# File lib/biointerchange/sofa.rb, line 573 def self.primary_transcript return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000185') end
class BioInterchange::SOFA
Public Class Methods
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
– 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
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
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 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
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 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 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 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 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
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 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 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
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
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
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 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
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 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
– 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
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
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
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
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
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
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
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
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
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
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 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
– 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
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
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
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
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
– 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
– 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
– 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
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
– 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
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
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
– 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
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
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 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 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
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
– 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
– 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
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
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
– 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
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
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
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
– 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
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
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
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
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
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
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
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
– 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
– 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
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
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
– 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
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
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
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
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
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
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
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
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
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
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
– 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
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
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
A transcript that in its initial state requires modification to be functional. (purl.obolibrary.org/obo/SO_0000185)
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
– 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
– 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
– 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
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
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
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
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
– 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
– 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
– 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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