class BioInterchange::SOFA

Public Class Methods

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/sofa.rb, line 1071
def self.ARS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000436')
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/sofa.rb, line 765
def self.CDS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000316')
end
CDS_region() click to toggle source

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

# File lib/biointerchange/sofa.rb, line 1587
def self.CDS_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000851')
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/sofa.rb, line 1491
def self.CRM
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000727')
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/sofa.rb, line 1197
def self.C_D_box_snoRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000593')
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/sofa.rb, line 747
def self.CpG_island
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000307')
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/sofa.rb, line 867
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/sofa.rb, line 1353
def self.EST_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000668')
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/sofa.rb, line 669
def self.ORF
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000236')
end
PCR_product() click to toggle source

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

# File lib/biointerchange/sofa.rb, line 339
def self.PCR_product
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000006')
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/sofa.rb, line 591
def self.RFLP_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000193')
end
RNA_motif() click to toggle source

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

# File lib/biointerchange/sofa.rb, line 1461
def self.RNA_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000715')
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/sofa.rb, line 837
def self.RNAi_reagent
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000337')
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/sofa.rb, line 939
def self.RNase_MRP_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000385')
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/sofa.rb, line 945
def self.RNase_P_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000386')
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/sofa.rb, line 795
def self.SAGE_tag
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000326')
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/sofa.rb, line 1389
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/sofa.rb, line 1725
def self.SNV
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001483')
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/sofa.rb, line 1191
def self.SRP_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000590')
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/sofa.rb, line 807
def self.STS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000331')
end
Sequence_Ontology() click to toggle source

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

# File lib/biointerchange/sofa.rb, line 315
def self.Sequence_Ontology
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000000')
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/sofa.rb, line 663
def self.TF_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000235')
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/sofa.rb, line 759
def self.TSS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000315')
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/sofa.rb, line 999
def self.U11_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000398')
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/sofa.rb, line 1005
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/sofa.rb, line 1011
def self.U14_snoRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000403')
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/sofa.rb, line 957
def self.U1_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000391')
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/sofa.rb, line 963
def self.U2_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000392')
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/sofa.rb, line 969
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/sofa.rb, line 975
def self.U4atac_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000394')
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/sofa.rb, line 981
def self.U5_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000395')
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/sofa.rb, line 987
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/sofa.rb, line 993
def self.U6atac_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000397')
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/sofa.rb, line 627
def self.UTR
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000203')
end
UTR_region() click to toggle source

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

# File lib/biointerchange/sofa.rb, line 1563
def self.UTR_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000837')
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/sofa.rb, line 1023
def self.Y_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000405')
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/SOFA_2_5_2.obo#adjacent_to)

# File lib/biointerchange/sofa.rb, line 17
def self.adjacent_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#adjacent_to')
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/sofa.rb, line 1275
def self.antisense_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000644')
end
antisense_primary_transcript() click to toggle source

The reverse complement of the primary transcript. (purl.obolibrary.org/obo/SO_0000645)

# File lib/biointerchange/sofa.rb, line 1281
def self.antisense_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000645')
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/sofa.rb, line 1683
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/sofa.rb, line 465
def self.assembly_component
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000143')
end
associated_with() click to toggle source

This relationship is vague and up for discussion. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#associated_with)

# File lib/biointerchange/sofa.rb, line 23
def self.associated_with
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#associated_with')
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/sofa.rb, line 453
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/sofa.rb, line 1185
def self.autocatalytically_spliced_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000588')
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/sofa.rb, line 1677
def self.base
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001236')
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/sofa.rb, line 1035
def self.binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000409')
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/sofa.rb, line 1701
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/sofa.rb, line 1689
def self.biomaterial_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001409')
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/sofa.rb, line 1227
def self.branch_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000611')
end
cDNA_match() click to toggle source

A match against cDNA sequence. (purl.obolibrary.org/obo/SO_0000689)

