biointerchange 0.2.1 → 0.2.2
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- data/README.md +61 -18
- data/VERSION +1 -1
- data/examples/Saccharomyces_cerevisiae_incl_consequences.gvf.gz +0 -0
- data/examples/webservice_example.json +7 -0
- data/generators/GOxrefify.rb +36 -28
- data/generators/javaify.rb +131 -112
- data/generators/make_supplement_releases.rb +57 -0
- data/generators/pythonify.rb +68 -53
- data/lib/biointerchange/core.rb +4 -2
- data/lib/biointerchange/faldo.rb +160 -0
- data/lib/biointerchange/genomics/gff3_feature_set.rb +1 -1
- data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +1 -1
- data/lib/biointerchange/genomics/gff3_reader.rb +1 -1
- data/lib/biointerchange/model.rb +21 -0
- data/lib/biointerchange/registry.rb +1 -1
- data/lib/biointerchange/sio.rb +2035 -57
- data/lib/biointerchange/textmining/document.rb +1 -1
- data/lib/biointerchange/textmining/pdfx_xml_reader.rb +1 -15
- data/lib/biointerchange/textmining/pubannos_json_reader.rb +1 -3
- data/spec/gff3_rdfwriter_spec.rb +1 -0
- data/spec/gvf_rdfwriter_spec.rb +1 -0
- data/spec/text_mining_pdfx_xml_reader_spec.rb +4 -3
- data/spec/text_mining_pubannos_json_reader_spec.rb +6 -5
- data/spec/text_mining_rdfwriter_spec.rb +2 -1
- data/supplemental/java/biointerchange/pom.xml +1 -1
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/FALDO.java +219 -0
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GFF3O.java +2 -1
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GOXRef.java +1221 -0
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GVF1O.java +2 -1
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SIO.java +2283 -15
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SO.java +2 -1
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SOFA.java +5 -4
- data/supplemental/python/biointerchange/faldo.py +168 -0
- data/supplemental/python/biointerchange/gff3o.py +6 -4
- data/supplemental/python/biointerchange/goxref.py +1040 -0
- data/supplemental/python/biointerchange/gvf1o.py +6 -4
- data/supplemental/python/biointerchange/sio.py +1740 -21
- data/supplemental/python/biointerchange/so.py +6527 -6525
- data/supplemental/python/biointerchange/sofa.py +792 -790
- data/supplemental/python/setup.py +2 -2
- data/web/about.html +9 -29
- data/web/api.html +10 -30
- data/web/biointerchange.js +78 -27
- data/web/cli.html +137 -0
- data/web/index.html +19 -34
- data/web/ontologies.html +9 -29
- data/web/service/rdfizer.fcgi +19 -2
- data/web/webservices.html +70 -35
- metadata +13 -3
@@ -2,1829 +2,1825 @@ import rdflib
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from rdflib import Namespace
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__namespace_SOFA = Namespace('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:adjacent_to')
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def _namespace_SOFA(accession):
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return __namespace_SOFA[accession]
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class SOFA:
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@classmethod
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def adjacent_to(cls):
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return _namespace_SOFA('')
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return _namespace_SOFA('http_//purl.org/obo/owl:adjacent_to')
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@classmethod
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def complete_evidence_for_feature(cls):
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return _namespace_SOFA('
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return _namespace_SOFA('http_//purl.org/obo/owl:complete_evidence_for_feature')
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@classmethod
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def contained_by(cls):
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return _namespace_SOFA('
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return _namespace_SOFA('http_//purl.org/obo/owl:contained_by')
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@classmethod
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def contains(cls):
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return _namespace_SOFA('
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return _namespace_SOFA('http_//purl.org/obo/owl:contains')
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@classmethod
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def derives_from(cls):
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return _namespace_SOFA('
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return _namespace_SOFA('http_//purl.org/obo/owl:derives_from')
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@classmethod
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def evidence_for_feature(cls):
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return _namespace_SOFA('
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return _namespace_SOFA('http_//purl.org/obo/owl:evidence_for_feature')
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@classmethod
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def has_integral_part(cls):
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return _namespace_SOFA('
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return _namespace_SOFA('http_//purl.org/obo/owl:has_integral_part')
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@classmethod
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def has_part(cls):
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return _namespace_SOFA('
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return _namespace_SOFA('http_//purl.org/obo/owl:has_part')
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@classmethod
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def homologous_to(cls):
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return _namespace_SOFA('
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return _namespace_SOFA('http_//purl.org/obo/owl:homologous_to')
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@classmethod
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def integral_part_of(cls):
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return _namespace_SOFA('
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return _namespace_SOFA('http_//purl.org/obo/owl:integral_part_of')
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@classmethod
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def member_of(cls):
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return _namespace_SOFA('
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return _namespace_SOFA('http_//purl.org/obo/owl:member_of')
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@classmethod
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def non_functional_homolog_of(cls):
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return _namespace_SOFA('
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return _namespace_SOFA('http_//purl.org/obo/owl:non_functional_homolog_of')
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@classmethod
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def orthologous_to(cls):
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return _namespace_SOFA('
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return _namespace_SOFA('http_//purl.org/obo/owl:orthologous_to')
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@classmethod
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def paralogous_to(cls):
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return _namespace_SOFA('
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return _namespace_SOFA('http_//purl.org/obo/owl:paralogous_to')
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@classmethod
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def part_of(cls):
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return _namespace_SOFA('
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return _namespace_SOFA('http_//purl.org/obo/owl:part_of')
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@classmethod
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def partial_evidence_for_feature(cls):
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return _namespace_SOFA('
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return _namespace_SOFA('http_//purl.org/obo/owl:partial_evidence_for_feature')
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@classmethod
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def similar_to(cls):
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return _namespace_SOFA('
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return _namespace_SOFA('http_//purl.org/obo/owl:similar_to')
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@classmethod
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def Sequence_Ontology(cls):
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return _namespace_SOFA('
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return _namespace_SOFA('SO_0000000')
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@classmethod
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def region(cls):
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"""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. (cls, SO:ke)
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(SO_0000001)
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"""
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return _namespace_SOFA('
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return _namespace_SOFA('SO_0000001')
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@classmethod
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def interior_coding_exon(cls):
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return _namespace_SOFA('
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return _namespace_SOFA('SO_0000004')
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@classmethod
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def satellite_DNA(cls):
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"""The many tandem repeats (cls, 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. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
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(SO_0000005)
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"""
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return _namespace_SOFA('SO_0000005')
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@classmethod
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def PCR_product(cls):
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"""A region amplified by a PCR reaction. (cls, SO:ke)
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(SO_0000006)
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"""
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return _namespace_SOFA('SO_0000006')
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@classmethod
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def read_pair(cls):
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"""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. (cls, SO:ls)
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(SO_0000007)
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"""
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return _namespace_SOFA('SO_0000007')
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@classmethod
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def scRNA(cls):
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"""A small non coding RNA sequence, present in the cytoplasm. (cls, SO:ke)
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"""
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return _namespace_SOFA('SO_0000013')
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@classmethod
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def match_set(cls):
