end
histone_3_acetylation_site() click to toggle source

A histone 3 modification where the modification is the acylation of the residue. (purl.obolibrary.org/obo/SO_0001973)

# File lib/biointerchange/so.rb, line 12047
def self.histone_3_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001973')
end
histone_4_acylation_site() click to toggle source

A histone 4 modification where the modification is the acylation of the residue. (purl.obolibrary.org/obo/SO_0001972)

# File lib/biointerchange/so.rb, line 12041
def self.histone_4_acylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001972')
end
histone_acetylation_site() click to toggle source

A histone modification where the modification is the acylation of the residue. (purl.obolibrary.org/obo/SO_0001702)

# File lib/biointerchange/so.rb, line 10423
def self.histone_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001702')
end
histone_acylation_region() click to toggle source

A histone modification, whereby the histone protein is acylated at multiple sites in a region. (purl.obolibrary.org/obo/SO_0001737)

# File lib/biointerchange/so.rb, line 10633
def self.histone_acylation_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001737')
end
histone_binding_site() click to toggle source

A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone. (purl.obolibrary.org/obo/SO_0001383)

# File lib/biointerchange/so.rb, line 8563
def self.histone_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001383')
end
histone_methylation_site() click to toggle source

A histone modification site where the modification is the methylation of the residue. (purl.obolibrary.org/obo/SO_0001701)

# File lib/biointerchange/so.rb, line 10417
def self.histone_methylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001701')
end
histone_modification() click to toggle source

Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation. (purl.obolibrary.org/obo/SO_0001700)

# File lib/biointerchange/so.rb, line 10411
def self.histone_modification
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001700')
end
histone_ubiqitination_site() click to toggle source

A histone modification site where ubiquitin may be added. (purl.obolibrary.org/obo/SO_0001716)

# File lib/biointerchange/so.rb, line 10507
def self.histone_ubiqitination_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001716')
end
homing_endonuclease_binding_site() click to toggle source

The binding site (recognition site) of a homing endonuclease. The binding site is typically large. (purl.obolibrary.org/obo/SO_0001257)

# File lib/biointerchange/so.rb, line 7807
def self.homing_endonuclease_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001257')
end
homo_compound_chromosome() click to toggle source

A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved. (purl.obolibrary.org/obo/SO_1000138)

# File lib/biointerchange/so.rb, line 13169
def self.homo_compound_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000138')
end
homol_D_box() click to toggle source

A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence. (purl.obolibrary.org/obo/SO_0001848)

# File lib/biointerchange/so.rb, line 11293
def self.homol_D_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001848')
end
homol_E_box() click to toggle source

A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence. (purl.obolibrary.org/obo/SO_0001849)

# File lib/biointerchange/so.rb, line 11299
def self.homol_E_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001849')
end
homologous() click to toggle source

Similarity due to common ancestry. (purl.obolibrary.org/obo/SO_0000857)

# File lib/biointerchange/so.rb, line 5423
def self.homologous
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000857')
end
homologous_region() click to toggle source

A region that is homologous to another region. (purl.obolibrary.org/obo/SO_0000853)

# File lib/biointerchange/so.rb, line 5399
def self.homologous_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000853')
end
homologous_to() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/so_2_5_2.obo#homologous_to)

# File lib/biointerchange/so.rb, line 149
def self.homologous_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#homologous_to')
end
hydrophobic_region_of_peptide() click to toggle source

Hydrophobic regions are regions with a low affinity for water. (purl.obolibrary.org/obo/SO_0100013)

# File lib/biointerchange/so.rb, line 12425
def self.hydrophobic_region_of_peptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100013')
end
hydroxywybutosine() click to toggle source

Hydroxywybutosine is a modified guanosine base feature. (purl.obolibrary.org/obo/SO_0001334)

# File lib/biointerchange/so.rb, line 8269
def self.hydroxywybutosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001334')
end
hyperploid() click to toggle source

A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present. (purl.obolibrary.org/obo/SO_0000055)

# File lib/biointerchange/so.rb, line 643
def self.hyperploid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000055')
end
hypoploid() click to toggle source

A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing. (purl.obolibrary.org/obo/SO_0000056)

# File lib/biointerchange/so.rb, line 649
def self.hypoploid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000056')
end
iDNA() click to toggle source

Genomic sequence removed from the genome, as a normal event, by a process of recombination. (purl.obolibrary.org/obo/SO_0000723)

# File lib/biointerchange/so.rb, line 4661
def self.iDNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000723')
end
i_motif() click to toggle source

A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH. (purl.obolibrary.org/obo/SO_0001010)

# File lib/biointerchange/so.rb, line 6335
def self.i_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001010')
end
immature_peptide_region() click to toggle source

An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs. (purl.obolibrary.org/obo/SO_0001063)

# File lib/biointerchange/so.rb, line 6661
def self.immature_peptide_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001063')
end
immunoglobulin_region() click to toggle source

A region of immunoglobulin sequence, either constant or variable. (purl.obolibrary.org/obo/SO_0001832)

# File lib/biointerchange/so.rb, line 11197
def self.immunoglobulin_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001832')
end
improved_high_quality_draft() click to toggle source

The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution. (purl.obolibrary.org/obo/SO_0001488)

# File lib/biointerchange/so.rb, line 9187
def self.improved_high_quality_draft
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001488')
end
inactive_catalytic_site() click to toggle source

A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001618)

# File lib/biointerchange/so.rb, line 9949
def self.inactive_catalytic_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001618')
end
inactive_ligand_binding_site() click to toggle source

A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001560)

# File lib/biointerchange/so.rb, line 9619
def self.inactive_ligand_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001560')
end
incomplete_terminal_codon_variant() click to toggle source

A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed. (purl.obolibrary.org/obo/SO_0001626)

# File lib/biointerchange/so.rb, line 9991
def self.incomplete_terminal_codon_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001626')
end
increased_polyadenylation_variant() click to toggle source

A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference. (purl.obolibrary.org/obo/SO_0001802)

# File lib/biointerchange/so.rb, line 11017
def self.increased_polyadenylation_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001802')
end
increased_transcript_level_variant() click to toggle source

A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001542)

# File lib/biointerchange/so.rb, line 9511
def self.increased_transcript_level_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001542')
end
increased_transcript_stability_variant() click to toggle source

A sequence variant that increases transcript stability with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001548)

# File lib/biointerchange/so.rb, line 9547
def self.increased_transcript_stability_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001548')
end
increased_transcription_rate_variant() click to toggle source

A sequence variant that increases the rate of transcription with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001551)

# File lib/biointerchange/so.rb, line 9565
def self.increased_transcription_rate_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001551')
end
increased_translational_product_level() click to toggle source

A sequence variant which increases the translational product level with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001556)

# File lib/biointerchange/so.rb, line 9595
def self.increased_translational_product_level
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001556')
end
indel() click to toggle source

A sequence alteration which included an insertion and a deletion, affecting 2 or more bases. (purl.obolibrary.org/obo/SO_1000032)

# File lib/biointerchange/so.rb, line 12635
def self.indel
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000032')
end
independently_known() click to toggle source

Attribute to describe a feature that is independently known - not predicted. (purl.obolibrary.org/obo/SO_0000906)

# File lib/biointerchange/so.rb, line 5717
def self.independently_known
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000906')
end
inframe() click to toggle source

An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is divisible by 3. (purl.obolibrary.org/obo/SO_0001817)

# File lib/biointerchange/so.rb, line 11107
def self.inframe
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001817')
end
inframe_deletion() click to toggle source

An inframe non synonymous variant that deletes bases from the coding sequence. (purl.obolibrary.org/obo/SO_0001822)

# File lib/biointerchange/so.rb, line 11137
def self.inframe_deletion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001822')
end
inframe_indel() click to toggle source

A coding sequence variant where the change does not alter the frame of the transcript. (purl.obolibrary.org/obo/SO_0001820)

# File lib/biointerchange/so.rb, line 11125
def self.inframe_indel
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001820')
end
inframe_insertion() click to toggle source

An inframe non synonymous variant that inserts bases into in the coding sequence. (purl.obolibrary.org/obo/SO_0001821)

# File lib/biointerchange/so.rb, line 11131
def self.inframe_insertion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001821')
end
inframe_variant() click to toggle source

A sequence variant which does not cause a disruption of the translational reading frame. (purl.obolibrary.org/obo/SO_0001650)

# File lib/biointerchange/so.rb, line 10123
def self.inframe_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001650')
end
initiator_codon_variant() click to toggle source

A codon variant that changes at least one base of the first codon of a transcript. (purl.obolibrary.org/obo/SO_0001582)

# File lib/biointerchange/so.rb, line 9745
def self.initiator_codon_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001582')
end
inosine() click to toggle source

A modified RNA base in which hypoxanthine is bound to the ribose ring. (purl.obolibrary.org/obo/SO_0001230)

# File lib/biointerchange/so.rb, line 7651
def self.inosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001230')
end
insert() click to toggle source

To insert a subsection of sequence. (purl.obolibrary.org/obo/SO_0000046)

# File lib/biointerchange/so.rb, line 585
def self.insert
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000046')
end
insert_AA() click to toggle source

An edit to insert a AA dinucleotide. (purl.obolibrary.org/obo/SO_0000928)

# File lib/biointerchange/so.rb, line 5849
def self.insert_AA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000928')
end
insert_AU() click to toggle source

An edit to insert a AU dinucleotide. (purl.obolibrary.org/obo/SO_0000927)

# File lib/biointerchange/so.rb, line 5843
def self.insert_AU
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000927')
end
insert_C() click to toggle source

An edit to insert a cytidine. (purl.obolibrary.org/obo/SO_0000920)

# File lib/biointerchange/so.rb, line 5801
def self.insert_C
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000920')
end
insert_CU() click to toggle source

An edit to insert a CU dinucleotide. (purl.obolibrary.org/obo/SO_0000926)

# File lib/biointerchange/so.rb, line 5837
def self.insert_CU
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000926')
end
insert_G() click to toggle source

An edit to insert a G. (purl.obolibrary.org/obo/SO_0000923)

# File lib/biointerchange/so.rb, line 5819
def self.insert_G
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000923')
end
insert_GC() click to toggle source

An edit to insert a GC dinucleotide. (purl.obolibrary.org/obo/SO_0000924)

# File lib/biointerchange/so.rb, line 5825
def self.insert_GC
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000924')
end
insert_GU() click to toggle source

An edit to insert a GU dinucleotide. (purl.obolibrary.org/obo/SO_0000925)

# File lib/biointerchange/so.rb, line 5831
def self.insert_GU
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000925')
end
insert_U() click to toggle source

An edit to insert a U. (purl.obolibrary.org/obo/SO_0000917)

# File lib/biointerchange/so.rb, line 5783
def self.insert_U
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000917')
end
insert_dinucleotide() click to toggle source

An edit to insert a dinucleotide. (purl.obolibrary.org/obo/SO_0000921)

# File lib/biointerchange/so.rb, line 5807
def self.insert_dinucleotide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000921')
end
insertion() click to toggle source

The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence. (purl.obolibrary.org/obo/SO_0000667)

# File lib/biointerchange/so.rb, line 4325
def self.insertion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000667')
end
insertion_attribute() click to toggle source

A quality of a chromosomal insertion,. (purl.obolibrary.org/obo/SO_0001512)

# File lib/biointerchange/so.rb, line 9331
def self.insertion_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001512')
end
insertion_breakpoint() click to toggle source

The point within a chromosome where a insertion begins or ends. (purl.obolibrary.org/obo/SO_0001414)

# File lib/biointerchange/so.rb, line 8749
def self.insertion_breakpoint
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001414')
end
insertion_sequence() click to toggle source

A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats. (purl.obolibrary.org/obo/SO_0000973)

# File lib/biointerchange/so.rb, line 6119
def self.insertion_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000973')
end
insertion_site() click to toggle source

The junction where an insertion occurred. (purl.obolibrary.org/obo/SO_0000366)

# File lib/biointerchange/so.rb, line 2511
def self.insertion_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000366')
end
insertional() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001522)

# File lib/biointerchange/so.rb, line 9391
def self.insertional
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001522')
end
insertional_duplication() click to toggle source

A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication). (purl.obolibrary.org/obo/SO_1000154)

# File lib/biointerchange/so.rb, line 13259
def self.insertional_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000154')
end
inside_intron() click to toggle source

An attribute to describe a gene when it is located within the intron of another gene. (purl.obolibrary.org/obo/SO_0000069)

# File lib/biointerchange/so.rb, line 731
def self.inside_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000069')
end
inside_intron_antiparallel() click to toggle source

An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand. (purl.obolibrary.org/obo/SO_0000070)

# File lib/biointerchange/so.rb, line 737
def self.inside_intron_antiparallel
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000070')
end
inside_intron_parallel() click to toggle source

An attribute to describe a gene when it is located within the intron of another gene and on the same strand. (purl.obolibrary.org/obo/SO_0000071)

# File lib/biointerchange/so.rb, line 743
def self.inside_intron_parallel
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000071')
end
insulator() click to toggle source

A transcriptional cis regulatory region that when located between a CM and a gene’s promoter prevents the CRM from modulating that genes expression. (purl.obolibrary.org/obo/SO_0000627)

# File lib/biointerchange/so.rb, line 4085
def self.insulator
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000627')
end
insulator_binding_site() click to toggle source

A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues. (purl.obolibrary.org/obo/SO_0001460)

# File lib/biointerchange/so.rb, line 9019
def self.insulator_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001460')
end
integral_part_of() click to toggle source

X integral_part_of Y if and only if: X part_of Y and Y has_part X. (purl.obolibrary.org/obo/so_2_5_2.obo#integral_part_of)

# File lib/biointerchange/so.rb, line 155
def self.integral_part_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#integral_part_of')
end
integrase_coding_region() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000369)

# File lib/biointerchange/so.rb, line 2529
def self.integrase_coding_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000369')
end
integrated_mobile_genetic_element() click to toggle source

An MGE that is integrated into the host chromosome. (purl.obolibrary.org/obo/SO_0001039)

# File lib/biointerchange/so.rb, line 6509
def self.integrated_mobile_genetic_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001039')
end
integrated_plasmid() click to toggle source

A plasmid sequence that is integrated within the host chromosome. (purl.obolibrary.org/obo/SO_0001040)

# File lib/biointerchange/so.rb, line 6515
def self.integrated_plasmid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001040')
end
integration_excision_site() click to toggle source

A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site. (purl.obolibrary.org/obo/SO_0000946)

# File lib/biointerchange/so.rb, line 5957
def self.integration_excision_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000946')
end
integron() click to toggle source

A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site. (purl.obolibrary.org/obo/SO_0000365)

# File lib/biointerchange/so.rb, line 2505
def self.integron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000365')
end
intein() click to toggle source

A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond. (purl.obolibrary.org/obo/SO_0000728)

# File lib/biointerchange/so.rb, line 4691
def self.intein
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000728')
end
intein_containing() click to toggle source

An attribute of protein-coding genes where the initial protein product contains an intein. (purl.obolibrary.org/obo/SO_0000729)

# File lib/biointerchange/so.rb, line 4697
def self.intein_containing
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000729')
end
interband() click to toggle source

A light region between two darkly staining bands in a polytene chromosome. (purl.obolibrary.org/obo/SO_0000450)

# File lib/biointerchange/so.rb, line 3019
def self.interband
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000450')
end
interchromosomal() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001511)

# File lib/biointerchange/so.rb, line 9325
def self.interchromosomal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001511')
end
interchromosomal_breakpoint() click to toggle source

A rearrangement breakpoint between two different chromosomes. (purl.obolibrary.org/obo/SO_0001873)

# File lib/biointerchange/so.rb, line 11443
def self.interchromosomal_breakpoint
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001873')
end
interchromosomal_duplication() click to toggle source

A chromosome duplication involving an insertion from another chromosome. (purl.obolibrary.org/obo/SO_0000457)

# File lib/biointerchange/so.rb, line 3061
def self.interchromosomal_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000457')
end
interchromosomal_mutation() click to toggle source

A chromosomal structure variation whereby more than one chromosome is involved. (purl.obolibrary.org/obo/SO_1000031)

# File lib/biointerchange/so.rb, line 12629
def self.interchromosomal_mutation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000031')
end
interchromosomal_transposition() click to toggle source

A chromosome structure variation whereby a transposition occurred between chromosomes. (purl.obolibrary.org/obo/SO_1000155)

# File lib/biointerchange/so.rb, line 13265
def self.interchromosomal_transposition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000155')
end
intergenic_region() click to toggle source

A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome. (purl.obolibrary.org/obo/SO_0000605)

# File lib/biointerchange/so.rb, line 3953
def self.intergenic_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000605')
end
intergenic_variant() click to toggle source

A sequence variant located in the intergenic region, between genes. (purl.obolibrary.org/obo/SO_0001628)

# File lib/biointerchange/so.rb, line 10003
def self.intergenic_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001628')
end
interior_coding_exon() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000004)

# File lib/biointerchange/so.rb, line 339
def self.interior_coding_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000004')
end
interior_exon() click to toggle source

An exon that is bounded by 5’ and 3’ splice sites. (purl.obolibrary.org/obo/SO_0000201)

# File lib/biointerchange/so.rb, line 1527
def self.interior_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000201')
end
interior_intron() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000191)

# File lib/biointerchange/so.rb, line 1467
def self.interior_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000191')
end
intermediate() click to toggle source

An attribute to describe a feature between stages of processing. (purl.obolibrary.org/obo/SO_0000933)

# File lib/biointerchange/so.rb, line 5879
def self.intermediate
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000933')
end
intermediate_element() click to toggle source

A core promoter region of RNA polymerase III type 1 promoters. (purl.obolibrary.org/obo/SO_0001677)

# File lib/biointerchange/so.rb, line 10273
def self.intermediate_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001677')
end
internal_Shine_Dalgarno_sequence() click to toggle source

A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria. (purl.obolibrary.org/obo/SO_1001260)

# File lib/biointerchange/so.rb, line 13505
def self.internal_Shine_Dalgarno_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001260')
end
internal_UTR() click to toggle source

A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5’, 3’ or internal. (purl.obolibrary.org/obo/SO_0000241)

# File lib/biointerchange/so.rb, line 1767
def self.internal_UTR
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000241')
end
internal_eliminated_sequence() click to toggle source

A sequence eliminated from the genome of ciliates during nuclear differentiation. (purl.obolibrary.org/obo/SO_0000671)

# File lib/biointerchange/so.rb, line 4349
def self.internal_eliminated_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000671')
end
internal_feature_elongation() click to toggle source

A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence. (purl.obolibrary.org/obo/SO_0001908)

# File lib/biointerchange/so.rb, line 11653
def self.internal_feature_elongation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001908')
end
internal_guide_sequence() click to toggle source

A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity. (purl.obolibrary.org/obo/SO_0001016)

# File lib/biointerchange/so.rb, line 6371
def self.internal_guide_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001016')
end
internal_ribosome_entry_site() click to toggle source

Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation. (purl.obolibrary.org/obo/SO_0000243)

# File lib/biointerchange/so.rb, line 1779
def self.internal_ribosome_entry_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000243')
end
internal_transcribed_spacer_region() click to toggle source

Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs. (purl.obolibrary.org/obo/SO_0000639)

# File lib/biointerchange/so.rb, line 4157
def self.internal_transcribed_spacer_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000639')
end
intrachromosomal() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001510)

# File lib/biointerchange/so.rb, line 9319
def self.intrachromosomal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001510')
end
intrachromosomal_breakpoint() click to toggle source

A rearrangement breakpoint within the same chromosome. (purl.obolibrary.org/obo/SO_0001874)

# File lib/biointerchange/so.rb, line 11449
def self.intrachromosomal_breakpoint
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001874')
end
intrachromosomal_duplication() click to toggle source

A duplication that occurred within a chromosome. (purl.obolibrary.org/obo/SO_1000038)

# File lib/biointerchange/so.rb, line 12659
def self.intrachromosomal_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000038')
end
intrachromosomal_mutation() click to toggle source

A chromosomal structure variation within a single chromosome. (purl.obolibrary.org/obo/SO_1000028)

# File lib/biointerchange/so.rb, line 12611
def self.intrachromosomal_mutation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000028')
end
intrachromosomal_transposition() click to toggle source

A chromosome structure variation whereby a transposition occurred within a chromosome. (purl.obolibrary.org/obo/SO_1000041)

# File lib/biointerchange/so.rb, line 12677
def self.intrachromosomal_transposition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000041')
end
intramembrane_polypeptide_region() click to toggle source

Polypeptide region present in the lipid bilayer. (purl.obolibrary.org/obo/SO_0001075)

# File lib/biointerchange/so.rb, line 6721
def self.intramembrane_polypeptide_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001075')
end
intrinsically_unstructured_polypeptide_region() click to toggle source

A region of polypeptide chain with high conformational flexibility. (purl.obolibrary.org/obo/SO_0100003)

# File lib/biointerchange/so.rb, line 12365
def self.intrinsically_unstructured_polypeptide_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100003')
end
introgressed_chromosome_region() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000664)

# File lib/biointerchange/so.rb, line 4307
def self.introgressed_chromosome_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000664')
end
intron() click to toggle source

A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it. (purl.obolibrary.org/obo/SO_0000188)

# File lib/biointerchange/so.rb, line 1449
def self.intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000188')
end
intron_attribute() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000661)

# File lib/biointerchange/so.rb, line 4289
def self.intron_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000661')
end
intron_base_5() click to toggle source

Fifth intronic position after the intron exon boundary, close to the 5’ edge of the intron. (purl.obolibrary.org/obo/SO_0001994)

# File lib/biointerchange/so.rb, line 12167
def self.intron_base_5
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001994')
end
intron_domain() click to toggle source

Requested by Colin Batchelor, Feb 2007. (purl.obolibrary.org/obo/SO_0001014)

# File lib/biointerchange/so.rb, line 6359
def self.intron_domain
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001014')
end
intron_gain() click to toggle source

A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor. (purl.obolibrary.org/obo/SO_0001573)

# File lib/biointerchange/so.rb, line 9697
def self.intron_gain
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001573')
end
intron_variant() click to toggle source

A transcript variant occurring within an intron. (purl.obolibrary.org/obo/SO_0001627)

# File lib/biointerchange/so.rb, line 9997
def self.intron_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001627')
end
intronic_lncRNA() click to toggle source

A lnc_RNA totally contained within an intron. (purl.obolibrary.org/obo/SO_0001903)

# File lib/biointerchange/so.rb, line 11623
def self.intronic_lncRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001903')
end
intronic_regulatory_region() click to toggle source

A regulatory region that is part of an intron. (purl.obolibrary.org/obo/SO_0001492)

# File lib/biointerchange/so.rb, line 9211
def self.intronic_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001492')
end
intronic_splice_enhancer() click to toggle source

Sequences within the intron that modulate splice site selection for some introns. (purl.obolibrary.org/obo/SO_0000320)

# File lib/biointerchange/so.rb, line 2241
def self.intronic_splice_enhancer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000320')
end
invalidated() click to toggle source

An attribute describing a feature that is invalidated. (purl.obolibrary.org/obo/SO_0000790)

# File lib/biointerchange/so.rb, line 5057
def self.invalidated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000790')
end
invalidated_by_chimeric_cDNA() click to toggle source

A cDNA clone constructed from more than one mRNA. Usually an experimental artifact. (purl.obolibrary.org/obo/SO_0000362)

# File lib/biointerchange/so.rb, line 2487
def self.invalidated_by_chimeric_cDNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000362')
end
invalidated_by_genomic_contamination() click to toggle source

An attribute to describe a feature that is invalidated due to genomic contamination. (purl.obolibrary.org/obo/SO_0000414)

# File lib/biointerchange/so.rb, line 2799
def self.invalidated_by_genomic_contamination
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000414')
end
invalidated_by_genomic_polyA_primed_cDNA() click to toggle source

An attribute to describe a feature that is invalidated due to polyA priming. (purl.obolibrary.org/obo/SO_0000415)

# File lib/biointerchange/so.rb, line 2805
def self.invalidated_by_genomic_polyA_primed_cDNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000415')
end
invalidated_by_partial_processing() click to toggle source

An attribute to describe a feature that is invalidated due to partial processing. (purl.obolibrary.org/obo/SO_0000416)

# File lib/biointerchange/so.rb, line 2811
def self.invalidated_by_partial_processing
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000416')
end
invalidated_cDNA_clone() click to toggle source

A cDNA clone that is invalid. (purl.obolibrary.org/obo/SO_0000809)

# File lib/biointerchange/so.rb, line 5147
def self.invalidated_cDNA_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000809')
end
inversion() click to toggle source

A continuous nucleotide sequence is inverted in the same position. (purl.obolibrary.org/obo/SO_1000036)

# File lib/biointerchange/so.rb, line 12647
def self.inversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000036')
end
inversion_attribute() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001517)

# File lib/biointerchange/so.rb, line 9361
def self.inversion_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001517')
end
inversion_breakpoint() click to toggle source

The point within a chromosome where an inversion begins or ends. (purl.obolibrary.org/obo/SO_0001022)

# File lib/biointerchange/so.rb, line 6407
def self.inversion_breakpoint
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001022')
end
inversion_cum_translocation() click to toggle source

A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break. (purl.obolibrary.org/obo/SO_1000148)

# File lib/biointerchange/so.rb, line 13223
def self.inversion_cum_translocation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000148')
end
inversion_derived_aneuploid_chromosome() click to toggle source

A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion. (purl.obolibrary.org/obo/SO_0000567)

# File lib/biointerchange/so.rb, line 3725
def self.inversion_derived_aneuploid_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000567')
end
inversion_derived_bipartite_deficiency() click to toggle source

A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion. (purl.obolibrary.org/obo/SO_0000461)

# File lib/biointerchange/so.rb, line 3085
def self.inversion_derived_bipartite_deficiency
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000461')
end
inversion_derived_bipartite_duplication() click to toggle source

A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion. (purl.obolibrary.org/obo/SO_0000547)

# File lib/biointerchange/so.rb, line 3601
def self.inversion_derived_bipartite_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000547')
end
inversion_derived_deficiency_plus_aneuploid() click to toggle source

A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion. (purl.obolibrary.org/obo/SO_0000512)

# File lib/biointerchange/so.rb, line 3391
def self.inversion_derived_deficiency_plus_aneuploid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000512')
end
inversion_derived_deficiency_plus_duplication() click to toggle source

A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion. (purl.obolibrary.org/obo/SO_0000465)

# File lib/biointerchange/so.rb, line 3109
def self.inversion_derived_deficiency_plus_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000465')
end
inversion_derived_duplication_plus_aneuploid() click to toggle source

A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion. (purl.obolibrary.org/obo/SO_0000549)

# File lib/biointerchange/so.rb, line 3613
def self.inversion_derived_duplication_plus_aneuploid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000549')
end
inversion_site() click to toggle source

A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites. (purl.obolibrary.org/obo/SO_0000948)

# File lib/biointerchange/so.rb, line 5969
def self.inversion_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000948')
end
inversion_site_part() click to toggle source

A region located within an inversion site. (purl.obolibrary.org/obo/SO_0001048)

# File lib/biointerchange/so.rb, line 6563
def self.inversion_site_part
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001048')
end
invert() click to toggle source

To invert a subsection of sequence. (purl.obolibrary.org/obo/SO_0000047)

# File lib/biointerchange/so.rb, line 591
def self.invert
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000047')
end
inverted() click to toggle source

A quality of an insertion where the insert is in a cytologically inverted orientation. (purl.obolibrary.org/obo/SO_0001515)

# File lib/biointerchange/so.rb, line 9349
def self.inverted
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001515')
end
inverted_insertional_duplication() click to toggle source

An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments. (purl.obolibrary.org/obo/SO_1000153)

# File lib/biointerchange/so.rb, line 13253
def self.inverted_insertional_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000153')
end
inverted_interchromosomal_transposition() click to toggle source

An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment. (purl.obolibrary.org/obo/SO_1000156)

# File lib/biointerchange/so.rb, line 13271
def self.inverted_interchromosomal_transposition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000156')
end
inverted_intrachromosomal_transposition() click to toggle source

An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments. (purl.obolibrary.org/obo/SO_1000158)

# File lib/biointerchange/so.rb, line 13283
def self.inverted_intrachromosomal_transposition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000158')
end
inverted_repeat() click to toggle source

The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA—–TCAGC. (purl.obolibrary.org/obo/SO_0000294)

# File lib/biointerchange/so.rb, line 2085
def self.inverted_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000294')
end
inverted_ring_chromosome() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000439)

# File lib/biointerchange/so.rb, line 2953
def self.inverted_ring_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000439')
end
inverted_tandem_duplication() click to toggle source

A tandem duplication where the individual regions are not in the same orientation. (purl.obolibrary.org/obo/SO_1000040)

# File lib/biointerchange/so.rb, line 12671
def self.inverted_tandem_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000040')
end
iron_repressed_GATA_element() click to toggle source

A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron. (purl.obolibrary.org/obo/SO_0001851)

# File lib/biointerchange/so.rb, line 11311
def self.iron_repressed_GATA_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001851')
end
iron_responsive_element() click to toggle source

A regulatory sequence found in the 5’ and 3’ UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins. (purl.obolibrary.org/obo/SO_0001182)

# File lib/biointerchange/so.rb, line 7363
def self.iron_responsive_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001182')
end
is_class?(uri) click to toggle source

Determines whether the given URI is a class.

uri

URI that is tested for being a class

# File lib/biointerchange/so.rb, line 13847
def self.is_class?(uri)
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000000') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000001') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000002') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000003') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000004') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000005') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000006') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000007') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000008') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000009') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000010') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000011') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000012') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000013') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000014') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000015') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000016') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000017') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000018') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000020') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000021') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000022') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000023') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000024') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000025') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000026') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000027') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000028') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000029') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000030') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000031') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000032') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000033') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000034') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000035') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000036') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000037') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000038') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000039') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000040') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000041') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000042') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000043') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000044') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000045') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000046') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000047') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000048') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000052') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000053') then
    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000056') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000057') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000058') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000059') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000060') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000061') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000062') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000063') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000064') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000065') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000066') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000067') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000068') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000069') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000070') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000071') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000072') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000085') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000091') then
    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000094') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000095') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000096') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000097') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000098') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000100') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000102') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000109') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000110') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000116') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000117') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000118') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000120') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000124') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
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    return true
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    return true
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    return true
  end
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
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    return true
  end
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
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    return true
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    return true
  end
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    return true
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000247') then
    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001047') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001048') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001049') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001050') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001051') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001052') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001053') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001054') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001055') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001056') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001057') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001058') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001059') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001060') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001061') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001062') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001063') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001064') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001066') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001067') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001068') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001070') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001071') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001072') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001073') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001074') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001075') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001076') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001077') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001078') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001079') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001080') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001081') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001082') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001083') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001084') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001085') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001086') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001087') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001088') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001089') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001090') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001091') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001092') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001093') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001094') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001095') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001096') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001097') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001098') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001099') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001100') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001101') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001102') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001103') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001104') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001105') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001106') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001107') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001108') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001109') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001110') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001111') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001112') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001113') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001114') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001115') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001116') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001117') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001118') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001119') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001120') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001121') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001122') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001123') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001124') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001125') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001126') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001127') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001128') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001129') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001130') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001131') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001132') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001133') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001134') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001135') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001136') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001137') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001138') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001143') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001144') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001145') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001146') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001147') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001148') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001149') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001151') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001152') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001153') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001154') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001155') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001156') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001157') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001158') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001162') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001163') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001164') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001165') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001166') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001172') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001174') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001175') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001176') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001183') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001184') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001185') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001195') then
    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001202') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001204') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001205') then
    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001208') then
    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001211') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001212') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001213') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001214') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001216') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001217') then
    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001220') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001221') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001222') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001223') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001224') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001225') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001226') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001227') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001228') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001229') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001230') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001231') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001232') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001233') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001234') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001235') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001236') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001237') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001238') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001239') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001240') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001241') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001243') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001244') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001245') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001246') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001247') then
    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001250') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001251') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001252') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001253') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001254') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001255') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001256') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001257') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001258') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001259') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001260') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001261') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001262') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001263') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001264') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001265') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001266') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001267') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001268') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001269') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001270') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001271') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001272') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001282') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001288') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001289') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001290') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001292') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001293') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001294') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001295') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001296') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001297') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001299') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001300') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001301') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001305') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001307') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001308') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001309') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001310') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
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    return true
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
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    return true
  end
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    return true
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    return true
  end
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    return true
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    return true
  end
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001436') then
    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001439') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001440') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001447') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001449') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001450') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001451') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001452') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001453') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001454') then
    return true
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  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001455') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001456') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001457') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001458') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001459') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001460') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001461') then
    return true
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  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001462') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001463') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001464') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001465') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001466') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001467') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001468') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001469') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001470') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001471') then
    return true
  end
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    return true
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001495') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001496') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001501') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001507') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001508') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001509') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001515') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001637') then
    return true
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  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001638') then
    return true
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    return true
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  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001640') then
    return true
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    return true
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    return true
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  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001643') then
    return true
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  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001644') then
    return true
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    return true
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  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001646') then
    return true
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  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001647') then
    return true
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    return true
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001650') then
    return true
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001655') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001656') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001657') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001658') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001659') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001660') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001661') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001662') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001663') then
    return true
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  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001664') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001665') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001666') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001667') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001668') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001669') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001670') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001671') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001672') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001673') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001674') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001675') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001676') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001687') then
    return true
  end
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    return true
  end
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001695') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001696') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001697') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001698') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001699') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001700') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001701') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001702') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001703') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001704') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001705') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001706') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001708') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001712') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001713') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001714') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001715') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001717') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001718') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001719') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001720') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001721') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001722') then
    return true
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001727') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001728') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001730') then
    return true
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    return true
  end
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    return true
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    return true
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    return true
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    return true
  end
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    return true
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    return true
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    return true
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001818') then
    return true
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    return true
  end
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001824') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001825') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001826') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001827') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001828') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001830') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001831') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001832') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001833') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001834') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001835') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001836') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001837') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001838') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001839') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001840') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001841') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001842') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001843') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001844') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001845') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001846') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001847') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001848') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001849') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001850') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001851') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001853') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001854') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001855') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001856') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001857') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001858') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001859') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001860') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001861') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001862') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001863') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001864') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001865') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001866') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001868') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001869') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001870') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001871') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001872') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001873') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001874') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001875') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001876') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001881') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001882') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001884') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001886') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001887') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001888') then
    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001891') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001892') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001893') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001894') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001895') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001896') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001897') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001898') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001899') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001900') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001901') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001902') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001903') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001904') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001905') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001906') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001907') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001908') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001909') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001910') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001911') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001912') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001913') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001914') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001915') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001916') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001917') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001918') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001919') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001920') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001921') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001922') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001923') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001924') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001925') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001926') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001927') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001928') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001929') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001930') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001931') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001932') then
    return true
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  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001933') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001934') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001935') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001936') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001938') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001944') then
    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001950') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001951') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001952') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001953') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001954') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001955') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001956') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001957') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001958') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001959') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001960') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001961') then
    return true
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    return true
  end
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    return true
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    return true
  end
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001982') then
    return true
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    return true
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    return true
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001986') then
    return true
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001988') then
    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001994') then
    return true
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  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001995') then
    return true
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  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001996') then
    return true
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  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001997') then
    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005836') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005837') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005841') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005843') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005845') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005847') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005848') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005849') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005850') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005851') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005852') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005853') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005854') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005855') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005856') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005857') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005858') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100001') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100002') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100003') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100004') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100005') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100006') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100007') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100008') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100009') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100010') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100011') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100012') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100013') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100014') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100015') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100016') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100017') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100018') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100019') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100020') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100021') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000002') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000005') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000008') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000009') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000010') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000011') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000012') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000013') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000014') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000015') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000016') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000017') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000018') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000019') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000020') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000021') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000022') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000023') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000024') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000025') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000026') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000027') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000028') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000029') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000030') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000031') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000032') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000035') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000036') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000037') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000038') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000039') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000040') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000041') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000042') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000043') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000044') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000045') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000046') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000047') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000048') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000049') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000050') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000054') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000055') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000056') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000057') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000058') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000059') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000060') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000061') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000062') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000063') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000064') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000065') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000066') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000067') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000068') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000069') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000070') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000071') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000072') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000073') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000074') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000075') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000076') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000078') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000079') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000080') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000081') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000082') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000083') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000084') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000085') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000086') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000087') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000088') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000089') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000092') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000093') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000094') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000095') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000096') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000097') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000098') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000099') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000100') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000101') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000102') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000103') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000104') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000105') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000106') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000107') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000108') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000109') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000110') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000111') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000112') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000115') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000116') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000117') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000118') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000119') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000120') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000121') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000122') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000123') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000124') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000125') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000126') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000127') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000132') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000134') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000136') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000138') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000140') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000141') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000142') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000143') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000144') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000145') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000146') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000147') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000148') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000149') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000150') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000151') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000152') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000153') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000154') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000155') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000156') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000157') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000158') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000159') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000160') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000161') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000162') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000170') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000171') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000173') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000175') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000180') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000181') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000182') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000183') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000184') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000185') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000186') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001186') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001187') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001188') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001189') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001190') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001191') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001192') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001193') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001194') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001195') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001196') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001197') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001217') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001244') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001246') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001247') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001249') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001251') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001254') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001255') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001259') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001260') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001261') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001262') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001263') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001264') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001265') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001266') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001267') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001268') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001269') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001270') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001271') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001272') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001273') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001274') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001275') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001277') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001279') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001280') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001281') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001282') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001283') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001284') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001285') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001286') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001287') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001288') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_2000061') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_3000000') then
    return true
  end
  return false
end
is_consecutive_sequence_of() click to toggle source