# File lib/biointerchange/sofa.rb, line 1383
def self.cDNA_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000689')
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/sofa.rb, line 1173
def self.cap
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000581')
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/sofa.rb, line 1167
def self.centromere
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000577')
end
chromosomal_structural_element() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000628)

# File lib/biointerchange/sofa.rb, line 1263
def self.chromosomal_structural_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000628')
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/sofa.rb, line 843
def self.chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000340')
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/sofa.rb, line 849
def self.chromosome_band
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000341')
end
chromosome_part() click to toggle source

A region of a chromosome. (purl.obolibrary.org/obo/SO_0000830)

# File lib/biointerchange/sofa.rb, line 1527
def self.chromosome_part
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000830')
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/sofa.rb, line 1713
def self.cis_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001419')
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/sofa.rb, line 1785
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/sofa.rb, line 729
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/sofa.rb, line 495
def self.clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000151')
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/sofa.rb, line 1509
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/sofa.rb, line 399
def self.clone_insert_end
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000103')
end
clone_insert_start() click to toggle source

The start of the clone insert. (purl.obolibrary.org/obo/SO_0000179)

# File lib/biointerchange/sofa.rb, line 555
def self.clone_insert_start
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000179')
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/sofa.rb, line 813
def self.coding_conserved_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000332')
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/sofa.rb, line 597
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/sofa.rb, line 1665
def self.coding_region_of_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001215')
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/sofa.rb, line 891
def self.codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000360')
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/SOFA_2_5_2.obo#complete_evidence_for_feature)

# File lib/biointerchange/sofa.rb, line 29
def self.complete_evidence_for_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#complete_evidence_for_feature')
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/sofa.rb, line 1797
def self.complex_substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000005')
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/SOFA_2_5_2.obo#connects_on)

# File lib/biointerchange/sofa.rb, line 35
def self.connects_on
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#connects_on')
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/sofa.rb, line 801
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/SOFA_2_5_2.obo#contained_by)

# File lib/biointerchange/sofa.rb, line 41
def self.contained_by
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#contained_by')
end
contains() click to toggle source

The inverse of contained_by. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#contains)

# File lib/biointerchange/sofa.rb, line 47
def self.contains
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_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/sofa.rb, line 483
def self.contig
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000149')
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/sofa.rb, line 1617
def self.copy_number_variation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001019')
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/sofa.rb, line 543
def self.cross_genome_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000177')
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/sofa.rb, line 1821
def self.databank_entry
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_2000061')
end
decayed_exon() click to toggle source

A non-functional descendant of an exon. (purl.obolibrary.org/obo/SO_0000464)

# File lib/biointerchange/sofa.rb, line 1101
def self.decayed_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000464')
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/sofa.rb, line 501
def self.deletion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000159')
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/sofa.rb, line 1371
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/SOFA_2_5_2.obo#derives_from)

# File lib/biointerchange/sofa.rb, line 53
def self.derives_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#derives_from')
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/sofa.rb, line 753
def self.direct_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000314')
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/SOFA_2_5_2.obo#disconnected_from)

# File lib/biointerchange/sofa.rb, line 59
def self.disconnected_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#disconnected_from')
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/sofa.rb, line 1335
def self.dispersed_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000658')
end
ds_oligo() click to toggle source

A double stranded oligonucleotide. (purl.obolibrary.org/obo/SO_0000442)

# File lib/biointerchange/sofa.rb, line 1083
def self.ds_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000442')
end
edited_from() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#edited_from)

# File lib/biointerchange/sofa.rb, line 65
def self.edited_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#edited_from')
end
edited_to() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#edited_to)

# File lib/biointerchange/sofa.rb, line 71
def self.edited_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#edited_to')
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/sofa.rb, line 531
def self.enhancer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000165')
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/sofa.rb, line 915
def self.enzymatic_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000372')
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/sofa.rb, line 1761
def self.epigenetically_modified_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001720')
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/SOFA_2_5_2.obo#evidence_for_feature)