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"""A collection of match parts. (cls, SO:ke)
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return _namespace_SOFA('SO_0000038')
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@classmethod
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def match_part(cls):
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"""A part of a match, for example an hsp from blast is a match_part. (cls, SO:ke)
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return _namespace_SOFA('SO_0000039')
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@classmethod
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def gene_part(cls):
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"""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. (cls, SO:ke)
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"""
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@classmethod
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def operator(cls):
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"""A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon. (cls, SO:ma)
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return _namespace_SOFA('SO_0000057')
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@classmethod
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def nuclease_binding_site(cls):
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"""A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease. (cls, SO:cb)
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return _namespace_SOFA('SO_0000059')
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@classmethod
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def transposable_element(cls):
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"""A transposon or insertion sequence. An element that can insert in a variety of DNA sequences. (cls, http://www.sci.sdsu.edu/~smaloy/Glossary/T.html)
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@classmethod
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def expressed_sequence_match(cls):
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"""A match to an EST or cDNA sequence. (cls, SO:ke)
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@classmethod
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def clone_insert_end(cls):
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"""The end of the clone insert. (cls, SO:ke)
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@classmethod
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def polypeptide(cls):
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"""A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation. (cls, SO:ma)
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"""
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@classmethod
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def sequence_variant_obs(cls):
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"""A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. (cls, SO:ke)
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"""
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return _namespace_SOFA('SO_0000109')
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@classmethod
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def sequence_feature(cls):
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"""An extent of biological sequence. (cls, SO:ke)
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"""
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return _namespace_SOFA('SO_0000110')
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@classmethod
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def primer(cls):
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"""An oligo to which new deoxyribonucleotides can be added by DNA polymerase. (cls, SO:ke)
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return _namespace_SOFA('SO_0000112')
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@classmethod
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def proviral_region(cls):
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"""A viral sequence which has integrated into a host genome. (cls, SO:ke)
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"""
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return _namespace_SOFA('SO_0000113')
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@classmethod
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def methylated_C(cls):
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"""A methylated deoxy-cytosine. (cls, SO:ke)
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(SO_0000114)
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"""
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return _namespace_SOFA('SO_0000114')
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@classmethod
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def protein_coding_primary_transcript(cls):
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"""A primary transcript that, at least in part, encodes one or more proteins. (cls, SO:ke)
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"""
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return _namespace_SOFA('SO_0000120')
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@classmethod
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def ribosome_entry_site(cls):
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"""Region in mRNA where ribosome assembles. (cls, SO:ke)
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(SO_0000139)
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"""
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return _namespace_SOFA('SO_0000139')
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@classmethod
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def attenuator(cls):
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"""A sequence segment located within the five prime end of an mRNA that causes premature termination of translation. (cls, SO:as)
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"""
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return _namespace_SOFA('SO_0000140')
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@classmethod
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def terminator(cls):
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"""The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription. (cls, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
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"""
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return _namespace_SOFA('SO_0000141')
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@classmethod
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def assembly_component(cls):
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"""A region of known length which may be used to manufacture a longer region. (cls, SO:ke)
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(SO_0000143)
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"""
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return _namespace_SOFA('
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return _namespace_SOFA('SO_0000143')
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@classmethod
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def exon(cls):
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"""A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing. (cls, SO:ke)
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(SO_0000147)
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"""
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return _namespace_SOFA('
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|
+
return _namespace_SOFA('SO_0000147')
|
262
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|
|
263
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|
@classmethod
|
264
260
|
def supercontig(cls):
|
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|
"""One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's. (cls, SO:ls)
|
266
|
-
(
|
262
|
+
(SO_0000148)
|
267
263
|
"""
|
268
|
-
return _namespace_SOFA('
|
264
|
+
return _namespace_SOFA('SO_0000148')
|
269
265
|
|
270
266
|
@classmethod
|
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267
|
def contig(cls):
|
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|
"""A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. (cls, SO:ls)
|
273
|
-
(
|
269
|
+
(SO_0000149)
|
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|
"""
|
275
|
-
return _namespace_SOFA('
|
271
|
+
return _namespace_SOFA('SO_0000149')
|
276
272
|
|
277
273
|
@classmethod
|
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|
def read(cls):
|
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|
"""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. (cls, SO:rd)
|
280
|
-
(
|
276
|
+
(SO_0000150)
|
281
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|
"""
|
282
|
-
return _namespace_SOFA('
|
278
|
+
return _namespace_SOFA('SO_0000150')
|
283
279
|
|
284
280
|
@classmethod
|
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|
def clone(cls):
|
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|
"""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. (cls, SO:ke)
|
287
|
-
(
|
283
|
+
(SO_0000151)
|
288
284
|
"""
|
289
|
-
return _namespace_SOFA('
|
285
|
+
return _namespace_SOFA('SO_0000151')
|
290
286
|
|
291
287
|
@classmethod
|
292
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|
def deletion(cls):
|
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|
"""The point at which one or more contiguous nucleotides were excised. (cls, SO:ke)
|
294
|
-
(
|
290
|
+
(SO_0000159)
|
295
291
|
"""
|
296
|
-
return _namespace_SOFA('
|
292
|
+
return _namespace_SOFA('SO_0000159')
|
297
293
|
|
298
294
|
@classmethod
|
299
295
|
def methylated_A(cls):
|
300
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|
"""A modified RNA base in which adenine has been methylated. (cls, SO:ke)
|
301
|
-
(
|
297
|
+
(SO_0000161)
|
302
298
|
"""
|
303
|
-
return _namespace_SOFA('
|
299
|
+
return _namespace_SOFA('SO_0000161')
|
304
300
|
|
305
301
|
@classmethod
|
306
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|
def splice_site(cls):
|
307
303
|
"""Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction. (cls, SO:cjm, SO:ke)
|
308
|
-
(
|
304
|
+
(SO_0000162)
|
309
305
|
"""
|
310
|
-
return _namespace_SOFA('
|
306
|
+
return _namespace_SOFA('SO_0000162')
|
311
307
|
|
312
308
|
@classmethod
|
313
309
|
def five_prime_cis_splice_site(cls):
|
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|
"""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. (cls, http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke)
|
315
|
-
(
|
311
|
+
(SO_0000163)
|
316
312
|
"""
|
317
|
-
return _namespace_SOFA('
|
313
|
+
return _namespace_SOFA('SO_0000163')
|
318
314
|
|
319
315
|
@classmethod
|
320
316
|
def three_prime_cis_splice_site(cls):
|
321
317
|
"""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. (cls, http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke)
|
322
|
-
(
|
318
|
+
(SO_0000164)
|
323
319
|
"""
|
324
|
-
return _namespace_SOFA('
|
320
|
+
return _namespace_SOFA('SO_0000164')
|
325
321
|
|
326
322
|
@classmethod
|
327
323
|
def enhancer(cls):
|
328
324
|
"""A cis-acting sequence that increases the utilization of (cls, some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
|
329
|
-
(
|
325
|
+
(SO_0000165)
|
330
326
|
"""
|
331
|
-
return _namespace_SOFA('
|
327
|
+
return _namespace_SOFA('SO_0000165')
|
332
328
|
|
333
329
|
@classmethod
|
334
330
|
def promoter(cls):
|
335
331
|
"""A regulatory_region composed of the TSS(cls, s) and binding sites for TF_complexes of the basal transcription machinery. (SO:regcreative)
|
336
|
-
(
|
332
|
+
(SO_0000167)
|
337
333
|
"""
|
338
|
-
return _namespace_SOFA('
|
334
|
+
return _namespace_SOFA('SO_0000167')
|
339
335
|
|
340
336
|
@classmethod
|
341
337
|