R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical). (purl.obolibrary.org/obo/so_2_5_2.obo#is_consecutive_sequence_of)

# File lib/biointerchange/so.rb, line 161
def self.is_consecutive_sequence_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#is_consecutive_sequence_of')
end
is_datatype_property?(uri) click to toggle source

Determines whether the given URI is a datatype property.

uri

URI that is tested for being a datatype property

# File lib/biointerchange/so.rb, line 13840
def self.is_datatype_property?(uri)
  return false
end
is_named_individual?(uri) click to toggle source

Determines whether the given URI is a named individual.

uri

URI that is tested for being a named individual

# File lib/biointerchange/so.rb, line 20544
def self.is_named_individual?(uri)
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/anonymous#variant_of') then
    return true
  end
  return false
end
is_object_property?(uri) click to toggle source

Determines whether the given URI is an object property.

uri

URI that is tested for being an object property

# File lib/biointerchange/so.rb, line 13680
def self.is_object_property?(uri)
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/part_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#adjacent_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#associated_with') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#complete_evidence_for_feature') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#connects_on') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#contained_by') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#contains') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#derives_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#disconnected_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#edited_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#edited_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#evidence_for_feature') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#exemplar_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#finished_by') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#finishes') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#gained') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#genome_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#guided_by') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#guides') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#has_integral_part') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#has_origin') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#has_part') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#has_quality') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#homologous_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#integral_part_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#is_consecutive_sequence_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#lost') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#maximally_overlaps') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#member_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#non_functional_homolog_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#orthologous_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#overlaps') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#paralogous_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#part_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#partial_evidence_for_feature') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#position_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#processed_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#processed_into') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#recombined_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#recombined_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#sequence_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#similar_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#started_by') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#starts') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#trans_spliced_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#trans_spliced_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#transcribed_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#transcribed_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#translates_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#translation_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#variant_of') then
    return true
  end
  return false
end
isoleucine() click to toggle source

A place holder for a cross product with chebi. (purl.obolibrary.org/obo/SO_0001438)

# File lib/biointerchange/so.rb, line 8887
def self.isoleucine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001438')
end
isoleucine_tRNA_primary_transcript() click to toggle source

A primary transcript encoding isoleucyl tRNA (SO:0000263). (purl.obolibrary.org/obo/SO_0000220)

# File lib/biointerchange/so.rb, line 1641
def self.isoleucine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000220')
end
isoleucyl_tRNA() click to toggle source

A tRNA sequence that has an isoleucine anticodon, and a 3’ isoleucine binding region. (purl.obolibrary.org/obo/SO_0000263)

# File lib/biointerchange/so.rb, line 1899
def self.isoleucyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000263')
end
isowyosine() click to toggle source

Isowyosine is a modified guanosine base feature. (purl.obolibrary.org/obo/SO_0001342)

# File lib/biointerchange/so.rb, line 8317
def self.isowyosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001342')
end
junction() click to toggle source

A sequence_feature with an extent of zero. (purl.obolibrary.org/obo/SO_0000699)

# File lib/biointerchange/so.rb, line 4517
def self.junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000699')
end
kinetoplast() click to toggle source

A kinetoplast is an interlocked network of thousands of minicircles and tens of maxi circles, located near the base of the flagellum of some protozoan species. (purl.obolibrary.org/obo/SO_0000741)

# File lib/biointerchange/so.rb, line 4769
def self.kinetoplast
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000741')
end
kinetoplast_gene() click to toggle source

A gene located in kinetoplast sequence. (purl.obolibrary.org/obo/SO_0000089)

# File lib/biointerchange/so.rb, line 851
def self.kinetoplast_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000089')
end
kozak_sequence() click to toggle source

A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5’ UTR and CDS sequence. (purl.obolibrary.org/obo/SO_0001647)

# File lib/biointerchange/so.rb, line 10117
def self.kozak_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001647')
end
laevosynaptic_chromosome() click to toggle source

LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres. (purl.obolibrary.org/obo/SO_1000143)

# File lib/biointerchange/so.rb, line 13193
def self.laevosynaptic_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000143')
end
lambda_clone() click to toggle source

A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome. (purl.obolibrary.org/obo/SO_0000160)

# File lib/biointerchange/so.rb, line 1277
def self.lambda_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000160')
end
lambda_vector() click to toggle source

The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome. (purl.obolibrary.org/obo/SO_0000754)

# File lib/biointerchange/so.rb, line 4847
def self.lambda_vector
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000754')
end
large_subunit_rRNA() click to toggle source

Ribosomal RNA transcript that structures the large subunit of the ribosome. (purl.obolibrary.org/obo/SO_0000651)

# File lib/biointerchange/so.rb, line 4229
def self.large_subunit_rRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000651')
end
lariat_intron() click to toggle source

A kind of intron whereby the excision is driven by lariat formation. (purl.obolibrary.org/obo/SO_0001958)

# File lib/biointerchange/so.rb, line 11957
def self.lariat_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001958')
end
left_handed_peptide_helix() click to toggle source

A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw. (purl.obolibrary.org/obo/SO_0001115)

# File lib/biointerchange/so.rb, line 6961
def self.left_handed_peptide_helix
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001115')
end
lethal_variant() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001773)

# File lib/biointerchange/so.rb, line 10849
def self.lethal_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001773')
end
leucine() click to toggle source

A place holder for a cross product with chebi. (purl.obolibrary.org/obo/SO_0001437)

# File lib/biointerchange/so.rb, line 8881
def self.leucine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001437')
end
leucine_tRNA_primary_transcript() click to toggle source

A primary transcript encoding leucyl tRNA (SO:0000264). (purl.obolibrary.org/obo/SO_0000221)

# File lib/biointerchange/so.rb, line 1647
def self.leucine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000221')
end
leucoplast_chromosome() click to toggle source

A chromosome with origin in a leucoplast. (purl.obolibrary.org/obo/SO_0000823)

# File lib/biointerchange/so.rb, line 5231
def self.leucoplast_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000823')
end
leucoplast_gene() click to toggle source

A plastid gene from leucoplast sequence. (purl.obolibrary.org/obo/SO_0000095)

# File lib/biointerchange/so.rb, line 887
def self.leucoplast_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000095')
end
leucoplast_sequence() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000747)

# File lib/biointerchange/so.rb, line 4805
def self.leucoplast_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000747')
end
leucyl_tRNA() click to toggle source

A tRNA sequence that has a leucine anticodon, and a 3’ leucine binding region. (purl.obolibrary.org/obo/SO_0000264)

# File lib/biointerchange/so.rb, line 1905
def self.leucyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000264')
end
level_of_transcript_variant() click to toggle source

A sequence variant which alters the level of a transcript. (purl.obolibrary.org/obo/SO_0001540)

# File lib/biointerchange/so.rb, line 9499
def self.level_of_transcript_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001540')
end
ligand_binding_site() click to toggle source

A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone. (purl.obolibrary.org/obo/SO_0001657)

# File lib/biointerchange/so.rb, line 10153
def self.ligand_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001657')
end
ligation_based_read() click to toggle source

A read produced by ligation based sequencing technologies. (purl.obolibrary.org/obo/SO_0001425)

# File lib/biointerchange/so.rb, line 8815
def self.ligation_based_read
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001425')
end
lincRNA() click to toggle source

A multiexonic non-coding RNA transcribed by RNA polymerase II. (purl.obolibrary.org/obo/SO_0001463)

# File lib/biointerchange/so.rb, line 9037
def self.lincRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001463')
end
lincRNA_gene() click to toggle source

A gene that encodes large intervening non-coding RNA. (purl.obolibrary.org/obo/SO_0001641)

# File lib/biointerchange/so.rb, line 10081
def self.lincRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001641')
end
linear() click to toggle source

A quality of a nucleotide polymer that has a 3’-terminal residue and a 5’-terminal residue. (purl.obolibrary.org/obo/SO_0000987)

# File lib/biointerchange/so.rb, line 6197
def self.linear
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000987')
end
linear_double_stranded_DNA_chromosome() click to toggle source

Structural unit composed of a self-replicating, double-stranded, linear DNA molecule. (purl.obolibrary.org/obo/SO_0000957)

# File lib/biointerchange/so.rb, line 6023
def self.linear_double_stranded_DNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000957')
end
linear_double_stranded_RNA_chromosome() click to toggle source

Structural unit composed of a self-replicating, double-stranded, linear RNA molecule. (purl.obolibrary.org/obo/SO_0000964)

# File lib/biointerchange/so.rb, line 6065
def self.linear_double_stranded_RNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000964')
end
linear_single_stranded_DNA_chromosome() click to toggle source

Structural unit composed of a self-replicating, single-stranded, linear DNA molecule. (purl.obolibrary.org/obo/SO_0000959)

# File lib/biointerchange/so.rb, line 6035
def self.linear_single_stranded_DNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000959')
end
linear_single_stranded_RNA_chromosome() click to toggle source

Structural unit composed of a self-replicating, single-stranded, linear RNA molecule. (purl.obolibrary.org/obo/SO_0000963)

# File lib/biointerchange/so.rb, line 6059
def self.linear_single_stranded_RNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000963')
end
linkage_group() click to toggle source

A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned. (purl.obolibrary.org/obo/SO_0000018)

# File lib/biointerchange/so.rb, line 423
def self.linkage_group
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000018')
end
lipoprotein_signal_peptide() click to toggle source

A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes. (purl.obolibrary.org/obo/SO_0100009)

# File lib/biointerchange/so.rb, line 12401
def self.lipoprotein_signal_peptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100009')
end
lnc_RNA() click to toggle source

A non-coding RNA over 200nucleotides in length. (purl.obolibrary.org/obo/SO_0001877)

# File lib/biointerchange/so.rb, line 11467
def self.lnc_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001877')
end
locus_control_region() click to toggle source

A DNA region that includes DNAse hypersensitive sites located 5’ to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene. (purl.obolibrary.org/obo/SO_0000037)

# File lib/biointerchange/so.rb, line 531
def self.locus_control_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000037')
end
long_terminal_repeat() click to toggle source

A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses. (purl.obolibrary.org/obo/SO_0000286)

# File lib/biointerchange/so.rb, line 2037
def self.long_terminal_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000286')
end
loss_of_heterozygosity() click to toggle source

A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene. (purl.obolibrary.org/obo/SO_0001786)

# File lib/biointerchange/so.rb, line 10921
def self.loss_of_heterozygosity
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001786')
end
lost() click to toggle source

X lost Y if X is a variant_of X’ and Y part of X’ but not X. (purl.obolibrary.org/obo/so_2_5_2.obo#lost)

# File lib/biointerchange/so.rb, line 167
def self.lost
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#lost')
end
low_complexity() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001004)

# File lib/biointerchange/so.rb, line 6299
def self.low_complexity
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001004')
end
low_complexity_region() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001005)

# File lib/biointerchange/so.rb, line 6305
def self.low_complexity_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001005')
end
loxP_site() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000346)

# File lib/biointerchange/so.rb, line 2397
def self.loxP_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000346')
end
lysidine() click to toggle source

Lysidine is a modified cytidine. (purl.obolibrary.org/obo/SO_0001289)

# File lib/biointerchange/so.rb, line 7999
def self.lysidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001289')
end
lysine() click to toggle source

A place holder for a cross product with chebi. (purl.obolibrary.org/obo/SO_0001450)

# File lib/biointerchange/so.rb, line 8959
def self.lysine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001450')
end
lysine_tRNA_primary_transcript() click to toggle source

A primary transcript encoding lysyl tRNA (SO:0000265). (purl.obolibrary.org/obo/SO_0000222)

# File lib/biointerchange/so.rb, line 1653
def self.lysine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000222')
end
lysosomal_localization_signal() click to toggle source

A polypeptide region that targets a polypeptide to the lysosome. (purl.obolibrary.org/obo/SO_0001530)

# File lib/biointerchange/so.rb, line 9439
def self.lysosomal_localization_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001530')
end
lysyl_tRNA() click to toggle source

A tRNA sequence that has a lysine anticodon, and a 3’ lysine binding region. (purl.obolibrary.org/obo/SO_0000265)

# File lib/biointerchange/so.rb, line 1911
def self.lysyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000265')
end
mRNA() click to toggle source

Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns. (purl.obolibrary.org/obo/SO_0000234)

# File lib/biointerchange/so.rb, line 1725
def self.mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000234')
end
mRNA_attribute() click to toggle source

An attribute describing an mRNA feature. (purl.obolibrary.org/obo/SO_0000863)

# File lib/biointerchange/so.rb, line 5459
def self.mRNA_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000863')
end
mRNA_by_polyadenylation_status() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000245)

# File lib/biointerchange/so.rb, line 1791
def self.mRNA_by_polyadenylation_status
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000245')
end
mRNA_contig() click to toggle source

A contig composed of mRNA_reads. (purl.obolibrary.org/obo/SO_0001829)

# File lib/biointerchange/so.rb, line 11179
def self.mRNA_contig
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001829')
end
mRNA_not_polyadenylated() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000247)

# File lib/biointerchange/so.rb, line 1803
def self.mRNA_not_polyadenylated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000247')
end
mRNA_read() click to toggle source

A sequencer read of an mRNA substrate. (purl.obolibrary.org/obo/SO_0001827)

# File lib/biointerchange/so.rb, line 11167
def self.mRNA_read
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001827')
end
mRNA_recoded_by_codon_redefinition() click to toggle source

A recoded_mRNA that was modified by an alteration of codon meaning. (purl.obolibrary.org/obo/SO_1001265)

# File lib/biointerchange/so.rb, line 13535
def self.mRNA_recoded_by_codon_redefinition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001265')
end
mRNA_recoded_by_translational_bypass() click to toggle source

A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon. (purl.obolibrary.org/obo/SO_1001264)

# File lib/biointerchange/so.rb, line 13529
def self.mRNA_recoded_by_translational_bypass
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001264')
end
mRNA_region() click to toggle source

A region of an mRNA. (purl.obolibrary.org/obo/SO_0000836)

# File lib/biointerchange/so.rb, line 5297
def self.mRNA_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000836')
end
mRNA_with_frameshift() click to toggle source

An mRNA with a frameshift. (purl.obolibrary.org/obo/SO_0000108)

# File lib/biointerchange/so.rb, line 965
def self.mRNA_with_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000108')
end
mRNA_with_minus_1_frameshift() click to toggle source

An mRNA with a minus 1 frameshift. (purl.obolibrary.org/obo/SO_0000282)

# File lib/biointerchange/so.rb, line 2013
def self.mRNA_with_minus_1_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000282')
end
mRNA_with_minus_2_frameshift() click to toggle source

A mRNA with a minus 2 frameshift. (purl.obolibrary.org/obo/SO_0000335)

# File lib/biointerchange/so.rb, line 2331
def self.mRNA_with_minus_2_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000335')
end
mRNA_with_plus_1_frameshift() click to toggle source

An mRNA with a plus 1 frameshift. (purl.obolibrary.org/obo/SO_0000321)

# File lib/biointerchange/so.rb, line 2247
def self.mRNA_with_plus_1_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000321')
end
mRNA_with_plus_2_frameshift() click to toggle source

An mRNA with a plus 2 frameshift. (purl.obolibrary.org/obo/SO_0000329)

# File lib/biointerchange/so.rb, line 2295
def self.mRNA_with_plus_2_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000329')
end
macronuclear_chromosome() click to toggle source

A chromosome originating in a macronucleus. (purl.obolibrary.org/obo/SO_0000824)

# File lib/biointerchange/so.rb, line 5237
def self.macronuclear_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000824')
end
macronuclear_sequence() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000083)

# File lib/biointerchange/so.rb, line 815
def self.macronuclear_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000083')
end
macronucleus_destined_segment() click to toggle source

A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome. (purl.obolibrary.org/obo/SO_0000672)

# File lib/biointerchange/so.rb, line 4355
def self.macronucleus_destined_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000672')
end
major_TSS() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001238)

# File lib/biointerchange/so.rb, line 7699
def self.major_TSS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001238')
end
mannosyl_queuosine() click to toggle source

Mannosyl_queuosine is a modified 7-deazoguanosine. (purl.obolibrary.org/obo/SO_0001320)

# File lib/biointerchange/so.rb, line 8185
def self.mannosyl_queuosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001320')
end
match() click to toggle source

A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. (purl.obolibrary.org/obo/SO_0000343)

# File lib/biointerchange/so.rb, line 2379
def self.match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000343')
end
match_part() click to toggle source

A part of a match, for example an hsp from blast is a match_part. (purl.obolibrary.org/obo/SO_0000039)

# File lib/biointerchange/so.rb, line 543
def self.match_part
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000039')
end
match_set() click to toggle source

A collection of match parts. (purl.obolibrary.org/obo/SO_0000038)

# File lib/biointerchange/so.rb, line 537
def self.match_set
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000038')
end
maternal_uniparental_disomy() click to toggle source

Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father. (purl.obolibrary.org/obo/SO_0001745)

# File lib/biointerchange/so.rb, line 10681
def self.maternal_uniparental_disomy
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001745')
end
maternal_variant() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001775)

# File lib/biointerchange/so.rb, line 10861
def self.maternal_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001775')
end
maternally_imprinted() click to toggle source

The maternal copy of the gene is modified, rendering it transcriptionally silent. (purl.obolibrary.org/obo/SO_0000135)

# File lib/biointerchange/so.rb, line 1127
def self.maternally_imprinted
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000135')
end
maternally_imprinted_gene() click to toggle source

A gene that is maternally_imprinted. (purl.obolibrary.org/obo/SO_0000888)

# File lib/biointerchange/so.rb, line 5609
def self.maternally_imprinted_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000888')
end
mathematically_defined_repeat() click to toggle source

A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness. (purl.obolibrary.org/obo/SO_0001642)

# File lib/biointerchange/so.rb, line 10087
def self.mathematically_defined_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001642')
end
mating_type_M_box() click to toggle source

A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc. (purl.obolibrary.org/obo/SO_0001852)

# File lib/biointerchange/so.rb, line 11317
def self.mating_type_M_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001852')
end
mating_type_region() click to toggle source

A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type. (purl.obolibrary.org/obo/SO_0001789)

# File lib/biointerchange/so.rb, line 10939
def self.mating_type_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001789')
end
mating_type_region_motif() click to toggle source

DNA motif that is a component of a mating type region. (purl.obolibrary.org/obo/SO_0001999)

# File lib/biointerchange/so.rb, line 12197
def self.mating_type_region_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001999')
end
matrix_attachment_site() click to toggle source

A DNA region that is required for the binding of chromatin to the nuclear matrix. (purl.obolibrary.org/obo/SO_0000036)

# File lib/biointerchange/so.rb, line 525
def self.matrix_attachment_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000036')
end
mature_miRNA_variant() click to toggle source

A transcript variant located with the sequence of the mature miRNA. (purl.obolibrary.org/obo/SO_0001620)

# File lib/biointerchange/so.rb, line 9961
def self.mature_miRNA_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001620')
end
mature_protein_region() click to toggle source

The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide. (purl.obolibrary.org/obo/SO_0000419)

# File lib/biointerchange/so.rb, line 2829
def self.mature_protein_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000419')
end
mature_transcript() click to toggle source

A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5’ and/or the 3’ ends, other than addition of bases. In bacteria functional mRNAs are usually not modified. (purl.obolibrary.org/obo/SO_0000233)

# File lib/biointerchange/so.rb, line 1719
def self.mature_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000233')
end
mature_transcript_region() click to toggle source

A region of a mature transcript. (purl.obolibrary.org/obo/SO_0000834)

# File lib/biointerchange/so.rb, line 5285
def self.mature_transcript_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000834')
end
maxicircle() click to toggle source

A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method. (purl.obolibrary.org/obo/SO_0000742)

# File lib/biointerchange/so.rb, line 4775
def self.maxicircle
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000742')
end
maxicircle_gene() click to toggle source

A mitochondrial gene located in a maxicircle. (purl.obolibrary.org/obo/SO_0000654)

# File lib/biointerchange/so.rb, line 4247
def self.maxicircle_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000654')
end
maximally_overlaps() click to toggle source

A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y. (purl.obolibrary.org/obo/so_2_5_2.obo#maximally_overlaps)

# File lib/biointerchange/so.rb, line 173
def self.maximally_overlaps
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#maximally_overlaps')
end
member_of() click to toggle source

A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444. (purl.obolibrary.org/obo/so_2_5_2.obo#member_of)

# File lib/biointerchange/so.rb, line 179
def self.member_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#member_of')
end
member_of_regulon() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_1001217)

# File lib/biointerchange/so.rb, line 13451
def self.member_of_regulon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001217')
end
membrane_peptide_loop() click to toggle source

Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane. (purl.obolibrary.org/obo/SO_0001076)

# File lib/biointerchange/so.rb, line 6727
def self.membrane_peptide_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001076')
end
membrane_structure() click to toggle source

Arrangement of the polypeptide with respect to the lipid bilayer. (purl.obolibrary.org/obo/SO_0001071)

# File lib/biointerchange/so.rb, line 6697
def self.membrane_structure
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001071')
end
metabolic_island() click to toggle source

A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria. (purl.obolibrary.org/obo/SO_0000774)

# File lib/biointerchange/so.rb, line 4961
def self.metabolic_island
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000774')
end
metal_binding_site() click to toggle source

A binding site that, in the molecule, interacts selectively and non-covalently with metal ions. (purl.obolibrary.org/obo/SO_0001656)

# File lib/biointerchange/so.rb, line 10147
def self.metal_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001656')
end
methionine() click to toggle source

A place holder for a cross product with chebi. (purl.obolibrary.org/obo/SO_0001442)

# File lib/biointerchange/so.rb, line 8911
def self.methionine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001442')
end
methionine_tRNA_primary_transcript() click to toggle source

A primary transcript encoding methionyl tRNA (SO:0000266). (purl.obolibrary.org/obo/SO_0000223)

# File lib/biointerchange/so.rb, line 1659
def self.methionine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000223')
end
methionyl_tRNA() click to toggle source

A tRNA sequence that has a methionine anticodon, and a 3’ methionine binding region. (purl.obolibrary.org/obo/SO_0000266)

# File lib/biointerchange/so.rb, line 1917
def self.methionyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000266')
end
methylated_DNA_base_feature() click to toggle source

A nucleotide modified by methylation. (purl.obolibrary.org/obo/SO_0000306)

# File lib/biointerchange/so.rb, line 2157
def self.methylated_DNA_base_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000306')
end
methylated_adenine() click to toggle source

A modified base in which adenine has been methylated. (purl.obolibrary.org/obo/SO_0000161)

# File lib/biointerchange/so.rb, line 1283
def self.methylated_adenine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000161')
end
methylated_cytosine() click to toggle source

A methylated deoxy-cytosine. (purl.obolibrary.org/obo/SO_0000114)

# File lib/biointerchange/so.rb, line 1001
def self.methylated_cytosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000114')
end
methylation_guide_snoRNA() click to toggle source

A snoRNA that specifies the site of 2’-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue. (purl.obolibrary.org/obo/SO_0005841)

# File lib/biointerchange/so.rb, line 12263
def self.methylation_guide_snoRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005841')
end
methylation_guide_snoRNA_primary_transcript() click to toggle source

A primary transcript encoding a methylation guide small nucleolar RNA. (purl.obolibrary.org/obo/SO_0000580)

# File lib/biointerchange/so.rb, line 3803
def self.methylation_guide_snoRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000580')
end
methylinosine() click to toggle source

A modified RNA base in which methylhypoxanthine is bound to the ribose ring. (purl.obolibrary.org/obo/SO_0001233)

# File lib/biointerchange/so.rb, line 7669
def self.methylinosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001233')
end
methylwyosine() click to toggle source

Methylwyosine is a modified guanosine base feature. (purl.obolibrary.org/obo/SO_0001337)

# File lib/biointerchange/so.rb, line 8287
def self.methylwyosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001337')
end
miRNA() click to toggle source

Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors. (purl.obolibrary.org/obo/SO_0000276)

# File lib/biointerchange/so.rb, line 1977
def self.miRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000276')
end
miRNA_antiguide() click to toggle source

A region of the pri miRNA that basepairs with the guide to form the hairpin. (purl.obolibrary.org/obo/SO_0001473)

# File lib/biointerchange/so.rb, line 9097
def self.miRNA_antiguide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001473')
end
miRNA_encoding() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000571)

# File lib/biointerchange/so.rb, line 3749
def self.miRNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000571')
end
miRNA_gene() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001265)

# File lib/biointerchange/so.rb, line 7855
def self.miRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001265')
end
miRNA_loop() click to toggle source

The loop of the hairpin loop formed by folding of the pre-miRNA. (purl.obolibrary.org/obo/SO_0001246)

# File lib/biointerchange/so.rb, line 7741
def self.miRNA_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001246')
end
miRNA_primary_transcript() click to toggle source

A primary transcript encoding a micro RNA. (purl.obolibrary.org/obo/SO_0000647)

# File lib/biointerchange/so.rb, line 4205
def self.miRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000647')
end
miRNA_primary_transcript_region() click to toggle source

A part of an miRNA primary_transcript. (purl.obolibrary.org/obo/SO_0001243)

# File lib/biointerchange/so.rb, line 7723
def self.miRNA_primary_transcript_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001243')
end
miRNA_stem() click to toggle source

The stem of the hairpin loop formed by folding of the pre-miRNA. (purl.obolibrary.org/obo/SO_0001245)

# File lib/biointerchange/so.rb, line 7735
def self.miRNA_stem
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001245')
end
miRNA_target_site() click to toggle source

A miRNA target site is a binding site where the molecule is a micro RNA. (purl.obolibrary.org/obo/SO_0000934)

# File lib/biointerchange/so.rb, line 5885
def self.miRNA_target_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000934')
end
microarray_oligo() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000328)

# File lib/biointerchange/so.rb, line 2289
def self.microarray_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000328')
end
micronuclear_chromosome() click to toggle source

A chromosome originating in a micronucleus. (purl.obolibrary.org/obo/SO_0000825)

# File lib/biointerchange/so.rb, line 5243
def self.micronuclear_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000825')
end
micronuclear_sequence() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000084)

# File lib/biointerchange/so.rb, line 821
def self.micronuclear_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000084')
end
microsatellite() click to toggle source

A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem. (purl.obolibrary.org/obo/SO_0000289)

# File lib/biointerchange/so.rb, line 2055
def self.microsatellite
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000289')
end
mini_exon_donor_RNA() click to toggle source

A primary transcript that donates the spliced leader to other mRNA. (purl.obolibrary.org/obo/SO_0000635)

# File lib/biointerchange/so.rb, line 4133
def self.mini_exon_donor_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000635')
end
mini_gene() click to toggle source

By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually ‘T-helpers’ (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA. (purl.obolibrary.org/obo/SO_0000815)

# File lib/biointerchange/so.rb, line 5183
def self.mini_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000815')
end
minicircle() click to toggle source

A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs. (purl.obolibrary.org/obo/SO_0000980)

# File lib/biointerchange/so.rb, line 6155
def self.minicircle
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000980')
end
minicircle_gene() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000975)

# File lib/biointerchange/so.rb, line 6125
def self.minicircle_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000975')
end
minisatellite() click to toggle source

A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp. (purl.obolibrary.org/obo/SO_0000643)

# File lib/biointerchange/so.rb, line 4181
def self.minisatellite
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000643')
end
minor_TSS() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001239)

# File lib/biointerchange/so.rb, line 7705
def self.minor_TSS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001239')
end
minus_10_signal() click to toggle source

A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70. (purl.obolibrary.org/obo/SO_0000175)

# File lib/biointerchange/so.rb, line 1367
def self.minus_10_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000175')
end
minus_12_signal() click to toggle source

A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54. (purl.obolibrary.org/obo/SO_0001673)

# File lib/biointerchange/so.rb, line 10249
def self.minus_12_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001673')
end
minus_1_frameshift() click to toggle source

A frameshift caused by deleting one base. (purl.obolibrary.org/obo/SO_0000866)

# File lib/biointerchange/so.rb, line 5477
def self.minus_1_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000866')
end
minus_1_frameshift_variant() click to toggle source

A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead. (purl.obolibrary.org/obo/SO_0001592)

# File lib/biointerchange/so.rb, line 9793
def self.minus_1_frameshift_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001592')
end
minus_1_translationally_frameshifted() click to toggle source

An attribute describing a translational frameshift of -1. (purl.obolibrary.org/obo/SO_1001262)

# File lib/biointerchange/so.rb, line 13517
def self.minus_1_translationally_frameshifted
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001262')
end
minus_24_signal() click to toggle source

A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54. (purl.obolibrary.org/obo/SO_0001674)

# File lib/biointerchange/so.rb, line 10255
def self.minus_24_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001674')
end
minus_2_frameshift() click to toggle source

A frameshift caused by deleting two bases. (purl.obolibrary.org/obo/SO_0000867)

# File lib/biointerchange/so.rb, line 5483
def self.minus_2_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000867')
end
minus_2_frameshift_variant() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001593)

# File lib/biointerchange/so.rb, line 9799
def self.minus_2_frameshift_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001593')
end
minus_35_signal() click to toggle source

A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70. (purl.obolibrary.org/obo/SO_0000176)

# File lib/biointerchange/so.rb, line 1373
def self.minus_35_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000176')
end
mirtron() click to toggle source

A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage. (purl.obolibrary.org/obo/SO_0001034)

# File lib/biointerchange/so.rb, line 6479
def self.mirtron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001034')
end
missense_variant() click to toggle source

A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved. (purl.obolibrary.org/obo/SO_0001583)

# File lib/biointerchange/so.rb, line 9751
def self.missense_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001583')
end
mitochondrial_DNA() click to toggle source

This terms is used by MO. (purl.obolibrary.org/obo/SO_0001032)

# File lib/biointerchange/so.rb, line 6467
def self.mitochondrial_DNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001032')
end
mitochondrial_DNA_read() click to toggle source