# File lib/biointerchange/sofa.rb, line 77
def self.evidence_for_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#evidence_for_feature')
end
exemplar_of() click to toggle source

X is exemplar of Y if X is the best evidence for Y. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#exemplar_of)

# File lib/biointerchange/sofa.rb, line 83
def self.exemplar_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_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/sofa.rb, line 471
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/sofa.rb, line 819
def self.exon_junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000333')
end
exon_region() click to toggle source

A region of an exon. (purl.obolibrary.org/obo/SO_0000852)

# File lib/biointerchange/sofa.rb, line 1593
def self.exon_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000852')
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/sofa.rb, line 1695
def self.experimental_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001410')
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/sofa.rb, line 1431
def self.experimental_result_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000703')
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/sofa.rb, line 393
def self.expressed_sequence_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000102')
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/SOFA_2_5_2.obo#finished_by)

# File lib/biointerchange/sofa.rb, line 89
def self.finished_by
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#finished_by')
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/SOFA_2_5_2.obo#finishes)

# File lib/biointerchange/sofa.rb, line 95
def self.finishes
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#finishes')
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/sofa.rb, line 633
def self.five_prime_UTR
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000204')
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/sofa.rb, line 519
def self.five_prime_cis_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000163')
end
five_prime_coding_exon() click to toggle source

The 5' most coding exon. (purl.obolibrary.org/obo/SO_0000200)

# File lib/biointerchange/sofa.rb, line 621
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/sofa.rb, line 603
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/sofa.rb, line 1137
def self.five_prime_coding_exon_noncoding_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000486')
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/sofa.rb, line 675
def self.flanking_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000239')
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/SOFA_2_5_2.obo#gained)

# File lib/biointerchange/sofa.rb, line 101
def self.gained
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#gained')
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/sofa.rb, line 1497
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/sofa.rb, line 1437
def self.gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000704')
end
gene_component_region() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000842)

# File lib/biointerchange/sofa.rb, line 1581
def self.gene_component_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000842')
end
gene_group() click to toggle source

A collection of related genes. (purl.obolibrary.org/obo/SO_0005855)

# File lib/biointerchange/sofa.rb, line 1779
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/sofa.rb, line 1503
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/sofa.rb, line 1533
def self.gene_member_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000831')
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/sofa.rb, line 369
def self.gene_part
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000050')
end
genome_of() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#genome_of)

# File lib/biointerchange/sofa.rb, line 107
def self.genome_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#genome_of')
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/sofa.rb, line 1377
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/sofa.rb, line 1107
def self.golden_path_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000468')
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/sofa.rb, line 1209
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/sofa.rb, line 1179
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/sofa.rb, line 1203
def self.guide_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000602')
end
guided_by() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#guided_by)

# File lib/biointerchange/sofa.rb, line 113
def self.guided_by
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#guided_by')
end
guides() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#guides)

# File lib/biointerchange/sofa.rb, line 119
def self.guides
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_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/sofa.rb, line 933
def self.hammerhead_ribozyme
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000380')
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/SOFA_2_5_2.obo#has_integral_part)

# File lib/biointerchange/sofa.rb, line 125
def self.has_integral_part
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_integral_part')
end
has_origin() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_origin)

# File lib/biointerchange/sofa.rb, line 131
def self.has_origin
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_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/sofa.rb, line 2777
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/SOFA_2_5_2.obo#has_part)

# File lib/biointerchange/sofa.rb, line 137
def self.has_part
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_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/SOFA_2_5_2.obo#has_quality)

# File lib/biointerchange/sofa.rb, line 143
def self.has_quality
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_quality')
end
homologous_to() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#homologous_to)

# File lib/biointerchange/sofa.rb, line 149
def self.homologous_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#homologous_to')
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/sofa.rb, line 1653
def self.immature_peptide_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001063')
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/sofa.rb, line 1347
def self.insertion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000667')
end
insertion_site() click to toggle source