def cross_genome_match(cls):
|
342
338
|
"""A nucleotide match against a sequence from another organism. (cls, SO:ma)
|
343
|
-
(
|
339
|
+
(SO_0000177)
|
344
340
|
"""
|
345
|
-
return _namespace_SOFA('
|
341
|
+
return _namespace_SOFA('SO_0000177')
|
346
342
|
|
347
343
|
@classmethod
|
348
344
|
def operon(cls):
|
349
345
|
"""A group of contiguous genes transcribed as a single (cls, polycistronic) mRNA from a single regulatory region. (SO:ma)
|
350
|
-
(
|
346
|
+
(SO_0000178)
|
351
347
|
"""
|
352
|
-
return _namespace_SOFA('
|
348
|
+
return _namespace_SOFA('SO_0000178')
|
353
349
|
|
354
350
|
@classmethod
|
355
351
|
def clone_insert_start(cls):
|
356
352
|
"""The start of the clone insert. (cls, SO:ke)
|
357
|
-
(
|
353
|
+
(SO_0000179)
|
358
354
|
"""
|
359
|
-
return _namespace_SOFA('
|
355
|
+
return _namespace_SOFA('SO_0000179')
|
360
356
|
|
361
357
|
@classmethod
|
362
358
|
def translated_nucleotide_match(cls):
|
363
359
|
"""A match against a translated sequence. (cls, SO:ke)
|
364
|
-
(
|
360
|
+
(SO_0000181)
|
365
361
|
"""
|
366
|
-
return _namespace_SOFA('
|
362
|
+
return _namespace_SOFA('SO_0000181')
|
367
363
|
|
368
364
|
@classmethod
|
369
365
|
def non_transcribed_region(cls):
|
370
366
|
"""A region of the gene which is not transcribed. (cls, SO:ke)
|
371
|
-
(
|
367
|
+
(SO_0000183)
|
372
368
|
"""
|
373
|
-
return _namespace_SOFA('
|
369
|
+
return _namespace_SOFA('SO_0000183')
|
374
370
|
|
375
371
|
@classmethod
|
376
372
|
def primary_transcript(cls):
|
377
373
|
"""A transcript that in its initial state requires modification to be functional. (cls, SO:ma)
|
378
|
-
(
|
374
|
+
(SO_0000185)
|
379
375
|
"""
|
380
|
-
return _namespace_SOFA('
|
376
|
+
return _namespace_SOFA('SO_0000185')
|
381
377
|
|
382
378
|
@classmethod
|
383
379
|
def repeat_family(cls):
|
384
380
|
"""A group of characterized repeat sequences. (cls, SO:ke)
|
385
|
-
(
|
381
|
+
(SO_0000187)
|
386
382
|
"""
|
387
|
-
return _namespace_SOFA('
|
383
|
+
return _namespace_SOFA('SO_0000187')
|
388
384
|
|
389
385
|
@classmethod
|
390
386
|
def intron(cls):
|
391
387
|
"""A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (cls, exons) on either side of it. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
|
392
|
-
(
|
388
|
+
(SO_0000188)
|
393
389
|
"""
|
394
|
-
return _namespace_SOFA('
|
390
|
+
return _namespace_SOFA('SO_0000188')
|
395
391
|
|
396
392
|
@classmethod
|
397
393
|
def RFLP_fragment(cls):
|
398
394
|
"""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. (cls, GOC:pj)
|
399
|
-
(
|
395
|
+
(SO_0000193)
|
400
396
|
"""
|
401
|
-
return _namespace_SOFA('
|
397
|
+
return _namespace_SOFA('SO_0000193')
|
402
398
|
|
403
399
|
@classmethod
|
404
400
|
def coding_exon(cls):
|
405
401
|
"""An exon whereby at least one base is part of a codon (cls, here, 'codon' is inclusive of the stop_codon). (SO:ke)
|
406
|
-
(
|
402
|
+
(SO_0000195)
|
407
403
|
"""
|
408
|
-
return _namespace_SOFA('
|
404
|
+
return _namespace_SOFA('SO_0000195')
|
409
405
|
|
410
406
|
@classmethod
|
411
407
|
def five_prime_coding_exon_coding_region(cls):
|
412
408
|
"""The sequence of the five_prime_coding_exon that codes for protein. (cls, SO:cjm)
|
413
|
-
(
|
409
|
+
(SO_0000196)
|
414
410
|
"""
|
415
|
-
return _namespace_SOFA('
|
411
|
+
return _namespace_SOFA('SO_0000196')
|
416
412
|
|
417
413
|
@classmethod
|
418
414
|
def three_prime_coding_exon_coding_region(cls):
|
419
415
|
"""The sequence of the three_prime_coding_exon that codes for protein. (cls, SO:cjm)
|
420
|
-
(
|
416
|
+
(SO_0000197)
|
421
417
|
"""
|
422
|
-
return _namespace_SOFA('
|
418
|
+
return _namespace_SOFA('SO_0000197')
|
423
419
|
|
424
420
|
@classmethod
|
425
421
|
def noncoding_exon(cls):
|
426
422
|
"""An exon that does not contain any codons. (cls, SO:ke)
|
427
|
-
(
|
423
|
+
(SO_0000198)
|
428
424
|
"""
|
429
|
-
return _namespace_SOFA('
|
425
|
+
return _namespace_SOFA('SO_0000198')
|
430
426
|
|
431
427
|
@classmethod
|
432
428
|
def five_prime_coding_exon(cls):
|
433
429
|
"""The 5' most coding exon. (cls, SO:ke)
|
434
|
-
(
|
430
|
+
(SO_0000200)
|
435
431
|
"""
|
436
|
-
return _namespace_SOFA('
|
432
|
+
return _namespace_SOFA('SO_0000200')
|
437
433
|
|
438
434
|
@classmethod
|
439
435
|
def UTR(cls):
|
440
436
|
"""Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated. (cls, SO:ke)
|
441
|
-
(
|
437
|
+
(SO_0000203)
|
442
438
|
"""
|
443
|
-
return _namespace_SOFA('
|
439
|
+
return _namespace_SOFA('SO_0000203')
|
444
440
|
|
445
441
|
@classmethod
|
446
442
|
def five_prime_UTR(cls):
|
447
443
|
"""A region at the 5' end of a mature transcript (cls, preceding the initiation codon) that is not translated into a protein. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
|
448
|
-
(
|
444
|
+
(SO_0000204)
|
449
445
|
"""
|
450
|
-
return _namespace_SOFA('
|
446
|
+
return _namespace_SOFA('SO_0000204')
|
451
447
|
|
452
448
|
@classmethod
|
453
449
|
def three_prime_UTR(cls):
|
454
450
|
"""A region at the 3' end of a mature transcript (cls, following the stop codon) that is not translated into a protein. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
|
455
|
-
(
|
451
|
+
(SO_0000205)
|
456
452
|
"""
|
457
|
-
return _namespace_SOFA('
|
453
|
+
return _namespace_SOFA('SO_0000205')
|
458
454
|
|
459
455
|
@classmethod
|
460
456
|
def rRNA_primary_transcript(cls):
|
461
457
|
"""A primary transcript encoding a ribosomal RNA. (cls, SO:ke)
|
462
|
-
(
|
458
|
+
(SO_0000209)
|
463
459
|
"""
|
464
|
-
return _namespace_SOFA('
|
460
|
+
return _namespace_SOFA('SO_0000209')
|
465
461
|
|
466
462
|
@classmethod
|
467
463
|
def mature_transcript(cls):
|
468
464
|
"""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. (cls, SO:ke)
|
469
|
-
(
|
465
|
+
(SO_0000233)
|
470
466
|
"""
|
471
|
-
return _namespace_SOFA('
|
467
|
+
return _namespace_SOFA('SO_0000233')
|
472
468
|
|
473
469
|
@classmethod
|
474
470
|
def mRNA(cls):
|
475
471
|
"""Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns. (cls, SO:ma)
|
476
|
-
(
|
472
|
+
(SO_0000234)
|
477
473
|
"""
|
478
|
-
return _namespace_SOFA('
|
474
|
+
return _namespace_SOFA('SO_0000234')
|
479
475
|
|
480
476
|
@classmethod
|
481
477
|
def TF_binding_site(cls):
|
482
478
|
"""A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]. (cls, SO:ke)
|
483
|
-
(
|
479
|
+
(SO_0000235)
|
484
480
|
"""
|
485
|
-
return _namespace_SOFA('
|
481
|
+
return _namespace_SOFA('SO_0000235')
|
486
482
|
|
487
483
|
@classmethod
|
488
484
|
def ORF(cls):
|
489
485
|
"""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(cls, NNN)nTER. (SGD:rb, SO:ma)
|
490
|
-
(
|
486
|
+
(SO_0000236)
|
491
487
|
"""
|
492
|
-
return _namespace_SOFA('
|
488
|
+
return _namespace_SOFA('SO_0000236')
|
493
489
|
|
494
490
|
@classmethod
|
495
491
|
def flanking_region(cls):
|
496
492
|
"""The sequences extending on either side of a specific region. (cls, SO:ke)
|
497
|
-
(
|
493
|
+
(SO_0000239)
|
498
494
|
"""
|
499
|
-
return _namespace_SOFA('
|
495
|
+
return _namespace_SOFA('SO_0000239')
|
500
496
|
|
501
497
|
@classmethod
|
502
498
|
def rRNA(cls):
|
503
499
|
"""RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity. (cls, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732)
|
504
|
-
(
|
500
|
+
(SO_0000252)
|
505
501
|
"""
|
506
|
-
return _namespace_SOFA('
|
502
|
+
return _namespace_SOFA('SO_0000252')
|
507
503
|
|
508
504
|
@classmethod
|
509
505
|
def tRNA(cls):
|
510
506
|
"""Transfer RNA (cls, 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. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732)
|
511
|
-
(
|
507
|
+
(SO_0000253)
|
512
508
|
"""
|
513
|
-
return _namespace_SOFA('
|
509
|
+
return _namespace_SOFA('SO_0000253')
|
514
510
|
|
515
511
|
@classmethod
|
516
512
|
def snRNA(cls):
|
517
513
|
"""A small nuclear RNA molecule involved in pre-mRNA splicing and processing. (cls, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems)
|
518
|
-
(
|
514
|
+
(SO_0000274)
|
519
515
|
"""
|
520
|
-
return _namespace_SOFA('
|
516
|
+
return _namespace_SOFA('SO_0000274')
|
521
517
|
|
522
518
|
@classmethod
|
523
519
|
def snoRNA(cls):
|
524
520
|
"""A snoRNA (cls, 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. (GOC:kgc)
|
525
|
-
(
|
521
|
+
(SO_0000275)
|
526
522
|
"""
|
527
|
-
return _namespace_SOFA('
|
523
|
+
return _namespace_SOFA('SO_0000275')
|
528
524
|
|
529
525
|
@classmethod
|
530
526
|
def miRNA(cls):
|
531
527
|
"""Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (cls, 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. (PMID:12592000)
|
532
|
-
(
|
528
|
+
(SO_0000276)
|
533
529
|
"""
|
534
|
-
return _namespace_SOFA('
|
530
|
+
return _namespace_SOFA('SO_0000276')
|
535
531
|
|
536
532
|
@classmethod
|
537
533
|
def microsatellite(cls):
|
538
534
|
"""A repeat_region containing repeat_units (cls, 2 to 4 bp) that is repeated multiple times in tandem. (http://www.informatics.jax.org/silver/glossary.shtml)
|
539
|
-
(
|
535
|
+
(SO_0000289)
|
540
536
|
"""
|
541
|
-
return _namespace_SOFA('
|
537
|
+
return _namespace_SOFA('SO_0000289')
|
542
538
|
|
543
539
|
@classmethod
|
544
540
|
def inverted_repeat(cls):
|
545
541
|
"""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. (cls, SO:ke)
|
546
|
-
(
|
542
|
+
(SO_0000294)
|
547
543
|
"""
|
548
|
-
return _namespace_SOFA('
|
544
|
+
return _namespace_SOFA('SO_0000294')
|
549
545
|
|
550
546
|
@classmethod
|
551
547
|
def origin_of_replication(cls):
|
552
548
|
"""The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies. (cls, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
|
553
|
-
(
|
549
|
+
(SO_0000296)
|
554
550
|
"""
|
555
|
-
return _namespace_SOFA('
|
551
|
+
return _namespace_SOFA('SO_0000296')
|
556
552
|
|
557
553
|
@classmethod
|
558
554
|
def clip(cls):
|
559
555
|
"""Part of the primary transcript that is clipped off during processing. (cls, SO:ke)
|
560
|
-
(
|
556
|
+
(SO_0000303)
|
561
557
|
"""
|
562
|
-
return _namespace_SOFA('
|
558
|
+
return _namespace_SOFA('SO_0000303')
|
563
559
|
|
564
560
|
@classmethod
|
565
561
|
def modified_base(cls):
|
566
562
|
"""A modified nucleotide, i.e. a nucleotide other than A, T, C. G. (cls, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
|
567
|
-
(
|
563
|
+
(SO_0000305)
|
568
564
|
"""
|
569
|
-
return _namespace_SOFA('
|
565
|
+
return _namespace_SOFA('SO_0000305')
|
570
566
|
|
571
567
|
@classmethod
|
572
568
|
def methylated_base_feature(cls):
|
573
569
|
"""A nucleotide modified by methylation. (cls, SO:ke)
|
574
|
-
(
|
570
|
+
(SO_0000306)
|
575
571
|
"""
|
576
|
-
return _namespace_SOFA('
|
572
|
+
return _namespace_SOFA('SO_0000306')
|
577
573
|
|
578
574
|
@classmethod
|
579
575
|
def CpG_island(cls):
|
580
576
|
"""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. (cls, SO:rd)
|
581
|
-
(
|
577
|
+
(SO_0000307)
|
582
578
|
"""
|
583
|
-
return _namespace_SOFA('
|
579
|
+
return _namespace_SOFA('SO_0000307')
|
584
580
|
|
585
581
|
@classmethod
|
586
582
|
def direct_repeat(cls):
|
587
583
|
"""A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA. (cls, SO:ke)
|
588
|
-
(
|
584
|
+
(SO_0000314)
|
589
585
|
"""
|
590
|
-
return _namespace_SOFA('
|
586
|
+
return _namespace_SOFA('SO_0000314')
|
591
587
|
|
592
588
|
@classmethod
|
593
589
|
def TSS(cls):
|
594
590
|
"""The first base where RNA polymerase begins to synthesize the RNA transcript. (cls, SO:ke)
|
595
|
-
(
|
591
|
+
(SO_0000315)
|
596
592
|
"""
|
597
|
-
return _namespace_SOFA('
|
593
|
+
return _namespace_SOFA('SO_0000315')
|
598
594
|
|
599
595
|
@classmethod
|
600
596
|
def CDS(cls):
|
601
597
|
"""A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon. (cls, SO:ma)
|
602
|
-
(
|
598
|
+
(SO_0000316)
|
603
599
|
"""
|
604
|
-
return _namespace_SOFA('
|
600
|
+
return _namespace_SOFA('SO_0000316')
|
605
601
|
|
606
602
|
@classmethod
|
607
603
|
def start_codon(cls):
|
608
604
|
"""First codon to be translated by a ribosome. (cls, SO:ke)
|
609
|
-
(
|
605
|
+
(SO_0000318)
|
610
606
|
"""
|
611
|
-
return _namespace_SOFA('
|
607
|
+
return _namespace_SOFA('SO_0000318')
|
612
608
|
|