A sequencer read of a mitochondrial DNA sample. (purl.obolibrary.org/obo/SO_0001929)

# File lib/biointerchange/so.rb, line 11779
def self.mitochondrial_DNA_read
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001929')
end
mitochondrial_chromosome() click to toggle source

A chromosome originating in a mitochondria. (purl.obolibrary.org/obo/SO_0000819)

# File lib/biointerchange/so.rb, line 5207
def self.mitochondrial_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000819')
end
mitochondrial_contig() click to toggle source

A contig of mitochondria derived sequences. (purl.obolibrary.org/obo/SO_0001921)

# File lib/biointerchange/so.rb, line 11731
def self.mitochondrial_contig
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001921')
end
mitochondrial_sequence() click to toggle source

This term is mapped to MGED. Do not obsolete without consulting MGED ontology. (purl.obolibrary.org/obo/SO_0000737)

# File lib/biointerchange/so.rb, line 4745
def self.mitochondrial_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000737')
end
mitochondrial_supercontig() click to toggle source

A scaffold composed of mitochondrial contigs. (purl.obolibrary.org/obo/SO_0001922)

# File lib/biointerchange/so.rb, line 11737
def self.mitochondrial_supercontig
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001922')
end
mitochondrial_targeting_signal() click to toggle source

A polypeptide region that targets a polypeptide to the mitochondrion. (purl.obolibrary.org/obo/SO_0001808)

# File lib/biointerchange/so.rb, line 11053
def self.mitochondrial_targeting_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001808')
end
mobile() click to toggle source

An attribute describing a feature that has either intra-genome or intracellular mobility. (purl.obolibrary.org/obo/SO_0001234)

# File lib/biointerchange/so.rb, line 7675
def self.mobile
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001234')
end
mobile_element_insertion() click to toggle source

A kind of insertion where the inserted sequence is a mobile element. (purl.obolibrary.org/obo/SO_0001837)

# File lib/biointerchange/so.rb, line 11227
def self.mobile_element_insertion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001837')
end
mobile_genetic_element() click to toggle source

A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome. (purl.obolibrary.org/obo/SO_0001037)

# File lib/biointerchange/so.rb, line 6497
def self.mobile_genetic_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001037')
end
mobile_intron() click to toggle source

An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility. (purl.obolibrary.org/obo/SO_0000666)

# File lib/biointerchange/so.rb, line 4319
def self.mobile_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000666')
end
modified_DNA_base() click to toggle source

A modified nucleotide, i.e. a nucleotide other than A, T, C. G. (purl.obolibrary.org/obo/SO_0000305)

# File lib/biointerchange/so.rb, line 2151
def self.modified_DNA_base
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000305')
end
modified_L_alanine() click to toggle source

A post translationally modified alanine amino acid feature. (purl.obolibrary.org/obo/SO_0001387)

# File lib/biointerchange/so.rb, line 8587
def self.modified_L_alanine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001387')
end
modified_L_arginine() click to toggle source

A post translationally modified arginine amino acid feature. (purl.obolibrary.org/obo/SO_0001406)

# File lib/biointerchange/so.rb, line 8701
def self.modified_L_arginine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001406')
end
modified_L_asparagine() click to toggle source

A post translationally modified asparagine amino acid feature. (purl.obolibrary.org/obo/SO_0001388)

# File lib/biointerchange/so.rb, line 8593
def self.modified_L_asparagine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001388')
end
modified_L_aspartic_acid() click to toggle source

A post translationally modified aspartic acid amino acid feature. (purl.obolibrary.org/obo/SO_0001389)

# File lib/biointerchange/so.rb, line 8599
def self.modified_L_aspartic_acid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001389')
end
modified_L_cysteine() click to toggle source

A post translationally modified cysteine amino acid feature. (purl.obolibrary.org/obo/SO_0001390)

# File lib/biointerchange/so.rb, line 8605
def self.modified_L_cysteine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001390')
end
modified_L_glutamic_acid() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001391)

# File lib/biointerchange/so.rb, line 8611
def self.modified_L_glutamic_acid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001391')
end
modified_L_glutamine() click to toggle source

A post translationally modified glutamine amino acid feature. (purl.obolibrary.org/obo/SO_0001394)

# File lib/biointerchange/so.rb, line 8629
def self.modified_L_glutamine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001394')
end
modified_L_histidine() click to toggle source

A post translationally modified histidie amino acid feature. (purl.obolibrary.org/obo/SO_0001398)

# File lib/biointerchange/so.rb, line 8653
def self.modified_L_histidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001398')
end
modified_L_isoleucine() click to toggle source

A post translationally modified isoleucine amino acid feature. (purl.obolibrary.org/obo/SO_0001396)

# File lib/biointerchange/so.rb, line 8641
def self.modified_L_isoleucine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001396')
end
modified_L_leucine() click to toggle source

A post translationally modified leucine amino acid feature. (purl.obolibrary.org/obo/SO_0001401)

# File lib/biointerchange/so.rb, line 8671
def self.modified_L_leucine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001401')
end
modified_L_lysine() click to toggle source

A post translationally modified lysine amino acid feature. (purl.obolibrary.org/obo/SO_0001400)

# File lib/biointerchange/so.rb, line 8665
def self.modified_L_lysine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001400')
end
modified_L_methionine() click to toggle source

A post translationally modified methionine amino acid feature. (purl.obolibrary.org/obo/SO_0001395)

# File lib/biointerchange/so.rb, line 8635
def self.modified_L_methionine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001395')
end
modified_L_phenylalanine() click to toggle source

A post translationally modified phenylalanine amino acid feature. (purl.obolibrary.org/obo/SO_0001397)

# File lib/biointerchange/so.rb, line 8647
def self.modified_L_phenylalanine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001397')
end
modified_L_proline() click to toggle source

A post translationally modified proline amino acid feature. (purl.obolibrary.org/obo/SO_0001404)

# File lib/biointerchange/so.rb, line 8689
def self.modified_L_proline
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001404')
end
modified_L_selenocysteine() click to toggle source

A post translationally modified selenocysteine amino acid feature. (purl.obolibrary.org/obo/SO_0001402)

# File lib/biointerchange/so.rb, line 8677
def self.modified_L_selenocysteine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001402')
end
modified_L_serine() click to toggle source

A post translationally modified serine amino acid feature. (purl.obolibrary.org/obo/SO_0001399)

# File lib/biointerchange/so.rb, line 8659
def self.modified_L_serine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001399')
end
modified_L_threonine() click to toggle source

A post translationally modified threonine amino acid feature. (purl.obolibrary.org/obo/SO_0001392)

# File lib/biointerchange/so.rb, line 8617
def self.modified_L_threonine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001392')
end
modified_L_tryptophan() click to toggle source

A post translationally modified tryptophan amino acid feature. (purl.obolibrary.org/obo/SO_0001393)

# File lib/biointerchange/so.rb, line 8623
def self.modified_L_tryptophan
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001393')
end
modified_L_tyrosine() click to toggle source

A post translationally modified tyrosine amino acid feature. (purl.obolibrary.org/obo/SO_0001405)

# File lib/biointerchange/so.rb, line 8695
def self.modified_L_tyrosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001405')
end
modified_L_valine() click to toggle source

A post translationally modified valine amino acid feature. (purl.obolibrary.org/obo/SO_0001403)

# File lib/biointerchange/so.rb, line 8683
def self.modified_L_valine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001403')
end
modified_RNA_base_feature() click to toggle source

A post_transcriptionally modified base. (purl.obolibrary.org/obo/SO_0000250)

# File lib/biointerchange/so.rb, line 1821
def self.modified_RNA_base_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000250')
end
modified_adenine() click to toggle source

A modified adenine DNA base feature. (purl.obolibrary.org/obo/SO_0001962)

# File lib/biointerchange/so.rb, line 11981
def self.modified_adenine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001962')
end
modified_adenosine() click to toggle source

A modified adenine is an adenine base feature that has been altered. (purl.obolibrary.org/obo/SO_0001273)

# File lib/biointerchange/so.rb, line 7903
def self.modified_adenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001273')
end
modified_amino_acid_feature() click to toggle source

A post translationally modified amino acid feature. (purl.obolibrary.org/obo/SO_0001385)

# File lib/biointerchange/so.rb, line 8575
def self.modified_amino_acid_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001385')
end
modified_cytidine() click to toggle source

A modified cytidine is a cytidine base feature which has been altered. (purl.obolibrary.org/obo/SO_0001275)

# File lib/biointerchange/so.rb, line 7915
def self.modified_cytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001275')
end
modified_cytosine() click to toggle source

A modified cytosine DNA base feature. (purl.obolibrary.org/obo/SO_0001963)

# File lib/biointerchange/so.rb, line 11987
def self.modified_cytosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001963')
end
modified_glycine() click to toggle source

A post translationally modified glycine amino acid feature. (purl.obolibrary.org/obo/SO_0001386)

# File lib/biointerchange/so.rb, line 8581
def self.modified_glycine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001386')
end
modified_guanine() click to toggle source

A modified guanine DNA base feature. (purl.obolibrary.org/obo/SO_0001964)

# File lib/biointerchange/so.rb, line 11993
def self.modified_guanine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001964')
end
modified_guanosine() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001276)

# File lib/biointerchange/so.rb, line 7921
def self.modified_guanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001276')
end
modified_inosine() click to toggle source

A modified inosine is an inosine base feature that has been altered. (purl.obolibrary.org/obo/SO_0001274)

# File lib/biointerchange/so.rb, line 7909
def self.modified_inosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001274')
end
modified_uridine() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001277)

# File lib/biointerchange/so.rb, line 7927
def self.modified_uridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001277')
end
molecular_contact_region() click to toggle source

A region that is involved a contact with another molecule. (purl.obolibrary.org/obo/SO_0100002)

# File lib/biointerchange/so.rb, line 12359
def self.molecular_contact_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100002')
end
monocistronic() click to toggle source

An attribute describing a sequence that contains the code for one gene product. (purl.obolibrary.org/obo/SO_0000878)

# File lib/biointerchange/so.rb, line 5549
def self.monocistronic
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000878')
end
monocistronic_mRNA() click to toggle source

An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap. (purl.obolibrary.org/obo/SO_0000633)

# File lib/biointerchange/so.rb, line 4121
def self.monocistronic_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000633')
end
monocistronic_primary_transcript() click to toggle source

A primary transcript encoding for one gene product. (purl.obolibrary.org/obo/SO_0000632)

# File lib/biointerchange/so.rb, line 4115
def self.monocistronic_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000632')
end
monocistronic_transcript() click to toggle source

A transcript that is monocistronic. (purl.obolibrary.org/obo/SO_0000665)

# File lib/biointerchange/so.rb, line 4313
def self.monocistronic_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000665')
end
monomeric_repeat() click to toggle source

A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem. (purl.obolibrary.org/obo/SO_0001934)

# File lib/biointerchange/so.rb, line 11809
def self.monomeric_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001934')
end
morpholino_backbone() click to toggle source

An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages. (purl.obolibrary.org/obo/SO_0001183)

# File lib/biointerchange/so.rb, line 7369
def self.morpholino_backbone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001183')
end
morpholino_oligo() click to toggle source

Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino. (purl.obolibrary.org/obo/SO_0000034)

# File lib/biointerchange/so.rb, line 513
def self.morpholino_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000034')
end
mt_gene() click to toggle source

A gene located in mitochondrial sequence. (purl.obolibrary.org/obo/SO_0000088)

# File lib/biointerchange/so.rb, line 845
def self.mt_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000088')
end
mutated_variant_site() click to toggle source

Site which has been experimentally altered. (purl.obolibrary.org/obo/SO_0001148)

# File lib/biointerchange/so.rb, line 7159
def self.mutated_variant_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001148')
end
mutation_causing_inframe_polypeptide_N_terminal_elongation() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000106)

# File lib/biointerchange/so.rb, line 13031
def self.mutation_causing_inframe_polypeptide_N_terminal_elongation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000106')
end
mutation_causing_out_of_frame_polypeptide_C_terminal_elongation() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000109)

# File lib/biointerchange/so.rb, line 13049
def self.mutation_causing_out_of_frame_polypeptide_C_terminal_elongation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000109')
end
mutation_causing_out_of_frame_polypeptide_N_terminal_elongation() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000107)

# File lib/biointerchange/so.rb, line 13037
def self.mutation_causing_out_of_frame_polypeptide_N_terminal_elongation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000107')
end
mutation_causing_polypeptide_C_terminal_elongation() click to toggle source

. (purl.obolibrary.org/obo/SO_1000101)

# File lib/biointerchange/so.rb, line 13001
def self.mutation_causing_polypeptide_C_terminal_elongation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000101')
end
mutation_causing_polypeptide_N_terminal_elongation() click to toggle source

. (purl.obolibrary.org/obo/SO_1000100)

# File lib/biointerchange/so.rb, line 12995
def self.mutation_causing_polypeptide_N_terminal_elongation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000100')
end
mutaton_causing_inframe_polypeptide_C_terminal_elongation() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_1000108)

# File lib/biointerchange/so.rb, line 13043
def self.mutaton_causing_inframe_polypeptide_C_terminal_elongation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000108')
end
n_terminal_region() click to toggle source

The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa). (purl.obolibrary.org/obo/SO_0100014)

# File lib/biointerchange/so.rb, line 12431
def self.n_terminal_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100014')
end
natural() click to toggle source

An attribute describing a feature that occurs in nature. (purl.obolibrary.org/obo/SO_0000782)

# File lib/biointerchange/so.rb, line 5009
def self.natural
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000782')
end
natural_plasmid() click to toggle source

A plasmid that occurs naturally. (purl.obolibrary.org/obo/SO_0001476)

# File lib/biointerchange/so.rb, line 9115
def self.natural_plasmid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001476')
end
natural_transposable_element() click to toggle source

TE that exists (or existed) in nature. (purl.obolibrary.org/obo/SO_0000797)

# File lib/biointerchange/so.rb, line 5099
def self.natural_transposable_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000797')
end
natural_variant_site() click to toggle source

Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars. (purl.obolibrary.org/obo/SO_0001147)

# File lib/biointerchange/so.rb, line 7153
def self.natural_variant_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001147')
end
ncRNA() click to toggle source

An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product. (purl.obolibrary.org/obo/SO_0000655)

# File lib/biointerchange/so.rb, line 4253
def self.ncRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000655')
end
ncRNA_gene() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001263)

# File lib/biointerchange/so.rb, line 7843
def self.ncRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001263')
end
nc_conserved_region() click to toggle source

Non-coding region of sequence similarity by descent from a common ancestor. (purl.obolibrary.org/obo/SO_0000334)

# File lib/biointerchange/so.rb, line 2325
def self.nc_conserved_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000334')
end
nc_primary_transcript() click to toggle source

A primary transcript that is never translated into a protein. (purl.obolibrary.org/obo/SO_0000483)

# File lib/biointerchange/so.rb, line 3217
def self.nc_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000483')
end
negative_sense_ssRNA_viral_sequence() click to toggle source

A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation. (purl.obolibrary.org/obo/SO_0001200)

# File lib/biointerchange/so.rb, line 7471
def self.negative_sense_ssRNA_viral_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001200')
end
negatively_autoregulated() click to toggle source

The gene product is involved in its own transcriptional regulation where it decreases transcription. (purl.obolibrary.org/obo/SO_0000473)

# File lib/biointerchange/so.rb, line 3157
def self.negatively_autoregulated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000473')
end
negatively_autoregulated_gene() click to toggle source

A gene that is negatively autoreguated. (purl.obolibrary.org/obo/SO_0000891)

# File lib/biointerchange/so.rb, line 5627
def self.negatively_autoregulated_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000891')
end
nested_region() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001051)

# File lib/biointerchange/so.rb, line 6581
def self.nested_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001051')
end
nested_repeat() click to toggle source

Either:

-- No comment or description provided. --
(http://purl.obolibrary.org/obo/SO_0001052)

Or:

A repeat that is disrupted by the insertion of another element.
(http://purl.obolibrary.org/obo/SO_0001649)
# File lib/biointerchange/so.rb, line 6591
def self.nested_repeat
  return [ RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001052'), RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001649') ]
end
nested_tandem_repeat() click to toggle source

An NTR is a nested repeat of two distinct tandem motifs interspersed with each other. (purl.obolibrary.org/obo/SO_0001658)

# File lib/biointerchange/so.rb, line 10159
def self.nested_tandem_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001658')
end
nested_transposon() click to toggle source

Either:

-- No comment or description provided. --
(http://purl.obolibrary.org/obo/SO_0001053)

Or:

A transposon that is disrupted by the insertion of another element.
(http://purl.obolibrary.org/obo/SO_0001648)
# File lib/biointerchange/so.rb, line 6601
def self.nested_transposon
  return [ RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001053'), RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001648') ]
end
no_output() click to toggle source

An experimental region wherean analysis has been run and not produced any annotation. (purl.obolibrary.org/obo/SO_0100010)

# File lib/biointerchange/so.rb, line 12407
def self.no_output
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100010')
end
non_LTR_retrotransposon() click to toggle source

A retrotransposon without long terminal repeat sequences. (purl.obolibrary.org/obo/SO_0000189)

# File lib/biointerchange/so.rb, line 1455
def self.non_LTR_retrotransposon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000189')
end
non_LTR_retrotransposon_polymeric_tract() click to toggle source

A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon. (purl.obolibrary.org/obo/SO_0000433)

# File lib/biointerchange/so.rb, line 2913
def self.non_LTR_retrotransposon_polymeric_tract
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000433')
end
non_adjacent_residues() click to toggle source

Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them. (purl.obolibrary.org/obo/SO_0001083)

# File lib/biointerchange/so.rb, line 6769
def self.non_adjacent_residues
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001083')
end
non_canonical_five_prime_splice_site() click to toggle source

A 5’ splice site which does not have the sequence "GT". (SO:ke) (purl.obolibrary.org/obo/SO_0000679)

# File lib/biointerchange/so.rb, line 4397
def self.non_canonical_five_prime_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000679')
end
non_canonical_splice_site() click to toggle source

A splice site where the donor and acceptor sites differ from the canonical form. (purl.obolibrary.org/obo/SO_0000674)

# File lib/biointerchange/so.rb, line 4367
def self.non_canonical_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000674')
end
non_canonical_start_codon() click to toggle source

A start codon that is not the usual AUG sequence. (purl.obolibrary.org/obo/SO_0000680)

# File lib/biointerchange/so.rb, line 4403
def self.non_canonical_start_codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000680')
end
non_canonical_three_prime_splice_site() click to toggle source

A 3’ splice site that does not have the sequence "AG". (SO:ke) (purl.obolibrary.org/obo/SO_0000678)

# File lib/biointerchange/so.rb, line 4391
def self.non_canonical_three_prime_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000678')
end
non_capped_primary_transcript() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000106)

# File lib/biointerchange/so.rb, line 953
def self.non_capped_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000106')
end
non_coding_transcript_exon_variant() click to toggle source

A sequence variant that changes non-coding exon sequence in a non-coding transcript. (purl.obolibrary.org/obo/SO_0001792)

# File lib/biointerchange/so.rb, line 10957
def self.non_coding_transcript_exon_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001792')
end
non_coding_transcript_intron_variant() click to toggle source

A transcript variant occurring within an intron of a non coding transcript. (purl.obolibrary.org/obo/SO_0001970)

# File lib/biointerchange/so.rb, line 12029
def self.non_coding_transcript_intron_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001970')
end
non_coding_transcript_variant() click to toggle source

A transcript variant of a non coding RNA gene. (purl.obolibrary.org/obo/SO_0001619)

# File lib/biointerchange/so.rb, line 9955
def self.non_coding_transcript_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001619')
end
non_conservative_amino_acid_substitution() click to toggle source

A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide. (purl.obolibrary.org/obo/SO_0001608)

# File lib/biointerchange/so.rb, line 9889
def self.non_conservative_amino_acid_substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001608')
end
non_conservative_missense_variant() click to toggle source

A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties. (purl.obolibrary.org/obo/SO_0001586)

# File lib/biointerchange/so.rb, line 9763
def self.non_conservative_missense_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001586')
end
non_covalent_binding_site() click to toggle source

Binding site for any chemical group (co-enzyme, prosthetic group, etc.). (purl.obolibrary.org/obo/SO_0001091)

# File lib/biointerchange/so.rb, line 6817
def self.non_covalent_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001091')
end
non_cytoplasmic_polypeptide_region() click to toggle source

Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm. (purl.obolibrary.org/obo/SO_0001074)

# File lib/biointerchange/so.rb, line 6715
def self.non_cytoplasmic_polypeptide_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001074')
end
non_functional_homolog_of() click to toggle source

A relationship between a pseudogenic feature and its functional ancestor. (purl.obolibrary.org/obo/so_2_5_2.obo#non_functional_homolog_of)

# File lib/biointerchange/so.rb, line 185
def self.non_functional_homolog_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#non_functional_homolog_of')
end
non_processed_pseudogene() click to toggle source

A pseudogene that arose from a means other than retrotransposition. (purl.obolibrary.org/obo/SO_0001760)

# File lib/biointerchange/so.rb, line 10771
def self.non_processed_pseudogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001760')
end
non_protein_coding() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000011)

# File lib/biointerchange/so.rb, line 381
def self.non_protein_coding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000011')
end
non_synonymous() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001816)

# File lib/biointerchange/so.rb, line 11101
def self.non_synonymous
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001816')
end
non_terminal_residue() click to toggle source

The residue at an extremity of the sequence is not the terminal residue. (purl.obolibrary.org/obo/SO_0001084)

# File lib/biointerchange/so.rb, line 6775
def self.non_terminal_residue
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001084')
end
non_transcribed_region() click to toggle source

A region of the gene which is not transcribed. (purl.obolibrary.org/obo/SO_0000183)

# File lib/biointerchange/so.rb, line 1419
def self.non_transcribed_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000183')
end
nonamer_of_recombination_feature_of_vertebrate_immune_system_gene() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000562)

# File lib/biointerchange/so.rb, line 3695
def self.nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000562')
end
noncoding_exon() click to toggle source

An exon that does not contain any codons. (purl.obolibrary.org/obo/SO_0000198)

# File lib/biointerchange/so.rb, line 1509
def self.noncoding_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000198')
end
noncoding_region_of_exon() click to toggle source

The maximal intersection of exon and UTR. (purl.obolibrary.org/obo/SO_0001214)

# File lib/biointerchange/so.rb, line 7555
def self.noncoding_region_of_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001214')
end
noncontiguous_finished() click to toggle source

The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions. (purl.obolibrary.org/obo/SO_0001490)

# File lib/biointerchange/so.rb, line 9199
def self.noncontiguous_finished
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001490')
end
nonsynonymous_variant() click to toggle source

A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change. (purl.obolibrary.org/obo/SO_0001992)

# File lib/biointerchange/so.rb, line 12155
def self.nonsynonymous_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001992')
end
novel_sequence_insertion() click to toggle source

An insertion the sequence of which cannot be mapped to the reference genome. (purl.obolibrary.org/obo/SO_0001838)

# File lib/biointerchange/so.rb, line 11233
def self.novel_sequence_insertion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001838')
end
nuclear_chromosome() click to toggle source

A chromosome originating in a nucleus. (purl.obolibrary.org/obo/SO_0000828)

# File lib/biointerchange/so.rb, line 5249
def self.nuclear_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000828')
end
nuclear_export_signal() click to toggle source

A polypeptide region that targets a polypeptide to he cytoplasm. (purl.obolibrary.org/obo/SO_0001531)

# File lib/biointerchange/so.rb, line 9445
def self.nuclear_export_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001531')
end
nuclear_gene() click to toggle source

A gene from nuclear sequence. (purl.obolibrary.org/obo/SO_0000087)

# File lib/biointerchange/so.rb, line 839
def self.nuclear_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000087')
end
nuclear_localization_signal() click to toggle source

A polypeptide region that targets a polypeptide to the nucleus. (purl.obolibrary.org/obo/SO_0001528)

# File lib/biointerchange/so.rb, line 9427
def self.nuclear_localization_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001528')
end
nuclear_mitochondrial() click to toggle source

An attribute describing a nuclear pseudogene of a mitochndrial gene. (purl.obolibrary.org/obo/SO_0000899)

# File lib/biointerchange/so.rb, line 5675
def self.nuclear_mitochondrial
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000899')
end
nuclear_mt_pseudogene() click to toggle source

A nuclear pseudogene of either coding or non-coding mitochondria derived sequence. (purl.obolibrary.org/obo/SO_0001044)

# File lib/biointerchange/so.rb, line 6539
def self.nuclear_mt_pseudogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001044')
end
nuclear_rim_localization_signal() click to toggle source

A polypeptide region that targets a polypeptide to the nuclear rim. (purl.obolibrary.org/obo/SO_0001534)

# File lib/biointerchange/so.rb, line 9463
def self.nuclear_rim_localization_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001534')
end
nuclear_sequence() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000738)

# File lib/biointerchange/so.rb, line 4751
def self.nuclear_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000738')
end
nuclease_binding_site() click to toggle source

A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease. (purl.obolibrary.org/obo/SO_0000059)

# File lib/biointerchange/so.rb, line 671
def self.nuclease_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000059')
end
nuclease_hypersensitive_site() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000322)

# File lib/biointerchange/so.rb, line 2253
def self.nuclease_hypersensitive_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000322')
end
nuclease_sensitive_site() click to toggle source

A region of nucleotide sequence targeted by a nuclease enzyme. (purl.obolibrary.org/obo/SO_0000684)

# File lib/biointerchange/so.rb, line 4427
def self.nuclease_sensitive_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000684')
end
nucleic_acid() click to toggle source

An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone. (purl.obolibrary.org/obo/SO_0000348)

# File lib/biointerchange/so.rb, line 2409
def self.nucleic_acid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000348')
end
nucleomorph_gene() click to toggle source

A gene from nucleomorph sequence. (purl.obolibrary.org/obo/SO_0000097)

# File lib/biointerchange/so.rb, line 899
def self.nucleomorph_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000097')
end
nucleomorphic_chromosome() click to toggle source

A chromosome originating in a nucleomorph. (purl.obolibrary.org/obo/SO_0000829)

# File lib/biointerchange/so.rb, line 5255
def self.nucleomorphic_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000829')
end
nucleomorphic_sequence() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000739)

# File lib/biointerchange/so.rb, line 4757
def self.nucleomorphic_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000739')
end
nucleotide_binding_site() click to toggle source

A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues. (purl.obolibrary.org/obo/SO_0001655)

# File lib/biointerchange/so.rb, line 10141
def self.nucleotide_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001655')
end
nucleotide_match() click to toggle source

A match against a nucleotide sequence. (purl.obolibrary.org/obo/SO_0000347)

# File lib/biointerchange/so.rb, line 2403
def self.nucleotide_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000347')
end
nucleotide_motif() click to toggle source

A region of nucleotide sequence corresponding to a known motif. (purl.obolibrary.org/obo/SO_0000714)

# File lib/biointerchange/so.rb, line 4607
def self.nucleotide_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000714')
end
nucleotide_to_protein_binding_site() click to toggle source

A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues. (purl.obolibrary.org/obo/SO_0001654)

# File lib/biointerchange/so.rb, line 10135
def self.nucleotide_to_protein_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001654')
end
octamer_motif() click to toggle source

A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors. (purl.obolibrary.org/obo/SO_0001258)

# File lib/biointerchange/so.rb, line 7813
def self.octamer_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001258')
end
oligo() click to toggle source

A short oligonucleotide sequence, of length on the order of 10’s of bases; either single or double stranded. (purl.obolibrary.org/obo/SO_0000696)

# File lib/biointerchange/so.rb, line 4499
def self.oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000696')
end
oligo_U_tail() click to toggle source

The string of non-encoded U’s at the 3’ end of a guide RNA (SO:0000602). (purl.obolibrary.org/obo/SO_0000609)

# File lib/biointerchange/so.rb, line 3977
def self.oligo_U_tail
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000609')
end
one_methyl_three_three_amino_three_carboxypropyl_pseudouridine() click to toggle source

1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001373)

# File lib/biointerchange/so.rb, line 8503
def self.one_methyl_three_three_amino_three_carboxypropyl_pseudouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001373')
end
one_methyladenosine() click to toggle source

1_methyladenosine is a modified adenosine. (purl.obolibrary.org/obo/SO_0001295)

# File lib/biointerchange/so.rb, line 8035
def self.one_methyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001295')
end
one_methylguanosine() click to toggle source

1_methylguanosine is a modified guanosine base feature. (purl.obolibrary.org/obo/SO_0001324)

# File lib/biointerchange/so.rb, line 8209
def self.one_methylguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001324')
end
one_methylinosine() click to toggle source

1-methylinosine is a modified insosine. (purl.obolibrary.org/obo/SO_0001278)

# File lib/biointerchange/so.rb, line 7933
def self.one_methylinosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001278')
end
one_methylpseudouridine() click to toggle source

1_methylpseudouridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001347)

# File lib/biointerchange/so.rb, line 8347
def self.one_methylpseudouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001347')
end
one_two_prime_O_dimethyladenosine() click to toggle source

1,2’-O-dimethyladenosine is a modified adenosine. (purl.obolibrary.org/obo/SO_0001314)

# File lib/biointerchange/so.rb, line 8149
def self.one_two_prime_O_dimethyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001314')
end
one_two_prime_O_dimethylguanosine() click to toggle source

1_2prime_O_dimethylguanosine is a modified guanosine base feature. (purl.obolibrary.org/obo/SO_0001340)

# File lib/biointerchange/so.rb, line 8305
def self.one_two_prime_O_dimethylguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001340')
end
one_two_prime_O_dimethylinosine() click to toggle source

1,2’-O-dimethylinosine is a modified inosine. (purl.obolibrary.org/obo/SO_0001279)

# File lib/biointerchange/so.rb, line 7939
def self.one_two_prime_O_dimethylinosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001279')
end
open_chromatin_region() click to toggle source

A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA. (purl.obolibrary.org/obo/SO_0001747)

# File lib/biointerchange/so.rb, line 10693
def self.open_chromatin_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001747')
end
operator() click to toggle source

A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon. (purl.obolibrary.org/obo/SO_0000057)

# File lib/biointerchange/so.rb, line 655
def self.operator
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000057')
end
operon() click to toggle source

A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region. (purl.obolibrary.org/obo/SO_0000178)

# File lib/biointerchange/so.rb, line 1385
def self.operon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000178')
end
operon_member() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000080)

# File lib/biointerchange/so.rb, line 797
def self.operon_member
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000080')
end
organelle_sequence() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000736)

# File lib/biointerchange/so.rb, line 4739
def self.organelle_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000736')
end
oriC() click to toggle source

An origin of bacterial chromosome replication. (purl.obolibrary.org/obo/SO_0000953)

# File lib/biointerchange/so.rb, line 5999
def self.oriC
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000953')
end
oriT() click to toggle source

A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization. (purl.obolibrary.org/obo/SO_0000724)

# File lib/biointerchange/so.rb, line 4667
def self.oriT
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000724')
end
oriV() click to toggle source

An origin of vegetative replication in plasmids and phages. (purl.obolibrary.org/obo/SO_0000952)

# File lib/biointerchange/so.rb, line 5993
def self.oriV
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000952')
end
origin_of_replication() click to toggle source

The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies. (purl.obolibrary.org/obo/SO_0000296)

# File lib/biointerchange/so.rb, line 2097
def self.origin_of_replication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000296')
end
orphan() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000910)

# File lib/biointerchange/so.rb, line 5741
def self.orphan
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000910')
end
orphan_CDS() click to toggle source

A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence. (purl.obolibrary.org/obo/SO_1001247)

# File lib/biointerchange/so.rb, line 13469
def self.orphan_CDS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001247')
end
orthologous() click to toggle source

An attribute describing a kind of homology where divergence occured after a speciation event. (purl.obolibrary.org/obo/SO_0000858)

# File lib/biointerchange/so.rb, line 5429
def self.orthologous
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000858')
end
orthologous_region() click to toggle source

A homologous_region that is orthologous to another region. (purl.obolibrary.org/obo/SO_0000855)

# File lib/biointerchange/so.rb, line 5411
def self.orthologous_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000855')
end
orthologous_to() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/so_2_5_2.obo#orthologous_to)

# File lib/biointerchange/so.rb, line 191
def self.orthologous_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#orthologous_to')
end
outron() click to toggle source

A region of a primary transcript, that is removed via trans splicing. (purl.obolibrary.org/obo/SO_0001475)

# File lib/biointerchange/so.rb, line 9109
def self.outron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001475')
end
overlapping() click to toggle source

An attribute describing a gene that has a sequence that overlaps the sequence of another gene. (purl.obolibrary.org/obo/SO_0000068)

# File lib/biointerchange/so.rb, line 725
def self.overlapping
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000068')
end
overlapping_EST_set() click to toggle source

A continous experimental result region extending the length of multiple overlapping EST’s. (purl.obolibrary.org/obo/SO_0001262)

# File lib/biointerchange/so.rb, line 7837
def self.overlapping_EST_set
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001262')
end
overlapping_feature_set() click to toggle source

A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature. (purl.obolibrary.org/obo/SO_0001261)

# File lib/biointerchange/so.rb, line 7831
def self.overlapping_feature_set
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001261')
end
overlaps() click to toggle source

X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y. (purl.obolibrary.org/obo/so_2_5_2.obo#overlaps)

# File lib/biointerchange/so.rb, line 197
def self.overlaps
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#overlaps')
end
p_element() click to toggle source

A P_element is a DNA transposon responsible for hybrid dysgenesis. (purl.obolibrary.org/obo/SO_0001535)

# File lib/biointerchange/so.rb, line 9469
def self.p_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001535')
end
paired_end_fragment() click to toggle source

An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair). (purl.obolibrary.org/obo/SO_0001790)