The junction where an insertion occurred. (purl.obolibrary.org/obo/SO_0000366)

# File lib/biointerchange/sofa.rb, line 897
def self.insertion_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000366')
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/sofa.rb, line 1257
def self.insulator
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000627')
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/SOFA_2_5_2.obo#integral_part_of)

# File lib/biointerchange/sofa.rb, line 155
def self.integral_part_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#integral_part_of')
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/sofa.rb, line 1629
def self.integrated_mobile_genetic_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001039')
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/sofa.rb, line 1215
def self.intergenic_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000605')
end
interior_coding_exon() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000004)

# File lib/biointerchange/sofa.rb, line 327
def self.interior_coding_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000004')
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/sofa.rb, line 585
def self.intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000188')
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/sofa.rb, line 1809
def self.inversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000036')
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/sofa.rb, line 717
def self.inverted_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000294')
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/sofa.rb, line 1995
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_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_0000013') 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_0000050') 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_0000059') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000101') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000102') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000103') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000104') then
    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
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000112') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000113') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000114') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000120') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000139') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000140') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000141') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000143') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000147') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000148') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000149') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000150') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000151') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000159') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000161') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000162') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000163') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000164') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000165') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000167') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000177') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000178') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000179') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000181') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000183') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000185') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000187') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000188') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000193') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000195') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000196') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000197') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000198') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000200') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000203') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000204') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000205') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000209') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000233') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000234') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000235') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000236') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000239') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000252') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000253') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000274') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000275') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000276') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000289') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000294') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000296') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000303') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000305') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000306') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000307') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000314') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000315') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000316') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000318') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000319') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000324') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000325') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000326') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000330') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000331') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000332') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000333') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000334') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000336') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000337') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000340') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000341') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000343') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000344') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000345') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000347') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000349') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000353') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000360') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000366') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000368') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000370') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000372') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000374') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000375') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000380') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000385') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000386') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000390') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000391') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000392') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000393') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000394') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000395') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000396') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000397') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000398') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000399') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000403') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000404') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000405') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000407') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000409') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000410') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000412') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000413') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000418') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000419') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000436') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000441') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000442') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000454') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000462') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000464') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000468') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000472') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000474') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000483') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000484') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000486') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000499') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000502') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000551') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000553') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000577') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000581') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000587') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000588') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000590') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000593') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000602') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000603') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000605') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000610') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000611') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000612') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000616') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000624') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000625') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000627') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000628') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000643') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000644') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000645') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000646') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000649') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000650') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000651') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000652') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000653') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000655') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000657') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000658') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000662') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000667') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000668') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000673') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000684') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000687') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000688') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000689') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000694') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000695') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000696') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000699') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000700') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000701') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000702') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000703') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000704') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000705') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000706') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000714') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000715') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000717') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000719') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000724') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000725') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000727') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000730') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000752') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000753') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000777') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000778') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000830') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000831') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000833') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000834') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000835') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000836') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000837') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000839') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000841') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000842') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000851') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000852') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001000') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001001') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001002') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001019') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001037') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001039') 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_0001059') 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_0001214') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001215') 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_0001248') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001409') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001410') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001411') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001412') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001419') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001420') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001483') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001527') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001647') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001654') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001679') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001683') 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_0001790') then
    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_0005855') 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_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_1000036') 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_2000061') 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/SOFA_2_5_2.obo#is_consecutive_sequence_of)