613
609
|
@classmethod
|
614
610
|
def stop_codon(cls):
|
615
611
|
"""In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis. (cls, SO:ke)
|
616
|
-
(
|
612
|
+
(SO_0000319)
|
617
613
|
"""
|
618
|
-
return _namespace_SOFA('
|
614
|
+
return _namespace_SOFA('SO_0000319')
|
619
615
|
|
620
616
|
@classmethod
|
621
617
|
def tag(cls):
|
622
618
|
"""A nucleotide sequence that may be used to identify a larger sequence. (cls, SO:ke)
|
623
|
-
(
|
619
|
+
(SO_0000324)
|
624
620
|
"""
|
625
|
-
return _namespace_SOFA('
|
621
|
+
return _namespace_SOFA('SO_0000324')
|
626
622
|
|
627
623
|
@classmethod
|
628
624
|
def rRNA_large_subunit_primary_transcript(cls):
|
629
625
|
"""A primary transcript encoding a large ribosomal subunit RNA. (cls, SO:ke)
|
630
|
-
(
|
626
|
+
(SO_0000325)
|
631
627
|
"""
|
632
|
-
return _namespace_SOFA('
|
628
|
+
return _namespace_SOFA('SO_0000325')
|
633
629
|
|
634
630
|
@classmethod
|
635
631
|
def SAGE_tag(cls):
|
636
632
|
"""A short diagnostic sequence tag, serial analysis of gene expression (cls, SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract)
|
637
|
-
(
|
633
|
+
(SO_0000326)
|
638
634
|
"""
|
639
|
-
return _namespace_SOFA('
|
635
|
+
return _namespace_SOFA('SO_0000326')
|
640
636
|
|
641
637
|
@classmethod
|
642
638
|
def conserved_region(cls):
|
643
639
|
"""Region of sequence similarity by descent from a common ancestor. (cls, SO:ke)
|
644
|
-
(
|
640
|
+
(SO_0000330)
|
645
641
|
"""
|
646
|
-
return _namespace_SOFA('
|
642
|
+
return _namespace_SOFA('SO_0000330')
|
647
643
|
|
648
644
|
@classmethod
|
649
645
|
def STS(cls):
|
650
646
|
"""Short (cls, typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known. (http://www.biospace.com)
|
651
|
-
(
|
647
|
+
(SO_0000331)
|
652
648
|
"""
|
653
|
-
return _namespace_SOFA('
|
649
|
+
return _namespace_SOFA('SO_0000331')
|
654
650
|
|
655
651
|
@classmethod
|
656
652
|
def coding_conserved_region(cls):
|
657
653
|
"""Coding region of sequence similarity by descent from a common ancestor. (cls, SO:ke)
|
658
|
-
(
|
654
|
+
(SO_0000332)
|
659
655
|
"""
|
660
|
-
return _namespace_SOFA('
|
656
|
+
return _namespace_SOFA('SO_0000332')
|
661
657
|
|
662
658
|
@classmethod
|
663
659
|
def exon_junction(cls):
|
664
660
|
"""The boundary between two exons in a processed transcript. (cls, SO:ke)
|
665
|
-
(
|
661
|
+
(SO_0000333)
|
666
662
|
"""
|
667
|
-
return _namespace_SOFA('
|
663
|
+
return _namespace_SOFA('SO_0000333')
|
668
664
|
|
669
665
|
@classmethod
|
670
666
|
def nc_conserved_region(cls):
|
671
667
|
"""Non-coding region of sequence similarity by descent from a common ancestor. (cls, SO:ke)
|
672
|
-
(
|
668
|
+
(SO_0000334)
|
673
669
|
"""
|
674
|
-
return _namespace_SOFA('
|
670
|
+
return _namespace_SOFA('SO_0000334')
|
675
671
|
|
676
672
|
@classmethod
|
677
673
|
def pseudogene(cls):
|
678
674
|
"""A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (cls, 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). (http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html)
|
679
|
-
(
|
675
|
+
(SO_0000336)
|
680
676
|
"""
|
681
|
-
return _namespace_SOFA('
|
677
|
+
return _namespace_SOFA('SO_0000336')
|
682
678
|
|
683
679
|
@classmethod
|
684
680
|
def RNAi_reagent(cls):
|
685
681
|
"""A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference. (cls, SO:rd)
|
686
|
-
(
|
682
|
+
(SO_0000337)
|
687
683
|
"""
|
688
|
-
return _namespace_SOFA('
|
684
|
+
return _namespace_SOFA('SO_0000337')
|
689
685
|
|
690
686
|
@classmethod
|
691
687
|
def chromosome(cls):
|
692
688
|
"""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. (cls, SO:ma)
|
693
|
-
(
|
689
|
+
(SO_0000340)
|
694
690
|
"""
|
695
|
-
return _namespace_SOFA('
|
691
|
+
return _namespace_SOFA('SO_0000340')
|
696
692
|
|
697
693
|
@classmethod
|
698
694
|
def chromosome_band(cls):
|
699
695
|
"""A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark. (cls, SO:ma)
|
700
|
-
(
|
696
|
+
(SO_0000341)
|
701
697
|
"""
|
702
|
-
return _namespace_SOFA('
|
698
|
+
return _namespace_SOFA('SO_0000341')
|
703
699
|
|
704
700
|
@classmethod
|
705
701
|
def match(cls):
|
706
702
|
"""A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. (cls, SO:ke)
|
707
|
-
(
|
703
|
+
(SO_0000343)
|
708
704
|
"""
|
709
|
-
return _namespace_SOFA('
|
705
|
+
return _namespace_SOFA('SO_0000343')
|
710
706
|
|
711
707
|
@classmethod
|
712
708
|
def splice_enhancer(cls):
|
713
709
|
"""Region of a transcript that regulates splicing. (cls, SO:ke)
|
714
|
-
(
|
710
|
+
(SO_0000344)
|
715
711
|
"""
|
716
|
-
return _namespace_SOFA('
|
712
|
+
return _namespace_SOFA('SO_0000344')
|
717
713
|
|
718
714
|
@classmethod
|
719
715
|
def EST(cls):
|
720
716
|
"""A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long. (cls, SO:ke)
|
721
|
-
(
|
717
|
+
(SO_0000345)
|
722
718
|
"""
|
723
|
-
return _namespace_SOFA('
|
719
|
+
return _namespace_SOFA('SO_0000345')
|
724
720
|
|
725
721
|
@classmethod
|
726
722
|
def nucleotide_match(cls):
|
727
723
|
"""A match against a nucleotide sequence. (cls, SO:ke)
|
728
|
-
(
|
724
|
+
(SO_0000347)
|
729
725
|
"""
|
730
|
-
return _namespace_SOFA('
|
726
|
+
return _namespace_SOFA('SO_0000347')
|
731
727
|
|
732
728
|
@classmethod
|
733
729
|
def protein_match(cls):
|
734
730
|
"""A match against a protein sequence. (cls, SO:ke)
|
735
|
-
(
|
731
|
+
(SO_0000349)
|
736
732
|
"""
|
737
|
-
return _namespace_SOFA('
|
733
|
+
return _namespace_SOFA('SO_0000349')
|
738
734
|
|
739
735
|
@classmethod
|
740
736
|
def sequence_assembly(cls):
|
741
737
|
"""A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. (cls, SO:ma)
|
742
|
-
(
|
738
|
+
(SO_0000353)
|
743
739
|
"""
|
744
|
-
return _namespace_SOFA('
|
740
|
+
return _namespace_SOFA('SO_0000353')
|
745
741
|
|
746
742
|
@classmethod
|
747
743
|
def codon(cls):
|
748
744
|
"""A set of (cls, 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. (http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke)
|
749
|
-
(
|
745
|
+
(SO_0000360)
|
750
746
|
"""
|
751
|
-
return _namespace_SOFA('
|
747
|
+
return _namespace_SOFA('SO_0000360')
|
752
748
|
|
753
749
|
@classmethod
|
754
750
|
def insertion_site(cls):
|
755
751
|
"""The junction where an insertion occurred. (cls, SO:ke)
|
756
|
-
(
|
752
|
+
(SO_0000366)
|
757
753
|
"""
|
758
|
-
return _namespace_SOFA('
|
754
|
+
return _namespace_SOFA('SO_0000366')
|
759
755
|
|
760
756
|
@classmethod
|
761
757
|
def transposable_element_insertion_site(cls):
|
762
758
|
"""The junction in a genome where a transposable_element has inserted. (cls, SO:ke)
|
763
|
-
(
|
759
|
+
(SO_0000368)
|
764
760
|
"""
|
765
|
-
return _namespace_SOFA('
|
761
|
+
return _namespace_SOFA('SO_0000368')
|
766
762
|
|
767
763
|
@classmethod
|
768
764
|
def small_regulatory_ncRNA(cls):
|
769
765
|
"""A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression. (cls, SO:ma)
|
770
|
-
(
|
766
|
+
(SO_0000370)
|
771
767
|
"""
|
772
|
-
return _namespace_SOFA('
|
768
|
+
return _namespace_SOFA('SO_0000370')
|
773
769
|
|
774
770
|
@classmethod
|
775
771
|
def enzymatic_RNA(cls):
|
776
772
|
"""An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein. (cls, RSC:cb)
|
777
|
-
(
|
773
|
+
(SO_0000372)
|
778
774
|
"""
|
779
|
-
return _namespace_SOFA('
|
775
|
+
return _namespace_SOFA('SO_0000372')
|
780
776
|
|
781
777
|
@classmethod
|
782
778
|
def ribozyme(cls):
|
783
779
|
"""An RNA with catalytic activity. (cls, SO:ma)
|
784
|
-
(
|
780
|
+
(SO_0000374)
|
785
781
|
"""
|
786
|
-
return _namespace_SOFA('
|
782
|
+
return _namespace_SOFA('SO_0000374')
|
787
783
|
|
788
784
|
@classmethod
|
789
785
|
def rRNA_5_8S(cls):
|
790
786
|
"""5_8S ribosomal RNA (cls, 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. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002)
|
791
|
-
(
|
787
|
+
(SO_0000375)
|
792
788
|
"""
|
793
|
-
return _namespace_SOFA('
|
789
|
+
return _namespace_SOFA('SO_0000375')
|
794
790
|
|
795
791
|
@classmethod
|
796
792
|
def hammerhead_ribozyme(cls):
|
797
793
|
"""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. (cls, PMID:2436805)
|
798
|
-
(
|
794
|
+
(SO_0000380)
|
799
795
|
"""
|
800
|
-
return _namespace_SOFA('
|
796
|
+
return _namespace_SOFA('SO_0000380')
|
801
797
|
|
802
798
|
@classmethod
|
803
799
|
def RNase_MRP_RNA(cls):
|
804
800
|
"""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. (cls, http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030)
|
805
|
-
(
|
801
|
+
(SO_0000385)
|
806
802
|
"""
|
807
|
-
return _namespace_SOFA('
|
803
|
+
return _namespace_SOFA('SO_0000385')
|
808
804
|
|
809
805
|
@classmethod
|
810
806
|
def RNase_P_RNA(cls):
|
811
807
|
"""The RNA component of Ribonuclease P (cls, 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. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010)
|
812
|
-
(
|
808
|
+
(SO_0000386)
|
813
809
|
"""
|
814
|
-
return _namespace_SOFA('
|
810
|
+
return _namespace_SOFA('SO_0000386')
|
815
811
|
|
816
812
|
@classmethod
|
817
813
|
def telomerase_RNA(cls):
|
818
814
|
"""The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA. (cls, http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025)
|
819
|
-
(
|
815
|
+
(SO_0000390)
|
820
816
|
"""
|
821
|
-
return _namespace_SOFA('
|
817
|
+
return _namespace_SOFA('SO_0000390')
|
822
818
|
|
823
819
|
@classmethod
|
824
820
|
def U1_snRNA(cls):
|
825
821
|
"""U1 is a small nuclear RNA (cls, 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. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003)
|
826
|
-
(
|
822
|
+
(SO_0000391)
|
827
823
|
"""
|
828
|
-
return _namespace_SOFA('
|
824
|
+
return _namespace_SOFA('SO_0000391')
|
829
825
|
|
830
826
|
@classmethod
|
831
827
|
def U2_snRNA(cls):
|
832
828
|
"""U2 is a small nuclear RNA (cls, 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. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004)
|
833
|
-
(
|
829
|
+
(SO_0000392)
|
834
830
|
"""
|
835
|
-
return _namespace_SOFA('
|
831
|
+
return _namespace_SOFA('SO_0000392')
|
836
832
|
|
837
833
|
@classmethod
|
838
834
|
def U4_snRNA(cls):
|
839
835
|
"""U4 small nuclear RNA (cls, 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. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015)
|
840
|
-
(
|
836
|
+
(SO_0000393)
|
841
837
|
"""
|
842
|
-
return _namespace_SOFA('
|
838
|
+
return _namespace_SOFA('SO_0000393')
|
843
839
|
|
844
840
|
@classmethod
|
845
841
|
def U4atac_snRNA(cls):
|
846
842
|
"""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 (cls, SO:0000397). (PMID:=12409455)
|
847
|
-
(
|
843
|
+
(SO_0000394)
|
848
844
|
"""
|
849
|
-
return _namespace_SOFA('
|
845
|
+
return _namespace_SOFA('SO_0000394')
|
850
846
|
|
851
847
|
@classmethod
|
852
848
|
def U5_snRNA(cls):
|
853
849
|
"""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. (cls, http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020)
|
854
|
-
(
|
850
|
+
(SO_0000395)
|
855
851
|
"""
|
856
|
-
return _namespace_SOFA('
|
852
|
+
return _namespace_SOFA('SO_0000395')
|
857
853
|
|
858
854
|
@classmethod
|
859
855
|
def U6_snRNA(cls):
|
860
856
|
"""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. (cls, http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015)
|
861
|
-
(
|
857
|
+
(SO_0000396)
|
862
858
|
"""
|
863
|
-
return _namespace_SOFA('
|
859
|
+
return _namespace_SOFA('SO_0000396')
|
864
860
|
|
865
861
|
@classmethod
|
866
862
|
def U6atac_snRNA(cls):
|
867
863
|
"""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 (cls, SO:0000394). (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract)
|
868
|
-
(
|
864
|
+
(SO_0000397)
|
869
865
|
"""
|
870
|
-
return _namespace_SOFA('
|
866
|
+
return _namespace_SOFA('SO_0000397')
|
871
867
|
|
872
868
|
@classmethod
|
873
869
|
def U11_snRNA(cls):
|
874
870
|
"""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. (cls, PMID:9622129)
|
875
|
-
(
|
871
|
+
(SO_0000398)
|
876
872
|
"""
|
877
|
-
return _namespace_SOFA('
|
873
|
+
return _namespace_SOFA('SO_0000398')
|
878
874
|
|
879
875
|
@classmethod
|
880
876
|
def U12_snRNA(cls):
|
881
877
|