# File lib/biointerchange/so.rb, line 10945
def self.paired_end_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001790')
end
paracentric() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001519)

# File lib/biointerchange/so.rb, line 9373
def self.paracentric
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001519')
end
paracentric_inversion() click to toggle source

A chromosomal inversion that does not include the centromere. (purl.obolibrary.org/obo/SO_1000047)

# File lib/biointerchange/so.rb, line 12713
def self.paracentric_inversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000047')
end
parallel_beta_strand() click to toggle source

A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets. (purl.obolibrary.org/obo/SO_0001113)

# File lib/biointerchange/so.rb, line 6949
def self.parallel_beta_strand
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001113')
end
paralogous() click to toggle source

An attribute describing a kind of homology where divergence occurred after a duplication event. (purl.obolibrary.org/obo/SO_0000859)

# File lib/biointerchange/so.rb, line 5435
def self.paralogous
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000859')
end
paralogous_region() click to toggle source

A homologous_region that is paralogous to another region. (purl.obolibrary.org/obo/SO_0000854)

# File lib/biointerchange/so.rb, line 5405
def self.paralogous_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000854')
end
paralogous_to() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/so_2_5_2.obo#paralogous_to)

# File lib/biointerchange/so.rb, line 203
def self.paralogous_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#paralogous_to')
end
part_of() click to toggle source

Either:

Example: amino_acid part_of polypeptide.
(http://purl.obolibrary.org/obo/part_of)

Or:

X part_of Y if X is a subregion of Y.
(http://purl.obolibrary.org/obo/so_2_5_2.obo#part_of)
# File lib/biointerchange/so.rb, line 11
def self.part_of
  return [ RDF::URI.new('http://purl.obolibrary.org/obo/part_of'), RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#part_of') ]
end
partial_evidence_for_feature() click to toggle source

B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A. (purl.obolibrary.org/obo/so_2_5_2.obo#partial_evidence_for_feature)

# File lib/biointerchange/so.rb, line 209
def self.partial_evidence_for_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#partial_evidence_for_feature')
end
partial_genomic_sequence_assembly() click to toggle source

A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N’s. (purl.obolibrary.org/obo/SO_0001876)

# File lib/biointerchange/so.rb, line 11461
def self.partial_genomic_sequence_assembly
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001876')
end
partially_characterised_chromosomal_mutation() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_1000175)

# File lib/biointerchange/so.rb, line 13331
def self.partially_characterised_chromosomal_mutation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000175')
end
partially_processed_cDNA_clone() click to toggle source

A cDNA invalidated clone by partial processing. (purl.obolibrary.org/obo/SO_0000813)

# File lib/biointerchange/so.rb, line 5171
def self.partially_processed_cDNA_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000813')
end
paternal_uniparental_disomy() click to toggle source

Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother. (purl.obolibrary.org/obo/SO_0001746)

# File lib/biointerchange/so.rb, line 10687
def self.paternal_uniparental_disomy
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001746')
end
paternal_variant() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001776)

# File lib/biointerchange/so.rb, line 10867
def self.paternal_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001776')
end
paternally_imprinted() click to toggle source

The paternal copy of the gene is modified, rendering it transcriptionally silent. (purl.obolibrary.org/obo/SO_0000136)

# File lib/biointerchange/so.rb, line 1133
def self.paternally_imprinted
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000136')
end
paternally_imprinted_gene() click to toggle source

A gene that is paternally imprinted. (purl.obolibrary.org/obo/SO_0000889)

# File lib/biointerchange/so.rb, line 5615
def self.paternally_imprinted_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000889')
end
pathogenic_island() click to toggle source

Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species. (purl.obolibrary.org/obo/SO_0000773)

# File lib/biointerchange/so.rb, line 4955
def self.pathogenic_island
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000773')
end
pedigree_specific_variant() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001779)

# File lib/biointerchange/so.rb, line 10885
def self.pedigree_specific_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001779')
end
peptide_coil() click to toggle source

Irregular, unstructured regions of a protein’s backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds). (purl.obolibrary.org/obo/SO_0100012)

# File lib/biointerchange/so.rb, line 12419
def self.peptide_coil
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100012')
end
peptide_collection() click to toggle source

A collection of peptide sequences. (purl.obolibrary.org/obo/SO_0001501)

# File lib/biointerchange/so.rb, line 9265
def self.peptide_collection
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001501')
end
peptide_helix() click to toggle source

A helix is a secondary_structure conformation where the peptide backbone forms a coil. (purl.obolibrary.org/obo/SO_0001114)

# File lib/biointerchange/so.rb, line 6955
def self.peptide_helix
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001114')
end
peptide_localization_signal() click to toggle source

A region of peptide sequence used to target the polypeptide molecule to a specific organelle. (purl.obolibrary.org/obo/SO_0001527)

# File lib/biointerchange/so.rb, line 9421
def self.peptide_localization_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001527')
end
peptidyl() click to toggle source

An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds. (purl.obolibrary.org/obo/SO_0001407)

# File lib/biointerchange/so.rb, line 8707
def self.peptidyl
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001407')
end
pericentric() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001518)

# File lib/biointerchange/so.rb, line 9367
def self.pericentric
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001518')
end
pericentric_inversion() click to toggle source

A chromosomal inversion that includes the centromere. (purl.obolibrary.org/obo/SO_1000046)

# File lib/biointerchange/so.rb, line 12707
def self.pericentric_inversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000046')
end
peroxywybutosine() click to toggle source

Peroxywybutosine is a modified guanosine base feature. (purl.obolibrary.org/obo/SO_0001333)

# File lib/biointerchange/so.rb, line 8263
def self.peroxywybutosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001333')
end
phage_sequence() click to toggle source

The nucleotide sequence of a virus that infects bacteria. (purl.obolibrary.org/obo/SO_0001042)

# File lib/biointerchange/so.rb, line 6527
def self.phage_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001042')
end
phagemid() click to toggle source

A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with "helper" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids. (SO:ma) (purl.obolibrary.org/obo/SO_0000157)

# File lib/biointerchange/so.rb, line 1259
def self.phagemid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000157')
end
phagemid_clone() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000761)

# File lib/biointerchange/so.rb, line 4889
def self.phagemid_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000761')
end
phenylalanine() click to toggle source

A place holder for a cross product with chebi. (purl.obolibrary.org/obo/SO_0001441)

# File lib/biointerchange/so.rb, line 8905
def self.phenylalanine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001441')
end
phenylalanine_tRNA_primary_transcript() click to toggle source

A primary transcript encoding phenylalanyl tRNA (SO:0000267). (purl.obolibrary.org/obo/SO_0000224)

# File lib/biointerchange/so.rb, line 1665
def self.phenylalanine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000224')
end
phenylalanyl_tRNA() click to toggle source

A tRNA sequence that has a phenylalanine anticodon, and a 3’ phenylalanine binding region. (purl.obolibrary.org/obo/SO_0000267)

# File lib/biointerchange/so.rb, line 1923
def self.phenylalanyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000267')
end
phosphorylation_site() click to toggle source

A post-translationally modified region in which residues of the protein are modified by phosphorylation. (purl.obolibrary.org/obo/SO_0001811)

# File lib/biointerchange/so.rb, line 11071
def self.phosphorylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001811')
end
piRNA() click to toggle source

A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements. (purl.obolibrary.org/obo/SO_0001035)

# File lib/biointerchange/so.rb, line 6485
def self.piRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001035')
end
piRNA_gene() click to toggle source

A gene that encodes for an piwi associated RNA. (purl.obolibrary.org/obo/SO_0001638)

# File lib/biointerchange/so.rb, line 10063
def self.piRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001638')
end
pi_helix() click to toggle source

The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier. (purl.obolibrary.org/obo/SO_0001118)

# File lib/biointerchange/so.rb, line 6979
def self.pi_helix
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001118')
end
plasmid() click to toggle source

A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism. (purl.obolibrary.org/obo/SO_0000155)

# File lib/biointerchange/so.rb, line 1247
def self.plasmid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000155')
end
plasmid_clone() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000759)

# File lib/biointerchange/so.rb, line 4877
def self.plasmid_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000759')
end
plasmid_gene() click to toggle source

A gene from plasmid sequence. (purl.obolibrary.org/obo/SO_0000098)

# File lib/biointerchange/so.rb, line 905
def self.plasmid_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000098')
end
plasmid_location() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000749)

# File lib/biointerchange/so.rb, line 4817
def self.plasmid_location
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000749')
end
plasmid_vector() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000755)

# File lib/biointerchange/so.rb, line 4853
def self.plasmid_vector
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000755')
end
plastid_gene() click to toggle source

A gene from plastid sequence. (purl.obolibrary.org/obo/SO_0000090)

# File lib/biointerchange/so.rb, line 857
def self.plastid_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000090')
end
plastid_sequence() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000740)

# File lib/biointerchange/so.rb, line 4763
def self.plastid_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000740')
end
plus_1_frameshift() click to toggle source

A frameshift caused by inserting one base. (purl.obolibrary.org/obo/SO_0000868)

# File lib/biointerchange/so.rb, line 5489
def self.plus_1_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000868')
end
plus_1_frameshift_variant() click to toggle source

A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward. (purl.obolibrary.org/obo/SO_0001594)

# File lib/biointerchange/so.rb, line 9805
def self.plus_1_frameshift_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001594')
end
plus_1_translational_frameshift() click to toggle source

The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different. (purl.obolibrary.org/obo/SO_0001211)

# File lib/biointerchange/so.rb, line 7537
def self.plus_1_translational_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001211')
end
plus_1_translationally_frameshifted() click to toggle source

An attribute describing a translational frameshift of +1. (purl.obolibrary.org/obo/SO_1001263)

# File lib/biointerchange/so.rb, line 13523
def self.plus_1_translationally_frameshifted
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001263')
end
plus_2_frameshift_variant() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001595)

# File lib/biointerchange/so.rb, line 9811
def self.plus_2_frameshift_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001595')
end
plus_2_framshift() click to toggle source

A frameshift caused by inserting two bases. (purl.obolibrary.org/obo/SO_0000869)

# File lib/biointerchange/so.rb, line 5495
def self.plus_2_framshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000869')
end
plus_2_translational_frameshift() click to toggle source

The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different. (purl.obolibrary.org/obo/SO_0001212)

# File lib/biointerchange/so.rb, line 7543
def self.plus_2_translational_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001212')
end
point_centromere() click to toggle source

A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae. (purl.obolibrary.org/obo/SO_0001794)

# File lib/biointerchange/so.rb, line 10969
def self.point_centromere
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001794')
end
point_mutation() click to toggle source

A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. (purl.obolibrary.org/obo/SO_1000008)

# File lib/biointerchange/so.rb, line 12491
def self.point_mutation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000008')
end
polinton() click to toggle source

A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5’-AG and TC-3’ termini. Polintons exist as autonomous and nonautonomous elements. (purl.obolibrary.org/obo/SO_0001170)

# File lib/biointerchange/so.rb, line 7291
def self.polinton
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001170')
end
polyA_primed_cDNA_clone() click to toggle source

A cDNA clone invalidated by polyA priming. (purl.obolibrary.org/obo/SO_0000812)

# File lib/biointerchange/so.rb, line 5165
def self.polyA_primed_cDNA_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000812')
end
polyA_sequence() click to toggle source

Sequence of about 100 nucleotides of A added to the 3’ end of most eukaryotic mRNAs. (purl.obolibrary.org/obo/SO_0000610)

# File lib/biointerchange/so.rb, line 3983
def self.polyA_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000610')
end
polyA_signal_sequence() click to toggle source

The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA. (purl.obolibrary.org/obo/SO_0000551)

# File lib/biointerchange/so.rb, line 3625
def self.polyA_signal_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000551')
end
polyA_site() click to toggle source

The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence. (purl.obolibrary.org/obo/SO_0000553)

# File lib/biointerchange/so.rb, line 3637
def self.polyA_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000553')
end
polyadenylated() click to toggle source

A attribute describing the addition of a poly A tail to the 3’ end of a mRNA molecule. (purl.obolibrary.org/obo/SO_0000246)

# File lib/biointerchange/so.rb, line 1797
def self.polyadenylated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000246')
end
polyadenylated_mRNA() click to toggle source

An mRNA that is polyadenylated. (purl.obolibrary.org/obo/SO_0000871)

# File lib/biointerchange/so.rb, line 5507
def self.polyadenylated_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000871')
end
polyadenylation_variant() click to toggle source

A sequence variant that changes polyadenylation with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001545)

# File lib/biointerchange/so.rb, line 9529
def self.polyadenylation_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001545')
end
polycistronic() click to toggle source

An attribute describing a sequence that contains the code for more than one gene product. (purl.obolibrary.org/obo/SO_0000880)

# File lib/biointerchange/so.rb, line 5561
def self.polycistronic
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000880')
end
polycistronic_gene() click to toggle source

A gene that is polycistronic. (purl.obolibrary.org/obo/SO_0000477)

# File lib/biointerchange/so.rb, line 3181
def self.polycistronic_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000477')
end
polycistronic_mRNA() click to toggle source

An mRNA that encodes multiple proteins from at least two non-overlapping regions. (purl.obolibrary.org/obo/SO_0000634)

# File lib/biointerchange/so.rb, line 4127
def self.polycistronic_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000634')
end
polycistronic_primary_transcript() click to toggle source

A primary transcript encoding for more than one gene product. (purl.obolibrary.org/obo/SO_0000631)

# File lib/biointerchange/so.rb, line 4109
def self.polycistronic_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000631')
end
polycistronic_transcript() click to toggle source

A transcript that is polycistronic. (purl.obolibrary.org/obo/SO_0000078)

# File lib/biointerchange/so.rb, line 785
def self.polycistronic_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000078')
end
polymer_attribute() click to toggle source

An attribute to describe the kind of biological sequence. (purl.obolibrary.org/obo/SO_0000443)

# File lib/biointerchange/so.rb, line 2977
def self.polymer_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000443')
end
polymerase_synthesis_read() click to toggle source

A read produced by the polymerase based sequence by synthesis method. (purl.obolibrary.org/obo/SO_0001426)

# File lib/biointerchange/so.rb, line 8821
def self.polymerase_synthesis_read
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001426')
end
polymorphic_pseudogene() click to toggle source

Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated. (purl.obolibrary.org/obo/SO_0001841)

# File lib/biointerchange/so.rb, line 11251
def self.polymorphic_pseudogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001841')
end
polymorphic_sequence_variant() click to toggle source

A sequence variant that is segregating in one or more natural populations of a species. (purl.obolibrary.org/obo/SO_0001025)

# File lib/biointerchange/so.rb, line 6425
def self.polymorphic_sequence_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001025')
end
polymorphic_variant() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001766)

# File lib/biointerchange/so.rb, line 10807
def self.polymorphic_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001766')
end
polypeptide() click to toggle source

A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation. (purl.obolibrary.org/obo/SO_0000104)

# File lib/biointerchange/so.rb, line 941
def self.polypeptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000104')
end
polypeptide_DNA_contact() click to toggle source

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA. (purl.obolibrary.org/obo/SO_0100020)

# File lib/biointerchange/so.rb, line 12467
def self.polypeptide_DNA_contact
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100020')
end
polypeptide_binding_motif() click to toggle source

A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand. (purl.obolibrary.org/obo/SO_0100018)

# File lib/biointerchange/so.rb, line 12455
def self.polypeptide_binding_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100018')
end
polypeptide_calcium_ion_contact_site() click to toggle source

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions. (purl.obolibrary.org/obo/SO_0001094)

# File lib/biointerchange/so.rb, line 6835
def self.polypeptide_calcium_ion_contact_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001094')
end
polypeptide_catalytic_motif() click to toggle source

A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues. (purl.obolibrary.org/obo/SO_0100019)

# File lib/biointerchange/so.rb, line 12461
def self.polypeptide_catalytic_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100019')
end
polypeptide_cobalt_ion_contact_site() click to toggle source

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions. (purl.obolibrary.org/obo/SO_0001095)

# File lib/biointerchange/so.rb, line 6841
def self.polypeptide_cobalt_ion_contact_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001095')
end
polypeptide_conserved_motif() click to toggle source

A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found. (purl.obolibrary.org/obo/SO_0100017)

# File lib/biointerchange/so.rb, line 12449
def self.polypeptide_conserved_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100017')
end
polypeptide_conserved_region() click to toggle source

A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found. (purl.obolibrary.org/obo/SO_0100021)

# File lib/biointerchange/so.rb, line 12473
def self.polypeptide_conserved_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100021')
end
polypeptide_copper_ion_contact_site() click to toggle source

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions. (purl.obolibrary.org/obo/SO_0001096)

# File lib/biointerchange/so.rb, line 6847
def self.polypeptide_copper_ion_contact_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001096')
end
polypeptide_domain() click to toggle source

A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution. (purl.obolibrary.org/obo/SO_0000417)

# File lib/biointerchange/so.rb, line 2817
def self.polypeptide_domain
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000417')
end
polypeptide_function_variant() click to toggle source

A sequence variant which changes polypeptide functioning with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001554)

# File lib/biointerchange/so.rb, line 9583
def self.polypeptide_function_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001554')
end
polypeptide_fusion() click to toggle source

A sequence variant that causes a fusion of two polypeptide sequences. (purl.obolibrary.org/obo/SO_0001616)

# File lib/biointerchange/so.rb, line 9937
def self.polypeptide_fusion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001616')
end
polypeptide_gain_of_function_variant() click to toggle source

A sequence variant which causes gain of polypeptide function with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001557)

# File lib/biointerchange/so.rb, line 9601
def self.polypeptide_gain_of_function_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001557')
end
polypeptide_iron_ion_contact_site() click to toggle source

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions. (purl.obolibrary.org/obo/SO_0001097)

# File lib/biointerchange/so.rb, line 6853
def self.polypeptide_iron_ion_contact_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001097')
end
polypeptide_ligand_contact() click to toggle source

Residues which interact with a ligand. (purl.obolibrary.org/obo/SO_0001105)

# File lib/biointerchange/so.rb, line 6901
def self.polypeptide_ligand_contact
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001105')
end
polypeptide_localization_variant() click to toggle source

A sequence variant which changes the localization of a polypeptide with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001558)

# File lib/biointerchange/so.rb, line 9607
def self.polypeptide_localization_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001558')
end
polypeptide_loss_of_function_variant() click to toggle source

A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001559)

# File lib/biointerchange/so.rb, line 9613
def self.polypeptide_loss_of_function_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001559')
end
polypeptide_magnesium_ion_contact_site() click to toggle source

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions. (purl.obolibrary.org/obo/SO_0001098)

# File lib/biointerchange/so.rb, line 6859
def self.polypeptide_magnesium_ion_contact_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001098')
end
polypeptide_manganese_ion_contact_site() click to toggle source

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions. (purl.obolibrary.org/obo/SO_0001099)

# File lib/biointerchange/so.rb, line 6865
def self.polypeptide_manganese_ion_contact_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001099')
end
polypeptide_metal_contact() click to toggle source

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions. (purl.obolibrary.org/obo/SO_0001092)

# File lib/biointerchange/so.rb, line 6823
def self.polypeptide_metal_contact
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001092')
end
polypeptide_molybdenum_ion_contact_site() click to toggle source

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions. (purl.obolibrary.org/obo/SO_0001100)

# File lib/biointerchange/so.rb, line 6871
def self.polypeptide_molybdenum_ion_contact_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001100')
end
polypeptide_motif() click to toggle source

A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.). (purl.obolibrary.org/obo/SO_0001067)

# File lib/biointerchange/so.rb, line 6679
def self.polypeptide_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001067')
end
polypeptide_nest_left_right_motif() click to toggle source

A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. (purl.obolibrary.org/obo/SO_0001121)

# File lib/biointerchange/so.rb, line 6997
def self.polypeptide_nest_left_right_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001121')
end
polypeptide_nest_motif() click to toggle source

A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops. (purl.obolibrary.org/obo/SO_0001120)

# File lib/biointerchange/so.rb, line 6991
def self.polypeptide_nest_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001120')
end
polypeptide_nest_right_left_motif() click to toggle source

A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. (purl.obolibrary.org/obo/SO_0001122)

# File lib/biointerchange/so.rb, line 7003
def self.polypeptide_nest_right_left_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001122')
end
polypeptide_nickel_ion_contact_site() click to toggle source

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions. (purl.obolibrary.org/obo/SO_0001101)

# File lib/biointerchange/so.rb, line 6877
def self.polypeptide_nickel_ion_contact_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001101')
end
polypeptide_partial_loss_of_function() click to toggle source

A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001561)

# File lib/biointerchange/so.rb, line 9625
def self.polypeptide_partial_loss_of_function
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001561')
end
polypeptide_post_translational_processing_affected() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_1000123)

# File lib/biointerchange/so.rb, line 13121
def self.polypeptide_post_translational_processing_affected
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000123')
end
polypeptide_post_translational_processing_variant() click to toggle source

A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001562)

# File lib/biointerchange/so.rb, line 9631
def self.polypeptide_post_translational_processing_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001562')
end
polypeptide_region() click to toggle source

Biological sequence region that can be assigned to a specific subsequence of a polypeptide. (purl.obolibrary.org/obo/SO_0000839)

# File lib/biointerchange/so.rb, line 5315
def self.polypeptide_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000839')
end
polypeptide_repeat() click to toggle source

A polypeptide_repeat is a single copy of an internal sequence repetition. (purl.obolibrary.org/obo/SO_0001068)

# File lib/biointerchange/so.rb, line 6685
def self.polypeptide_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001068')
end
polypeptide_secondary_structure() click to toggle source

A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain. (purl.obolibrary.org/obo/SO_0001078)

# File lib/biointerchange/so.rb, line 6739
def self.polypeptide_secondary_structure
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001078')
end
polypeptide_sequence_variant() click to toggle source

A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence. (purl.obolibrary.org/obo/SO_0001603)

# File lib/biointerchange/so.rb, line 9859
def self.polypeptide_sequence_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001603')
end
polypeptide_sequencing_information() click to toggle source

Incompatibility in the sequence due to some experimental problem. (purl.obolibrary.org/obo/SO_0001082)

# File lib/biointerchange/so.rb, line 6763
def self.polypeptide_sequencing_information
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001082')
end
polypeptide_structural_motif() click to toggle source

Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit. (purl.obolibrary.org/obo/SO_0001079)

# File lib/biointerchange/so.rb, line 6745
def self.polypeptide_structural_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001079')
end
polypeptide_structural_region() click to toggle source

Region of polypeptide with a given structural property. (purl.obolibrary.org/obo/SO_0001070)

# File lib/biointerchange/so.rb, line 6691
def self.polypeptide_structural_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001070')
end
polypeptide_truncation() click to toggle source

A sequence variant of the CD that causes a truncation of the resulting polypeptide. (purl.obolibrary.org/obo/SO_0001617)

# File lib/biointerchange/so.rb, line 9943
def self.polypeptide_truncation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001617')
end
polypeptide_tungsten_ion_contact_site() click to toggle source

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions. (purl.obolibrary.org/obo/SO_0001102)

# File lib/biointerchange/so.rb, line 6883
def self.polypeptide_tungsten_ion_contact_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001102')
end
polypeptide_turn_motif() click to toggle source

A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues. (purl.obolibrary.org/obo/SO_0001128)

# File lib/biointerchange/so.rb, line 7039
def self.polypeptide_turn_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001128')
end
polypeptide_variation_site() click to toggle source

A site of sequence variation (alteration). Alternative sequence due to naturally occuring events such as polymorphisms and altermatve splicing or experimental methods such as site directed mutagenesis. (purl.obolibrary.org/obo/SO_0001146)

# File lib/biointerchange/so.rb, line 7147
def self.polypeptide_variation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001146')
end
polypeptide_zinc_ion_contact_site() click to toggle source

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions. (purl.obolibrary.org/obo/SO_0001103)

# File lib/biointerchange/so.rb, line 6889
def self.polypeptide_zinc_ion_contact_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001103')
end
polyploid() click to toggle source

A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number. (purl.obolibrary.org/obo/SO_0001254)

# File lib/biointerchange/so.rb, line 7789
def self.polyploid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001254')
end
polypyrimidine_tract() click to toggle source

The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing. (purl.obolibrary.org/obo/SO_0000612)

# File lib/biointerchange/so.rb, line 3995
def self.polypyrimidine_tract
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000612')
end
population_specific_variant() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001780)

# File lib/biointerchange/so.rb, line 10891
def self.population_specific_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001780')
end
position_of() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/so_2_5_2.obo#position_of)

# File lib/biointerchange/so.rb, line 215
def self.position_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#position_of')
end
positional_candidate_gene() click to toggle source

A candidate gene whose association with a trait is based on the gene’s location on a chromosome. (purl.obolibrary.org/obo/SO_0001868)

# File lib/biointerchange/so.rb, line 11413
def self.positional_candidate_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001868')
end
positive_sense_ssRNA_viral_sequence() click to toggle source

A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host. (purl.obolibrary.org/obo/SO_0001201)

# File lib/biointerchange/so.rb, line 7477
def self.positive_sense_ssRNA_viral_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001201')
end
positively_autoregulated() click to toggle source

The gene product is involved in its own transcriptional regulation, where it increases transcription. (purl.obolibrary.org/obo/SO_0000475)

# File lib/biointerchange/so.rb, line 3169
def self.positively_autoregulated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000475')
end
positively_autoregulated_gene() click to toggle source

A gene that is positively autoregulated. (purl.obolibrary.org/obo/SO_0000892)

# File lib/biointerchange/so.rb, line 5633
def self.positively_autoregulated_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000892')
end
possible_assembly_error() click to toggle source

A region of sequence where there may have been an error in the assembly. (purl.obolibrary.org/obo/SO_0000702)

# File lib/biointerchange/so.rb, line 4535
def self.possible_assembly_error
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000702')
end
possible_base_call_error() click to toggle source

A region of sequence where the validity of the base calling is questionable. (purl.obolibrary.org/obo/SO_0000701)

# File lib/biointerchange/so.rb, line 4529
def self.possible_base_call_error
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000701')
end
post_translationally_modified_region() click to toggle source

A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein. (purl.obolibrary.org/obo/SO_0001089)

# File lib/biointerchange/so.rb, line 6805
def self.post_translationally_modified_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001089')
end
post_translationally_regulated() click to toggle source

An attribute describing a gene that is regulated after it has been translated. (purl.obolibrary.org/obo/SO_0000130)

# File lib/biointerchange/so.rb, line 1097
def self.post_translationally_regulated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000130')
end
post_translationally_regulated_by_protein_modification() click to toggle source

An attribute describing a gene sequence where the resulting protein is modified to regulate it. (purl.obolibrary.org/obo/SO_0000469)

# File lib/biointerchange/so.rb, line 3133
def self.post_translationally_regulated_by_protein_modification
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000469')
end
post_translationally_regulated_by_protein_stability() click to toggle source

An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein. (purl.obolibrary.org/obo/SO_0000467)

# File lib/biointerchange/so.rb, line 3121
def self.post_translationally_regulated_by_protein_stability
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000467')
end
post_translationally_regulated_gene() click to toggle source

A gene that is post translationally regulated. (purl.obolibrary.org/obo/SO_0000890)

# File lib/biointerchange/so.rb, line 5621
def self.post_translationally_regulated_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000890')
end
pre_edited_mRNA() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000932)

# File lib/biointerchange/so.rb, line 5873
def self.pre_edited_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000932')
end
pre_edited_region() click to toggle source

The region of a transcript that will be edited. (purl.obolibrary.org/obo/SO_0000583)

# File lib/biointerchange/so.rb, line 3821
def self.pre_edited_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000583')
end
pre_miRNA() click to toggle source

The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin sructure. (purl.obolibrary.org/obo/SO_0001244)

# File lib/biointerchange/so.rb, line 7729
def self.pre_miRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001244')
end
predicted() click to toggle source

An attribute describing an unverified region. (purl.obolibrary.org/obo/SO_0000732)

# File lib/biointerchange/so.rb, line 4715
def self.predicted
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000732')
end
predicted_ab_initio_computation() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000310)

# File lib/biointerchange/so.rb, line 2181
def self.predicted_ab_initio_computation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000310')
end
predicted_by_ab_initio_computation() click to toggle source

An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity. (purl.obolibrary.org/obo/SO_0000911)

# File lib/biointerchange/so.rb, line 5747
def self.predicted_by_ab_initio_computation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000911')
end
predicted_gene() click to toggle source

This term is mapped to MGED. Do not obsolete without consulting MGED ontology. (purl.obolibrary.org/obo/SO_0000996)

# File lib/biointerchange/so.rb, line 6251
def self.predicted_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000996')
end
primary_transcript() click to toggle source

A transcript that in its initial state requires modification to be functional. (purl.obolibrary.org/obo/SO_0000185)

# File lib/biointerchange/so.rb, line 1431
def self.primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000185')
end
primary_transcript_attribute() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000144)

# File lib/biointerchange/so.rb, line 1181
def self.primary_transcript_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000144')
end
primary_transcript_region() click to toggle source

A part of a primary transcript. (purl.obolibrary.org/obo/SO_0000835)

# File lib/biointerchange/so.rb, line 5291
def self.primary_transcript_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000835')
end
primer() click to toggle source

An oligo to which new deoxyribonucleotides can be added by DNA polymerase. (purl.obolibrary.org/obo/SO_0000112)

# File lib/biointerchange/so.rb, line 989
def self.primer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000112')
end
primer_binding_site() click to toggle source

Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription. (purl.obolibrary.org/obo/SO_0005850)

# File lib/biointerchange/so.rb, line 12299
def self.primer_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005850')
end
primer_match() click to toggle source

A nucleotide match to a primer sequence. (purl.obolibrary.org/obo/SO_0001472)

# File lib/biointerchange/so.rb, line 9091
def self.primer_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001472')
end
probe() click to toggle source

A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid. (purl.obolibrary.org/obo/SO_0000051)

# File lib/biointerchange/so.rb, line 615
def self.probe
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000051')
end
processed() click to toggle source

An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail. (purl.obolibrary.org/obo/SO_0000900)

# File lib/biointerchange/so.rb, line 5681
def self.processed
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000900')
end
processed_from() click to toggle source

Inverse of processed_into. (purl.obolibrary.org/obo/so_2_5_2.obo#processed_from)

# File lib/biointerchange/so.rb, line 221
def self.processed_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#processed_from')
end
processed_into() click to toggle source

X is processed_into Y if a region X is modified to create Y. (purl.obolibrary.org/obo/so_2_5_2.obo#processed_into)

# File lib/biointerchange/so.rb, line 227
def self.processed_into
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#processed_into')
end
processed_pseudogene() click to toggle source

A pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promoters, but often including a polyA tail. (purl.obolibrary.org/obo/SO_0000043)

# File lib/biointerchange/so.rb, line 567
def self.processed_pseudogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000043')
end
processed_transcript() click to toggle source

A transcript for which no open reading frame has been identified and for which no other function has been determined. (purl.obolibrary.org/obo/SO_0001503)

# File lib/biointerchange/so.rb, line 9277
def self.processed_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001503')
end
processed_transcript_attribute() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000082)

# File lib/biointerchange/so.rb, line 809
def self.processed_transcript_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000082')
end
proline() click to toggle source

A place holder for a cross product with chebi. (purl.obolibrary.org/obo/SO_0001439)

# File lib/biointerchange/so.rb, line 8893
def self.proline
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001439')
end
proline_tRNA_primary_transcript() click to toggle source

A primary transcript encoding prolyl tRNA (SO:0000268). (purl.obolibrary.org/obo/SO_0000225)

# File lib/biointerchange/so.rb, line 1671
def self.proline_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000225')
end
prolyl_tRNA() click to toggle source

A tRNA sequence that has a proline anticodon, and a 3’ proline binding region. (purl.obolibrary.org/obo/SO_0000268)

# File lib/biointerchange/so.rb, line 1929
def self.prolyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000268')
end
promoter() click to toggle source

A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery. (purl.obolibrary.org/obo/SO_0000167)

# File lib/biointerchange/so.rb, line 1319
def self.promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000167')
end
promoter_element() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001659)

# File lib/biointerchange/so.rb, line 10165
def self.promoter_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001659')
end
promoter_flanking_region() click to toggle source

A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites. (purl.obolibrary.org/obo/SO_0001952)

# File lib/biointerchange/so.rb, line 11917
def self.promoter_flanking_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001952')
end
promoter_region() click to toggle source

A region of sequence which is part of a promoter. (purl.obolibrary.org/obo/SO_0000832)

# File lib/biointerchange/so.rb, line 5273
def self.promoter_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000832')
end
promoter_targeting_sequence() click to toggle source

A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter. (purl.obolibrary.org/obo/SO_0001058)

# File lib/biointerchange/so.rb, line 6631
def self.promoter_targeting_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001058')
end
promoter_trap_construct() click to toggle source

A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic. (purl.obolibrary.org/obo/SO_0001478)

# File lib/biointerchange/so.rb, line 9127
def self.promoter_trap_construct
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001478')
end
propeptide() click to toggle source

Part of a peptide chain which is cleaved off during the formation of the mature protein. (purl.obolibrary.org/obo/SO_0001062)

# File lib/biointerchange/so.rb, line 6655
def self.propeptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001062')
end
propeptide_cleavage_site() click to toggle source

The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs. (purl.obolibrary.org/obo/SO_0001061)

# File lib/biointerchange/so.rb, line 6649
def self.propeptide_cleavage_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001061')
end
prophage() click to toggle source

A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated "island". (GOC:jl) (purl.obolibrary.org/obo/SO_0001006)

# File lib/biointerchange/so.rb, line 6311
def self.prophage
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001006')
end
proplastid_gene() click to toggle source

A gene from proplastid sequence. (purl.obolibrary.org/obo/SO_0000096)

# File lib/biointerchange/so.rb, line 893
def self.proplastid_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000096')
end
proplastid_sequence() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000748)