# File lib/biointerchange/sofa.rb, line 161
def self.is_consecutive_sequence_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_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/sofa.rb, line 1988
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/sofa.rb, line 2758
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/sofa.rb, line 1828
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/SOFA_2_5_2.obo#adjacent_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#associated_with') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#complete_evidence_for_feature') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#connects_on') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#contained_by') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#contains') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#derives_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#disconnected_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#edited_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#edited_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#evidence_for_feature') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#exemplar_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#finished_by') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#finishes') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#gained') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#genome_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#guided_by') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#guides') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_integral_part') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_origin') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_part') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_quality') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#homologous_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#integral_part_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#is_consecutive_sequence_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#lost') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#maximally_overlaps') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#member_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#non_functional_homolog_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#orthologous_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#overlaps') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#paralogous_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#part_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#partial_evidence_for_feature') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#position_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#processed_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#processed_into') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#recombined_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#recombined_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#sequence_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#similar_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#started_by') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#starts') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#trans_spliced_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#trans_spliced_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#transcribed_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#transcribed_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#translates_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#translation_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#variant_of') then
    return true
  end
  return false
end
junction() click to toggle source

A sequence_feature with an extent of zero. (purl.obolibrary.org/obo/SO_0000699)

# File lib/biointerchange/sofa.rb, line 1407
def self.junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000699')
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/sofa.rb, line 1737
def self.kozak_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001647')
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/sofa.rb, line 1305
def self.large_subunit_rRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000651')
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/SOFA_2_5_2.obo#lost)

# File lib/biointerchange/sofa.rb, line 167
def self.lost
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#lost')
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/sofa.rb, line 657
def self.mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000234')
end
mRNA_region() click to toggle source

A region of an mRNA. (purl.obolibrary.org/obo/SO_0000836)

# File lib/biointerchange/sofa.rb, line 1557
def self.mRNA_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000836')
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/sofa.rb, line 855
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/sofa.rb, line 363
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/sofa.rb, line 357
def self.match_set
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000038')
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/sofa.rb, line 1065
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/sofa.rb, line 651
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/sofa.rb, line 1545
def self.mature_transcript_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000834')
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/SOFA_2_5_2.obo#maximally_overlaps)

# File lib/biointerchange/sofa.rb, line 173
def self.maximally_overlaps
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_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/SOFA_2_5_2.obo#member_of)

# File lib/biointerchange/sofa.rb, line 179
def self.member_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#member_of')
end
methylated_DNA_base_feature() click to toggle source

A nucleotide modified by methylation. (purl.obolibrary.org/obo/SO_0000306)

# File lib/biointerchange/sofa.rb, line 741
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/sofa.rb, line 507
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/sofa.rb, line 435
def self.methylated_cytosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000114')
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/sofa.rb, line 705
def self.miRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000276')
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/sofa.rb, line 711
def self.microsatellite
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000289')
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/sofa.rb, line 1269
def self.minisatellite
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000643')
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/sofa.rb, line 1623
def self.mobile_genetic_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001037')
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/sofa.rb, line 735
def self.modified_DNA_base
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000305')
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/sofa.rb, line 1323
def self.ncRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000655')
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/sofa.rb, line 825
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/sofa.rb, line 1125
def self.nc_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000483')
end
non_functional_homolog_of() click to toggle source

A relationship between a pseudogenic feature and its functional ancestor. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#non_functional_homolog_of)

# File lib/biointerchange/sofa.rb, line 185
def self.non_functional_homolog_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#non_functional_homolog_of')
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/sofa.rb, line 567
def self.non_transcribed_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000183')
end
noncoding_exon() click to toggle source

An exon that does not contain any codons. (purl.obolibrary.org/obo/SO_0000198)

# File lib/biointerchange/sofa.rb, line 615
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/sofa.rb, line 1659
def self.noncoding_region_of_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001214')
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/sofa.rb, line 381
def self.nuclease_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000059')
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/sofa.rb, line 1365
def self.nuclease_sensitive_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000684')
end
nucleotide_match() click to toggle source

A match against a nucleotide sequence. (purl.obolibrary.org/obo/SO_0000347)

# File lib/biointerchange/sofa.rb, line 873
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/sofa.rb, line 1455
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/sofa.rb, line 1743
def self.nucleotide_to_protein_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001654')
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/sofa.rb, line 1401
def self.oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000696')
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/sofa.rb, line 375
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/sofa.rb, line 549
def self.operon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000178')
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/sofa.rb, line 1479
def self.oriT
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000724')
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/sofa.rb, line 723
def self.origin_of_replication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000296')
end
orthologous_to() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#orthologous_to)