"""The U12 small nuclear (cls, 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. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007)
|
882
|
-
(
|
878
|
+
(SO_0000399)
|
883
879
|
"""
|
884
|
-
return _namespace_SOFA('
|
880
|
+
return _namespace_SOFA('SO_0000399')
|
885
881
|
|
886
882
|
@classmethod
|
887
883
|
def U14_snoRNA(cls):
|
888
884
|
"""U14 small nucleolar RNA (cls, 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. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119)
|
889
|
-
(
|
885
|
+
(SO_0000403)
|
890
886
|
"""
|
891
|
-
return _namespace_SOFA('
|
887
|
+
return _namespace_SOFA('SO_0000403')
|
892
888
|
|
893
889
|
@classmethod
|
894
890
|
def vault_RNA(cls):
|
895
891
|
"""A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (cls, 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. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006)
|
896
|
-
(
|
892
|
+
(SO_0000404)
|
897
893
|
"""
|
898
|
-
return _namespace_SOFA('
|
894
|
+
return _namespace_SOFA('SO_0000404')
|
899
895
|
|
900
896
|
@classmethod
|
901
897
|
def Y_RNA(cls):
|
902
898
|
"""Y RNAs are components of the Ro ribonucleoprotein particle (cls, 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. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019)
|
903
|
-
(
|
899
|
+
(SO_0000405)
|
904
900
|
"""
|
905
|
-
return _namespace_SOFA('
|
901
|
+
return _namespace_SOFA('SO_0000405')
|
906
902
|
|
907
903
|
@classmethod
|
908
904
|
def rRNA_18S(cls):
|
909
905
|
"""A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome. (cls, SO:ke)
|
910
|
-
(
|
906
|
+
(SO_0000407)
|
911
907
|
"""
|
912
|
-
return _namespace_SOFA('
|
908
|
+
return _namespace_SOFA('SO_0000407')
|
913
909
|
|
914
910
|
@classmethod
|
915
911
|
def binding_site(cls):
|
916
912
|
"""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. (cls, EBIBS:GAR, SO:ke)
|
917
|
-
(
|
913
|
+
(SO_0000409)
|
918
914
|
"""
|
919
|
-
return _namespace_SOFA('
|
915
|
+
return _namespace_SOFA('SO_0000409')
|
920
916
|
|
921
917
|
@classmethod
|
922
918
|
def protein_binding_site(cls):
|
923
919
|
"""A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules. (cls, SO:ke)
|
924
|
-
(
|
920
|
+
(SO_0000410)
|
925
921
|
"""
|
926
|
-
return _namespace_SOFA('
|
922
|
+
return _namespace_SOFA('SO_0000410')
|
927
923
|
|
928
924
|
@classmethod
|
929
925
|
def restriction_fragment(cls):
|
930
926
|
"""A region of polynucleotide sequence produced by digestion with a restriction endonuclease. (cls, SO:ke)
|
931
|
-
(
|
927
|
+
(SO_0000412)
|
932
928
|
"""
|
933
|
-
return _namespace_SOFA('
|
929
|
+
return _namespace_SOFA('SO_0000412')
|
934
930
|
|
935
931
|
@classmethod
|
936
932
|
def sequence_difference(cls):
|
937
933
|
"""A region where the sequence differs from that of a specified sequence. (cls, SO:ke)
|
938
|
-
(
|
934
|
+
(SO_0000413)
|
939
935
|
"""
|
940
|
-
return _namespace_SOFA('
|
936
|
+
return _namespace_SOFA('SO_0000413')
|
941
937
|
|
942
938
|
@classmethod
|
943
939
|
def signal_peptide(cls):
|
944
940
|
"""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. (cls, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
|
945
|
-
(
|
941
|
+
(SO_0000418)
|
946
942
|
"""
|
947
|
-
return _namespace_SOFA('
|
943
|
+
return _namespace_SOFA('SO_0000418')
|
948
944
|
|
949
945
|
@classmethod
|
950
946
|
def mature_protein_region(cls):
|
951
947
|
"""The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide. (cls, EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb)
|
952
|
-
(
|
948
|
+
(SO_0000419)
|
953
949
|
"""
|
954
|
-
return _namespace_SOFA('
|
950
|
+
return _namespace_SOFA('SO_0000419')
|
955
951
|
|
956
952
|
@classmethod
|
957
953
|
def ARS(cls):
|
958
954
|
"""A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host. (cls, SO:ma)
|
959
|
-
(
|
955
|
+
(SO_0000436)
|
960
956
|
"""
|
961
|
-
return _namespace_SOFA('
|
957
|
+
return _namespace_SOFA('SO_0000436')
|
962
958
|
|
963
959
|
@classmethod
|
964
960
|
def ss_oligo(cls):
|
965
961
|
"""A single stranded oligonucleotide. (cls, SO:ke)
|
966
|
-
(
|
962
|
+
(SO_0000441)
|
967
963
|
"""
|
968
|
-
return _namespace_SOFA('
|
964
|
+
return _namespace_SOFA('SO_0000441')
|
969
965
|
|
970
966
|
@classmethod
|
971
967
|
def ds_oligo(cls):
|
972
968
|
"""A double stranded oligonucleotide. (cls, SO:ke)
|
973
|
-
(
|
969
|
+
(SO_0000442)
|
974
970
|
"""
|
975
|
-
return _namespace_SOFA('
|
971
|
+
return _namespace_SOFA('SO_0000442')
|
976
972
|
|
977
973
|
@classmethod
|
978
974
|
def rasiRNA(cls):
|
979
975
|
"""A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements. (cls, http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284)
|
980
|
-
(
|
976
|
+
(SO_0000454)
|
981
977
|
"""
|
982
|
-
return _namespace_SOFA('
|
978
|
+
return _namespace_SOFA('SO_0000454')
|
983
979
|
|
984
980
|
@classmethod
|
985
981
|
def pseudogenic_region(cls):
|
986
982
|
"""A non-functional descendent of a functional entity. (cls, SO:cjm)
|
987
|
-
(
|
983
|
+
(SO_0000462)
|
988
984
|
"""
|
989
|
-
return _namespace_SOFA('
|
985
|
+
return _namespace_SOFA('SO_0000462')
|
990
986
|
|
991
987
|
@classmethod
|
992
988
|
def decayed_exon(cls):
|
993
989
|
"""A non-functional descendant of an exon. (cls, SO:ke)
|
994
|
-
(
|
990
|
+
(SO_0000464)
|
995
991
|
"""
|
996
|
-
return _namespace_SOFA('
|
992
|
+
return _namespace_SOFA('SO_0000464')
|
997
993
|
|
998
994
|
@classmethod
|
999
995
|
def golden_path_fragment(cls):
|
1000
996
|
"""One of the pieces of sequence that make up a golden path. (cls, SO:rd)
|
1001
|
-
(
|
997
|
+
(SO_0000468)
|
1002
998
|
"""
|
1003
|
-
return _namespace_SOFA('
|
999
|
+
return _namespace_SOFA('SO_0000468')
|
1004
1000
|
|
1005
1001
|
@classmethod
|
1006
1002
|
def tiling_path(cls):
|
1007
1003
|
"""A set of regions which overlap with minimal polymorphism to form a linear sequence. (cls, SO:cjm)
|
1008
|
-
(
|
1004
|
+
(SO_0000472)
|
1009
1005
|
"""
|
1010
|
-
return _namespace_SOFA('
|
1006
|
+
return _namespace_SOFA('SO_0000472')
|
1011
1007
|
|
1012
1008
|
@classmethod
|
1013
1009
|
def tiling_path_fragment(cls):
|
1014
1010
|
"""A piece of sequence that makes up a tiling_path (cls, SO:0000472). (SO:ke)
|
1015
|
-
(
|
1011
|
+
(SO_0000474)
|
1016
1012
|
"""
|
1017
|
-
return _namespace_SOFA('
|
1013
|
+
return _namespace_SOFA('SO_0000474')
|
1018
1014
|
|
1019
1015
|
@classmethod
|
1020
1016
|
def nc_primary_transcript(cls):
|
1021
1017
|
"""A primary transcript that is never translated into a protein. (cls, SO:ke)
|
1022
|
-
(
|
1018
|
+
(SO_0000483)
|
1023
1019
|
"""
|
1024
|
-
return _namespace_SOFA('
|
1020
|
+
return _namespace_SOFA('SO_0000483')
|
1025
1021
|
|
1026
1022
|
@classmethod
|
1027
1023
|
def three_prime_coding_exon_noncoding_region(cls):
|
1028
1024
|
"""The sequence of the 3' exon that is not coding. (cls, SO:ke)
|
1029
|
-
(
|
1025
|
+
(SO_0000484)
|
1030
1026
|
"""
|
1031
|
-
return _namespace_SOFA('
|
1027
|
+
return _namespace_SOFA('SO_0000484')
|
1032
1028
|
|
1033
1029
|
@classmethod
|
1034
1030
|
def five_prime_coding_exon_noncoding_region(cls):
|
1035
1031
|
"""The sequence of the 5' exon preceding the start codon. (cls, SO:ke)
|
1036
|
-
(
|
1032
|
+
(SO_0000486)
|
1037
1033
|
"""
|
1038
|
-
return _namespace_SOFA('
|
1034
|
+
return _namespace_SOFA('SO_0000486')
|
1039
1035
|
|
1040
1036
|
@classmethod
|
1041
1037
|
def virtual_sequence(cls):
|
1042
1038
|
"""A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database. (cls, SO:ke)
|
1043
|
-
(
|
1039
|
+
(SO_0000499)
|
1044
1040
|
"""
|
1045
|
-
return _namespace_SOFA('
|
1041
|
+
return _namespace_SOFA('SO_0000499')
|
1046
1042
|
|
1047
1043
|
@classmethod
|
1048
1044
|
def transcribed_region(cls):
|
1049
1045
|
"""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. (cls, SO:ke)
|
1050
|
-
(
|
1046
|
+
(SO_0000502)
|
1051
1047
|
"""
|
1052
|
-
return _namespace_SOFA('
|
1048
|
+
return _namespace_SOFA('SO_0000502')
|
1053
1049
|
|
1054
1050
|
@classmethod
|
1055
1051
|
def polyA_signal_sequence(cls):
|
1056
1052
|
"""The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA. (cls, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
|
1057
|
-
(
|
1053
|
+
(SO_0000551)
|
1058
1054
|
"""
|
1059
|
-
return _namespace_SOFA('
|
1055
|
+
return _namespace_SOFA('SO_0000551')
|
1060
1056
|
|
1061
1057
|
@classmethod
|
1062
1058
|
def polyA_site(cls):
|
1063
1059
|
"""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. (cls, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
|
1064
|
-
(
|
1060
|
+
(SO_0000553)
|
1065
1061
|
"""
|
1066
|
-
return _namespace_SOFA('
|
1062
|
+
return _namespace_SOFA('SO_0000553')
|
1067
1063
|
|
1068
1064
|
@classmethod
|
1069
1065
|
def centromere(cls):
|
1070
1066
|
"""A region of chromosome where the spindle fibers attach during mitosis and meiosis. (cls, SO:ke)
|
1071
|
-
(
|
1067
|
+
(SO_0000577)
|
1072
1068
|
"""
|
1073
|
-
return _namespace_SOFA('
|
1069
|
+
return _namespace_SOFA('SO_0000577')
|
1074
1070
|
|
1075
1071
|
@classmethod
|
1076
1072
|
def cap(cls):
|
1077
1073
|
"""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. (cls, http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html)
|
1078
|
-
(
|
1074
|
+
(SO_0000581)
|
1079
1075
|
"""
|
1080
|
-
return _namespace_SOFA('
|
1076
|
+
return _namespace_SOFA('SO_0000581')
|
1081
1077
|
|
1082
1078
|
@classmethod
|
1083
1079
|
def group_I_intron(cls):
|
1084
1080
|
"""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 (cls, 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. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028)
|
1085
|
-
(
|
1081
|
+
(SO_0000587)
|
1086
1082
|
"""
|
1087
|
-
return _namespace_SOFA('
|
1083
|
+
return _namespace_SOFA('SO_0000587')
|
1088
1084
|
|
1089
1085
|
@classmethod
|
1090
1086
|
def autocatalytically_spliced_intron(cls):
|
1091
1087
|
"""A self spliced intron. (cls, SO:ke)
|
1092
|
-
(
|
1088
|
+
(SO_0000588)
|
1093
1089
|
"""
|
1094
|
-
return _namespace_SOFA('
|
1090
|
+
return _namespace_SOFA('SO_0000588')
|
1095
1091
|
|
1096
1092
|
@classmethod
|
1097
1093
|
def SRP_RNA(cls):
|
1098
1094
|
"""The signal recognition particle (cls, 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. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017)
|
1099
|
-
(
|
1095
|
+
(SO_0000590)
|
1100
1096
|
"""
|
1101
|
-
return _namespace_SOFA('
|
1097
|
+
return _namespace_SOFA('SO_0000590')
|
1102
1098
|
|
1103
1099
|
@classmethod
|
1104
1100
|
def C_D_box_snoRNA(cls):
|
1105
1101
|
"""Most box C/D snoRNAs also contain long (cls, >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'. (http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html)
|
1106
|
-
(
|
1102
|
+
(SO_0000593)
|
1107
1103
|
"""
|
1108
|
-
return _namespace_SOFA('
|
1104
|
+
return _namespace_SOFA('SO_0000593')
|
1109
1105
|
|
1110
1106
|
@classmethod
|
1111
1107
|
def guide_RNA(cls):
|
1112
1108
|
"""A short 3'-uridylated RNA that can form a duplex (cls, except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA. (http://www.rna.ucla.edu/index.html)
|
1113
|
-
(
|
1109
|
+
(SO_0000602)
|
1114
1110
|
"""
|
1115
|
-
return _namespace_SOFA('
|
1111
|
+
return _namespace_SOFA('SO_0000602')
|
1116
1112
|
|
1117
1113
|
@classmethod
|
1118
1114
|
def group_II_intron(cls):
|
1119
1115
|
"""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 (cls, 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. (http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml)
|
1120
|
-
(
|
1116
|
+
(SO_0000603)
|
1121
1117
|
"""
|
1122
|
-
return _namespace_SOFA('
|
1118
|
+
return _namespace_SOFA('SO_0000603')
|
1123
1119
|
|
1124
1120
|
@classmethod
|
1125
1121
|
def intergenic_region(cls):
|
1126
1122
|
"""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. (cls, SO:cjm)
|
1127
|
-
(
|
1123
|
+
(SO_0000605)
|
1128
1124
|
"""
|
1129
|
-
return _namespace_SOFA('
|
1125
|
+
return _namespace_SOFA('SO_0000605')
|
1130
1126
|
|
1131
1127
|
@classmethod
|
1132
1128
|
def polyA_sequence(cls):
|
1133
1129
|
"""Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs. (cls, SO:ke)
|
1134
|
-
(
|
1130
|
+
(SO_0000610)
|
1135