# File lib/biointerchange/so.rb, line 4811
def self.proplastid_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000748')
end
protease_site() click to toggle source

A polypeptide_region that codes for a protease cleavage site. (purl.obolibrary.org/obo/SO_0001956)

# File lib/biointerchange/so.rb, line 11941
def self.protease_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001956')
end
protein_altering_variant() click to toggle source

A sequence_variant which is predicted to change the protein encoded in the coding sequence. (purl.obolibrary.org/obo/SO_0001818)

# File lib/biointerchange/so.rb, line 11113
def self.protein_altering_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001818')
end
protein_binding_site() click to toggle source

A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules. (purl.obolibrary.org/obo/SO_0000410)

# File lib/biointerchange/so.rb, line 2775
def self.protein_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000410')
end
protein_coding() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000010)

# File lib/biointerchange/so.rb, line 375
def self.protein_coding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000010')
end
protein_coding_gene() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001217)

# File lib/biointerchange/so.rb, line 7573
def self.protein_coding_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001217')
end
protein_coding_primary_transcript() click to toggle source

A primary transcript that, at least in part, encodes one or more proteins. (purl.obolibrary.org/obo/SO_0000120)

# File lib/biointerchange/so.rb, line 1037
def self.protein_coding_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000120')
end
protein_hmm_match() click to toggle source

A match to a protein HMM such as pfam. (purl.obolibrary.org/obo/SO_0001831)

# File lib/biointerchange/so.rb, line 11191
def self.protein_hmm_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001831')
end
protein_match() click to toggle source

A match against a protein sequence. (purl.obolibrary.org/obo/SO_0000349)

# File lib/biointerchange/so.rb, line 2415
def self.protein_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000349')
end
protein_protein_contact() click to toggle source

A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues. (purl.obolibrary.org/obo/SO_0001093)

# File lib/biointerchange/so.rb, line 6829
def self.protein_protein_contact
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001093')
end
protein_stability_element() click to toggle source

A polypeptide region that proves structure in a protein that affects the stability of the protein. (purl.obolibrary.org/obo/SO_0001955)

# File lib/biointerchange/so.rb, line 11935
def self.protein_stability_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001955')
end
proviral_gene() click to toggle source

A gene from proviral sequence. (purl.obolibrary.org/obo/SO_0000099)

# File lib/biointerchange/so.rb, line 911
def self.proviral_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000099')
end
proviral_location() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000751)

# File lib/biointerchange/so.rb, line 4829
def self.proviral_location
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000751')
end
proviral_region() click to toggle source

A viral sequence which has integrated into a host genome. (purl.obolibrary.org/obo/SO_0000113)

# File lib/biointerchange/so.rb, line 995
def self.proviral_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000113')
end
proximal_promoter_element() click to toggle source

DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor). (purl.obolibrary.org/obo/SO_0001668)

# File lib/biointerchange/so.rb, line 10219
def self.proximal_promoter_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001668')
end
pseudogene() click to toggle source

A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their "normal" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its "normal" paralog). (www.ucl.ac.uk/~ucbhjow/b241/glossary.html) (purl.obolibrary.org/obo/SO_0000336)

# File lib/biointerchange/so.rb, line 2337
def self.pseudogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000336')
end
pseudogene_attribute() click to toggle source

An attribute of a pseudogene (SO:0000336). (purl.obolibrary.org/obo/SO_0000042)

# File lib/biointerchange/so.rb, line 561
def self.pseudogene_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000042')
end
pseudogene_by_unequal_crossing_over() click to toggle source

A pseudogene caused by unequal crossing over at recombination. (purl.obolibrary.org/obo/SO_0000044)

# File lib/biointerchange/so.rb, line 573
def self.pseudogene_by_unequal_crossing_over
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000044')
end
pseudogenic_exon() click to toggle source

A non functional descendant of an exon, part of a pseudogene. (purl.obolibrary.org/obo/SO_0000507)

# File lib/biointerchange/so.rb, line 3361
def self.pseudogenic_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000507')
end
pseudogenic_gene_segment() click to toggle source

A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product. (purl.obolibrary.org/obo/SO_0001741)

# File lib/biointerchange/so.rb, line 10657
def self.pseudogenic_gene_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001741')
end
pseudogenic_rRNA() click to toggle source

A non functional descendent of an rRNA. (purl.obolibrary.org/obo/SO_0000777)

# File lib/biointerchange/so.rb, line 4979
def self.pseudogenic_rRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000777')
end
pseudogenic_region() click to toggle source

A non-functional descendent of a functional entity. (purl.obolibrary.org/obo/SO_0000462)

# File lib/biointerchange/so.rb, line 3091
def self.pseudogenic_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000462')
end
pseudogenic_tRNA() click to toggle source

A non functional descendent of a tRNA. (purl.obolibrary.org/obo/SO_0000778)

# File lib/biointerchange/so.rb, line 4985
def self.pseudogenic_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000778')
end
pseudogenic_transcript() click to toggle source

A non functional descendant of a transcript, part of a pseudogene. (purl.obolibrary.org/obo/SO_0000516)

# File lib/biointerchange/so.rb, line 3415
def self.pseudogenic_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000516')
end
pseudoknot() click to toggle source

A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop. (purl.obolibrary.org/obo/SO_0000591)

# File lib/biointerchange/so.rb, line 3869
def self.pseudoknot
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000591')
end
pseudouridine() click to toggle source

A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position. (purl.obolibrary.org/obo/SO_0001229)

# File lib/biointerchange/so.rb, line 7645
def self.pseudouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001229')
end
pseudouridylation_guide_snoRNA() click to toggle source

A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue. (purl.obolibrary.org/obo/SO_0001187)

# File lib/biointerchange/so.rb, line 7393
def self.pseudouridylation_guide_snoRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001187')
end
purine_to_pyrimidine_transversion() click to toggle source

Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T. (purl.obolibrary.org/obo/SO_1000023)

# File lib/biointerchange/so.rb, line 12581
def self.purine_to_pyrimidine_transversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000023')
end
purine_transition() click to toggle source

A substitution of a purine, A or G, for another purine. (purl.obolibrary.org/obo/SO_1000014)

# File lib/biointerchange/so.rb, line 12527
def self.purine_transition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000014')
end
pyrimidine_to_purine_transversion() click to toggle source

Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G. (purl.obolibrary.org/obo/SO_1000018)

# File lib/biointerchange/so.rb, line 12551
def self.pyrimidine_to_purine_transversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000018')
end
pyrimidine_transition() click to toggle source

A substitution of a pyrimidine, C or T, for another pyrimidine. (purl.obolibrary.org/obo/SO_1000010)

# File lib/biointerchange/so.rb, line 12503
def self.pyrimidine_transition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000010')
end
pyrosequenced_read() click to toggle source

A read produced by pyrosequencing technology. (purl.obolibrary.org/obo/SO_0001424)

# File lib/biointerchange/so.rb, line 8809
def self.pyrosequenced_read
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001424')
end
pyrrolysine() click to toggle source

A place holder for a cross product with chebi. (purl.obolibrary.org/obo/SO_0001456)

# File lib/biointerchange/so.rb, line 8995
def self.pyrrolysine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001456')
end
pyrrolysine_tRNA_primary_transcript() click to toggle source

A primary transcript encoding pyrrolysyl tRNA (SO:0000766). (purl.obolibrary.org/obo/SO_0001178)

# File lib/biointerchange/so.rb, line 7339
def self.pyrrolysine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001178')
end
pyrrolysyl_tRNA() click to toggle source

A tRNA sequence that has a pyrrolysine anticodon, and a 3’ pyrrolysine binding region. (purl.obolibrary.org/obo/SO_0000766)

# File lib/biointerchange/so.rb, line 4919
def self.pyrrolysyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000766')
end
quality_value() click to toggle source

An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score. (purl.obolibrary.org/obo/SO_0001686)

# File lib/biointerchange/so.rb, line 10327
def self.quality_value
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001686')
end
quantitative_variant() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001774)

# File lib/biointerchange/so.rb, line 10855
def self.quantitative_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001774')
end
queuosine() click to toggle source

Queuosine is a modified 7-deazoguanosine. (purl.obolibrary.org/obo/SO_0001317)

# File lib/biointerchange/so.rb, line 8167
def self.queuosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001317')
end
rDNA_intergenic_spacer_element() click to toggle source

A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1). (purl.obolibrary.org/obo/SO_0001860)

# File lib/biointerchange/so.rb, line 11365
def self.rDNA_intergenic_spacer_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001860')
end
rDNA_replication_fork_barrier() click to toggle source

A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing. (purl.obolibrary.org/obo/SO_0001914)

# File lib/biointerchange/so.rb, line 11689
def self.rDNA_replication_fork_barrier
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001914')
end
rRNA() click to toggle source

RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity. (purl.obolibrary.org/obo/SO_0000252)

# File lib/biointerchange/so.rb, line 1833
def self.rRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000252')
end
rRNA_16S() click to toggle source

A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome. (purl.obolibrary.org/obo/SO_0001000)

# File lib/biointerchange/so.rb, line 6275
def self.rRNA_16S
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001000')
end
rRNA_18S() click to toggle source

A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome. (purl.obolibrary.org/obo/SO_0000407)

# File lib/biointerchange/so.rb, line 2757
def self.rRNA_18S
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000407')
end
rRNA_21S() click to toggle source

A component of the large ribosomal subunit in mitochondrial rRNA. (purl.obolibrary.org/obo/SO_0001171)

# File lib/biointerchange/so.rb, line 7297
def self.rRNA_21S
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001171')
end
rRNA_23S() click to toggle source

A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome. (purl.obolibrary.org/obo/SO_0001001)

# File lib/biointerchange/so.rb, line 6281
def self.rRNA_23S
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001001')
end
rRNA_25S() click to toggle source

A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes. (purl.obolibrary.org/obo/SO_0001002)

# File lib/biointerchange/so.rb, line 6287
def self.rRNA_25S
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001002')
end
rRNA_28S() click to toggle source

A component of the large ribosomal subunit. (purl.obolibrary.org/obo/SO_0000653)

# File lib/biointerchange/so.rb, line 4241
def self.rRNA_28S
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000653')
end
rRNA_5S() click to toggle source

5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription. (purl.obolibrary.org/obo/SO_0000652)

# File lib/biointerchange/so.rb, line 4235
def self.rRNA_5S
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000652')
end
rRNA_5_8S() click to toggle source

5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea. (purl.obolibrary.org/obo/SO_0000375)

# File lib/biointerchange/so.rb, line 2565
def self.rRNA_5_8S
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000375')
end
rRNA_cleavage_RNA() click to toggle source

An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules. (purl.obolibrary.org/obo/SO_0005843)

# File lib/biointerchange/so.rb, line 12269
def self.rRNA_cleavage_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005843')
end
rRNA_cleavage_snoRNA_primary_transcript() click to toggle source

A primary transcript encoding an rRNA cleavage snoRNA. (purl.obolibrary.org/obo/SO_0000582)

# File lib/biointerchange/so.rb, line 3815
def self.rRNA_cleavage_snoRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000582')
end
rRNA_encoding() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000573)

# File lib/biointerchange/so.rb, line 3761
def self.rRNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000573')
end
rRNA_gene() click to toggle source

A gene that encodes for ribosomal RNA. (purl.obolibrary.org/obo/SO_0001637)

# File lib/biointerchange/so.rb, line 10057
def self.rRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001637')
end
rRNA_large_subunit_primary_transcript() click to toggle source

A primary transcript encoding a large ribosomal subunit RNA. (purl.obolibrary.org/obo/SO_0000325)

# File lib/biointerchange/so.rb, line 2271
def self.rRNA_large_subunit_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000325')
end
rRNA_primary_transcript() click to toggle source

A primary transcript encoding a ribosomal RNA. (purl.obolibrary.org/obo/SO_0000209)

# File lib/biointerchange/so.rb, line 1575
def self.rRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000209')
end
rRNA_primary_transcript_region() click to toggle source

A region of an rRNA primary transcript. (purl.obolibrary.org/obo/SO_0000838)

# File lib/biointerchange/so.rb, line 5309
def self.rRNA_primary_transcript_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000838')
end
rRNA_small_subunit_primary_transcript() click to toggle source

A primary transcript encoding a small ribosomal subunit RNA. (purl.obolibrary.org/obo/SO_0000255)

# File lib/biointerchange/so.rb, line 1851
def self.rRNA_small_subunit_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000255')
end
random_sequence() click to toggle source

A sequence of nucleotides or amino acids which, by design, has a "random" order of components, given a predetermined input frequency of these components. (SO:ma) (purl.obolibrary.org/obo/SO_0000449)

# File lib/biointerchange/so.rb, line 3013
def self.random_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000449')
end
rare_variant() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001765)

# File lib/biointerchange/so.rb, line 10801
def self.rare_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001765')
end
rasiRNA() click to toggle source

A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements. (purl.obolibrary.org/obo/SO_0000454)

# File lib/biointerchange/so.rb, line 3043
def self.rasiRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000454')
end
rate_of_transcription_variant() click to toggle source

A sequence variant that changes the rate of transcription with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001550)

# File lib/biointerchange/so.rb, line 9559
def self.rate_of_transcription_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001550')
end
read() click to toggle source

A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine. (purl.obolibrary.org/obo/SO_0000150)

# File lib/biointerchange/so.rb, line 1217
def self.read
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000150')
end
read_pair() click to toggle source

One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert. (purl.obolibrary.org/obo/SO_0000007)

# File lib/biointerchange/so.rb, line 357
def self.read_pair
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000007')
end
reading_frame() click to toggle source

A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon. (purl.obolibrary.org/obo/SO_0000717)

# File lib/biointerchange/so.rb, line 4625
def self.reading_frame
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000717')
end
reagent() click to toggle source

A sequence used in experiment. (purl.obolibrary.org/obo/SO_0000695)

# File lib/biointerchange/so.rb, line 4493
def self.reagent
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000695')
end
reagent_attribute() click to toggle source

Added jan 2006 by KE. (purl.obolibrary.org/obo/SO_0000786)

# File lib/biointerchange/so.rb, line 5033
def self.reagent_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000786')
end
rearranged_at_DNA_level() click to toggle source

An attribute to describe the sequence of a feature, where the DNA is rearranged. (purl.obolibrary.org/obo/SO_0000904)

# File lib/biointerchange/so.rb, line 5705
def self.rearranged_at_DNA_level
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000904')
end
rearrangement_breakpoint() click to toggle source

A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome. (purl.obolibrary.org/obo/SO_0001872)

# File lib/biointerchange/so.rb, line 11437
def self.rearrangement_breakpoint
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001872')
end
reciprocal() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001521)

# File lib/biointerchange/so.rb, line 9385
def self.reciprocal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001521')
end
reciprocal_chromosomal_translocation() click to toggle source

A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged. (purl.obolibrary.org/obo/SO_1000048)

# File lib/biointerchange/so.rb, line 12719
def self.reciprocal_chromosomal_translocation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000048')
end
recoded() click to toggle source

An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations. (purl.obolibrary.org/obo/SO_0000881)

# File lib/biointerchange/so.rb, line 5567
def self.recoded
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000881')
end
recoded_by_translational_bypass() click to toggle source

Recoded mRNA where a block of nucleotides is not translated. (purl.obolibrary.org/obo/SO_0000886)

# File lib/biointerchange/so.rb, line 5597
def self.recoded_by_translational_bypass
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000886')
end
recoded_codon() click to toggle source

A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough. (purl.obolibrary.org/obo/SO_0000145)

# File lib/biointerchange/so.rb, line 1187
def self.recoded_codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000145')
end
recoded_mRNA() click to toggle source

The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals. (purl.obolibrary.org/obo/SO_1001261)

# File lib/biointerchange/so.rb, line 13511
def self.recoded_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001261')
end
recoding_pseudoknot() click to toggle source

The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding. (purl.obolibrary.org/obo/SO_0000545)

# File lib/biointerchange/so.rb, line 3589
def self.recoding_pseudoknot
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000545')
end
recoding_stimulatory_region() click to toggle source

A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA. (purl.obolibrary.org/obo/SO_1001268)

# File lib/biointerchange/so.rb, line 13553
def self.recoding_stimulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001268')
end
recombination_feature() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000298)

# File lib/biointerchange/so.rb, line 2109
def self.recombination_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000298')
end
recombination_feature_of_rearranged_gene() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000300)

# File lib/biointerchange/so.rb, line 2121
def self.recombination_feature_of_rearranged_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000300')
end
recombination_hotspot() click to toggle source

A region in a genome which promotes recombination. (purl.obolibrary.org/obo/SO_0000339)

# File lib/biointerchange/so.rb, line 2355
def self.recombination_hotspot
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000339')
end
recombination_regulatory_region() click to toggle source

A regulatory region that is involved in the control of the process of recombination. (purl.obolibrary.org/obo/SO_0001681)

# File lib/biointerchange/so.rb, line 10297
def self.recombination_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001681')
end
recombination_signal_sequence() click to toggle source

A region recognized by a recombinase. (purl.obolibrary.org/obo/SO_0001532)

# File lib/biointerchange/so.rb, line 9451
def self.recombination_signal_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001532')
end
recombinationally_inverted_gene() click to toggle source

A recombinationally rearranged gene by inversion. (purl.obolibrary.org/obo/SO_0000373)

# File lib/biointerchange/so.rb, line 2553
def self.recombinationally_inverted_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000373')
end
recombinationally_rearranged() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000940)

# File lib/biointerchange/so.rb, line 5921
def self.recombinationally_rearranged
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000940')
end
recombinationally_rearranged_gene() click to toggle source

A gene that is recombinationally rearranged. (purl.obolibrary.org/obo/SO_0000456)

# File lib/biointerchange/so.rb, line 3055
def self.recombinationally_rearranged_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000456')
end
recombinationally_rearranged_vertebrate_immune_system_gene() click to toggle source

A recombinationally rearranged gene of the vertebrate immune system. (purl.obolibrary.org/obo/SO_0000941)

# File lib/biointerchange/so.rb, line 5927
def self.recombinationally_rearranged_vertebrate_immune_system_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000941')
end
recombined_from() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/so_2_5_2.obo#recombined_from)

# File lib/biointerchange/so.rb, line 233
def self.recombined_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#recombined_from')
end
recombined_to() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/so_2_5_2.obo#recombined_to)

# File lib/biointerchange/so.rb, line 239
def self.recombined_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#recombined_to')
end
recursive_splice_site() click to toggle source

A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons. (purl.obolibrary.org/obo/SO_0000998)

# File lib/biointerchange/so.rb, line 6263
def self.recursive_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000998')
end
reference_genome() click to toggle source

A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly. (purl.obolibrary.org/obo/SO_0001505)

# File lib/biointerchange/so.rb, line 9289
def self.reference_genome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001505')
end
region() click to toggle source

A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. (purl.obolibrary.org/obo/SO_0000001)

# File lib/biointerchange/so.rb, line 321
def self.region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000001')
end
regional_centromere() click to toggle source

A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions. (purl.obolibrary.org/obo/SO_0001795)

# File lib/biointerchange/so.rb, line 10975
def self.regional_centromere
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001795')
end
regional_centromere_central_core() click to toggle source

A conserved region within the central region of a modular centromere, where the kinetochore is formed. (purl.obolibrary.org/obo/SO_0001796)

# File lib/biointerchange/so.rb, line 10981
def self.regional_centromere_central_core
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001796')
end
regional_centromere_inner_repeat_region() click to toggle source

The inner inverted repeat region of a modular centromere and part of the entral core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm. (purl.obolibrary.org/obo/SO_0001798)

# File lib/biointerchange/so.rb, line 10993
def self.regional_centromere_inner_repeat_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001798')
end
regional_centromere_outer_repeat_region() click to toggle source

The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms. (purl.obolibrary.org/obo/SO_0001799)

# File lib/biointerchange/so.rb, line 10999
def self.regional_centromere_outer_repeat_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001799')
end
regional_centromere_outer_repeat_transcript() click to toggle source

A transcript that is transcribed from the outer repeat region of a regional centromere. (purl.obolibrary.org/obo/SO_0001905)

# File lib/biointerchange/so.rb, line 11635
def self.regional_centromere_outer_repeat_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001905')
end
regulated() click to toggle source

An attribute to describe a sequence that is regulated. (purl.obolibrary.org/obo/SO_0000119)

# File lib/biointerchange/so.rb, line 1031
def self.regulated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000119')
end
regulatory_promoter_element() click to toggle source

A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region. (purl.obolibrary.org/obo/SO_0001678)

# File lib/biointerchange/so.rb, line 10279
def self.regulatory_promoter_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001678')
end
regulatory_region() click to toggle source

A region of sequence that is involved in the control of a biological process. (purl.obolibrary.org/obo/SO_0005836)

# File lib/biointerchange/so.rb, line 12251
def self.regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005836')
end
regulatory_region_ablation() click to toggle source

A feature ablation whereby the deleted region includes a regulatory region. (purl.obolibrary.org/obo/SO_0001894)

# File lib/biointerchange/so.rb, line 11569
def self.regulatory_region_ablation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001894')
end
regulatory_region_amplification() click to toggle source

A feature amplification of a region containing a regulatory region. (purl.obolibrary.org/obo/SO_0001891)

# File lib/biointerchange/so.rb, line 11551
def self.regulatory_region_amplification
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001891')
end
regulatory_region_fusion() click to toggle source

A feature fusion where the deletion brings together regulatory regions. (purl.obolibrary.org/obo/SO_0001887)

# File lib/biointerchange/so.rb, line 11527
def self.regulatory_region_fusion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001887')
end
regulatory_region_translocation() click to toggle source

A feature translocation where the region contains a regulatory region. (purl.obolibrary.org/obo/SO_0001884)

# File lib/biointerchange/so.rb, line 11509
def self.regulatory_region_translocation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001884')
end
regulatory_region_variant() click to toggle source

A sequence variant located within a regulatory region. (purl.obolibrary.org/obo/SO_0001566)

# File lib/biointerchange/so.rb, line 9655
def self.regulatory_region_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001566')
end
regulon() click to toggle source

A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal. (purl.obolibrary.org/obo/SO_1001284)

# File lib/biointerchange/so.rb, line 13637
def self.regulon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001284')
end
remark() click to toggle source

A comment about the sequence. (purl.obolibrary.org/obo/SO_0000700)

# File lib/biointerchange/so.rb, line 4523
def self.remark
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000700')
end
repeat_component() click to toggle source

A region of a repeated sequence. (purl.obolibrary.org/obo/SO_0000840)

# File lib/biointerchange/so.rb, line 5321
def self.repeat_component
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000840')
end
repeat_family() click to toggle source

A group of characterized repeat sequences. (purl.obolibrary.org/obo/SO_0000187)

# File lib/biointerchange/so.rb, line 1443
def self.repeat_family
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000187')
end
repeat_fragment() click to toggle source

A portion of a repeat, interrupted by the insertion of another element. (purl.obolibrary.org/obo/SO_0001050)

# File lib/biointerchange/so.rb, line 6575
def self.repeat_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001050')
end
repeat_region() click to toggle source

A region of sequence containing one or more repeat units. (purl.obolibrary.org/obo/SO_0000657)

# File lib/biointerchange/so.rb, line 4265
def self.repeat_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000657')
end
repeat_unit() click to toggle source

The simplest repeated component of a repeat region. A single repeat. (purl.obolibrary.org/obo/SO_0000726)

# File lib/biointerchange/so.rb, line 4679
def self.repeat_unit
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000726')
end
repetitive_element() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000292)

# File lib/biointerchange/so.rb, line 2073
def self.repetitive_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000292')
end
replication_regulatory_region() click to toggle source

A regulatory region that is involved in the control of the process of nucleotide replication. (purl.obolibrary.org/obo/SO_0001682)

# File lib/biointerchange/so.rb, line 10303
def self.replication_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001682')
end
replicon() click to toggle source

A region containing at least one unique origin of replication and a unique termination site. (purl.obolibrary.org/obo/SO_0001235)

# File lib/biointerchange/so.rb, line 7681
def self.replicon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001235')
end
rescue() click to toggle source

An attribute describing a region’s ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype. (purl.obolibrary.org/obo/SO_0000814)

# File lib/biointerchange/so.rb, line 5177
def self.rescue
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000814')
end
rescue_gene() click to toggle source

A gene that rescues. (purl.obolibrary.org/obo/SO_0000816)

# File lib/biointerchange/so.rb, line 5189
def self.rescue_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000816')
end
rescue_mini_gene() click to toggle source

A mini_gene that rescues. (purl.obolibrary.org/obo/SO_0000795)

# File lib/biointerchange/so.rb, line 5087
def self.rescue_mini_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000795')
end
rescue_region() click to toggle source

A region that rescues. (purl.obolibrary.org/obo/SO_0000411)

# File lib/biointerchange/so.rb, line 2781
def self.rescue_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000411')
end
resolution_site() click to toggle source

A region specifically recognised by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles. (purl.obolibrary.org/obo/SO_0000947)

# File lib/biointerchange/so.rb, line 5963
def self.resolution_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000947')
end
restriction_enzyme_assembly_scar() click to toggle source

A region of DNA sequence formed from the ligation of two sticky ends where the palindrome is broken and no longer comprises the recognition site and thus cannot be re-cut by the restriction enzymes used to create the sticky ends. (purl.obolibrary.org/obo/SO_0001953)

# File lib/biointerchange/so.rb, line 11923
def self.restriction_enzyme_assembly_scar
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001953')
end
restriction_enzyme_binding_site() click to toggle source

A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme. (purl.obolibrary.org/obo/SO_0000061)

# File lib/biointerchange/so.rb, line 683
def self.restriction_enzyme_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000061')
end
restriction_enzyme_cleavage_junction() click to toggle source

The boundary at which a restriction enzyme breaks the nucleotide sequence. (purl.obolibrary.org/obo/SO_0001688)

# File lib/biointerchange/so.rb, line 10339
def self.restriction_enzyme_cleavage_junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001688')
end
restriction_enzyme_cut_site() click to toggle source

A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA. (purl.obolibrary.org/obo/SO_0000168)

# File lib/biointerchange/so.rb, line 1325
def self.restriction_enzyme_cut_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000168')
end
restriction_enzyme_five_prime_single_strand_overhang() click to toggle source

A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5’ end. (purl.obolibrary.org/obo/SO_0001932)

# File lib/biointerchange/so.rb, line 11797
def self.restriction_enzyme_five_prime_single_strand_overhang
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001932')
end
restriction_enzyme_recognition_site() click to toggle source

The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site. (purl.obolibrary.org/obo/SO_0001687)

# File lib/biointerchange/so.rb, line 10333
def self.restriction_enzyme_recognition_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001687')
end
restriction_enzyme_region() click to toggle source

A region related to restriction enzyme function. (purl.obolibrary.org/obo/SO_0001954)

# File lib/biointerchange/so.rb, line 11929
def self.restriction_enzyme_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001954')
end
restriction_enzyme_single_strand_overhang() click to toggle source

A terminal region of DNA sequence where the end of the region is not blunt ended. (purl.obolibrary.org/obo/SO_0001695)

# File lib/biointerchange/so.rb, line 10381
def self.restriction_enzyme_single_strand_overhang
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001695')
end
restriction_enzyme_three_prime_single_strand_overhang() click to toggle source

A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3’ end. (purl.obolibrary.org/obo/SO_0001933)

# File lib/biointerchange/so.rb, line 11803
def self.restriction_enzyme_three_prime_single_strand_overhang
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001933')
end
restriction_fragment() click to toggle source

A region of polynucleotide sequence produced by digestion with a restriction endonuclease. (purl.obolibrary.org/obo/SO_0000412)

# File lib/biointerchange/so.rb, line 2787
def self.restriction_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000412')
end
retinoic_acid_responsive_element() click to toggle source

A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind. (purl.obolibrary.org/obo/SO_0001653)

# File lib/biointerchange/so.rb, line 10129
def self.retinoic_acid_responsive_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001653')
end
retrogene() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001219)

# File lib/biointerchange/so.rb, line 7585
def self.retrogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001219')
end
retron() click to toggle source

Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes. (purl.obolibrary.org/obo/SO_1001275)

# File lib/biointerchange/so.rb, line 13595
def self.retron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001275')
end
retrotransposed() click to toggle source

An attribute of a feature that occurred as the product of a reverse transcriptase mediated event. (purl.obolibrary.org/obo/SO_0000569)

# File lib/biointerchange/so.rb, line 3737
def self.retrotransposed
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000569')
end
retrotransposon() click to toggle source

A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase. (purl.obolibrary.org/obo/SO_0000180)

# File lib/biointerchange/so.rb, line 1401
def self.retrotransposon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000180')
end
reverse() click to toggle source

Reverse is an attribute of the feature, where the feature is in the 3’ to 5’ direction. Again could be applied to primer. (purl.obolibrary.org/obo/SO_0001031)

# File lib/biointerchange/so.rb, line 6461
def self.reverse
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001031')
end
reverse_Hoogsteen_base_pair() click to toggle source

A type of non-canonical base-pairing. (purl.obolibrary.org/obo/SO_0000501)

# File lib/biointerchange/so.rb, line 3325
def self.reverse_Hoogsteen_base_pair
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000501')
end
reverse_primer() click to toggle source

A single stranded oligo used for polymerase chain reaction. (purl.obolibrary.org/obo/SO_0000132)

# File lib/biointerchange/so.rb, line 1109
def self.reverse_primer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000132')
end
rho_dependent_bacterial_terminator() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000981)

# File lib/biointerchange/so.rb, line 6161
def self.rho_dependent_bacterial_terminator
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000981')
end
rho_independent_bacterial_terminator() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000982)

# File lib/biointerchange/so.rb, line 6167
def self.rho_independent_bacterial_terminator
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000982')
end
ribonuclease_site() click to toggle source

A region of a transcript encoding the cleavage site for a ribonuclease enzyme. (purl.obolibrary.org/obo/SO_0001977)

# File lib/biointerchange/so.rb, line 12071
def self.ribonuclease_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001977')
end
ribosome_entry_site() click to toggle source

Region in mRNA where ribosome assembles. (purl.obolibrary.org/obo/SO_0000139)

# File lib/biointerchange/so.rb, line 1151
def self.ribosome_entry_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000139')
end
riboswitch() click to toggle source

A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5’ end of an mRNA, that acts as a direct sensor of metabolites. (purl.obolibrary.org/obo/SO_0000035)

# File lib/biointerchange/so.rb, line 519
def self.riboswitch
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000035')
end
ribothymidine() click to toggle source

A modified RNA base in which thymine is bound to the ribose ring. (purl.obolibrary.org/obo/SO_0001232)

# File lib/biointerchange/so.rb, line 7663
def self.ribothymidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001232')
end
ribozyme() click to toggle source

An RNA with catalytic activity. (purl.obolibrary.org/obo/SO_0000374)

# File lib/biointerchange/so.rb, line 2559
def self.ribozyme
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000374')
end
ribozymic() click to toggle source

An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein. (purl.obolibrary.org/obo/SO_0001186)

# File lib/biointerchange/so.rb, line 7387
def self.ribozymic
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001186')
end
right_handed_peptide_helix() click to toggle source

A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw. (purl.obolibrary.org/obo/SO_0001116)

# File lib/biointerchange/so.rb, line 6967
def self.right_handed_peptide_helix
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001116')
end
ring_chromosome() click to toggle source

A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome. (purl.obolibrary.org/obo/SO_1000045)

# File lib/biointerchange/so.rb, line 12701
def self.ring_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000045')
end
rolling_circle() click to toggle source

This has been obsoleted as it represents a process. replaced_by: GO:0070581. (purl.obolibrary.org/obo/SO_0000969)

# File lib/biointerchange/so.rb, line 6095
def self.rolling_circle
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000969')
end
sarcin_like_RNA_motif() click to toggle source

A loop in ribosomal RNA containing the sites of attack for ricin and sarcin. (purl.obolibrary.org/obo/SO_0000024)

# File lib/biointerchange/so.rb, line 453
def self.sarcin_like_RNA_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000024')
end
satellite_DNA() click to toggle source

The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA. (purl.obolibrary.org/obo/SO_0000005)

# File lib/biointerchange/so.rb, line 345
def self.satellite_DNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000005')
end
scRNA() click to toggle source

A small non coding RNA sequence, present in the cytoplasm. (purl.obolibrary.org/obo/SO_0000013)

# File lib/biointerchange/so.rb, line 393
def self.scRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000013')
end
scRNA_encoding() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000575)

# File lib/biointerchange/so.rb, line 3773
def self.scRNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000575')
end
scRNA_gene() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001266)

# File lib/biointerchange/so.rb, line 7861
def self.scRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001266')
end
scRNA_primary_transcript() click to toggle source

The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a eukaryote. (purl.obolibrary.org/obo/SO_0000012)

# File lib/biointerchange/so.rb, line 387
def self.scRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000012')
end
schellmann_loop() click to toggle source

A motif of six or seven consecutive residues that contains two H-bonds. (purl.obolibrary.org/obo/SO_0001123)

# File lib/biointerchange/so.rb, line 7009
def self.schellmann_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001123')
end
schellmann_loop_seven() click to toggle source

Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5). (purl.obolibrary.org/obo/SO_0001124)

# File lib/biointerchange/so.rb, line 7015
def self.schellmann_loop_seven
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001124')
end
schellmann_loop_six() click to toggle source

Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4). (purl.obolibrary.org/obo/SO_0001125)

# File lib/biointerchange/so.rb, line 7021
def self.schellmann_loop_six
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001125')
end
score() click to toggle source

The score of an experimentally derived feature such as a p-value. (purl.obolibrary.org/obo/SO_0001685)

# File lib/biointerchange/so.rb, line 10321
def self.score
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001685')
end
selenocysteine() click to toggle source