# File lib/biointerchange/sofa.rb, line 191
def self.orthologous_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#orthologous_to')
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/SOFA_2_5_2.obo#overlaps)

# File lib/biointerchange/sofa.rb, line 197
def self.overlaps
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#overlaps')
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/sofa.rb, line 1767
def self.paired_end_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001790')
end
paralogous_to() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#paralogous_to)

# File lib/biointerchange/sofa.rb, line 203
def self.paralogous_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_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/SOFA_2_5_2.obo#part_of)
# File lib/biointerchange/sofa.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/SOFA_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/SOFA_2_5_2.obo#partial_evidence_for_feature)

# File lib/biointerchange/sofa.rb, line 209
def self.partial_evidence_for_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#partial_evidence_for_feature')
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/sofa.rb, line 1731
def self.peptide_localization_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001527')
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/sofa.rb, line 1803
def self.point_mutation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000008')
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/sofa.rb, line 1221
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/sofa.rb, line 1155
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/sofa.rb, line 1161
def self.polyA_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000553')
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/sofa.rb, line 405
def self.polypeptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000104')
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/sofa.rb, line 1569
def self.polypeptide_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000839')
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/sofa.rb, line 1233
def self.polypyrimidine_tract
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000612')
end
position_of() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#position_of)

# File lib/biointerchange/sofa.rb, line 215
def self.position_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#position_of')
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/sofa.rb, line 1425
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/sofa.rb, line 1419
def self.possible_base_call_error
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000701')
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/sofa.rb, line 573
def self.primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000185')
end
primary_transcript_region() click to toggle source

A part of a primary transcript. (purl.obolibrary.org/obo/SO_0000835)

# File lib/biointerchange/sofa.rb, line 1551
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/sofa.rb, line 423
def self.primer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000112')
end
processed_from() click to toggle source

Inverse of processed_into. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#processed_from)

# File lib/biointerchange/sofa.rb, line 221
def self.processed_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_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/SOFA_2_5_2.obo#processed_into)

# File lib/biointerchange/sofa.rb, line 227
def self.processed_into
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#processed_into')
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/sofa.rb, line 537
def self.promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000167')
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/sofa.rb, line 1041
def self.protein_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000410')
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/sofa.rb, line 441
def self.protein_coding_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000120')
end
protein_match() click to toggle source

A match against a protein sequence. (purl.obolibrary.org/obo/SO_0000349)

# File lib/biointerchange/sofa.rb, line 879
def self.protein_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000349')
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/sofa.rb, line 429
def self.proviral_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000113')
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/sofa.rb, line 831
def self.pseudogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000336')
end
pseudogenic_rRNA() click to toggle source

A non functional descendent of an rRNA. (purl.obolibrary.org/obo/SO_0000777)

# File lib/biointerchange/sofa.rb, line 1515
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/sofa.rb, line 1095
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/sofa.rb, line 1521
def self.pseudogenic_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000778')
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/sofa.rb, line 681
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/sofa.rb, line 1599
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/sofa.rb, line 1029
def self.rRNA_18S
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000407')
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/sofa.rb, line 1605
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/sofa.rb, line 1611
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/sofa.rb, line 1317
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/sofa.rb, line 1311
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/sofa.rb, line 927
def self.rRNA_5_8S
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000375')
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/sofa.rb, line 789
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/sofa.rb, line 645
def self.rRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000209')
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/sofa.rb, line 1089
def self.rasiRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000454')
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/sofa.rb, line 489
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/sofa.rb, line 345
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/sofa.rb, line 1467
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/sofa.rb, line 1395
def self.reagent
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000695')
end
recombined_from() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#recombined_from)