1131
|
"""
|
1136
|
-
return _namespace_SOFA('
|
1132
|
+
return _namespace_SOFA('SO_0000610')
|
1137
1133
|
|
1138
1134
|
@classmethod
|
1139
1135
|
def branch_site(cls):
|
1140
1136
|
"""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. (cls, SO:ke)
|
1141
|
-
(
|
1137
|
+
(SO_0000611)
|
1142
1138
|
"""
|
1143
|
-
return _namespace_SOFA('
|
1139
|
+
return _namespace_SOFA('SO_0000611')
|
1144
1140
|
|
1145
1141
|
@classmethod
|
1146
1142
|
def polypyrimidine_tract(cls):
|
1147
1143
|
"""The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing. (cls, http://nar.oupjournals.org/cgi/content/full/25/4/888)
|
1148
|
-
(
|
1144
|
+
(SO_0000612)
|
1149
1145
|
"""
|
1150
|
-
return _namespace_SOFA('
|
1146
|
+
return _namespace_SOFA('SO_0000612')
|
1151
1147
|
|
1152
1148
|
@classmethod
|
1153
1149
|
def transcription_end_site(cls):
|
1154
1150
|
"""The base where transcription ends. (cls, SO:ke)
|
1155
|
-
(
|
1151
|
+
(SO_0000616)
|
1156
1152
|
"""
|
1157
|
-
return _namespace_SOFA('
|
1153
|
+
return _namespace_SOFA('SO_0000616')
|
1158
1154
|
|
1159
1155
|
@classmethod
|
1160
1156
|
def telomere(cls):
|
1161
1157
|
"""A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end. (cls, SO:ma)
|
1162
|
-
(
|
1158
|
+
(SO_0000624)
|
1163
1159
|
"""
|
1164
|
-
return _namespace_SOFA('
|
1160
|
+
return _namespace_SOFA('SO_0000624')
|
1165
1161
|
|
1166
1162
|
@classmethod
|
1167
1163
|
def silencer(cls):
|
1168
1164
|
"""A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control. (cls, SO:ke)
|
1169
|
-
(
|
1165
|
+
(SO_0000625)
|
1170
1166
|
"""
|
1171
|
-
return _namespace_SOFA('
|
1167
|
+
return _namespace_SOFA('SO_0000625')
|
1172
1168
|
|
1173
1169
|
@classmethod
|
1174
1170
|
def insulator(cls):
|
1175
1171
|
"""A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression. (cls, SO:regcreative)
|
1176
|
-
(
|
1172
|
+
(SO_0000627)
|
1177
1173
|
"""
|
1178
|
-
return _namespace_SOFA('
|
1174
|
+
return _namespace_SOFA('SO_0000627')
|
1179
1175
|
|
1180
1176
|
@classmethod
|
1181
1177
|
def chromosomal_structural_element(cls):
|
1182
|
-
return _namespace_SOFA('
|
1178
|
+
return _namespace_SOFA('SO_0000628')
|
1183
1179
|
|
1184
1180
|
@classmethod
|
1185
1181
|
def minisatellite(cls):
|
1186
1182
|
"""A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp. (cls, http://www.informatics.jax.org/silver/glossary.shtml)
|
1187
|
-
(
|
1183
|
+
(SO_0000643)
|
1188
1184
|
"""
|
1189
|
-
return _namespace_SOFA('
|
1185
|
+
return _namespace_SOFA('SO_0000643')
|
1190
1186
|
|
1191
1187
|
@classmethod
|
1192
1188
|
def antisense_RNA(cls):
|
1193
1189
|
"""Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA. (cls, SO:ke)
|
1194
|
-
(
|
1190
|
+
(SO_0000644)
|
1195
1191
|
"""
|
1196
|
-
return _namespace_SOFA('
|
1192
|
+
return _namespace_SOFA('SO_0000644')
|
1197
1193
|
|
1198
1194
|
@classmethod
|
1199
1195
|
def antisense_primary_transcript(cls):
|
1200
1196
|
"""The reverse complement of the primary transcript. (cls, SO:ke)
|
1201
|
-
(
|
1197
|
+
(SO_0000645)
|
1202
1198
|
"""
|
1203
|
-
return _namespace_SOFA('
|
1199
|
+
return _namespace_SOFA('SO_0000645')
|
1204
1200
|
|
1205
1201
|
@classmethod
|
1206
1202
|
def siRNA(cls):
|
1207
1203
|
"""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 (cls, via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules. (PMID:12592000)
|
1208
|
-
(
|
1204
|
+
(SO_0000646)
|
1209
1205
|
"""
|
1210
|
-
return _namespace_SOFA('
|
1206
|
+
return _namespace_SOFA('SO_0000646')
|
1211
1207
|
|
1212
1208
|
@classmethod
|
1213
1209
|
def stRNA(cls):
|
1214
1210
|
"""Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans. (cls, PMID:11081512)
|
1215
|
-
(
|
1211
|
+
(SO_0000649)
|
1216
1212
|
"""
|
1217
|
-
return _namespace_SOFA('
|
1213
|
+
return _namespace_SOFA('SO_0000649')
|
1218
1214
|
|
1219
1215
|
@classmethod
|
1220
1216
|
def small_subunit_rRNA(cls):
|
1221
1217
|
"""Ribosomal RNA transcript that structures the small subunit of the ribosome. (cls, SO:ke)
|
1222
|
-
(
|
1218
|
+
(SO_0000650)
|
1223
1219
|
"""
|
1224
|
-
return _namespace_SOFA('
|
1220
|
+
return _namespace_SOFA('SO_0000650')
|
1225
1221
|
|
1226
1222
|
@classmethod
|
1227
1223
|
def large_subunit_rRNA(cls):
|
1228
1224
|
"""Ribosomal RNA transcript that structures the large subunit of the ribosome. (cls, SO:ke)
|
1229
|
-
(
|
1225
|
+
(SO_0000651)
|
1230
1226
|
"""
|
1231
|
-
return _namespace_SOFA('
|
1227
|
+
return _namespace_SOFA('SO_0000651')
|
1232
1228
|
|
1233
1229
|
@classmethod
|
1234
1230
|
def rRNA_5S(cls):
|
1235
1231
|
"""5S ribosomal RNA (cls, 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. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001)
|
1236
|
-
(
|
1232
|
+
(SO_0000652)
|
1237
1233
|
"""
|
1238
|
-
return _namespace_SOFA('
|
1234
|
+
return _namespace_SOFA('SO_0000652')
|
1239
1235
|
|
1240
1236
|
@classmethod
|
1241
1237
|
def rRNA_28S(cls):
|
1242
1238
|
"""A component of the large ribosomal subunit. (cls, SO:ke)
|
1243
|
-
(
|
1239
|
+
(SO_0000653)
|
1244
1240
|
"""
|
1245
|
-
return _namespace_SOFA('
|
1241
|
+
return _namespace_SOFA('SO_0000653')
|
1246
1242
|
|
1247
1243
|
@classmethod
|
1248
1244
|
def ncRNA(cls):
|
1249
1245
|
"""An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product. (cls, SO:ke)
|
1250
|
-
(
|
1246
|
+
(SO_0000655)
|
1251
1247
|
"""
|
1252
|
-
return _namespace_SOFA('
|
1248
|
+
return _namespace_SOFA('SO_0000655')
|
1253
1249
|
|
1254
1250
|
@classmethod
|
1255
1251
|
def repeat_region(cls):
|
1256
1252
|
"""A region of sequence containing one or more repeat units. (cls, SO:ke)
|
1257
|
-
(
|
1253
|
+
(SO_0000657)
|
1258
1254
|
"""
|
1259
|
-
return _namespace_SOFA('
|
1255
|
+
return _namespace_SOFA('SO_0000657')
|
1260
1256
|
|
1261
1257
|
@classmethod
|
1262
1258
|
def dispersed_repeat(cls):
|
1263
1259
|
"""A repeat that is located at dispersed sites in the genome. (cls, SO:ke)
|
1264
|
-
(
|
1260
|
+
(SO_0000658)
|
1265
1261
|
"""
|
1266
|
-
return _namespace_SOFA('
|
1262
|
+
return _namespace_SOFA('SO_0000658')
|
1267
1263
|
|
1268
1264
|
@classmethod
|
1269
1265
|
def spliceosomal_intron(cls):
|
1270
1266
|
"""An intron which is spliced by the spliceosome. (cls, SO:ke)
|
1271
|
-
(
|
1267
|
+
(SO_0000662)
|
1272
1268
|
"""
|
1273
|
-
return _namespace_SOFA('
|
1269
|
+
return _namespace_SOFA('SO_0000662')
|
1274
1270
|
|
1275
1271
|
@classmethod
|
1276
1272
|
def insertion(cls):
|
1277
1273
|
"""The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence. (cls, SO:ke)
|
1278
|
-
(
|
1274
|
+
(SO_0000667)
|
1279
1275
|
"""
|
1280
|
-
return _namespace_SOFA('
|
1276
|
+
return _namespace_SOFA('SO_0000667')
|
1281
1277
|
|
1282
1278
|
@classmethod
|
1283
1279
|
def EST_match(cls):
|
1284
1280
|
"""A match against an EST sequence. (cls, SO:ke)
|
1285
|
-
(
|
1281
|
+
(SO_0000668)
|
1286
1282
|
"""
|
1287
|
-
return _namespace_SOFA('
|
1283
|
+
return _namespace_SOFA('SO_0000668')
|
1288
1284
|
|
1289
1285
|
@classmethod
|
1290
1286
|
def transcript(cls):
|
1291
1287
|
"""An RNA synthesized on a DNA or RNA template by an RNA polymerase. (cls, SO:ma)
|
1292
|
-
(
|
1288
|
+
(SO_0000673)
|
1293
1289
|
"""
|
1294
|
-
return _namespace_SOFA('
|
1290
|
+
return _namespace_SOFA('SO_0000673')
|
1295
1291
|
|
1296
1292
|
@classmethod
|
1297
1293
|
def nuclease_sensitive_site(cls):
|
1298
1294
|
"""A region of nucleotide sequence targeted by a nuclease enzyme. (cls, SO:ma)
|
1299
|
-
(
|
1295
|
+
(SO_0000684)
|
1300
1296
|
"""
|
1301
|
-
return _namespace_SOFA('
|
1297
|
+
return _namespace_SOFA('SO_0000684')
|
1302
1298
|
|
1303
1299
|
@classmethod
|
1304
1300
|
def deletion_junction(cls):
|
1305
1301
|
"""The space between two bases in a sequence which marks the position where a deletion has occurred. (cls, SO:ke)
|
1306
|
-
(
|
1302
|
+
(SO_0000687)
|
1307
1303
|
"""
|
1308
|
-
return _namespace_SOFA('
|
1304
|
+
return _namespace_SOFA('SO_0000687')
|
1309
1305
|
|
1310
1306
|
@classmethod
|
1311
1307
|
def golden_path(cls):
|
1312
1308
|
"""A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence. (cls, SO:ls)
|
1313
|
-
(
|
1309
|
+
(SO_0000688)
|
1314
1310
|
"""
|
1315
|
-
return _namespace_SOFA('
|
1311
|
+
return _namespace_SOFA('SO_0000688')
|
1316
1312
|
|
1317
1313
|
@classmethod
|
1318
1314
|
def cDNA_match(cls):
|
1319
1315
|
"""A match against cDNA sequence. (cls, SO:ke)
|
1320
|
-
(
|
1316
|
+
(SO_0000689)
|
1321
1317
|
"""
|
1322
|
-
return _namespace_SOFA('
|
1318
|
+
return _namespace_SOFA('SO_0000689')
|
1323
1319
|
|
1324
1320
|
@classmethod
|
1325
1321
|
def SNP(cls):
|
1326
1322
|
"""SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(cls, s), wherein the least frequent variant has an abundance of 1% or greater. (SO:cb)
|
1327
|
-
(
|
1323
|
+
(SO_0000694)
|
1328
1324
|
"""
|
1329
|
-
return _namespace_SOFA('
|
1325
|
+
return _namespace_SOFA('SO_0000694')
|
1330
1326
|
|
1331
1327
|
@classmethod
|
1332
1328
|
def reagent(cls):
|
1333
1329
|
"""A sequence used in experiment. (cls, SO:ke)
|
1334
|
-
(
|
1330
|
+
(SO_0000695)
|
1335
1331
|
"""
|
1336
|
-
return _namespace_SOFA('
|
1332
|
+
return _namespace_SOFA('SO_0000695')
|
1337
1333
|
|
1338
1334
|
@classmethod
|
1339
1335
|
def oligo(cls):
|
1340
1336
|
"""A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. (cls, SO:ma)
|
1341
|
-
(
|
1337
|
+
(SO_0000696)
|
1342
1338
|
"""
|
1343
|
-
return _namespace_SOFA('
|
1339
|
+
return _namespace_SOFA('SO_0000696')
|
1344
1340
|
|
1345
1341
|
@classmethod
|
1346
1342
|
def junction(cls):
|
1347
1343
|
"""A sequence_feature with an extent of zero. (cls, SO:ke)
|
1348
|
-
(
|
1344
|
+
(SO_0000699)
|
1349
1345
|
"""
|
1350
|
-
return _namespace_SOFA('
|
1346
|
+
return _namespace_SOFA('SO_0000699')
|
1351
1347
|
|
1352
1348
|
@classmethod
|
1353
1349
|
def remark(cls):
|
1354
1350
|
"""A comment about the sequence. (cls, SO:ke)
|
1355
|
-
(
|
1351
|
+
(SO_0000700)
|
1356
1352
|
"""
|
1357
|
-
return _namespace_SOFA('
|
1353
|
+
return _namespace_SOFA('SO_0000700')
|
1358
1354
|
|
1359
1355
|
@classmethod
|
1360
1356
|
def possible_base_call_error(cls):
|
1361
1357
|
"""A region of sequence where the validity of the base calling is questionable. (cls, SO:ke)
|
1362
|
-
(
|
1358
|
+
(SO_0000701)
|
1363
1359
|
"""
|
1364
|
-
return _namespace_SOFA('
|
1360
|
+
return _namespace_SOFA('SO_0000701')
|
1365
1361
|
|
1366
1362
|
@classmethod
|
1367
1363
|
def possible_assembly_error(cls):
|
1368
1364
|
"""A region of sequence where there may have been an error in the assembly. (cls, SO:ke)
|
1369
|
-
(
|
1365
|
+
(SO_0000702)
|
1370
1366
|
"""
|
1371
|
-
return _namespace_SOFA('
|
1367
|
+
return _namespace_SOFA('SO_0000702')
|
1372
1368
|
|
1373
1369
|
@classmethod
|
1374
1370
|
def experimental_result_region(cls):
|
1375
1371
|
"""A region of sequence implicated in an experimental result. (cls, SO:ke)
|
1376
|
-
(
|
1372
|
+
(SO_0000703)
|
1377
1373
|
"""
|
1378
|
-
return _namespace_SOFA('
|
1374
|
+
return _namespace_SOFA('SO_0000703')
|
1379
1375
|
|
1380
1376
|
@classmethod
|
1381
1377
|
def gene(cls):
|
1382
1378
|
"""A region (cls, 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. (SO:immuno_workshop)
|
1383
|
-
(
|
1379
|
+
(SO_0000704)
|
1384
1380
|
"""
|
1385
|
-
return _namespace_SOFA('
|
1381
|
+
return _namespace_SOFA('SO_0000704')
|
1386
1382
|
|
1387
1383
|
@classmethod
|
1388
1384
|
def tandem_repeat(cls):
|
1389
1385
|
"""Two or more adjcent copies of a region (cls, of length greater than 1). (SO:ke)
|
1390
|
-
(
|
1386
|
+
(SO_0000705)
|
1391
1387
|
"""
|
1392
|
-
return _namespace_SOFA('
|
1388
|
+
return _namespace_SOFA('SO_0000705')
|
1393
1389
|
|
1394
1390
|
@classmethod
|
1395
1391
|
def trans_splice_acceptor_site(cls):
|
1396
1392
|
"""The 3' splice site of the acceptor primary transcript. (cls, SO:ke)
|
1397
|
-
(
|
1393
|
+
(SO_0000706)
|
1398
1394
|
"""
|
1399
|
-
return _namespace_SOFA('
|
1395
|
+
return _namespace_SOFA('SO_0000706')
|
1400
1396
|
|
1401
1397
|
@classmethod
|
1402
1398
|
def nucleotide_motif(cls):
|
1403
1399
|
"""A region of nucleotide sequence corresponding to a known motif. (cls, SO:ke)