A place holder for a cross product with chebi. (purl.obolibrary.org/obo/SO_0001455)

# File lib/biointerchange/so.rb, line 8989
def self.selenocysteine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001455')
end
selenocysteine_tRNA_primary_transcript() click to toggle source

A primary transcript encoding seryl tRNA (SO:000269). (purl.obolibrary.org/obo/SO_0005856)

# File lib/biointerchange/so.rb, line 12335
def self.selenocysteine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005856')
end
selenocysteinyl_tRNA() click to toggle source

A tRNA sequence that has a selenocysteine anticodon, and a 3’ selenocysteine binding region. (purl.obolibrary.org/obo/SO_0005857)

# File lib/biointerchange/so.rb, line 12341
def self.selenocysteinyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005857')
end
sequence_alteration() click to toggle source

A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. (purl.obolibrary.org/obo/SO_0001059)

# File lib/biointerchange/so.rb, line 6637
def self.sequence_alteration
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001059')
end
sequence_assembly() click to toggle source

A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. (purl.obolibrary.org/obo/SO_0000353)

# File lib/biointerchange/so.rb, line 2439
def self.sequence_assembly
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000353')
end
sequence_attribute() click to toggle source

An attribute describes a quality of sequence. (purl.obolibrary.org/obo/SO_0000400)

# File lib/biointerchange/so.rb, line 2715
def self.sequence_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000400')
end
sequence_collection() click to toggle source

A collection of discontinuous sequences. (purl.obolibrary.org/obo/SO_0001260)

# File lib/biointerchange/so.rb, line 7825
def self.sequence_collection
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001260')
end
sequence_conflict() click to toggle source

Different sources report differing sequences. (purl.obolibrary.org/obo/SO_0001085)

# File lib/biointerchange/so.rb, line 6781
def self.sequence_conflict
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001085')
end
sequence_difference() click to toggle source

A region where the sequence differs from that of a specified sequence. (purl.obolibrary.org/obo/SO_0000413)

# File lib/biointerchange/so.rb, line 2793
def self.sequence_difference
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000413')
end
sequence_feature() click to toggle source

Any extent of continuous biological sequence. (purl.obolibrary.org/obo/SO_0000110)

# File lib/biointerchange/so.rb, line 977
def self.sequence_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000110')
end
sequence_feature_locating_method() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000308)

# File lib/biointerchange/so.rb, line 2169
def self.sequence_feature_locating_method
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000308')
end
sequence_length_variation() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000248)

# File lib/biointerchange/so.rb, line 1809
def self.sequence_length_variation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000248')
end
sequence_location() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000735)

# File lib/biointerchange/so.rb, line 4733
def self.sequence_location
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000735')
end
sequence_motif() click to toggle source

A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance. (purl.obolibrary.org/obo/SO_0001683)

# File lib/biointerchange/so.rb, line 10309
def self.sequence_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001683')
end
sequence_of() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/so_2_5_2.obo#sequence_of)

# File lib/biointerchange/so.rb, line 245
def self.sequence_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#sequence_of')
end
sequence_operation() click to toggle source

An operation that can be applied to a sequence, that results in a change. (purl.obolibrary.org/obo/SO_0000041)

# File lib/biointerchange/so.rb, line 555
def self.sequence_operation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000041')
end
sequence_rearrangement_feature() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000669)

# File lib/biointerchange/so.rb, line 4337
def self.sequence_rearrangement_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000669')
end
sequence_replication_mode() click to toggle source

This has been obsoleted as it represents a process. replaced_by: GO:0034961. (purl.obolibrary.org/obo/SO_0000968)

# File lib/biointerchange/so.rb, line 6089
def self.sequence_replication_mode
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000968')
end
sequence_secondary_structure() click to toggle source

A folded sequence. (purl.obolibrary.org/obo/SO_0000002)

# File lib/biointerchange/so.rb, line 327
def self.sequence_secondary_structure
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000002')
end
sequence_uncertainty() click to toggle source

Describes the positions in a sequence where the authors are unsure about the sequence assignment. (purl.obolibrary.org/obo/SO_0001086)

# File lib/biointerchange/so.rb, line 6787
def self.sequence_uncertainty
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001086')
end
sequence_variant() click to toggle source

A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. (purl.obolibrary.org/obo/SO_0001060)

# File lib/biointerchange/so.rb, line 6643
def self.sequence_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001060')
end
sequence_variant_affecting_3D_structure_of_polypeptide() click to toggle source

A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule. (purl.obolibrary.org/obo/SO_1000111)

# File lib/biointerchange/so.rb, line 13061
def self.sequence_variant_affecting_3D_structure_of_polypeptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000111')
end
sequence_variant_affecting_copy_number() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_0001020)

# File lib/biointerchange/so.rb, line 6395
def self.sequence_variant_affecting_copy_number
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001020')
end
sequence_variant_affecting_editing() click to toggle source

Sequence variant affects the editing of the transcript. (purl.obolibrary.org/obo/SO_1000075)

# File lib/biointerchange/so.rb, line 12863
def self.sequence_variant_affecting_editing
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000075')
end
sequence_variant_affecting_gene_structure() click to toggle source

A sequence_variant_effect that changes the gene structure. (purl.obolibrary.org/obo/SO_1000180)

# File lib/biointerchange/so.rb, line 13337
def self.sequence_variant_affecting_gene_structure
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000180')
end
sequence_variant_affecting_level_of_translational_product() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000102)

# File lib/biointerchange/so.rb, line 13007
def self.sequence_variant_affecting_level_of_translational_product
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000102')
end
sequence_variant_affecting_polyadenylation() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_0001432)

# File lib/biointerchange/so.rb, line 8851
def self.sequence_variant_affecting_polyadenylation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001432')
end
sequence_variant_affecting_polypeptide_amino_acid_sequence() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000105)

# File lib/biointerchange/so.rb, line 13025
def self.sequence_variant_affecting_polypeptide_amino_acid_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000105')
end
sequence_variant_affecting_polypeptide_function() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000117)

# File lib/biointerchange/so.rb, line 13085
def self.sequence_variant_affecting_polypeptide_function
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000117')
end
sequence_variant_affecting_rate_of_transcription() click to toggle source

A mutation that alters the rate a which transcription of the sequence occurs. (purl.obolibrary.org/obo/SO_1000081)

# File lib/biointerchange/so.rb, line 12893
def self.sequence_variant_affecting_rate_of_transcription
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000081')
end
sequence_variant_affecting_regulatory_region() click to toggle source

A sequence_variant_effect which changes the regulatory region of a gene. (purl.obolibrary.org/obo/SO_0000053)

# File lib/biointerchange/so.rb, line 631
def self.sequence_variant_affecting_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000053')
end
sequence_variant_affecting_splice_acceptor() click to toggle source

A sequence_variant_effect that changes the splice acceptor sequence. (purl.obolibrary.org/obo/SO_1000073)

# File lib/biointerchange/so.rb, line 12851
def self.sequence_variant_affecting_splice_acceptor
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000073')
end
sequence_variant_affecting_splice_donor() click to toggle source

A sequence_variant_effect that changes the splice donor sequence. (purl.obolibrary.org/obo/SO_1000072)

# File lib/biointerchange/so.rb, line 12845
def self.sequence_variant_affecting_splice_donor
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000072')
end
sequence_variant_affecting_splicing() click to toggle source

A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed. (purl.obolibrary.org/obo/SO_1000071)

# File lib/biointerchange/so.rb, line 12839
def self.sequence_variant_affecting_splicing
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000071')
end
sequence_variant_affecting_transcript_processing() click to toggle source

Sequence variant affects the way in which the primary transcriptional product is processed to form the mature transcript. (purl.obolibrary.org/obo/SO_1000070)

# File lib/biointerchange/so.rb, line 12833
def self.sequence_variant_affecting_transcript_processing
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000070')
end
sequence_variant_affecting_transcript_secondary_structure() click to toggle source

A sequence variant that affects the secondary structure (folding) of the RNA transcript molecule. (purl.obolibrary.org/obo/SO_1000126)

# File lib/biointerchange/so.rb, line 13139
def self.sequence_variant_affecting_transcript_secondary_structure
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000126')
end
sequence_variant_affecting_transcript_stability() click to toggle source

Sequence variant affects the stability of the transcript. (purl.obolibrary.org/obo/SO_1000082)

# File lib/biointerchange/so.rb, line 12899
def self.sequence_variant_affecting_transcript_stability
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000082')
end
sequence_variant_affecting_transcription() click to toggle source

Mutation affects the process of transcription, its initiation, progression or termination. (purl.obolibrary.org/obo/SO_1000076)

# File lib/biointerchange/so.rb, line 12869
def self.sequence_variant_affecting_transcription
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000076')
end
sequence_variant_affecting_translational_product() click to toggle source

A sequence variant causing a change in primary translation product of a transcript. (purl.obolibrary.org/obo/SO_1000088)

# File lib/biointerchange/so.rb, line 12935
def self.sequence_variant_affecting_translational_product
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000088')
end
sequence_variant_causes_exon_loss() click to toggle source

A sequence variant affecting splicing and causes an exon loss. (purl.obolibrary.org/obo/SO_1000184)

# File lib/biointerchange/so.rb, line 13361
def self.sequence_variant_causes_exon_loss
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000184')
end
sequence_variant_causes_intron_gain() click to toggle source

A sequence variant effect, causing an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072). (purl.obolibrary.org/obo/SO_1000185)

# File lib/biointerchange/so.rb, line 13367
def self.sequence_variant_causes_intron_gain
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000185')
end
sequence_variant_causing_amino_acid_coding_codon_change_in_transcript() click to toggle source

The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons. (purl.obolibrary.org/obo/SO_1000056)

# File lib/biointerchange/so.rb, line 12749
def self.sequence_variant_causing_amino_acid_coding_codon_change_in_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000056')
end
sequence_variant_causing_amino_acid_deletion() click to toggle source

The deletion of one or more amino acids from the polypeptide, without affecting the surrounding sequence. (purl.obolibrary.org/obo/SO_1000097)

# File lib/biointerchange/so.rb, line 12977
def self.sequence_variant_causing_amino_acid_deletion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000097')
end
sequence_variant_causing_amino_acid_insertion() click to toggle source

The insertion of one or more amino acids from the polypeptide, without affecting the surrounding sequence. (purl.obolibrary.org/obo/SO_1000096)

# File lib/biointerchange/so.rb, line 12971
def self.sequence_variant_causing_amino_acid_insertion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000096')
end
sequence_variant_causing_amino_acid_substitution() click to toggle source

The replacement of a single amino acid by another. (purl.obolibrary.org/obo/SO_1000093)

# File lib/biointerchange/so.rb, line 12953
def self.sequence_variant_causing_amino_acid_substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000093')
end
sequence_variant_causing_compensatory_transcript_secondary_structure_mutation() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000127)

# File lib/biointerchange/so.rb, line 13145
def self.sequence_variant_causing_compensatory_transcript_secondary_structure_mutation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000127')
end
sequence_variant_causing_complex_3D_structural_change() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000115)

# File lib/biointerchange/so.rb, line 13073
def self.sequence_variant_causing_complex_3D_structural_change
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000115')
end
sequence_variant_causing_complex_change_of_translational_product() click to toggle source

Any sequence variant effect that is known at nucleotide level but cannot be explained by using other key terms. (purl.obolibrary.org/obo/SO_1000092)

# File lib/biointerchange/so.rb, line 12947
def self.sequence_variant_causing_complex_change_of_translational_product
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000092')
end
sequence_variant_causing_conformational_change() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000116)

# File lib/biointerchange/so.rb, line 13079
def self.sequence_variant_causing_conformational_change
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000116')
end
sequence_variant_causing_conservative_amino_acid_substitution() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000094)

# File lib/biointerchange/so.rb, line 12959
def self.sequence_variant_causing_conservative_amino_acid_substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000094')
end
sequence_variant_causing_conservative_missense_codon_change_in_transcript() click to toggle source

The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position. (purl.obolibrary.org/obo/SO_1000060)

# File lib/biointerchange/so.rb, line 12773
def self.sequence_variant_causing_conservative_missense_codon_change_in_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000060')
end
sequence_variant_causing_cryptic_splice_acceptor_activation() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1001186)

# File lib/biointerchange/so.rb, line 13379
def self.sequence_variant_causing_cryptic_splice_acceptor_activation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001186')
end
sequence_variant_causing_cryptic_splice_activation() click to toggle source

A sequence variant causing a new (functional) splice site. (purl.obolibrary.org/obo/SO_1000074)

# File lib/biointerchange/so.rb, line 12857
def self.sequence_variant_causing_cryptic_splice_activation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000074')
end
sequence_variant_causing_cryptic_splice_donor_activation() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000186)

# File lib/biointerchange/so.rb, line 13373
def self.sequence_variant_causing_cryptic_splice_donor_activation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000186')
end
sequence_variant_causing_gain_of_function_of_polypeptide() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000125)

# File lib/biointerchange/so.rb, line 13133
def self.sequence_variant_causing_gain_of_function_of_polypeptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000125')
end
sequence_variant_causing_gene_fusion() click to toggle source

A sequence_variant_effect that changes the gene structure by causing a fusion to another gene. (purl.obolibrary.org/obo/SO_1000181)

# File lib/biointerchange/so.rb, line 13343
def self.sequence_variant_causing_gene_fusion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000181')
end
sequence_variant_causing_inactive_catalytic_site() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000120)

# File lib/biointerchange/so.rb, line 13103
def self.sequence_variant_causing_inactive_catalytic_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000120')
end
sequence_variant_causing_inactive_ligand_binding_site() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000119)

# File lib/biointerchange/so.rb, line 13097
def self.sequence_variant_causing_inactive_ligand_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000119')
end
sequence_variant_causing_initiator_codon_change_in_transcript() click to toggle source

The DNA mutation changes, usually destroys, the first coding triplet of a gene. Usually prevents translation although another initiator codon may be used. (purl.obolibrary.org/obo/SO_1000055)

# File lib/biointerchange/so.rb, line 12743
def self.sequence_variant_causing_initiator_codon_change_in_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000055')
end
sequence_variant_causing_loss_of_function_of_polypeptide() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000118)

# File lib/biointerchange/so.rb, line 13091
def self.sequence_variant_causing_loss_of_function_of_polypeptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000118')
end
sequence_variant_causing_minus_1_frameshift() click to toggle source

A mutation causing a disruption of the translational reading frame, due to the deletion of a nucleotide. (purl.obolibrary.org/obo/SO_1000067)

# File lib/biointerchange/so.rb, line 12815
def self.sequence_variant_causing_minus_1_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000067')
end
sequence_variant_causing_minus_2_frameshift() click to toggle source

A mutation causing a disruption of the translational reading frame, due to the deletion of two nucleotides. (purl.obolibrary.org/obo/SO_1000069)

# File lib/biointerchange/so.rb, line 12827
def self.sequence_variant_causing_minus_2_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000069')
end
sequence_variant_causing_missense_codon_change_in_transcript() click to toggle source

The nucleotide change in the codon leads to a new codon coding for a new amino acid. (purl.obolibrary.org/obo/SO_1000059)

# File lib/biointerchange/so.rb, line 12767
def self.sequence_variant_causing_missense_codon_change_in_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000059')
end
sequence_variant_causing_no_3D_structural_change() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is no effect, it is not a good term. (purl.obolibrary.org/obo/SO_1000112)

# File lib/biointerchange/so.rb, line 13067
def self.sequence_variant_causing_no_3D_structural_change
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000112')
end
sequence_variant_causing_no_change_in_transcript() click to toggle source

No effect on the state of the RNA. (purl.obolibrary.org/obo/SO_1000050)

# File lib/biointerchange/so.rb, line 12731
def self.sequence_variant_causing_no_change_in_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000050')
end
sequence_variant_causing_no_change_of_translational_product() click to toggle source

The sequence variant at RNA level does not lead to any change in polypeptide. (purl.obolibrary.org/obo/SO_1000089)

# File lib/biointerchange/so.rb, line 12941
def self.sequence_variant_causing_no_change_of_translational_product
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000089')
end
sequence_variant_causing_non_synonymous_codon_change_in_transcript() click to toggle source

A DNA point mutation that causes a substitution of an amino acid by an other. (purl.obolibrary.org/obo/SO_1000058)

# File lib/biointerchange/so.rb, line 12761
def self.sequence_variant_causing_non_synonymous_codon_change_in_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000058')
end
sequence_variant_causing_nonconservative_amino_acid_substitution() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000095)

# File lib/biointerchange/so.rb, line 12965
def self.sequence_variant_causing_nonconservative_amino_acid_substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000095')
end
sequence_variant_causing_nonconservative_missense_codon_change_in_transcript() click to toggle source

The amino acid change following from the codon change changes the gross properties (size, charge, hydrophobicity) of the amino acid in that position. (purl.obolibrary.org/obo/SO_1000061)

# File lib/biointerchange/so.rb, line 12779
def self.sequence_variant_causing_nonconservative_missense_codon_change_in_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000061')
end
sequence_variant_causing_nonsense_codon_change_in_transcript() click to toggle source

The nucleotide change in the codon triplet creates a terminator codon. (purl.obolibrary.org/obo/SO_1000062)

# File lib/biointerchange/so.rb, line 12785
def self.sequence_variant_causing_nonsense_codon_change_in_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000062')
end
sequence_variant_causing_partial_loss_of_function_of_polypeptide() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000124)

# File lib/biointerchange/so.rb, line 13127
def self.sequence_variant_causing_partial_loss_of_function_of_polypeptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000124')
end
sequence_variant_causing_plus_1_frameshift_mutation() click to toggle source

A mutation causing a disruption of the translational reading frame, due to the insertion of a nucleotide. (purl.obolibrary.org/obo/SO_1000066)

# File lib/biointerchange/so.rb, line 12809
def self.sequence_variant_causing_plus_1_frameshift_mutation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000066')
end
sequence_variant_causing_plus_2_frameshift() click to toggle source

A mutation causing a disruption of the translational reading frame, due to the insertion of two nucleotides. (purl.obolibrary.org/obo/SO_1000068)

# File lib/biointerchange/so.rb, line 12821
def self.sequence_variant_causing_plus_2_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000068')
end
sequence_variant_causing_polypeptide_elongation() click to toggle source

The extension of the translational product at either (or both) the N-terminus and/or the C-terminus. (purl.obolibrary.org/obo/SO_1000099)

# File lib/biointerchange/so.rb, line 12989
def self.sequence_variant_causing_polypeptide_elongation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000099')
end
sequence_variant_causing_polypeptide_fusion() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000134)

# File lib/biointerchange/so.rb, line 13157
def self.sequence_variant_causing_polypeptide_fusion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000134')
end
sequence_variant_causing_polypeptide_localization_change() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000121)

# File lib/biointerchange/so.rb, line 13109
def self.sequence_variant_causing_polypeptide_localization_change
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000121')
end
sequence_variant_causing_polypeptide_post_translational_processing_change() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000122)

# File lib/biointerchange/so.rb, line 13115
def self.sequence_variant_causing_polypeptide_post_translational_processing_change
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000122')
end
sequence_variant_causing_polypeptide_truncation() click to toggle source

The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062). (purl.obolibrary.org/obo/SO_1000098)

# File lib/biointerchange/so.rb, line 12983
def self.sequence_variant_causing_polypeptide_truncation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000098')
end
sequence_variant_causing_synonymous_codon_change_in_transcript() click to toggle source

The changed codon has the same translation product as the original codon. (purl.obolibrary.org/obo/SO_1000057)

# File lib/biointerchange/so.rb, line 12755
def self.sequence_variant_causing_synonymous_codon_change_in_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000057')
end
sequence_variant_causing_terminator_codon_change_in_transcript() click to toggle source

The nucleotide change in the codon triplet changes the stop codon, causing an elongated transcript sequence. (purl.obolibrary.org/obo/SO_1000063)

# File lib/biointerchange/so.rb, line 12791
def self.sequence_variant_causing_terminator_codon_change_in_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000063')
end
sequence_variant_decreasing_level_of_translation_product() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000103)

# File lib/biointerchange/so.rb, line 13013
def self.sequence_variant_decreasing_level_of_translation_product
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000103')
end
sequence_variant_decreasing_rate_of_transcription() click to toggle source

A sequence variation that decreases the rate a which transcription of the sequence occurs. (purl.obolibrary.org/obo/SO_1000078)

# File lib/biointerchange/so.rb, line 12875
def self.sequence_variant_decreasing_rate_of_transcription
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000078')
end
sequence_variant_decreasing_transcript_stability() click to toggle source

Sequence variant decreases the stability (half-life) of the transcript. (purl.obolibrary.org/obo/SO_1000084)

# File lib/biointerchange/so.rb, line 12911
def self.sequence_variant_decreasing_transcript_stability
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000084')
end
sequence_variant_effect() click to toggle source

The effect of a change in nucleotide sequence. (purl.obolibrary.org/obo/SO_1000132)

# File lib/biointerchange/so.rb, line 13151
def self.sequence_variant_effect
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000132')
end
sequence_variant_increasing_level_of_translation_product() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000104)

# File lib/biointerchange/so.rb, line 13019
def self.sequence_variant_increasing_level_of_translation_product
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000104')
end
sequence_variant_increasing_rate_of_transcription() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000080)

# File lib/biointerchange/so.rb, line 12887
def self.sequence_variant_increasing_rate_of_transcription
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000080')
end
sequence_variant_increasing_transcript_stability() click to toggle source

Sequence variant increases the stability (half-life) of the transcript. (purl.obolibrary.org/obo/SO_1000083)

# File lib/biointerchange/so.rb, line 12905
def self.sequence_variant_increasing_transcript_stability
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000083')
end
sequence_variant_obs() click to toggle source

A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. (purl.obolibrary.org/obo/SO_0000109)

# File lib/biointerchange/so.rb, line 971
def self.sequence_variant_obs
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000109')
end
sequence_variation_affecting_coding_sequence() click to toggle source

Any of the amino acid coding triplets of a gene are affected by the DNA mutation. (purl.obolibrary.org/obo/SO_1000054)

# File lib/biointerchange/so.rb, line 12737
def self.sequence_variation_affecting_coding_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000054')
end
sequence_variation_affecting_level_of_transcript() click to toggle source

A sequence variation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence. (purl.obolibrary.org/obo/SO_1000085)

# File lib/biointerchange/so.rb, line 12917
def self.sequence_variation_affecting_level_of_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000085')
end
sequence_variation_affecting_reading_frame() click to toggle source

An umbrella term for terms describing an effect of a sequence variation on the frame of translation. (purl.obolibrary.org/obo/SO_1000064)

# File lib/biointerchange/so.rb, line 12797
def self.sequence_variation_affecting_reading_frame
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000064')
end
sequence_variation_affecting_transcript() click to toggle source

Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. (purl.obolibrary.org/obo/SO_1000049)

# File lib/biointerchange/so.rb, line 12725
def self.sequence_variation_affecting_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000049')
end
sequence_variation_affecting_transcript_sequence() click to toggle source

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (purl.obolibrary.org/obo/SO_1000079)

# File lib/biointerchange/so.rb, line 12881
def self.sequence_variation_affecting_transcript_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000079')
end
sequence_variation_decreasing_level_of_transcript() click to toggle source

A sequence variation that causes a decrease in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence. (purl.obolibrary.org/obo/SO_1000086)

# File lib/biointerchange/so.rb, line 12923
def self.sequence_variation_decreasing_level_of_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000086')
end
sequence_variation_increasing_level_of_transcript() click to toggle source

A sequence_variation that causes an increase in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence. (purl.obolibrary.org/obo/SO_1000087)

# File lib/biointerchange/so.rb, line 12929
def self.sequence_variation_increasing_level_of_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000087')
end
sequencing_primer() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000107)

# File lib/biointerchange/so.rb, line 959
def self.sequencing_primer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000107')
end
serine() click to toggle source

A place holder for a cross product with chebi. (purl.obolibrary.org/obo/SO_0001444)

# File lib/biointerchange/so.rb, line 8923
def self.serine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001444')
end
serine_tRNA_primary_transcript() click to toggle source

A primary transcript encoding seryl tRNA (SO:000269). (purl.obolibrary.org/obo/SO_0000226)

# File lib/biointerchange/so.rb, line 1677
def self.serine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000226')
end
serine_threonine_motif() click to toggle source

A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4). (purl.obolibrary.org/obo/SO_0001126)

# File lib/biointerchange/so.rb, line 7027
def self.serine_threonine_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001126')
end
serine_threonine_staple_motif() click to toggle source

A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative. (purl.obolibrary.org/obo/SO_0001127)

# File lib/biointerchange/so.rb, line 7033
def self.serine_threonine_staple_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001127')
end
serine_threonine_turn() click to toggle source

A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2). (purl.obolibrary.org/obo/SO_0001141)

# File lib/biointerchange/so.rb, line 7117
def self.serine_threonine_turn
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001141')
end
seryl_tRNA() click to toggle source

A tRNA sequence that has a serine anticodon, and a 3’ serine binding region. (purl.obolibrary.org/obo/SO_0000269)

# File lib/biointerchange/so.rb, line 1935
def self.seryl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000269')
end
seven_aminomethyl_seven_deazaguanosine() click to toggle source

7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine. (purl.obolibrary.org/obo/SO_0001322)

# File lib/biointerchange/so.rb, line 8197
def self.seven_aminomethyl_seven_deazaguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001322')
end
seven_cyano_seven_deazaguanosine() click to toggle source

7_cyano_7_deazaguanosine is a modified 7-deazoguanosine. (purl.obolibrary.org/obo/SO_0001321)

# File lib/biointerchange/so.rb, line 8191
def self.seven_cyano_seven_deazaguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001321')
end
seven_deazaguanosine() click to toggle source

7-deazaguanosine is a moddified guanosine. (purl.obolibrary.org/obo/SO_0001316)

# File lib/biointerchange/so.rb, line 8161
def self.seven_deazaguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001316')
end
seven_methylguanine() click to toggle source

A modified RNA base in which guanine is methylated at the 7- position. (purl.obolibrary.org/obo/SO_0001231)

# File lib/biointerchange/so.rb, line 7657
def self.seven_methylguanine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001231')
end
seven_methylguanosine() click to toggle source

7_methylguanosine is a modified guanosine base feature. (purl.obolibrary.org/obo/SO_0001326)

# File lib/biointerchange/so.rb, line 8221
def self.seven_methylguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001326')
end
sgRNA() click to toggle source

A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method. (purl.obolibrary.org/obo/SO_0001998)

# File lib/biointerchange/so.rb, line 12191
def self.sgRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001998')
end
shadow_enhancer() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001482)

# File lib/biointerchange/so.rb, line 9151
def self.shadow_enhancer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001482')
end
siRNA() click to toggle source

A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules. (purl.obolibrary.org/obo/SO_0000646)

# File lib/biointerchange/so.rb, line 4199
def self.siRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000646')
end
signal_anchor() click to toggle source

A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane. (purl.obolibrary.org/obo/SO_0001809)

# File lib/biointerchange/so.rb, line 11059
def self.signal_anchor
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001809')
end
signal_peptide() click to toggle source

The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components. (purl.obolibrary.org/obo/SO_0000418)

# File lib/biointerchange/so.rb, line 2823
def self.signal_peptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000418')
end
signature() click to toggle source

A region of sequence where developer information is encoded. (purl.obolibrary.org/obo/SO_0001978)

# File lib/biointerchange/so.rb, line 12077
def self.signature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001978')
end
silenced() click to toggle source

An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level. (purl.obolibrary.org/obo/SO_0000893)

# File lib/biointerchange/so.rb, line 5639
def self.silenced
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000893')
end
silenced_by_DNA_methylation() click to toggle source

An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription. (purl.obolibrary.org/obo/SO_0000895)

# File lib/biointerchange/so.rb, line 5651
def self.silenced_by_DNA_methylation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000895')
end
silenced_by_DNA_modification() click to toggle source

An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription. (purl.obolibrary.org/obo/SO_0000894)

# File lib/biointerchange/so.rb, line 5645
def self.silenced_by_DNA_modification
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000894')
end
silenced_by_RNA_interference() click to toggle source

An attribute describing an epigenetic process where a gene is inactivated by RNA interference. (purl.obolibrary.org/obo/SO_0001220)

# File lib/biointerchange/so.rb, line 7591
def self.silenced_by_RNA_interference
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001220')
end
silenced_by_histone_deacetylation() click to toggle source

An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation. (purl.obolibrary.org/obo/SO_0001223)

# File lib/biointerchange/so.rb, line 7609
def self.silenced_by_histone_deacetylation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001223')
end
silenced_by_histone_methylation() click to toggle source

An attribute describing an epigenetic process where a gene is inactivated by histone methylation. (purl.obolibrary.org/obo/SO_0001222)

# File lib/biointerchange/so.rb, line 7603
def self.silenced_by_histone_methylation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001222')
end
silenced_by_histone_modification() click to toggle source

An attribute describing an epigenetic process where a gene is inactivated by histone modification. (purl.obolibrary.org/obo/SO_0001221)

# File lib/biointerchange/so.rb, line 7597
def self.silenced_by_histone_modification
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001221')
end
silenced_gene() click to toggle source

A gene that is silenced. (purl.obolibrary.org/obo/SO_0000127)

# File lib/biointerchange/so.rb, line 1079
def self.silenced_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000127')
end
silencer() click to toggle source

A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control. (purl.obolibrary.org/obo/SO_0000625)

# File lib/biointerchange/so.rb, line 4073
def self.silencer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000625')
end
silent_mating_type_cassette_array() click to toggle source

A gene cassette array that corresponds to a silenced version of a mating type region. (purl.obolibrary.org/obo/SO_0001984)

# File lib/biointerchange/so.rb, line 12107
def self.silent_mating_type_cassette_array
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001984')
end
silent_mutation() click to toggle source

A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation. (purl.obolibrary.org/obo/SO_0001017)

# File lib/biointerchange/so.rb, line 6377
def self.silent_mutation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001017')
end
similar_to() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/so_2_5_2.obo#similar_to)

# File lib/biointerchange/so.rb, line 251
def self.similar_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#similar_to')
end
simple_sequence_length_variation() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000207)

# File lib/biointerchange/so.rb, line 1563
def self.simple_sequence_length_variation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000207')
end
single() click to toggle source

Attributes added to describe the different kinds of replicon. SO workshop, September 2006. (purl.obolibrary.org/obo/SO_0000984)

# File lib/biointerchange/so.rb, line 6179
def self.single
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000984')
end
single_strand_restriction_enzyme_cleavage_site() click to toggle source

A restriction enzyme cleavage site whereby only one strand is cut. (purl.obolibrary.org/obo/SO_0001694)

# File lib/biointerchange/so.rb, line 10375
def self.single_strand_restriction_enzyme_cleavage_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001694')
end
single_stranded_DNA_chromosome() click to toggle source

Structural unit composed of a self-replicating, single-stranded DNA molecule. (purl.obolibrary.org/obo/SO_0000956)

# File lib/biointerchange/so.rb, line 6017
def self.single_stranded_DNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000956')
end
single_stranded_RNA_chromosome() click to toggle source

Structural unit composed of a self-replicating, single-stranded RNA molecule. (purl.obolibrary.org/obo/SO_0000962)

# File lib/biointerchange/so.rb, line 6053
def self.single_stranded_RNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000962')
end
single_stranded_cDNA() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000757)

# File lib/biointerchange/so.rb, line 4865
def self.single_stranded_cDNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000757')
end
site() click to toggle source

The interbase position where something (eg an aberration) occurred. (purl.obolibrary.org/obo/SO_0000408)

# File lib/biointerchange/so.rb, line 2763
def self.site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000408')
end
site_specific_recombination_target_region() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000342)

# File lib/biointerchange/so.rb, line 2373
def self.site_specific_recombination_target_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000342')
end
six_cutter_restriction_site() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000249)

# File lib/biointerchange/so.rb, line 1815
def self.six_cutter_restriction_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000249')
end
smFISH_probe() click to toggle source

A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment. (purl.obolibrary.org/obo/SO_0001854)

# File lib/biointerchange/so.rb, line 11329
def self.smFISH_probe
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001854')
end
small_regulatory_ncRNA() click to toggle source

A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression. (purl.obolibrary.org/obo/SO_0000370)

# File lib/biointerchange/so.rb, line 2535
def self.small_regulatory_ncRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000370')
end
small_subunit_rRNA() click to toggle source

Ribosomal RNA transcript that structures the small subunit of the ribosome. (purl.obolibrary.org/obo/SO_0000650)

# File lib/biointerchange/so.rb, line 4223
def self.small_subunit_rRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000650')
end
snRNA() click to toggle source

A small nuclear RNA molecule involved in pre-mRNA splicing and processing. (purl.obolibrary.org/obo/SO_0000274)

# File lib/biointerchange/so.rb, line 1965
def self.snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000274')
end
snRNA_encoding() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000623)

# File lib/biointerchange/so.rb, line 4061
def self.snRNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000623')
end
snRNA_gene() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001268)

# File lib/biointerchange/so.rb, line 7873
def self.snRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001268')
end
snRNA_primary_transcript() click to toggle source

A primary transcript encoding a small nuclear RNA (SO:0000274). (purl.obolibrary.org/obo/SO_0000231)

# File lib/biointerchange/so.rb, line 1707
def self.snRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000231')
end
snoRNA() click to toggle source

A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA. (purl.obolibrary.org/obo/SO_0000275)

# File lib/biointerchange/so.rb, line 1971
def self.snoRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000275')
end
snoRNA_encoding() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000578)

# File lib/biointerchange/so.rb, line 3791
def self.snoRNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000578')
end
snoRNA_gene() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001267)

# File lib/biointerchange/so.rb, line 7867
def self.snoRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001267')
end
snoRNA_primary_transcript() click to toggle source

A primary transcript encoding a small nucleolar mRNA (SO:0000275). (purl.obolibrary.org/obo/SO_0000232)