# File lib/biointerchange/sofa.rb, line 233
def self.recombined_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#recombined_from')
end
recombined_to() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#recombined_to)

# File lib/biointerchange/sofa.rb, line 239
def self.recombined_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#recombined_to')
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/sofa.rb, line 321
def self.region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000001')
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/sofa.rb, line 1773
def self.regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005836')
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/sofa.rb, line 1815
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/sofa.rb, line 1413
def self.remark
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000700')
end
repeat_family() click to toggle source

A group of characterized repeat sequences. (purl.obolibrary.org/obo/SO_0000187)

# File lib/biointerchange/sofa.rb, line 579
def self.repeat_family
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000187')
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/sofa.rb, line 1329
def self.repeat_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000657')
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/sofa.rb, line 1671
def self.replicon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001235')
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/sofa.rb, line 1047
def self.restriction_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000412')
end
ribosome_entry_site() click to toggle source

Region in mRNA where ribosome assembles. (purl.obolibrary.org/obo/SO_0000139)

# File lib/biointerchange/sofa.rb, line 447
def self.ribosome_entry_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000139')
end
ribozyme() click to toggle source

An RNA with catalytic activity. (purl.obolibrary.org/obo/SO_0000374)

# File lib/biointerchange/sofa.rb, line 921
def self.ribozyme
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000374')
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/sofa.rb, line 333
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/sofa.rb, line 351
def self.scRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000013')
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/sofa.rb, line 1647
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/sofa.rb, line 885
def self.sequence_assembly
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000353')
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/sofa.rb, line 1053
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/sofa.rb, line 417
def self.sequence_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000110')
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/sofa.rb, line 1755
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/SOFA_2_5_2.obo#sequence_of)

# File lib/biointerchange/sofa.rb, line 245
def self.sequence_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#sequence_of')
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/sofa.rb, line 411
def self.sequence_variant_obs
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000109')
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/sofa.rb, line 1287
def self.siRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000646')
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/sofa.rb, line 1059
def self.signal_peptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000418')
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/sofa.rb, line 1251
def self.silencer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000625')
end
similar_to() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#similar_to)

# File lib/biointerchange/sofa.rb, line 251
def self.similar_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#similar_to')
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/sofa.rb, line 909
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/sofa.rb, line 1299
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/sofa.rb, line 693
def self.snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000274')
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/sofa.rb, line 699
def self.snoRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000275')
end
splice_enhancer() click to toggle source

Region of a transcript that regulates splicing. (purl.obolibrary.org/obo/SO_0000344)

# File lib/biointerchange/sofa.rb, line 861
def self.splice_enhancer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000344')
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/sofa.rb, line 513
def self.splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000162')
end
spliceosomal_intron() click to toggle source

An intron which is spliced by the spliceosome. (purl.obolibrary.org/obo/SO_0000662)

# File lib/biointerchange/sofa.rb, line 1341
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/sofa.rb, line 1575
def self.spliceosomal_intron_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000841')
end
splicing_regulatory_region() click to toggle source

A regulatory_region that modulates splicing. (purl.obolibrary.org/obo/SO_0001056)

# File lib/biointerchange/sofa.rb, line 1641
def self.splicing_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001056')
end
ss_oligo() click to toggle source

A single stranded oligonucleotide. (purl.obolibrary.org/obo/SO_0000441)

# File lib/biointerchange/sofa.rb, line 1077
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/sofa.rb, line 1293
def self.stRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000649')
end
start_codon() click to toggle source

First codon to be translated by a ribosome. (purl.obolibrary.org/obo/SO_0000318)

# File lib/biointerchange/sofa.rb, line 771
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/SOFA_2_5_2.obo#started_by)

# File lib/biointerchange/sofa.rb, line 257
def self.started_by
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_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/SOFA_2_5_2.obo#starts)