|
1404
|
-
(
|
1400
|
+
(SO_0000714)
|
1405
1401
|
"""
|
1406
|
-
return _namespace_SOFA('
|
1402
|
+
return _namespace_SOFA('SO_0000714')
|
1407
1403
|
|
1408
1404
|
@classmethod
|
1409
1405
|
def RNA_motif(cls):
|
1410
1406
|
"""A motif that is active in RNA sequence. (cls, SO:ke)
|
1411
|
-
(
|
1407
|
+
(SO_0000715)
|
1412
1408
|
"""
|
1413
|
-
return _namespace_SOFA('
|
1409
|
+
return _namespace_SOFA('SO_0000715')
|
1414
1410
|
|
1415
1411
|
@classmethod
|
1416
1412
|
def reading_frame(cls):
|
1417
1413
|
"""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. (cls, SGD:rb)
|
1418
|
-
(
|
1414
|
+
(SO_0000717)
|
1419
1415
|
"""
|
1420
|
-
return _namespace_SOFA('
|
1416
|
+
return _namespace_SOFA('SO_0000717')
|
1421
1417
|
|
1422
1418
|
@classmethod
|
1423
1419
|
def ultracontig(cls):
|
1424
1420
|
"""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. (cls, FB:WG)
|
1425
|
-
(
|
1421
|
+
(SO_0000719)
|
1426
1422
|
"""
|
1427
|
-
return _namespace_SOFA('
|
1423
|
+
return _namespace_SOFA('SO_0000719')
|
1428
1424
|
|
1429
1425
|
@classmethod
|
1430
1426
|
def oriT(cls):
|
1431
1427
|
"""A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization. (cls, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
|
1432
|
-
(
|
1428
|
+
(SO_0000724)
|
1433
1429
|
"""
|
1434
|
-
return _namespace_SOFA('
|
1430
|
+
return _namespace_SOFA('SO_0000724')
|
1435
1431
|
|
1436
1432
|
@classmethod
|
1437
1433
|
def transit_peptide(cls):
|
1438
1434
|
"""The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (cls, chloroplast, mitochondrion, microbody or cyanelle). (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
|
1439
|
-
(
|
1435
|
+
(SO_0000725)
|
1440
1436
|
"""
|
1441
|
-
return _namespace_SOFA('
|
1437
|
+
return _namespace_SOFA('SO_0000725')
|
1442
1438
|
|
1443
1439
|
@classmethod
|
1444
1440
|
def CRM(cls):
|
1445
1441
|
"""A regulatory_region where more than 1 TF_binding_site together are regulatorily active. (cls, SO:SG)
|
1446
|
-
(
|
1442
|
+
(SO_0000727)
|
1447
1443
|
"""
|
1448
|
-
return _namespace_SOFA('
|
1444
|
+
return _namespace_SOFA('SO_0000727')
|
1449
1445
|
|
1450
1446
|
@classmethod
|
1451
1447
|
def gap(cls):
|
1452
1448
|
"""A gap in the sequence of known length. The unknown bases are filled in with N's. (cls, SO:ke)
|
1453
|
-
(
|
1449
|
+
(SO_0000730)
|
1454
1450
|
"""
|
1455
|
-
return _namespace_SOFA('
|
1451
|
+
return _namespace_SOFA('SO_0000730')
|
1456
1452
|
|
1457
1453
|
@classmethod
|
1458
1454
|
def gene_group_regulatory_region(cls):
|
1459
|
-
return _namespace_SOFA('
|
1455
|
+
return _namespace_SOFA('SO_0000752')
|
1460
1456
|
|
1461
1457
|
@classmethod
|
1462
1458
|
def clone_insert(cls):
|
1463
1459
|
"""The region of sequence that has been inserted and is being propagated by the clone. (cls, SO:ke)
|
1464
|
-
(
|
1460
|
+
(SO_0000753)
|
1465
1461
|
"""
|
1466
|
-
return _namespace_SOFA('
|
1462
|
+
return _namespace_SOFA('SO_0000753')
|
1467
1463
|
|
1468
1464
|
@classmethod
|
1469
1465
|
def pseudogenic_rRNA(cls):
|
1470
1466
|
"""A non functional descendent of an rRNA. (cls, SO:ke)
|
1471
|
-
(
|
1467
|
+
(SO_0000777)
|
1472
1468
|
"""
|
1473
|
-
return _namespace_SOFA('
|
1469
|
+
return _namespace_SOFA('SO_0000777')
|
1474
1470
|
|
1475
1471
|
@classmethod
|
1476
1472
|
def pseudogenic_tRNA(cls):
|
1477
1473
|
"""A non functional descendent of a tRNA. (cls, SO:ke)
|
1478
|
-
(
|
1474
|
+
(SO_0000778)
|
1479
1475
|
"""
|
1480
|
-
return _namespace_SOFA('
|
1476
|
+
return _namespace_SOFA('SO_0000778')
|
1481
1477
|
|
1482
1478
|
@classmethod
|
1483
1479
|
def chromosome_part(cls):
|
1484
1480
|
"""A region of a chromosome. (cls, SO:ke)
|
1485
|
-
(
|
1481
|
+
(SO_0000830)
|
1486
1482
|
"""
|
1487
|
-
return _namespace_SOFA('
|
1483
|
+
return _namespace_SOFA('SO_0000830')
|
1488
1484
|
|
1489
1485
|
@classmethod
|
1490
1486
|
def gene_member_region(cls):
|
1491
1487
|
"""A region of a gene. (cls, SO:ke)
|
1492
|
-
(
|
1488
|
+
(SO_0000831)
|
1493
1489
|
"""
|
1494
|
-
return _namespace_SOFA('
|
1490
|
+
return _namespace_SOFA('SO_0000831')
|
1495
1491
|
|
1496
1492
|
@classmethod
|
1497
1493
|
def transcript_region(cls):
|
1498
1494
|
"""A region of a transcript. (cls, SO:ke)
|
1499
|
-
(
|
1495
|
+
(SO_0000833)
|
1500
1496
|
"""
|
1501
|
-
return _namespace_SOFA('
|
1497
|
+
return _namespace_SOFA('SO_0000833')
|
1502
1498
|
|
1503
1499
|
@classmethod
|
1504
1500
|
def mature_transcript_region(cls):
|
1505
1501
|
"""A region of a mature transcript. (cls, SO:ke)
|
1506
|
-
(
|
1502
|
+
(SO_0000834)
|
1507
1503
|
"""
|
1508
|
-
return _namespace_SOFA('
|
1504
|
+
return _namespace_SOFA('SO_0000834')
|
1509
1505
|
|
1510
1506
|
@classmethod
|
1511
1507
|
def primary_transcript_region(cls):
|
1512
1508
|
"""A part of a primary transcript. (cls, SO:ke)
|
1513
|
-
(
|
1509
|
+
(SO_0000835)
|
1514
1510
|
"""
|
1515
|
-
return _namespace_SOFA('
|
1511
|
+
return _namespace_SOFA('SO_0000835')
|
1516
1512
|
|
1517
1513
|
@classmethod
|
1518
1514
|
def mRNA_region(cls):
|
1519
1515
|
"""A region of an mRNA. (cls, SO:cb)
|
1520
|
-
(
|
1516
|
+
(SO_0000836)
|
1521
1517
|
"""
|
1522
|
-
return _namespace_SOFA('
|
1518
|
+
return _namespace_SOFA('SO_0000836')
|
1523
1519
|
|
1524
1520
|
@classmethod
|
1525
1521
|
def UTR_region(cls):
|
1526
1522
|
"""A region of UTR. (cls, SO:ke)
|
1527
|
-
(
|
1523
|
+
(SO_0000837)
|
1528
1524
|
"""
|
1529
|
-
return _namespace_SOFA('
|
1525
|
+
return _namespace_SOFA('SO_0000837')
|
1530
1526
|
|
1531
1527
|
@classmethod
|
1532
1528
|
def polypeptide_region(cls):
|
1533
1529
|
"""Biological sequence region that can be assigned to a specific subsequence of a polypeptide. (cls, SO:GAR, SO:ke)
|
1534
|
-
(
|
1530
|
+
(SO_0000839)
|
1535
1531
|
"""
|
1536
|
-
return _namespace_SOFA('
|
1532
|
+
return _namespace_SOFA('SO_0000839')
|
1537
1533
|
|
1538
1534
|
@classmethod
|
1539
1535
|
def spliceosomal_intron_region(cls):
|
1540
1536
|
"""A region within an intron. (cls, SO:ke)
|
1541
|
-
(
|
1537
|
+
(SO_0000841)
|
1542
1538
|
"""
|
1543
|
-
return _namespace_SOFA('
|
1539
|
+
return _namespace_SOFA('SO_0000841')
|
1544
1540
|
|
1545
1541
|
@classmethod
|
1546
1542
|
def gene_component_region(cls):
|
1547
|
-
return _namespace_SOFA('
|
1543
|
+
return _namespace_SOFA('SO_0000842')
|
1548
1544
|
|
1549
1545
|
@classmethod
|
1550
1546
|
def CDS_region(cls):
|
1551
1547
|
"""A region of a CDS. (cls, SO:cb)
|
1552
|
-
(
|
1548
|
+
(SO_0000851)
|
1553
1549
|
"""
|
1554
|
-
return _namespace_SOFA('
|
1550
|
+
return _namespace_SOFA('SO_0000851')
|
1555
1551
|
|
1556
1552
|
@classmethod
|
1557
1553
|
def exon_region(cls):
|
1558
1554
|
"""A region of an exon. (cls, RSC:cb)
|
1559
|
-
(
|
1555
|
+
(SO_0000852)
|
1560
1556
|
"""
|
1561
|
-
return _namespace_SOFA('
|
1557
|
+
return _namespace_SOFA('SO_0000852')
|
1562
1558
|
|
1563
1559
|
@classmethod
|
1564
1560
|
def rRNA_16S(cls):
|
1565
1561
|
"""A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome. (cls, SO:ke)
|
1566
|
-
(
|
1562
|
+
(SO_0001000)
|
1567
1563
|
"""
|
1568
|
-
return _namespace_SOFA('
|
1564
|
+
return _namespace_SOFA('SO_0001000')
|
1569
1565
|
|
1570
1566
|
@classmethod
|
1571
1567
|
def rRNA_23S(cls):
|
1572
1568
|
"""A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome. (cls, SO:ke)
|
1573
|
-
(
|
1569
|
+
(SO_0001001)
|
1574
1570
|
"""
|
1575
|
-
return _namespace_SOFA('
|
1571
|
+
return _namespace_SOFA('SO_0001001')
|
1576
1572
|
|
1577
1573
|
@classmethod
|
1578
1574
|
def rRNA_25S(cls):
|
1579
1575
|
"""A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes. (cls, RSC:cb)
|
1580
|
-
(
|
1576
|
+
(SO_0001002)
|
1581
1577
|
"""
|
1582
|
-
return _namespace_SOFA('
|
1578
|
+
return _namespace_SOFA('SO_0001002')
|
1583
1579
|
|
1584
1580
|
@classmethod
|
1585
1581
|
def copy_number_variation(cls):
|
1586
1582
|
"""A variation that increases or decreases the copy number of a given region. (cls, SO:ke)
|
1587
|
-
(
|
1583
|
+
(SO_0001019)
|
1588
1584
|
"""
|
1589
|
-
return _namespace_SOFA('
|
1585
|
+
return _namespace_SOFA('SO_0001019')
|
1590
1586
|
|
1591
1587
|
@classmethod
|
1592
1588
|
def mobile_genetic_element(cls):
|
1593
1589
|
"""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. (cls, PMID:14681355)
|
1594
|
-
(
|
1590
|
+
(SO_0001037)
|
1595
1591
|
"""
|
1596
|
-
return _namespace_SOFA('
|
1592
|
+
return _namespace_SOFA('SO_0001037')
|
1597
1593
|
|
1598
1594
|
@classmethod
|
1599
1595
|
def integrated_mobile_genetic_element(cls):
|
1600
1596
|
"""An MGE that is integrated into the host chromosome. (cls, SO:ke)
|
1601
|
-
(
|
1597
|
+
(SO_0001039)
|
1602
1598
|
"""
|
1603
|
-
return _namespace_SOFA('
|
1599
|
+
return _namespace_SOFA('SO_0001039')
|
1604
1600
|
|
1605
1601
|
@classmethod
|
1606
1602
|
def transcriptional_cis_regulatory_region(cls):
|
1607
1603
|
"""A regulatory_region that modulates the transcription of a gene or genes. (cls, SO:regcreative)
|
1608
|
-
(
|
1604
|
+
(SO_0001055)
|
1609
1605
|
"""
|
1610
|
-
return _namespace_SOFA('
|
1606
|
+
return _namespace_SOFA('SO_0001055')
|
1611
1607
|
|
1612
1608
|
@classmethod
|
1613
1609
|
def splicing_regulatory_region(cls):
|
1614
1610
|
"""A regulatory_region that modulates splicing. (cls, SO:ke)
|
1615
|
-
(
|
1611
|
+
(SO_0001056)
|
1616
1612
|
"""
|
1617
|
-
return _namespace_SOFA('
|
1613
|
+
return _namespace_SOFA('SO_0001056')
|
1618
1614
|
|
1619
1615
|
@classmethod
|
1620
1616
|
def sequence_alteration(cls):
|
1621
1617
|
"""A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. (cls, SO:ke)
|
1622
|
-
(
|
1618
|
+
(SO_0001059)
|
1623
1619
|
"""
|
1624
|
-
return _namespace_SOFA('
|
1620
|
+
return _namespace_SOFA('SO_0001059')
|
1625
1621
|
|
1626
1622
|
@classmethod
|
1627
1623
|
def immature_peptide_region(cls):
|
1628
1624
|
"""An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs. (cls, EBIBS:GAR)
|
1629
|
-
(
|
1625
|
+
(SO_0001063)
|
1630
1626
|
"""
|
1631
|
-
return _namespace_SOFA('
|
1627
|
+
return _namespace_SOFA('SO_0001063')
|
1632
1628
|
|
1633
1629
|
@classmethod
|
1634
1630
|
def noncoding_region_of_exon(cls):
|
1635
1631
|
"""The maximal intersection of exon and UTR. (cls, SO:ke)
|
1636
|
-
(
|
1632
|
+
(SO_0001214)
|
1637
1633
|
"""
|
1638
|
-
return _namespace_SOFA('
|
1634
|
+
return _namespace_SOFA('SO_0001214')
|
1639
1635
|
|
1640
1636
|
@classmethod
|
1641
1637
|
def coding_region_of_exon(cls):
|
1642
1638
|
"""The region of an exon that encodes for protein sequence. (cls, SO:ke)
|
1643
|
-
(
|
1639
|
+
(SO_0001215)
|
1644
1640
|
"""
|
1645
|
-
return _namespace_SOFA('
|
1641
|
+
return _namespace_SOFA('SO_0001215')
|
1646
1642
|
|
1647
1643
|
@classmethod
|
1648
1644
|
def replicon(cls):
|
1649
1645
|
"""A region containing at least one unique origin of replication and a unique termination site. (cls, ISBN:0716719207)
|
1650
|
-
(
|
1646
|
+
(SO_0001235)
|
1651
1647
|
"""
|
1652
|
-
return _namespace_SOFA('
|
1648
|
+
return _namespace_SOFA('SO_0001235')
|
1653
1649
|
|
1654
1650
|
@classmethod
|
1655
1651
|
def base(cls):
|
1656
1652
|
"""A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. (cls, SO:ke)
|
1657
|
-
(
|
1653
|
+
(SO_0001236)
|
1658
1654
|
"""
|
1659
|
-
return _namespace_SOFA('
|
1655
|
+
return _namespace_SOFA('SO_0001236')
|
1660
1656
|
|
1661
1657
|
@classmethod
|
1662
1658
|
def assembly(cls):
|
1663
1659
|
"""A region of the genome of known length that is composed by ordering and aligning two or more different regions. (cls, SO:ke)
|
1664
|
-
(
|
1660
|
+
(SO_0001248)
|
1665
1661
|
"""
|
1666
|
-
return _namespace_SOFA('
|
1662
|
+
return _namespace_SOFA('SO_0001248')
|
1667
1663
|
|
1668
1664
|
@classmethod
|
1669
1665
|
def biomaterial_region(cls):
|
1670
1666
|
"""A region which is intended for use in an experiment. (cls, SO:cb)
|
1671
|
-
(
|
1667
|
+
(SO_0001409)
|
1672
1668
|
"""
|
1673
|
-
return _namespace_SOFA('
|
1669
|
+
return _namespace_SOFA('SO_0001409')
|
1674
1670
|
|
1675
1671
|
@classmethod
|
1676
1672
|
def experimental_feature(cls):
|
1677
1673
|
"""A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. (cls, SO:cb)
|
1678