# File lib/biointerchange/so.rb, line 1713
def self.snoRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000232')
end
solo_LTR() click to toggle source

A recombination product between the 2 LTR of the same element. (purl.obolibrary.org/obo/SO_0001003)

# File lib/biointerchange/so.rb, line 6293
def self.solo_LTR
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001003')
end
somatic_variant() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001777)

# File lib/biointerchange/so.rb, line 10873
def self.somatic_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001777')
end
sonicate_fragment() click to toggle source

A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments. (purl.obolibrary.org/obo/SO_0001253)

# File lib/biointerchange/so.rb, line 7783
def self.sonicate_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001253')
end
specific_recombination_site() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000299)

# File lib/biointerchange/so.rb, line 2115
def self.specific_recombination_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000299')
end
splice_acceptor_variant() click to toggle source

A splice variant that changes the 2 base region at the 3’ end of an intron. (purl.obolibrary.org/obo/SO_0001574)

# File lib/biointerchange/so.rb, line 9703
def self.splice_acceptor_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001574')
end
splice_donor_5th_base_variant() click to toggle source

A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript. (purl.obolibrary.org/obo/SO_0001787)

# File lib/biointerchange/so.rb, line 10927
def self.splice_donor_5th_base_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001787')
end
splice_donor_variant() click to toggle source

A splice variant that changes the 2 base pair region at the 5’ end of an intron. (purl.obolibrary.org/obo/SO_0001575)

# File lib/biointerchange/so.rb, line 9709
def self.splice_donor_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001575')
end
splice_enhancer() click to toggle source

Region of a transcript that regulates splicing. (purl.obolibrary.org/obo/SO_0000344)

# File lib/biointerchange/so.rb, line 2385
def self.splice_enhancer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000344')
end
splice_junction() click to toggle source

The boundary between an intron and an exon. (purl.obolibrary.org/obo/SO_0001421)

# File lib/biointerchange/so.rb, line 8791
def self.splice_junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001421')
end
splice_region() click to toggle source

A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron. (purl.obolibrary.org/obo/SO_0001902)

# File lib/biointerchange/so.rb, line 11617
def self.splice_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001902')
end
splice_region_variant() click to toggle source

A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron. (purl.obolibrary.org/obo/SO_0001630)

# File lib/biointerchange/so.rb, line 10015
def self.splice_region_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001630')
end
splice_site() click to toggle source

Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction. (purl.obolibrary.org/obo/SO_0000162)

# File lib/biointerchange/so.rb, line 1289
def self.splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000162')
end
splice_site_variant() click to toggle source

A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript. (purl.obolibrary.org/obo/SO_0001629)

# File lib/biointerchange/so.rb, line 10009
def self.splice_site_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001629')
end
spliced_leader_RNA() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000636)

# File lib/biointerchange/so.rb, line 4139
def self.spliced_leader_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000636')
end
spliceosomal_intron() click to toggle source

An intron which is spliced by the spliceosome. (purl.obolibrary.org/obo/SO_0000662)

# File lib/biointerchange/so.rb, line 4295
def self.spliceosomal_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000662')
end
spliceosomal_intron_region() click to toggle source

A region within an intron. (purl.obolibrary.org/obo/SO_0000841)

# File lib/biointerchange/so.rb, line 5327
def self.spliceosomal_intron_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000841')
end
splicing_feature() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000682)

# File lib/biointerchange/so.rb, line 4415
def self.splicing_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000682')
end
splicing_regulatory_region() click to toggle source

A regulatory_region that modulates splicing. (purl.obolibrary.org/obo/SO_0001056)

# File lib/biointerchange/so.rb, line 6619
def self.splicing_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001056')
end
splicing_variant() click to toggle source

A sequence variant that changes the process of splicing. (purl.obolibrary.org/obo/SO_0001568)

# File lib/biointerchange/so.rb, line 9667
def self.splicing_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001568')
end
spot_42_RNA() click to toggle source

A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels. (purl.obolibrary.org/obo/SO_0000389)

# File lib/biointerchange/so.rb, line 2649
def self.spot_42_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000389')
end
ss_RNA_viral_sequence() click to toggle source

A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA. (purl.obolibrary.org/obo/SO_0001199)

# File lib/biointerchange/so.rb, line 7465
def self.ss_RNA_viral_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001199')
end
ss_oligo() click to toggle source

A single stranded oligonucleotide. (purl.obolibrary.org/obo/SO_0000441)

# File lib/biointerchange/so.rb, line 2965
def self.ss_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000441')
end
stRNA() click to toggle source

Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans. (purl.obolibrary.org/obo/SO_0000649)

# File lib/biointerchange/so.rb, line 4217
def self.stRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000649')
end
stRNA_encoding() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000656)

# File lib/biointerchange/so.rb, line 4259
def self.stRNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000656')
end
stRNA_gene() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001270)

# File lib/biointerchange/so.rb, line 7885
def self.stRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001270')
end
stRNA_primary_transcript() click to toggle source

A primary transcript encoding a small temporal mRNA (SO:0000649). (purl.obolibrary.org/obo/SO_0000648)

# File lib/biointerchange/so.rb, line 4211
def self.stRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000648')
end
st_turn_left_handed_type_one() click to toggle source

The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees. (purl.obolibrary.org/obo/SO_0001142)

# File lib/biointerchange/so.rb, line 7123
def self.st_turn_left_handed_type_one
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001142')
end
st_turn_left_handed_type_two() click to toggle source

The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees. (purl.obolibrary.org/obo/SO_0001143)

# File lib/biointerchange/so.rb, line 7129
def self.st_turn_left_handed_type_two
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001143')
end
st_turn_right_handed_type_one() click to toggle source

The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees. (purl.obolibrary.org/obo/SO_0001144)

# File lib/biointerchange/so.rb, line 7135
def self.st_turn_right_handed_type_one
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001144')
end
st_turn_right_handed_type_two() click to toggle source

The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees. (purl.obolibrary.org/obo/SO_0001145)

# File lib/biointerchange/so.rb, line 7141
def self.st_turn_right_handed_type_two
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001145')
end
standard_draft() click to toggle source

The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete. (purl.obolibrary.org/obo/SO_0001486)

# File lib/biointerchange/so.rb, line 9175
def self.standard_draft
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001486')
end
start_codon() click to toggle source

First codon to be translated by a ribosome. (purl.obolibrary.org/obo/SO_0000318)

# File lib/biointerchange/so.rb, line 2229
def self.start_codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000318')
end
started_by() click to toggle source

X is strted_by Y if Y is part_of X and X and Y share a 5’ boundary. (purl.obolibrary.org/obo/so_2_5_2.obo#started_by)

# File lib/biointerchange/so.rb, line 257
def self.started_by
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#started_by')
end
starts() click to toggle source

X starts Y if X is part of Y, and A and Y share a 5’ or N-terminal boundary. (purl.obolibrary.org/obo/so_2_5_2.obo#starts)

# File lib/biointerchange/so.rb, line 263
def self.starts
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#starts')
end
status() click to toggle source

An attribute describing the status of a feature, based on the available evidence. (purl.obolibrary.org/obo/SO_0000905)

# File lib/biointerchange/so.rb, line 5711
def self.status
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000905')
end
status_of_coding_sequence() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_1001255)

# File lib/biointerchange/so.rb, line 13493
def self.status_of_coding_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001255')
end
stem_loop() click to toggle source

A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences. (purl.obolibrary.org/obo/SO_0000313)

# File lib/biointerchange/so.rb, line 2199
def self.stem_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000313')
end
sterol_regulatory_element() click to toggle source

A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs. (purl.obolibrary.org/obo/SO_0001861)

# File lib/biointerchange/so.rb, line 11371
def self.sterol_regulatory_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001861')
end
sticky_end_restriction_enzyme_cleavage_site() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001692)

# File lib/biointerchange/so.rb, line 10363
def self.sticky_end_restriction_enzyme_cleavage_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001692')
end
stop_codon() click to toggle source

In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis. (purl.obolibrary.org/obo/SO_0000319)

# File lib/biointerchange/so.rb, line 2235
def self.stop_codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000319')
end
stop_codon_read_through() click to toggle source

A stop codon redefined to be a new amino acid. (purl.obolibrary.org/obo/SO_0000883)

# File lib/biointerchange/so.rb, line 5579
def self.stop_codon_read_through
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000883')
end
stop_codon_readthrough() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_1001267)

# File lib/biointerchange/so.rb, line 13547
def self.stop_codon_readthrough
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001267')
end
stop_codon_redefined_as_pyrrolysine() click to toggle source

A stop codon redefined to be the new amino acid, pyrrolysine. (purl.obolibrary.org/obo/SO_0000884)

# File lib/biointerchange/so.rb, line 5585
def self.stop_codon_redefined_as_pyrrolysine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000884')
end
stop_codon_redefined_as_selenocysteine() click to toggle source

A stop codon redefined to be the new amino acid, selenocysteine. (purl.obolibrary.org/obo/SO_0000885)

# File lib/biointerchange/so.rb, line 5591
def self.stop_codon_redefined_as_selenocysteine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000885')
end
stop_codon_redefinition_as_pyrrolysine() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_1001270)

# File lib/biointerchange/so.rb, line 13565
def self.stop_codon_redefinition_as_pyrrolysine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001270')
end
stop_codon_redefinition_as_selenocysteine() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_1001266)

# File lib/biointerchange/so.rb, line 13541
def self.stop_codon_redefinition_as_selenocysteine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001266')
end
stop_codon_signal() click to toggle source

A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding. (purl.obolibrary.org/obo/SO_1001288)

# File lib/biointerchange/so.rb, line 13661
def self.stop_codon_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001288')
end
stop_gained() click to toggle source

A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript. (purl.obolibrary.org/obo/SO_0001587)

# File lib/biointerchange/so.rb, line 9769
def self.stop_gained
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001587')
end
stop_lost() click to toggle source

A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript. (purl.obolibrary.org/obo/SO_0001578)

# File lib/biointerchange/so.rb, line 9727
def self.stop_lost
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001578')
end
stop_retained_variant() click to toggle source

A sequence variant where at least one base in the terminator codon is changed, but the terminator remains. (purl.obolibrary.org/obo/SO_0001567)

# File lib/biointerchange/so.rb, line 9661
def self.stop_retained_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001567')
end
strand_attribute() click to toggle source

Attributes added to describe the different kinds of replicon. SO workshop, September 2006. (purl.obolibrary.org/obo/SO_0000983)

# File lib/biointerchange/so.rb, line 6173
def self.strand_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000983')
end
structural_alteration() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001785)

# File lib/biointerchange/so.rb, line 10915
def self.structural_alteration
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001785')
end
structural_variant() click to toggle source

A sequence variant that changes one or more sequence features. (purl.obolibrary.org/obo/SO_0001537)

# File lib/biointerchange/so.rb, line 9481
def self.structural_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001537')
end
substitute() click to toggle source

To substitute a subsection of sequence for another. (purl.obolibrary.org/obo/SO_0000048)

# File lib/biointerchange/so.rb, line 597
def self.substitute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000048')
end
substitute_A_to_I() click to toggle source

An edit to substitute an I for an A. (purl.obolibrary.org/obo/SO_0000919)

# File lib/biointerchange/so.rb, line 5795
def self.substitute_A_to_I
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000919')
end
substitute_C_to_U() click to toggle source

An edit to substitute an U for a C. (purl.obolibrary.org/obo/SO_0000922)

# File lib/biointerchange/so.rb, line 5813
def self.substitute_C_to_U
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000922')
end
substitution() click to toggle source

A sequence alteration where the length of the change in the variant is the same as that of the reference. (purl.obolibrary.org/obo/SO_1000002)

# File lib/biointerchange/so.rb, line 12479
def self.substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000002')
end
subtelomere() click to toggle source

A heterochromatic region of the chromosome, adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed. (purl.obolibrary.org/obo/SO_0001997)

# File lib/biointerchange/so.rb, line 12185
def self.subtelomere
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001997')
end
sugar_edge_base_pair() click to toggle source

A type of non-canonical base-pairing. (purl.obolibrary.org/obo/SO_0000030)

# File lib/biointerchange/so.rb, line 489
def self.sugar_edge_base_pair
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000030')
end
supercontig() click to toggle source

One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N’s. (purl.obolibrary.org/obo/SO_0000148)

# File lib/biointerchange/so.rb, line 1205
def self.supercontig
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000148')
end
supported_by_EST_or_cDNA() click to toggle source

An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data. (purl.obolibrary.org/obo/SO_0000909)

# File lib/biointerchange/so.rb, line 5735
def self.supported_by_EST_or_cDNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000909')
end
supported_by_domain_match() click to toggle source

An attribute to describe a feature that has been predicted using sequence similarity of a known domain. (purl.obolibrary.org/obo/SO_0000908)

# File lib/biointerchange/so.rb, line 5729
def self.supported_by_domain_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000908')
end
supported_by_sequence_similarity() click to toggle source

An attribute to describe a feature that has been predicted using sequence similarity techniques. (purl.obolibrary.org/obo/SO_0000907)

# File lib/biointerchange/so.rb, line 5723
def self.supported_by_sequence_similarity
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000907')
end
symbiosis_island() click to toggle source

A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria. (purl.obolibrary.org/obo/SO_0000776)

# File lib/biointerchange/so.rb, line 4973
def self.symbiosis_island
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000776')
end
symmetric_RNA_internal_loop() click to toggle source

An internal RNA loop where the extent of the loop on both stands is the same size. (purl.obolibrary.org/obo/SO_0000025)

# File lib/biointerchange/so.rb, line 459
def self.symmetric_RNA_internal_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000025')
end
synonymous() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001815)

# File lib/biointerchange/so.rb, line 11095
def self.synonymous
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001815')
end
synonymous_variant() click to toggle source

A sequence variant where there is no resulting change to the encoded amino acid. (purl.obolibrary.org/obo/SO_0001819)

# File lib/biointerchange/so.rb, line 11119
def self.synonymous_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001819')
end
syntenic() click to toggle source

Attribute describing sequence regions occurring in same order on chromosome of different species. (purl.obolibrary.org/obo/SO_0000860)

# File lib/biointerchange/so.rb, line 5441
def self.syntenic
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000860')
end
syntenic_region() click to toggle source

A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species. (purl.obolibrary.org/obo/SO_0005858)

# File lib/biointerchange/so.rb, line 12347
def self.syntenic_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005858')
end
synthetic_oligo() click to toggle source

An oligo composed of synthetic nucleotides. (purl.obolibrary.org/obo/SO_0001247)

# File lib/biointerchange/so.rb, line 7747
def self.synthetic_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001247')
end
synthetic_sequence() click to toggle source

An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence. (purl.obolibrary.org/obo/SO_0000351)

# File lib/biointerchange/so.rb, line 2427
def self.synthetic_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000351')
end
tRNA() click to toggle source

Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3’ end, to which the tRNA’s corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and ‘wobble’ base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position. (purl.obolibrary.org/obo/SO_0000253)

# File lib/biointerchange/so.rb, line 1839
def self.tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000253')
end
tRNA_encoding() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000663)

# File lib/biointerchange/so.rb, line 4301
def self.tRNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000663')
end
tRNA_gene() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001272)

# File lib/biointerchange/so.rb, line 7897
def self.tRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001272')
end
tRNA_intron() click to toggle source

An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification. (purl.obolibrary.org/obo/SO_1001272)

# File lib/biointerchange/so.rb, line 13577
def self.tRNA_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001272')
end
tRNA_primary_transcript() click to toggle source

A primary transcript encoding a transfer RNA (SO:0000253). (purl.obolibrary.org/obo/SO_0000210)

# File lib/biointerchange/so.rb, line 1581
def self.tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000210')
end
tRNA_region() click to toggle source

A region of a tRNA. (purl.obolibrary.org/obo/SO_0001172)

# File lib/biointerchange/so.rb, line 7303
def self.tRNA_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001172')
end
tag() click to toggle source

A nucleotide sequence that may be used to identify a larger sequence. (purl.obolibrary.org/obo/SO_0000324)

# File lib/biointerchange/so.rb, line 2265
def self.tag
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000324')
end
tandem() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001513)

# File lib/biointerchange/so.rb, line 9337
def self.tandem
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001513')
end
tandem_duplication() click to toggle source

A duplication consisting of 2 identical adjacent regions. (purl.obolibrary.org/obo/SO_1000173)

# File lib/biointerchange/so.rb, line 13325
def self.tandem_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000173')
end
tandem_repeat() click to toggle source

Two or more adjcent copies of a region (of length greater than 1). (purl.obolibrary.org/obo/SO_0000705)

# File lib/biointerchange/so.rb, line 4553
def self.tandem_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000705')
end
target_site_duplication() click to toggle source

A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion. (purl.obolibrary.org/obo/SO_0000434)

# File lib/biointerchange/so.rb, line 2919
def self.target_site_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000434')
end
targeting_vector() click to toggle source

An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications. (purl.obolibrary.org/obo/SO_0001644)

# File lib/biointerchange/so.rb, line 10099
def self.targeting_vector
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001644')
end
tasiRNA() click to toggle source

The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene. (purl.obolibrary.org/obo/SO_0001800)

# File lib/biointerchange/so.rb, line 11005
def self.tasiRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001800')
end
tasiRNA_primary_transcript() click to toggle source

A primary transcript encoding a tasiRNA. (purl.obolibrary.org/obo/SO_0001801)

# File lib/biointerchange/so.rb, line 11011
def self.tasiRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001801')
end
telomerase_RNA() click to toggle source

The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA. (purl.obolibrary.org/obo/SO_0000390)

# File lib/biointerchange/so.rb, line 2655
def self.telomerase_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000390')
end
telomerase_RNA_gene() click to toggle source

A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase. (purl.obolibrary.org/obo/SO_0001643)

# File lib/biointerchange/so.rb, line 10093
def self.telomerase_RNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001643')
end
telomere() click to toggle source

A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end. (purl.obolibrary.org/obo/SO_0000624)

# File lib/biointerchange/so.rb, line 4067
def self.telomere
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000624')
end
telomeric_repeat() click to toggle source

The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n. (purl.obolibrary.org/obo/SO_0001496)

# File lib/biointerchange/so.rb, line 9235
def self.telomeric_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001496')
end
telomeric_transcript() click to toggle source

A non-coding transcript derived from thetranscript of the telomere. (purl.obolibrary.org/obo/SO_0001927)

# File lib/biointerchange/so.rb, line 11767
def self.telomeric_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001927')
end
template_region() click to toggle source

A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA. (purl.obolibrary.org/obo/SO_0000978)

# File lib/biointerchange/so.rb, line 6143
def self.template_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000978')
end
terminal_inverted_repeat() click to toggle source

An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon. (purl.obolibrary.org/obo/SO_0000481)

# File lib/biointerchange/so.rb, line 3205
def self.terminal_inverted_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000481')
end
terminal_inverted_repeat_element() click to toggle source

A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long. (purl.obolibrary.org/obo/SO_0000208)

# File lib/biointerchange/so.rb, line 1569
def self.terminal_inverted_repeat_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000208')
end
terminator() click to toggle source

The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription. (purl.obolibrary.org/obo/SO_0000141)

# File lib/biointerchange/so.rb, line 1163
def self.terminator
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000141')
end
terminator_codon_variant() click to toggle source

A sequence variant whereby at least one of the bases in the terminator codon is changed. (purl.obolibrary.org/obo/SO_0001590)

# File lib/biointerchange/so.rb, line 9781
def self.terminator_codon_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001590')
end
terminator_of_type_2_RNApol_III_promoter() click to toggle source

A terminator signal for RNA polymerase III transcription. (purl.obolibrary.org/obo/SO_0000615)

# File lib/biointerchange/so.rb, line 4013
def self.terminator_of_type_2_RNApol_III_promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000615')
end
tetraloop() click to toggle source

A base-paired stem with loop of 4 non-hydrogen bonded nucleotides. (purl.obolibrary.org/obo/SO_0001008)

# File lib/biointerchange/so.rb, line 6323
def self.tetraloop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001008')
end
tetranucleotide_repeat_microsatellite_feature() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000641)

# File lib/biointerchange/so.rb, line 4169
def self.tetranucleotide_repeat_microsatellite_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000641')
end
theta_replication() click to toggle source

This has been obsoleted as it represents a process. replaced_by: GO:0070582 (purl.obolibrary.org/obo/SO_0000970)

# File lib/biointerchange/so.rb, line 6101
def self.theta_replication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000970')
end
three_methylcytidine() click to toggle source

3-methylcytidine is a modified cytidine. (purl.obolibrary.org/obo/SO_0001281)

# File lib/biointerchange/so.rb, line 7951
def self.three_methylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001281')
end
three_methylpseudouridine() click to toggle source

3_methylpseudouridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001377)

# File lib/biointerchange/so.rb, line 8527
def self.three_methylpseudouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001377')
end
three_methyluridine() click to toggle source

3_methyluridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001372)

# File lib/biointerchange/so.rb, line 8497
def self.three_methyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001372')
end
three_prime_D_heptamer() click to toggle source

7 nucleotide recombination site like CACAGTG, part of a 3’ D-recombination signal sequence of an immunoglobulin/T-cell receptor gene. (purl.obolibrary.org/obo/SO_0000493)

# File lib/biointerchange/so.rb, line 3277
def self.three_prime_D_heptamer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000493')
end
three_prime_D_nonamer() click to toggle source

A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3’ D-recombination signal sequence of an immunoglobulin/T-cell receptor gene. (purl.obolibrary.org/obo/SO_0000494)

# File lib/biointerchange/so.rb, line 3283
def self.three_prime_D_nonamer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000494')
end
three_prime_D_recombination_signal_sequence() click to toggle source

Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3’ D-heptamer (SO:0000493), 3’ D-spacer, and 3’ D-nonamer (SO:0000494) in 3’ of the D-region of a D-gene. (purl.obolibrary.org/obo/SO_0000570)

# File lib/biointerchange/so.rb, line 3743
def self.three_prime_D_recombination_signal_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000570')
end
three_prime_D_spacer() click to toggle source

A 12 or 23 nucleotide spacer between the 3’D-HEPTAMER and 3’D-NONAMER of a 3’D-RS. (purl.obolibrary.org/obo/SO_0000495)

# File lib/biointerchange/so.rb, line 3289
def self.three_prime_D_spacer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000495')
end
three_prime_EST() click to toggle source

An EST read from the 3’ end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs). (purl.obolibrary.org/obo/SO_0001209)

# File lib/biointerchange/so.rb, line 7525
def self.three_prime_EST
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001209')
end
three_prime_LTR() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000426)

# File lib/biointerchange/so.rb, line 2871
def self.three_prime_LTR
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000426')
end
three_prime_LTR_component() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000849)

# File lib/biointerchange/so.rb, line 5375
def self.three_prime_LTR_component
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000849')
end
three_prime_RACE_clone() click to toggle source

A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3’ end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5’ primer), and spliced into a vector for propagation in a suitable host. (purl.obolibrary.org/obo/SO_0001433)

# File lib/biointerchange/so.rb, line 8857
def self.three_prime_RACE_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001433')
end
three_prime_RST() click to toggle source

A tag produced from a single sequencing read from a 3’-RACE product; typically a few hundred base pairs long. (purl.obolibrary.org/obo/SO_0001468)

# File lib/biointerchange/so.rb, line 9067
def self.three_prime_RST
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001468')
end
three_prime_UST() click to toggle source

A UST located in the 3’UTR of a protein-coding transcript. (purl.obolibrary.org/obo/SO_0001465)

# File lib/biointerchange/so.rb, line 9049
def self.three_prime_UST
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001465')
end
three_prime_UTR() click to toggle source

A region at the 3’ end of a mature transcript (following the stop codon) that is not translated into a protein. (purl.obolibrary.org/obo/SO_0000205)

# File lib/biointerchange/so.rb, line 1551
def self.three_prime_UTR
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000205')
end
three_prime_UTR_intron() click to toggle source

An intron located in the 3’ UTR. (purl.obolibrary.org/obo/SO_0000448)

# File lib/biointerchange/so.rb, line 3007
def self.three_prime_UTR_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000448')
end
three_prime_cis_splice_site() click to toggle source

Intronic 2 bp region bordering the exon, at the 3’ edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron. (purl.obolibrary.org/obo/SO_0000164)

# File lib/biointerchange/so.rb, line 1301
def self.three_prime_cis_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000164')
end
three_prime_clip() click to toggle source

3’-most region of a precursor transcript that is clipped off during processing. (purl.obolibrary.org/obo/SO_0000557)

# File lib/biointerchange/so.rb, line 3665
def self.three_prime_clip
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000557')
end
three_prime_coding_exon() click to toggle source

The coding exon that is most 3-prime on a given transcript. (purl.obolibrary.org/obo/SO_0000202)

# File lib/biointerchange/so.rb, line 1533
def self.three_prime_coding_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000202')
end
three_prime_coding_exon_coding_region() click to toggle source

The sequence of the three_prime_coding_exon that codes for protein. (purl.obolibrary.org/obo/SO_0000197)

# File lib/biointerchange/so.rb, line 1503
def self.three_prime_coding_exon_coding_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000197')
end
three_prime_coding_exon_noncoding_region() click to toggle source

The sequence of the 3’ exon that is not coding. (purl.obolibrary.org/obo/SO_0000484)

# File lib/biointerchange/so.rb, line 3223
def self.three_prime_coding_exon_noncoding_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000484')
end
three_prime_five_prime_overlap() click to toggle source

An attribute to describe a gene when the 3’ region overlaps with another gene’s 5’ region. (purl.obolibrary.org/obo/SO_0000076)

# File lib/biointerchange/so.rb, line 773
def self.three_prime_five_prime_overlap
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000076')
end
three_prime_flanking_region() click to toggle source

A flanking region located three prime of a specific region. (purl.obolibrary.org/obo/SO_0001417)

# File lib/biointerchange/so.rb, line 8767
def self.three_prime_flanking_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001417')
end
three_prime_intron() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000192)

# File lib/biointerchange/so.rb, line 1473
def self.three_prime_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000192')
end
three_prime_noncoding_exon() click to toggle source

Non-coding exon in the 3’ UTR. (purl.obolibrary.org/obo/SO_0000444)

# File lib/biointerchange/so.rb, line 2983
def self.three_prime_noncoding_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000444')
end
three_prime_recoding_site() click to toggle source

The recoding stimulatory signal located downstream of the recoding site. (purl.obolibrary.org/obo/SO_1001277)

# File lib/biointerchange/so.rb, line 13601
def self.three_prime_recoding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001277')
end
three_prime_repeat_recoding_signal() click to toggle source

A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements. (purl.obolibrary.org/obo/SO_1001286)

# File lib/biointerchange/so.rb, line 13649
def self.three_prime_repeat_recoding_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001286')
end
three_prime_restriction_enzyme_junction() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001690)

# File lib/biointerchange/so.rb, line 10351
def self.three_prime_restriction_enzyme_junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001690')
end
three_prime_stem_loop_structure() click to toggle source

A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region. (purl.obolibrary.org/obo/SO_1001279)

# File lib/biointerchange/so.rb, line 13607
def self.three_prime_stem_loop_structure
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001279')
end
three_prime_sticky_end_restriction_enzyme_cleavage_site() click to toggle source

A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs. (purl.obolibrary.org/obo/SO_0001976)

# File lib/biointerchange/so.rb, line 12065
def self.three_prime_sticky_end_restriction_enzyme_cleavage_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001976')
end
three_prime_terminal_inverted_repeat() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000421)

# File lib/biointerchange/so.rb, line 2841
def self.three_prime_terminal_inverted_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000421')
end
three_prime_three_prime_overlap() click to toggle source

An attribute to describe a gene when the 3’ region overlaps with another gene’s 3’ region. (purl.obolibrary.org/obo/SO_0000075)

# File lib/biointerchange/so.rb, line 767
def self.three_prime_three_prime_overlap
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000075')
end
three_ten_helix() click to toggle source

The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier. (purl.obolibrary.org/obo/SO_0001119)

# File lib/biointerchange/so.rb, line 6985
def self.three_ten_helix
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001119')
end
three_three_amino_three_carboxypropyl_uridine() click to toggle source

3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001353)

# File lib/biointerchange/so.rb, line 8383
def self.three_three_amino_three_carboxypropyl_uridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001353')
end
three_two_prime_O_dimethyluridine() click to toggle source

3_2prime_O_dimethyluridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001375)

# File lib/biointerchange/so.rb, line 8515
def self.three_two_prime_O_dimethyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001375')
end
threonine() click to toggle source

A place holder for a cross product with chebi. (purl.obolibrary.org/obo/SO_0001445)

# File lib/biointerchange/so.rb, line 8929
def self.threonine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001445')
end
threonine_tRNA_primary_transcript() click to toggle source

A primary transcript encoding threonyl tRNA (SO:000270). (purl.obolibrary.org/obo/SO_0000227)

# File lib/biointerchange/so.rb, line 1683
def self.threonine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000227')
end
threonyl_tRNA() click to toggle source

A tRNA sequence that has a threonine anticodon, and a 3’ threonine binding region. (purl.obolibrary.org/obo/SO_0000270)

# File lib/biointerchange/so.rb, line 1941
def self.threonyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000270')
end
tiling_path() click to toggle source

A set of regions which overlap with minimal polymorphism to form a linear sequence. (purl.obolibrary.org/obo/SO_0000472)

# File lib/biointerchange/so.rb, line 3151
def self.tiling_path
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000472')
end
tiling_path_clone() click to toggle source

A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly. (purl.obolibrary.org/obo/SO_0000480)

# File lib/biointerchange/so.rb, line 3199
def self.tiling_path_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000480')
end
tiling_path_fragment() click to toggle source

A piece of sequence that makes up a tiling_path (SO:0000472). (purl.obolibrary.org/obo/SO_0000474)

# File lib/biointerchange/so.rb, line 3163
def self.tiling_path_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000474')
end
tmRNA() click to toggle source

A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes. (purl.obolibrary.org/obo/SO_0000584)

# File lib/biointerchange/so.rb, line 3827
def self.tmRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000584')
end
tmRNA_acceptor_piece() click to toggle source

The acceptor region of a two-piece tmRNA that when mature is charged at its 3’ end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together. (purl.obolibrary.org/obo/SO_0000770)

# File lib/biointerchange/so.rb, line 4937
def self.tmRNA_acceptor_piece
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000770')
end
tmRNA_coding_piece() click to toggle source

The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together. (purl.obolibrary.org/obo/SO_0000769)

# File lib/biointerchange/so.rb, line 4931
def self.tmRNA_coding_piece
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000769')
end
tmRNA_encoding() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000659)

# File lib/biointerchange/so.rb, line 4277
def self.tmRNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000659')
end
tmRNA_gene() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001271)

# File lib/biointerchange/so.rb, line 7891
def self.tmRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001271')
end
tmRNA_primary_transcript() click to toggle source

A primary transcript encoding a tmRNA (SO:0000584). (purl.obolibrary.org/obo/SO_0000586)

# File lib/biointerchange/so.rb, line 3839
def self.tmRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000586')
end
tmRNA_region() click to toggle source

A region of a tmRNA. (purl.obolibrary.org/obo/SO_0000847)

# File lib/biointerchange/so.rb, line 5363
def self.tmRNA_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000847')
end
topologically_defined_region() click to toggle source

A region that is defined according to its relations with other regions within the same sequence. (purl.obolibrary.org/obo/SO_0001412)

# File lib/biointerchange/so.rb, line 8737
def self.topologically_defined_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001412')
end
topology_attribute() click to toggle source

Attributes added to describe the different kinds of replicon. SO workshop, September 2006. (purl.obolibrary.org/obo/SO_0000986)

# File lib/biointerchange/so.rb, line 6191
def self.topology_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000986')
end
trans_splice_acceptor_site() click to toggle source

The 3’ splice site of the acceptor primary transcript. (purl.obolibrary.org/obo/SO_0000706)

# File lib/biointerchange/so.rb, line 4559
def self.trans_splice_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000706')
end
trans_splice_donor_site() click to toggle source

The 5’ five prime splice site region of the donor RNA. (purl.obolibrary.org/obo/SO_0000707)

# File lib/biointerchange/so.rb, line 4565
def self.trans_splice_donor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000707')
end
trans_splice_junction() click to toggle source

The boundary between the spliced leader and the first exon of the mRNA. (purl.obolibrary.org/obo/SO_0001474)

# File lib/biointerchange/so.rb, line 9103
def self.trans_splice_junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001474')
end
trans_splice_site() click to toggle source

Primary transcript region bordering trans-splice junction. (purl.obolibrary.org/obo/SO_0001420)

# File lib/biointerchange/so.rb, line 8785
def self.trans_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001420')
end
trans_spliced() click to toggle source

An attribute describing transcript sequence that is created by splicing exons from diferent genes. (purl.obolibrary.org/obo/SO_0000870)

# File lib/biointerchange/so.rb, line 5501
def self.trans_spliced
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000870')
end
trans_spliced_from() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/so_2_5_2.obo#trans_spliced_from)

# File lib/biointerchange/so.rb, line 269
def self.trans_spliced_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#trans_spliced_from')
end
trans_spliced_mRNA() click to toggle source

An mRNA that is trans-spliced. (purl.obolibrary.org/obo/SO_0000872)

# File lib/biointerchange/so.rb, line 5513
def self.trans_spliced_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000872')
end
trans_spliced_to() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/so_2_5_2.obo#trans_spliced_to)

# File lib/biointerchange/so.rb, line 275
def self.trans_spliced_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#trans_spliced_to')
end
trans_spliced_transcript() click to toggle source

A transcript that is trans-spliced. (purl.obolibrary.org/obo/SO_0000479)

# File lib/biointerchange/so.rb, line 3193
def self.trans_spliced_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000479')
end
transcribed_cluster() click to toggle source