# File lib/biointerchange/sofa.rb, line 263
def self.starts
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#starts')
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/sofa.rb, line 777
def self.stop_codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000319')
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/sofa.rb, line 1791
def self.substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000002')
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/sofa.rb, line 477
def self.supercontig
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000148')
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/sofa.rb, line 687
def self.tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000253')
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/sofa.rb, line 783
def self.tag
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000324')
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/sofa.rb, line 1443
def self.tandem_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000705')
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/sofa.rb, line 951
def self.telomerase_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000390')
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/sofa.rb, line 1245
def self.telomere
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000624')
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/sofa.rb, line 459
def self.terminator
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000141')
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/sofa.rb, line 639
def self.three_prime_UTR
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000205')
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/sofa.rb, line 525
def self.three_prime_cis_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000164')
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/sofa.rb, line 609
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/sofa.rb, line 1131
def self.three_prime_coding_exon_noncoding_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000484')
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/sofa.rb, line 1113
def self.tiling_path
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000472')
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/sofa.rb, line 1119
def self.tiling_path_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000474')
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/sofa.rb, line 1707
def self.topologically_defined_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001412')
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/sofa.rb, line 1449
def self.trans_splice_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000706')
end
trans_splice_site() click to toggle source

Primary transcript region bordering trans-splice junction. (purl.obolibrary.org/obo/SO_0001420)

# File lib/biointerchange/sofa.rb, line 1719
def self.trans_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001420')
end
trans_spliced_from() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#trans_spliced_from)

# File lib/biointerchange/sofa.rb, line 269
def self.trans_spliced_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#trans_spliced_from')
end
trans_spliced_to() click to toggle source

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#trans_spliced_to)

# File lib/biointerchange/sofa.rb, line 275
def self.trans_spliced_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#trans_spliced_to')
end
transcribed_from() click to toggle source

X is transcribed_from Y if X is synthesized from template Y. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#transcribed_from)

# File lib/biointerchange/sofa.rb, line 281
def self.transcribed_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_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/sofa.rb, line 1149
def self.transcribed_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000502')
end
transcribed_to() click to toggle source

Inverse of transcribed_from. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#transcribed_to)

# File lib/biointerchange/sofa.rb, line 287
def self.transcribed_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_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/sofa.rb, line 1359
def self.transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000673')
end
transcript_region() click to toggle source

A region of a transcript. (purl.obolibrary.org/obo/SO_0000833)

# File lib/biointerchange/sofa.rb, line 1539
def self.transcript_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000833')
end
transcription_end_site() click to toggle source

The base where transcription ends. (purl.obolibrary.org/obo/SO_0000616)

# File lib/biointerchange/sofa.rb, line 1239
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/sofa.rb, line 1749
def self.transcription_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001679')
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/sofa.rb, line 1635
def self.transcriptional_cis_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001055')
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/sofa.rb, line 1485
def self.transit_peptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000725')
end
translated_nucleotide_match() click to toggle source

A match against a translated sequence. (purl.obolibrary.org/obo/SO_0000181)

# File lib/biointerchange/sofa.rb, line 561
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/SOFA_2_5_2.obo#translates_to)

# File lib/biointerchange/sofa.rb, line 293
def self.translates_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_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/SOFA_2_5_2.obo#translation_of)

# File lib/biointerchange/sofa.rb, line 299
def self.translation_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#translation_of')
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/sofa.rb, line 387
def self.transposable_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000101')
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/sofa.rb, line 903
def self.transposable_element_insertion_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000368')
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/sofa.rb, line 1473
def self.ultracontig
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000719')
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/SOFA_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/sofa.rb, line 309
def self.variant_of
  return [ RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#variant_of'), RDF::URI.new('http://purl.obolibrary.org/obo/anonymous#variant_of') ]
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/sofa.rb, line 1017
def self.vault_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000404')
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/sofa.rb, line 1143
def self.virtual_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000499')
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/sofa.rb, line 2769
def self.with_parent(uris, parent)
  return uris.select { |uri| has_parent?(uri, parent) }
end