A region defined by a set of transcribed sequences from the same gene or expressed pseudogene. (purl.obolibrary.org/obo/SO_0001457)

# File lib/biointerchange/so.rb, line 9001
def self.transcribed_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001457')
end
transcribed_fragment() click to toggle source

An experimental region, defined by a tiling array experiment to be transcribed at some level. (purl.obolibrary.org/obo/SO_0001418)

# File lib/biointerchange/so.rb, line 8773
def self.transcribed_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001418')
end
transcribed_from() click to toggle source

X is transcribed_from Y if X is synthesized from template Y. (purl.obolibrary.org/obo/so_2_5_2.obo#transcribed_from)

# File lib/biointerchange/so.rb, line 281
def self.transcribed_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#transcribed_from')
end
transcribed_region() click to toggle source

A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes. (purl.obolibrary.org/obo/SO_0000502)

# File lib/biointerchange/so.rb, line 3331
def self.transcribed_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000502')
end
transcribed_spacer_region() click to toggle source

Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA. (purl.obolibrary.org/obo/SO_0000638)

# File lib/biointerchange/so.rb, line 4151
def self.transcribed_spacer_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000638')
end
transcribed_to() click to toggle source

Inverse of transcribed_from. (purl.obolibrary.org/obo/so_2_5_2.obo#transcribed_to)

# File lib/biointerchange/so.rb, line 287
def self.transcribed_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#transcribed_to')
end
transcript() click to toggle source

An RNA synthesized on a DNA or RNA template by an RNA polymerase. (purl.obolibrary.org/obo/SO_0000673)

# File lib/biointerchange/so.rb, line 4361
def self.transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000673')
end
transcript_ablation() click to toggle source

A feature ablation whereby the deleted region includes a transcript feature. (purl.obolibrary.org/obo/SO_0001893)

# File lib/biointerchange/so.rb, line 11563
def self.transcript_ablation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001893')
end
transcript_amplification() click to toggle source

A feature amplification of a region containing a transcript. (purl.obolibrary.org/obo/SO_0001889)

# File lib/biointerchange/so.rb, line 11539
def self.transcript_amplification
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001889')
end
transcript_attribute() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000237)

# File lib/biointerchange/so.rb, line 1743
def self.transcript_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000237')
end
transcript_bound_by_nucleic_acid() click to toggle source

A transcript that is bound by a nucleic acid. (purl.obolibrary.org/obo/SO_0000278)

# File lib/biointerchange/so.rb, line 1989
def self.transcript_bound_by_nucleic_acid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000278')
end
transcript_bound_by_protein() click to toggle source

A transcript that is bound by a protein. (purl.obolibrary.org/obo/SO_0000279)

# File lib/biointerchange/so.rb, line 1995
def self.transcript_bound_by_protein
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000279')
end
transcript_edited_by_U_insertion_deletion() click to toggle source

The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa. (purl.obolibrary.org/obo/SO_0000597)

# File lib/biointerchange/so.rb, line 3905
def self.transcript_edited_by_U_insertion_deletion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000597')
end
transcript_feature() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000115)

# File lib/biointerchange/so.rb, line 1007
def self.transcript_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000115')
end
transcript_function_variant() click to toggle source

A sequence variant which alters the functioning of a transcript with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001538)

# File lib/biointerchange/so.rb, line 9487
def self.transcript_function_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001538')
end
transcript_fusion() click to toggle source

A feature fusion where the deletion brings together transcript regions. (purl.obolibrary.org/obo/SO_0001886)

# File lib/biointerchange/so.rb, line 11521
def self.transcript_fusion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001886')
end
transcript_processing_variant() click to toggle source

A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001543)

# File lib/biointerchange/so.rb, line 9517
def self.transcript_processing_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001543')
end
transcript_region() click to toggle source

A region of a transcript. (purl.obolibrary.org/obo/SO_0000833)

# File lib/biointerchange/so.rb, line 5279
def self.transcript_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000833')
end
transcript_regulatory_region_fusion() click to toggle source

A feature fusion where the deletion brings together a regulatory region and a transcript region. (purl.obolibrary.org/obo/SO_0001890)

# File lib/biointerchange/so.rb, line 11545
def self.transcript_regulatory_region_fusion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001890')
end
transcript_secondary_structure_variant() click to toggle source

A sequence variant within a transcript that changes the secondary structure of the RNA product. (purl.obolibrary.org/obo/SO_0001596)

# File lib/biointerchange/so.rb, line 9817
def self.transcript_secondary_structure_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001596')
end
transcript_sequence_variant() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001579)

# File lib/biointerchange/so.rb, line 9733
def self.transcript_sequence_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001579')
end
transcript_stability_variant() click to toggle source

A variant that changes the stability of a transcript with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001546)

# File lib/biointerchange/so.rb, line 9535
def self.transcript_stability_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001546')
end
transcript_translocation() click to toggle source

A feature translocation where the region contains a transcript. (purl.obolibrary.org/obo/SO_0001883)

# File lib/biointerchange/so.rb, line 11503
def self.transcript_translocation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001883')
end
transcript_variant() click to toggle source

A sequence variant that changes the structure of the transcript. (purl.obolibrary.org/obo/SO_0001576)

# File lib/biointerchange/so.rb, line 9715
def self.transcript_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001576')
end
transcript_with_readthrough_stop_codon() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000117)

# File lib/biointerchange/so.rb, line 1019
def self.transcript_with_readthrough_stop_codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000117')
end
transcript_with_translational_frameshift() click to toggle source

A transcript with a translational frameshift. (purl.obolibrary.org/obo/SO_0000118)

# File lib/biointerchange/so.rb, line 1025
def self.transcript_with_translational_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000118')
end
transcription_end_site() click to toggle source

The base where transcription ends. (purl.obolibrary.org/obo/SO_0000616)

# File lib/biointerchange/so.rb, line 4019
def self.transcription_end_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000616')
end
transcription_regulatory_region() click to toggle source

A regulatory region that is involved in the control of the process of transcription. (purl.obolibrary.org/obo/SO_0001679)

# File lib/biointerchange/so.rb, line 10285
def self.transcription_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001679')
end
transcription_start_cluster() click to toggle source

A region defined by a cluster of experimentally determined transcription starting sites. (purl.obolibrary.org/obo/SO_0001915)

# File lib/biointerchange/so.rb, line 11695
def self.transcription_start_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001915')
end
transcription_variant() click to toggle source

A variant that changes alters the transcription of a transcript with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001549)

# File lib/biointerchange/so.rb, line 9553
def self.transcription_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001549')
end
transcriptional_cis_regulatory_region() click to toggle source

A regulatory_region that modulates the transcription of a gene or genes. (purl.obolibrary.org/obo/SO_0001055)

# File lib/biointerchange/so.rb, line 6613
def self.transcriptional_cis_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001055')
end
transcriptionally_constitutive() click to toggle source

Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate. (purl.obolibrary.org/obo/SO_0000124)

# File lib/biointerchange/so.rb, line 1061
def self.transcriptionally_constitutive
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000124')
end
transcriptionally_induced() click to toggle source

An inducer molecule is required for transcription to occur. (purl.obolibrary.org/obo/SO_0000125)

# File lib/biointerchange/so.rb, line 1067
def self.transcriptionally_induced
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000125')
end
transcriptionally_regulated() click to toggle source

An attribute describing a gene that is regulated at transcription. (purl.obolibrary.org/obo/SO_0000123)

# File lib/biointerchange/so.rb, line 1055
def self.transcriptionally_regulated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000123')
end
transcriptionally_repressed() click to toggle source

A repressor molecule is required for transcription to stop. (purl.obolibrary.org/obo/SO_0000126)

# File lib/biointerchange/so.rb, line 1073
def self.transcriptionally_repressed
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000126')
end
transgene() click to toggle source

A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another. (purl.obolibrary.org/obo/SO_0000902)

# File lib/biointerchange/so.rb, line 5693
def self.transgene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000902')
end
transgene_attribute() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000452)

# File lib/biointerchange/so.rb, line 3031
def self.transgene_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000452')
end
transgenic() click to toggle source

Attribute describing sequence that has been integrated with foreign sequence. (purl.obolibrary.org/obo/SO_0000781)

# File lib/biointerchange/so.rb, line 5003
def self.transgenic
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000781')
end
transgenic_insertion() click to toggle source

An insertion that derives from another organism, via the use of recombinant DNA technology. (purl.obolibrary.org/obo/SO_0001218)

# File lib/biointerchange/so.rb, line 7579
def self.transgenic_insertion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001218')
end
transgenic_transposable_element() click to toggle source

TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE. (purl.obolibrary.org/obo/SO_0000796)

# File lib/biointerchange/so.rb, line 5093
def self.transgenic_transposable_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000796')
end
transit_peptide() click to toggle source

The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle). (purl.obolibrary.org/obo/SO_0000725)

# File lib/biointerchange/so.rb, line 4673
def self.transit_peptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000725')
end
transition() click to toggle source

Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide. (purl.obolibrary.org/obo/SO_1000009)

# File lib/biointerchange/so.rb, line 12497
def self.transition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000009')
end
translated_nucleotide_match() click to toggle source

A match against a translated sequence. (purl.obolibrary.org/obo/SO_0000181)

# File lib/biointerchange/so.rb, line 1407
def self.translated_nucleotide_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000181')
end
translates_to() click to toggle source

Inverse of translation _of. (purl.obolibrary.org/obo/so_2_5_2.obo#translates_to)

# File lib/biointerchange/so.rb, line 293
def self.translates_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#translates_to')
end
translation_of() click to toggle source

X is translation of Y if Y is translated by ribosome to create X. (purl.obolibrary.org/obo/so_2_5_2.obo#translation_of)

# File lib/biointerchange/so.rb, line 299
def self.translation_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#translation_of')
end
translation_regulatory_region() click to toggle source

A regulatory region that is involved in the control of the process of translation. (purl.obolibrary.org/obo/SO_0001680)

# File lib/biointerchange/so.rb, line 10291
def self.translation_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001680')
end
translational_frameshift() click to toggle source

The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different. (purl.obolibrary.org/obo/SO_0001210)

# File lib/biointerchange/so.rb, line 7531
def self.translational_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001210')
end
translational_product_function_variant() click to toggle source

A sequence variant that affects the functioning of a translational product with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001539)

# File lib/biointerchange/so.rb, line 9493
def self.translational_product_function_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001539')
end
translational_product_level_variant() click to toggle source

A functional variant that changes the translational product level with respect to a reference sequence. (purl.obolibrary.org/obo/SO_0001553)

# File lib/biointerchange/so.rb, line 9577
def self.translational_product_level_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001553')
end
translational_product_structure_variant() click to toggle source

A sequence variant within the transcript that changes the structure of the translational product. (purl.obolibrary.org/obo/SO_0001598)

# File lib/biointerchange/so.rb, line 9829
def self.translational_product_structure_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001598')
end
translationally_frameshifted() click to toggle source

Recoding by frameshifting a particular site. (purl.obolibrary.org/obo/SO_0000887)

# File lib/biointerchange/so.rb, line 5603
def self.translationally_frameshifted
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000887')
end
translationally_regulated() click to toggle source

An attribute describing a gene that is regulated as it is translated. (purl.obolibrary.org/obo/SO_0000131)

# File lib/biointerchange/so.rb, line 1103
def self.translationally_regulated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000131')
end
translationally_regulated_gene() click to toggle source

A gene that is translationally regulated. (purl.obolibrary.org/obo/SO_0000896)

# File lib/biointerchange/so.rb, line 5657
def self.translationally_regulated_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000896')
end
translocate() click to toggle source

To translocate a subsection of sequence. (purl.obolibrary.org/obo/SO_0000049)

# File lib/biointerchange/so.rb, line 603
def self.translocate
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000049')
end
translocation() click to toggle source

A region of nucleotide sequence that has translocated to a new position. (purl.obolibrary.org/obo/SO_0000199)

# File lib/biointerchange/so.rb, line 1515
def self.translocation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000199')
end
translocation_breakpoint() click to toggle source

The point within a chromosome where a translocation begins or ends. (purl.obolibrary.org/obo/SO_0001413)

# File lib/biointerchange/so.rb, line 8743
def self.translocation_breakpoint
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001413')
end
translocation_element() click to toggle source

A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations. (purl.obolibrary.org/obo/SO_0000686)

# File lib/biointerchange/so.rb, line 4439
def self.translocation_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000686')
end
translocaton_attribute() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001520)

# File lib/biointerchange/so.rb, line 9379
def self.translocaton_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001520')
end
transmembrane_helix() click to toggle source

A region that traverses the lipid bilayer and adopts a helical secondary structure. (purl.obolibrary.org/obo/SO_0001812)

# File lib/biointerchange/so.rb, line 11077
def self.transmembrane_helix
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001812')
end
transmembrane_polypeptide_region() click to toggle source

Polypeptide region traversing the lipid bilayer. (purl.obolibrary.org/obo/SO_0001077)

# File lib/biointerchange/so.rb, line 6733
def self.transmembrane_polypeptide_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001077')
end
transposable_element() click to toggle source

A transposon or insertion sequence. An element that can insert in a variety of DNA sequences. (purl.obolibrary.org/obo/SO_0000101)

# File lib/biointerchange/so.rb, line 923
def self.transposable_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000101')
end
transposable_element_CDS() click to toggle source

A CDS that is part of a transposable element. (purl.obolibrary.org/obo/SO_0001896)

# File lib/biointerchange/so.rb, line 11581
def self.transposable_element_CDS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001896')
end
transposable_element_attribute() click to toggle source

Added by KE Jan 2006 to capture the kinds of attributes of TEs (purl.obolibrary.org/obo/SO_0000780)

# File lib/biointerchange/so.rb, line 4997
def self.transposable_element_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000780')
end
transposable_element_flanking_region() click to toggle source

The region of sequence surrounding a transposable element. (purl.obolibrary.org/obo/SO_0000364)

# File lib/biointerchange/so.rb, line 2499
def self.transposable_element_flanking_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000364')
end
transposable_element_gene() click to toggle source

A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast. (purl.obolibrary.org/obo/SO_0000111)

# File lib/biointerchange/so.rb, line 983
def self.transposable_element_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000111')
end
transposable_element_insertion_site() click to toggle source

The junction in a genome where a transposable_element has inserted. (purl.obolibrary.org/obo/SO_0000368)

# File lib/biointerchange/so.rb, line 2523
def self.transposable_element_insertion_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000368')
end
transposable_element_pseudogene() click to toggle source

A pseudogene contained within a transposable element. (purl.obolibrary.org/obo/SO_0001897)

# File lib/biointerchange/so.rb, line 11587
def self.transposable_element_pseudogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001897')
end
transposon_fragment() click to toggle source

A portion of a transposon, interrupted by the insertion of another element. (purl.obolibrary.org/obo/SO_0001054)

# File lib/biointerchange/so.rb, line 6607
def self.transposon_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001054')
end
transversion() click to toggle source

Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa. (purl.obolibrary.org/obo/SO_1000017)

# File lib/biointerchange/so.rb, line 12545
def self.transversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000017')
end
trinucleotide_repeat_microsatellite_feature() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000291)

# File lib/biointerchange/so.rb, line 2067
def self.trinucleotide_repeat_microsatellite_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000291')
end
tryptophan() click to toggle source

A place holder for a cross product with chebi. (purl.obolibrary.org/obo/SO_0001440)

# File lib/biointerchange/so.rb, line 8899
def self.tryptophan
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001440')
end
tryptophan_tRNA_primary_transcript() click to toggle source

A primary transcript encoding tryptophanyl tRNA (SO:000271). (purl.obolibrary.org/obo/SO_0000228)

# File lib/biointerchange/so.rb, line 1689
def self.tryptophan_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000228')
end
tryptophanyl_tRNA() click to toggle source

A tRNA sequence that has a tryptophan anticodon, and a 3’ tryptophan binding region. (purl.obolibrary.org/obo/SO_0000271)

# File lib/biointerchange/so.rb, line 1947
def self.tryptophanyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000271')
end
twintron() click to toggle source

An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed. (purl.obolibrary.org/obo/SO_0000406)

# File lib/biointerchange/so.rb, line 2751
def self.twintron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000406')
end
two_methyladenosine() click to toggle source

2_methyladenosine is a modified adenosine. (purl.obolibrary.org/obo/SO_0001296)

# File lib/biointerchange/so.rb, line 8041
def self.two_methyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001296')
end
two_methylthio_N6_cis_hydroxyisopentenyl_adenosine() click to toggle source

2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine. (purl.obolibrary.org/obo/SO_0001303)

# File lib/biointerchange/so.rb, line 8083
def self.two_methylthio_N6_cis_hydroxyisopentenyl_adenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001303')
end
two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine() click to toggle source

2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine. (purl.obolibrary.org/obo/SO_0001309)

# File lib/biointerchange/so.rb, line 8119
def self.two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001309')
end
two_methylthio_N6_isopentenyladenosine() click to toggle source

2_methylthio_N6_isopentenyladenosine is a modified adenosine. (purl.obolibrary.org/obo/SO_0001301)

# File lib/biointerchange/so.rb, line 8071
def self.two_methylthio_N6_isopentenyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001301')
end
two_methylthio_N6_methyladenosine() click to toggle source

2_methylthio_N6_methyladenosine is a modified adenosine. (purl.obolibrary.org/obo/SO_0001299)

# File lib/biointerchange/so.rb, line 8059
def self.two_methylthio_N6_methyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001299')
end
two_methylthio_N6_threonyl_carbamoyladenosine() click to toggle source

2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine. (purl.obolibrary.org/obo/SO_0001306)

# File lib/biointerchange/so.rb, line 8101
def self.two_methylthio_N6_threonyl_carbamoyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001306')
end
two_prime_O_methyladenosine() click to toggle source

2prime_O_methyladenosine is a modified adenosine. (purl.obolibrary.org/obo/SO_0001298)

# File lib/biointerchange/so.rb, line 8053
def self.two_prime_O_methyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001298')
end
two_prime_O_methylcytidine() click to toggle source

2’-O-methylcytidine is a modified cytidine. (purl.obolibrary.org/obo/SO_0001283)

# File lib/biointerchange/so.rb, line 7963
def self.two_prime_O_methylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001283')
end
two_prime_O_methylguanosine() click to toggle source

2prime_O_methylguanosine is a modified guanosine base feature. (purl.obolibrary.org/obo/SO_0001327)

# File lib/biointerchange/so.rb, line 8227
def self.two_prime_O_methylguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001327')
end
two_prime_O_methylinosine() click to toggle source

2’-O-methylinosine is a modified inosine. (purl.obolibrary.org/obo/SO_0001280)

# File lib/biointerchange/so.rb, line 7945
def self.two_prime_O_methylinosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001280')
end
two_prime_O_methylpseudouridine() click to toggle source

2prime_O_methylpseudouridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001348)

# File lib/biointerchange/so.rb, line 8353
def self.two_prime_O_methylpseudouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001348')
end
two_prime_O_methyluridine() click to toggle source

2prime_O_methyluridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001345)

# File lib/biointerchange/so.rb, line 8335
def self.two_prime_O_methyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001345')
end
two_prime_O_ribosyladenosine_phosphate() click to toggle source

2prime_O_ribosyladenosine_phosphate is a modified adenosine. (purl.obolibrary.org/obo/SO_0001310)

# File lib/biointerchange/so.rb, line 8125
def self.two_prime_O_ribosyladenosine_phosphate
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001310')
end
two_prime_O_ribosylguanosine_phosphate() click to toggle source

2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature. (purl.obolibrary.org/obo/SO_0001331)

# File lib/biointerchange/so.rb, line 8251
def self.two_prime_O_ribosylguanosine_phosphate
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001331')
end
two_thio_two_prime_O_methyluridine() click to toggle source

2_thio_2prime_O_methyluridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001352)

# File lib/biointerchange/so.rb, line 8377
def self.two_thio_two_prime_O_methyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001352')
end
two_thiocytidine() click to toggle source

2-thiocytidine is a modified cytidine. (purl.obolibrary.org/obo/SO_0001284)

# File lib/biointerchange/so.rb, line 7969
def self.two_thiocytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001284')
end
two_thiouridine() click to toggle source

2_thiouridine is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001349)

# File lib/biointerchange/so.rb, line 8359
def self.two_thiouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001349')
end
type_II_enzyme_restriction_site() click to toggle source

The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site. (purl.obolibrary.org/obo/SO_0000304)

# File lib/biointerchange/so.rb, line 2145
def self.type_II_enzyme_restriction_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000304')
end
type_I_enzyme_restriction_site() click to toggle source

The recognition site is bipartite and interrupted. (purl.obolibrary.org/obo/SO_0000284)

# File lib/biointerchange/so.rb, line 2025
def self.type_I_enzyme_restriction_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000284')
end
tyrosine() click to toggle source

A place holder for a cross product with chebi. (purl.obolibrary.org/obo/SO_0001446)

# File lib/biointerchange/so.rb, line 8935
def self.tyrosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001446')
end
tyrosine_tRNA_primary_transcript() click to toggle source

A primary transcript encoding tyrosyl tRNA (SO:000272). (purl.obolibrary.org/obo/SO_0000229)

# File lib/biointerchange/so.rb, line 1695
def self.tyrosine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000229')
end
tyrosyl_tRNA() click to toggle source

A tRNA sequence that has a tyrosine anticodon, and a 3’ tyrosine binding region. (purl.obolibrary.org/obo/SO_0000272)

# File lib/biointerchange/so.rb, line 1953
def self.tyrosyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000272')
end
ultracontig() click to toggle source

An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers. (purl.obolibrary.org/obo/SO_0000719)

# File lib/biointerchange/so.rb, line 4637
def self.ultracontig
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000719')
end
unassigned_supercontig() click to toggle source

A supercontig that is not been assigned to any ultracontig during a genome assembly project. (purl.obolibrary.org/obo/SO_0001875)

# File lib/biointerchange/so.rb, line 11455
def self.unassigned_supercontig
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001875')
end
uncharacterised_chromosomal_mutation() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_1000170)

# File lib/biointerchange/so.rb, line 13313
def self.uncharacterised_chromosomal_mutation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000170')
end
undermodified_hydroxywybutosine() click to toggle source

Undermodified_hydroxywybutosine is a modified guanosine base feature. (purl.obolibrary.org/obo/SO_0001335)

# File lib/biointerchange/so.rb, line 8275
def self.undermodified_hydroxywybutosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001335')
end
unedited_region() click to toggle source

The region of an edited transcript that will not be edited. (purl.obolibrary.org/obo/SO_0000607)

# File lib/biointerchange/so.rb, line 3965
def self.unedited_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000607')
end
unequally_crossed_over() click to toggle source

An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination. (purl.obolibrary.org/obo/SO_0000901)

# File lib/biointerchange/so.rb, line 5687
def self.unequally_crossed_over
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000901')
end
unigene_cluster() click to toggle source

A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene. (purl.obolibrary.org/obo/SO_0001458)

# File lib/biointerchange/so.rb, line 9007
def self.unigene_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001458')
end
uninverted_insertional_duplication() click to toggle source

An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments. (purl.obolibrary.org/obo/SO_1000152)

# File lib/biointerchange/so.rb, line 13247
def self.uninverted_insertional_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000152')
end
uninverted_interchromosomal_transposition() click to toggle source

An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments. (purl.obolibrary.org/obo/SO_1000157)

# File lib/biointerchange/so.rb, line 13277
def self.uninverted_interchromosomal_transposition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000157')
end
uninverted_intrachromosomal_transposition() click to toggle source

An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments. (purl.obolibrary.org/obo/SO_1000159)

# File lib/biointerchange/so.rb, line 13289
def self.uninverted_intrachromosomal_transposition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000159')
end
unique_variant() click to toggle source

A physical quality which inheres to the variant by virtue of the number instances of the variant within a population. (purl.obolibrary.org/obo/SO_0001764)

# File lib/biointerchange/so.rb, line 10795
def self.unique_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001764')
end
unitary_pseudogene() click to toggle source

A pseudogene, deactivated from original state by mutation, fixed in a population. (purl.obolibrary.org/obo/SO_0001759)

# File lib/biointerchange/so.rb, line 10765
def self.unitary_pseudogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001759')
end
unoriented_insertional_duplication() click to toggle source

An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded. (purl.obolibrary.org/obo/SO_1000160)

# File lib/biointerchange/so.rb, line 13295
def self.unoriented_insertional_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000160')
end
unoriented_interchromosomal_transposition() click to toggle source

An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded. (purl.obolibrary.org/obo/SO_1000161)

# File lib/biointerchange/so.rb, line 13301
def self.unoriented_interchromosomal_transposition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000161')
end
unoriented_intrachromosomal_transposition() click to toggle source

An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded. (purl.obolibrary.org/obo/SO_1000162)

# File lib/biointerchange/so.rb, line 13307
def self.unoriented_intrachromosomal_transposition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000162')
end
untranslated_region_polycistronic_mRNA() click to toggle source

The untranslated sequence separating the ‘cistrons’ of multicistronic mRNA. (purl.obolibrary.org/obo/SO_0000242)

# File lib/biointerchange/so.rb, line 1773
def self.untranslated_region_polycistronic_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000242')
end
upstream_AUG_codon() click to toggle source

A start codon upstream of the ORF. (purl.obolibrary.org/obo/SO_0000630)

# File lib/biointerchange/so.rb, line 4103
def self.upstream_AUG_codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000630')
end
upstream_gene_variant() click to toggle source

A sequence variant located 5’ of a gene. (purl.obolibrary.org/obo/SO_0001631)

# File lib/biointerchange/so.rb, line 10021
def self.upstream_gene_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001631')
end
upstream_transcript_variant() click to toggle source

A feature variant, where the alteration occurs upstream of the transcript TSS. (purl.obolibrary.org/obo/SO_0001986)

# File lib/biointerchange/so.rb, line 12119
def self.upstream_transcript_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001986')
end
uridine_five_oxyacetic_acid() click to toggle source

Uridine_5_oxyacetic_acid is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001356)

# File lib/biointerchange/so.rb, line 8401
def self.uridine_five_oxyacetic_acid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001356')
end
uridine_five_oxyacetic_acid_methyl_ester() click to toggle source

Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature. (purl.obolibrary.org/obo/SO_0001357)

# File lib/biointerchange/so.rb, line 8407
def self.uridine_five_oxyacetic_acid_methyl_ester
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001357')
end
vacuolar_sorting_signal() click to toggle source

A polypeptide region that targets a polypeptide to the vacuole. (purl.obolibrary.org/obo/SO_0001813)

# File lib/biointerchange/so.rb, line 11083
def self.vacuolar_sorting_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001813')
end
validated() click to toggle source

An attribute to describe a feature that has been proven. (purl.obolibrary.org/obo/SO_0000789)

# File lib/biointerchange/so.rb, line 5051
def self.validated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000789')
end
validated_cDNA_clone() click to toggle source

A cDNA clone that has been validated. (purl.obolibrary.org/obo/SO_0000808)

# File lib/biointerchange/so.rb, line 5141
def self.validated_cDNA_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000808')
end
valine() click to toggle source

A place holder for a cross product with chebi. (purl.obolibrary.org/obo/SO_0001436)

# File lib/biointerchange/so.rb, line 8875
def self.valine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001436')
end
valine_tRNA_primary_transcript() click to toggle source

A primary transcript encoding valyl tRNA (SO:000273). (purl.obolibrary.org/obo/SO_0000230)

# File lib/biointerchange/so.rb, line 1701
def self.valine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000230')
end
valyl_tRNA() click to toggle source

A tRNA sequence that has a valine anticodon, and a 3’ valine binding region. (purl.obolibrary.org/obo/SO_0000273)

# File lib/biointerchange/so.rb, line 1959
def self.valyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000273')
end
variant_collection() click to toggle source

A collection of one or more sequences of an individual. (purl.obolibrary.org/obo/SO_0001507)

# File lib/biointerchange/so.rb, line 9301
def self.variant_collection
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001507')
end
variant_frequency() click to toggle source

A physical quality which inheres to the variant by virtue of the number instances of the variant within a population. (purl.obolibrary.org/obo/SO_0001763)

# File lib/biointerchange/so.rb, line 10789
def self.variant_frequency
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001763')
end
variant_genome() click to toggle source

A collection of sequences (often chromosomes) of an individual. (purl.obolibrary.org/obo/SO_0001506)

# File lib/biointerchange/so.rb, line 9295
def self.variant_genome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001506')
end
variant_of() click to toggle source

Either:

A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.
(http://purl.obolibrary.org/obo/so_2_5_2.obo#variant_of)

Or:

A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.
(http://purl.obolibrary.org/obo/anonymous#variant_of)
# File lib/biointerchange/so.rb, line 309
def self.variant_of
  return [ RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#variant_of'), RDF::URI.new('http://purl.obolibrary.org/obo/anonymous#variant_of') ]
end
variant_origin() click to toggle source

A quality inhering in a variant by virtue of its origin. (purl.obolibrary.org/obo/SO_0001762)

# File lib/biointerchange/so.rb, line 10783
def self.variant_origin
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001762')
end
variant_phenotype() click to toggle source

A quality inhering in a variant by virtue of its phenotype. (purl.obolibrary.org/obo/SO_0001769)

# File lib/biointerchange/so.rb, line 10825
def self.variant_phenotype
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001769')
end
variant_quality() click to toggle source

A dependent entity that inheres in a bearer, a sequence variant. (purl.obolibrary.org/obo/SO_0001761)

# File lib/biointerchange/so.rb, line 10777
def self.variant_quality
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001761')
end
vault_RNA() click to toggle source

A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance. (purl.obolibrary.org/obo/SO_0000404)

# File lib/biointerchange/so.rb, line 2739
def self.vault_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000404')
end
vector_replicon() click to toggle source

A replicon that has been modified to act as a vector for foreign sequence. (purl.obolibrary.org/obo/SO_0000440)

# File lib/biointerchange/so.rb, line 2959
def self.vector_replicon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000440')
end
vertebrate_immune_system_feature() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000937)

# File lib/biointerchange/so.rb, line 5903
def self.vertebrate_immune_system_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000937')
end
vertebrate_immune_system_gene_recombination_feature() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000301)

# File lib/biointerchange/so.rb, line 2127
def self.vertebrate_immune_system_gene_recombination_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000301')
end
vertebrate_immune_system_gene_recombination_signal_feature() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000939)

# File lib/biointerchange/so.rb, line 5915
def self.vertebrate_immune_system_gene_recombination_signal_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000939')
end
vertebrate_immune_system_gene_recombination_spacer() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000563)

# File lib/biointerchange/so.rb, line 3701
def self.vertebrate_immune_system_gene_recombination_spacer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000563')
end
vertebrate_immunoglobulin_T_cell_receptor_gene_cluster() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000482)

# File lib/biointerchange/so.rb, line 3211
def self.vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000482')
end
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000938)

# File lib/biointerchange/so.rb, line 5909
def self.vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000938')
end
vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000936)

# File lib/biointerchange/so.rb, line 5897
def self.vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000936')
end
vertebrate_immunoglobulin_T_cell_receptor_segment() click to toggle source

I am using the term segment instead of gene here to avoid confusion with the region ‘gene’. (purl.obolibrary.org/obo/SO_0000460)

# File lib/biointerchange/so.rb, line 3079
def self.vertebrate_immunoglobulin_T_cell_receptor_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000460')
end
viral_sequence() click to toggle source

The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell. (purl.obolibrary.org/obo/SO_0001041)

# File lib/biointerchange/so.rb, line 6521
def self.viral_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001041')
end
virtual_sequence() click to toggle source

A continuous piece of sequence similar to the ‘virtual contig’ concept of the Ensembl database. (purl.obolibrary.org/obo/SO_0000499)

# File lib/biointerchange/so.rb, line 3313
def self.virtual_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000499')
end
whole_genome_sequence_status() click to toggle source

The status of whole genome sequence. (purl.obolibrary.org/obo/SO_0001499)

# File lib/biointerchange/so.rb, line 9253
def self.whole_genome_sequence_status
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001499')
end
wild_type() click to toggle source

An attribute describing sequence with the genotype found in nature and/or standard laboratory stock. (purl.obolibrary.org/obo/SO_0000817)

# File lib/biointerchange/so.rb, line 5195
def self.wild_type
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000817')
end
wild_type_rescue_gene() click to toggle source

A gene that rescues. (purl.obolibrary.org/obo/SO_0000818)

# File lib/biointerchange/so.rb, line 5201
def self.wild_type_rescue_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000818')
end
with_parent(uris, parent) click to toggle source

Returns only those URIs that fall under a designated parent URI.

uris

Set of URIs that are tested whether they have the given parent URI.

parent

Parent URI.

# File lib/biointerchange/so.rb, line 20555
def self.with_parent(uris, parent)
  return uris.select { |uri| has_parent?(uri, parent) }
end
wobble_base_pair() click to toggle source

A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C. (purl.obolibrary.org/obo/SO_0001015)

# File lib/biointerchange/so.rb, line 6365
def self.wobble_base_pair
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001015')
end
wybutosine() click to toggle source

Wybutosine is a modified guanosine base feature. (purl.obolibrary.org/obo/SO_0001332)

# File lib/biointerchange/so.rb, line 8257
def self.wybutosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001332')
end
wyosine() click to toggle source

Wyosine is a modified guanosine base feature. (purl.obolibrary.org/obo/SO_0001336)

# File lib/biointerchange/so.rb, line 8281
def self.wyosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001336')
end
zinc_finger_binding_site() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0001971)

# File lib/biointerchange/so.rb, line 12035
def self.zinc_finger_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001971')
end
zinc_repressed_element() click to toggle source

A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc. (purl.obolibrary.org/obo/SO_0002006)

# File lib/biointerchange/so.rb, line 12239
def self.zinc_repressed_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002006')
end