|
-
(
|
1674
|
+
(SO_0001410)
|
1679
1675
|
"""
|
1680
|
-
return _namespace_SOFA('
|
1676
|
+
return _namespace_SOFA('SO_0001410')
|
1681
1677
|
|
1682
1678
|
@classmethod
|
1683
1679
|
def biological_region(cls):
|
1684
1680
|
"""A region defined by its disposition to be involved in a biological process. (cls, SO:cb)
|
1685
|
-
(
|
1681
|
+
(SO_0001411)
|
1686
1682
|
"""
|
1687
|
-
return _namespace_SOFA('
|
1683
|
+
return _namespace_SOFA('SO_0001411')
|
1688
1684
|
|
1689
1685
|
@classmethod
|
1690
1686
|
def topologically_defined_region(cls):
|
1691
1687
|
"""A region that is defined according to its relations with other regions within the same sequence. (cls, SO:cb)
|
1692
|
-
(
|
1688
|
+
(SO_0001412)
|
1693
1689
|
"""
|
1694
|
-
return _namespace_SOFA('
|
1690
|
+
return _namespace_SOFA('SO_0001412')
|
1695
1691
|
|
1696
1692
|
@classmethod
|
1697
1693
|
def cis_splice_site(cls):
|
1698
1694
|
"""Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron. (cls, SO:cjm, SO:ke)
|
1699
|
-
(
|
1695
|
+
(SO_0001419)
|
1700
1696
|
"""
|
1701
|
-
return _namespace_SOFA('
|
1697
|
+
return _namespace_SOFA('SO_0001419')
|
1702
1698
|
|
1703
1699
|
@classmethod
|
1704
1700
|
def trans_splice_site(cls):
|
1705
1701
|
"""Primary transcript region bordering trans-splice junction. (cls, SO:ke)
|
1706
|
-
(
|
1702
|
+
(SO_0001420)
|
1707
1703
|
"""
|
1708
|
-
return _namespace_SOFA('
|
1704
|
+
return _namespace_SOFA('SO_0001420')
|
1709
1705
|
|
1710
1706
|
@classmethod
|
1711
1707
|
def SNV(cls):
|
1712
1708
|
"""SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist. (cls, SO:bm)
|
1713
|
-
(
|
1709
|
+
(SO_0001483)
|
1714
1710
|
"""
|
1715
|
-
return _namespace_SOFA('
|
1711
|
+
return _namespace_SOFA('SO_0001483')
|
1716
1712
|
|
1717
1713
|
@classmethod
|
1718
1714
|
def peptide_localization_signal(cls):
|
1719
1715
|
"""A region of peptide sequence used to target the polypeptide molecule to a specific organelle. (cls, SO:ke)
|
1720
|
-
(
|
1716
|
+
(SO_0001527)
|
1721
1717
|
"""
|
1722
|
-
return _namespace_SOFA('
|
1718
|
+
return _namespace_SOFA('SO_0001527')
|
1723
1719
|
|
1724
1720
|
@classmethod
|
1725
1721
|
def kozak_sequence(cls):
|
1726
1722
|
"""A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence. (cls, SO:ke)
|
1727
|
-
(
|
1723
|
+
(SO_0001647)
|
1728
1724
|
"""
|
1729
|
-
return _namespace_SOFA('
|
1725
|
+
return _namespace_SOFA('SO_0001647')
|
1730
1726
|
|
1731
1727
|
@classmethod
|
1732
1728
|
def nucleotide_to_protein_binding_site(cls):
|
1733
1729
|
"""A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues. (cls, SO:ke)
|
1734
|
-
(
|
1730
|
+
(SO_0001654)
|
1735
1731
|
"""
|
1736
|
-
return _namespace_SOFA('
|
1732
|
+
return _namespace_SOFA('SO_0001654')
|
1737
1733
|
|
1738
1734
|
@classmethod
|
1739
1735
|
def transcription_regulatory_region(cls):
|
1740
1736
|
"""A regulatory region that is involved in the control of the process of transcription. (cls, SO:ke)
|
1741
|
-
(
|
1737
|
+
(SO_0001679)
|
1742
1738
|
"""
|
1743
|
-
return _namespace_SOFA('
|
1739
|
+
return _namespace_SOFA('SO_0001679')
|
1744
1740
|
|
1745
1741
|
@classmethod
|
1746
1742
|
def sequence_motif(cls):
|
1747
1743
|
"""A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance. (cls, http://en.wikipedia.org/wiki/Sequence_motif)
|
1748
|
-
(
|
1744
|
+
(SO_0001683)
|
1749
1745
|
"""
|
1750
|
-
return _namespace_SOFA('
|
1746
|
+
return _namespace_SOFA('SO_0001683')
|
1751
1747
|
|
1752
1748
|
@classmethod
|
1753
1749
|
def epigenetically_modified_region(cls):
|
1754
1750
|
"""A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence. (cls, http://en.wikipedia.org/wiki/Epigenetics, SO:ke)
|
1755
|
-
(
|
1751
|
+
(SO_0001720)
|
1756
1752
|
"""
|
1757
|
-
return _namespace_SOFA('
|
1753
|
+
return _namespace_SOFA('SO_0001720')
|
1758
1754
|
|
1759
1755
|
@classmethod
|
1760
1756
|
def paired_end_fragment(cls):
|
1761
1757
|
"""An assembly region that has been sequenced from both ends resulting in a read_pair (cls, mate_pair). (SO:ke)
|
1762
|
-
(
|
1758
|
+
(SO_0001790)
|
1763
1759
|
"""
|
1764
|
-
return _namespace_SOFA('
|
1760
|
+
return _namespace_SOFA('SO_0001790')
|
1765
1761
|
|
1766
1762
|
@classmethod
|
1767
1763
|
def regulatory_region(cls):
|
1768
1764
|
"""A region of sequence that is involved in the control of a biological process. (cls, SO:ke)
|
1769
|
-
(
|
1765
|
+
(SO_0005836)
|
1770
1766
|
"""
|
1771
|
-
return _namespace_SOFA('
|
1767
|
+
return _namespace_SOFA('SO_0005836')
|
1772
1768
|
|
1773
1769
|
@classmethod
|
1774
1770
|
def gene_group(cls):
|
1775
1771
|
"""A collection of related genes. (cls, SO:ma)
|
1776
|
-
(
|
1772
|
+
(SO_0005855)
|
1777
1773
|
"""
|
1778
|
-
return _namespace_SOFA('
|
1774
|
+
return _namespace_SOFA('SO_0005855')
|
1779
1775
|
|
1780
1776
|
@classmethod
|
1781
1777
|
def cleaved_peptide_region(cls):
|
1782
1778
|
"""The cleaved_peptide_regon is the a region of peptide sequence that is cleaved during maturation. (cls, EBIBS:GAR)
|
1783
|
-
(
|
1779
|
+
(SO_0100011)
|
1784
1780
|
"""
|
1785
|
-
return _namespace_SOFA('
|
1781
|
+
return _namespace_SOFA('SO_0100011')
|
1786
1782
|
|
1787
1783
|
@classmethod
|
1788
1784
|
def substitution(cls):
|
1789
1785
|
"""A sequence alteration where the length of the change in the variant is the same as that of the reference. (cls, SO:ke)
|
1790
|
-
(
|
1786
|
+
(SO_1000002)
|
1791
1787
|
"""
|
1792
|
-
return _namespace_SOFA('
|
1788
|
+
return _namespace_SOFA('SO_1000002')
|
1793
1789
|
|
1794
1790
|
@classmethod
|
1795
1791
|
def complex_substitution(cls):
|
1796
1792
|
"""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. (cls, EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html)
|
1797
|
-
(
|
1793
|
+
(SO_1000005)
|
1798
1794
|
"""
|
1799
|
-
return _namespace_SOFA('
|
1795
|
+
return _namespace_SOFA('SO_1000005')
|
1800
1796
|
|
1801
1797
|
@classmethod
|
1802
1798
|
def point_mutation(cls):
|
1803
1799
|
"""A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. (cls, SO:immuno_workshop)
|
1804
|
-
(
|
1800
|
+
(SO_1000008)
|
1805
1801
|
"""
|
1806
|
-
return _namespace_SOFA('
|
1802
|
+
return _namespace_SOFA('SO_1000008')
|
1807
1803
|
|
1808
1804
|
@classmethod
|
1809
1805
|
def inversion(cls):
|
1810
1806
|
"""A continuous nucleotide sequence is inverted in the same position. (cls, EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html)
|
1811
|
-
(
|
1807
|
+
(SO_1000036)
|
1812
1808
|
"""
|
1813
|
-
return _namespace_SOFA('
|
1809
|
+
return _namespace_SOFA('SO_1000036')
|
1814
1810
|
|
1815
1811
|
@classmethod
|
1816
1812
|
def regulon(cls):
|
1817
1813
|
"""A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal. (cls, ISBN:0198506732)
|
1818
|
-
(
|
1814
|
+
(SO_1001284)
|
1819
1815
|
"""
|
1820
|
-
return _namespace_SOFA('
|
1816
|
+
return _namespace_SOFA('SO_1001284')
|
1821
1817
|
|
1822
1818
|
@classmethod
|
1823
1819
|
def databank_entry(cls):
|
1824
1820
|
"""The sequence referred to by an entry in a databank such as Genbank or SwissProt. (cls, SO:ke)
|
1825
|
-
(
|
1821
|
+
(SO_2000061)
|
1826
1822
|
"""
|
1827
|
-
return _namespace_SOFA('
|
1823
|
+
return _namespace_SOFA('SO_2000061')
|
1828
1824
|
|
1829
1825
|
@classmethod
|
1830
1826
|
def is_object_property(cls, uri):
|
@@ -1832,39 +1828,39 @@ class SOFA:
|
|
1832
1828
|
|
1833
1829
|
uri -- URI that is tested for being an object property
|
1834
1830
|
"""
|
1835
|
-
if uri == _namespace_SOFA(''):
|
1831
|
+
if uri == _namespace_SOFA('http_//purl.org/obo/owl:adjacent_to'):
|
1836
1832
|
return True
|
1837
|
-
if uri == _namespace_SOFA('
|
1833
|
+
if uri == _namespace_SOFA('http_//purl.org/obo/owl:complete_evidence_for_feature'):
|
1838
1834
|
return True
|
1839
|
-
if uri == _namespace_SOFA('
|
1835
|
+
if uri == _namespace_SOFA('http_//purl.org/obo/owl:contained_by'):
|
1840
1836
|
return True
|
1841
|
-
if uri == _namespace_SOFA('
|
1837
|
+
if uri == _namespace_SOFA('http_//purl.org/obo/owl:contains'):
|
1842
1838
|
return True
|
1843
|
-
if uri == _namespace_SOFA('
|
1839
|
+
if uri == _namespace_SOFA('http_//purl.org/obo/owl:derives_from'):
|
1844
1840
|
return True
|
1845
|
-
if uri == _namespace_SOFA('
|
1841
|
+
if uri == _namespace_SOFA('http_//purl.org/obo/owl:evidence_for_feature'):
|
1846
1842
|
return True
|
1847
|
-
if uri == _namespace_SOFA('
|
1843
|
+
if uri == _namespace_SOFA('http_//purl.org/obo/owl:has_integral_part'):
|
1848
1844
|
return True
|
1849
|
-
if uri == _namespace_SOFA('
|
1845
|
+
if uri == _namespace_SOFA('http_//purl.org/obo/owl:has_part'):
|
1850
1846
|
return True
|
1851
|
-
if uri == _namespace_SOFA('
|
1847
|
+
if uri == _namespace_SOFA('http_//purl.org/obo/owl:homologous_to'):
|
1852
1848
|
return True
|
1853
|
-
if uri == _namespace_SOFA('
|
1849
|
+
if uri == _namespace_SOFA('http_//purl.org/obo/owl:integral_part_of'):
|
1854
1850
|
return True
|
1855
|
-
if uri == _namespace_SOFA('
|
1851
|
+
if uri == _namespace_SOFA('http_//purl.org/obo/owl:member_of'):
|
1856
1852
|
return True
|
1857
|
-
if uri == _namespace_SOFA('
|
1853
|
+
if uri == _namespace_SOFA('http_//purl.org/obo/owl:non_functional_homolog_of'):
|
1858
1854
|
return True
|
1859
|
-
if uri == _namespace_SOFA('
|
1855
|
+
if uri == _namespace_SOFA('http_//purl.org/obo/owl:orthologous_to'):
|
1860
1856
|
return True
|
1861
|
-
if uri == _namespace_SOFA('
|
1857
|
+
if uri == _namespace_SOFA('http_//purl.org/obo/owl:paralogous_to'):
|
1862
1858
|
return True
|
1863
|
-
if uri == _namespace_SOFA('
|
1859
|
+
if uri == _namespace_SOFA('http_//purl.org/obo/owl:part_of'):
|
1864
1860
|
return True
|
1865
|
-
if uri == _namespace_SOFA('
|
1861
|
+
if uri == _namespace_SOFA('http_//purl.org/obo/owl:partial_evidence_for_feature'):
|
1866
1862
|
return True
|
1867
|
-
if uri == _namespace_SOFA('
|
1863
|
+
if uri == _namespace_SOFA('http_//purl.org/obo/owl:similar_to'):
|
1868
1864
|
return True
|
1869
1865
|
return False
|
1870
1866
|
|
@@ -1882,509 +1878,509 @@ class SOFA:
|
|
1882
1878
|
|
1883
1879
|
uri -- URI that is tested for being a class
|
1884
1880
|
"""
|
1885
|
-
if uri == _namespace_SOFA('
|
1881
|
+
if uri == _namespace_SOFA('SO_0000000'):
|
1886
1882
|
return True
|
1887
|
-
if uri == _namespace_SOFA('
|
1883
|
+
if uri == _namespace_SOFA('SO_0000001'):
|
1888
1884
|
return True
|
1889
|
-
if uri == _namespace_SOFA('
|
1885
|
+
if uri == _namespace_SOFA('SO_0000004'):
|
1890
1886
|
return True
|
1891
|
-
if uri == _namespace_SOFA('
|
1887
|
+
if uri == _namespace_SOFA('SO_0000005'):
|
1892
1888
|
return True
|
1893
|
-
if uri == _namespace_SOFA('
|
1889
|
+
if uri == _namespace_SOFA('SO_0000006'):
|
1894
1890
|
return True
|
1895
|
-
if uri == _namespace_SOFA('
|
1891
|
+
if uri == _namespace_SOFA('SO_0000007'):
|
1896
1892
|
return True
|
1897
|
-
if uri == _namespace_SOFA('
|
1893
|
+
if uri == _namespace_SOFA('SO_0000013'):
|
1898
1894
|
return True
|
1899
|
-
if uri == _namespace_SOFA('
|
1895
|
+
if uri == _namespace_SOFA('SO_0000038'):
|
1900
1896
|
return True
|
1901
|
-
if uri == _namespace_SOFA('
|
1897
|
+
if uri == _namespace_SOFA('SO_0000039'):
|
1902
1898
|
return True
|
1903
|
-
if uri == _namespace_SOFA('
|
1899
|
+
if uri == _namespace_SOFA('SO_0000050'):
|
1904
1900
|
return True
|
1905
|
-
if uri == _namespace_SOFA('
|
1901
|
+
if uri == _namespace_SOFA('SO_0000057'):
|
1906
1902
|
return True
|
1907
|
-
if uri == _namespace_SOFA('
|
1903
|
+
if uri == _namespace_SOFA('SO_0000059'):
|
1908
1904
|
return True
|
1909
|
-
if uri == _namespace_SOFA('
|
1905
|
+
if uri == _namespace_SOFA('SO_0000101'):
|
1910
1906
|
return True
|
1911
|
-
if uri == _namespace_SOFA('
|
1907
|
+
if uri == _namespace_SOFA('SO_0000102'):
|
1912
1908
|
return True
|
1913
|
-
if uri == _namespace_SOFA('
|
1909
|
+
if uri == _namespace_SOFA('SO_0000103'):
|
1914
1910
|
return True
|
1915
|
-
if uri == _namespace_SOFA('
|
1911
|
+
if uri == _namespace_SOFA('SO_0000104'):
|
1916
1912
|
return True
|
1917
|
-
if uri == _namespace_SOFA('
|
1913
|
+
if uri == _namespace_SOFA('SO_0000109'):
|
1918
1914
|
return True
|
1919
|
-
if uri == _namespace_SOFA('
|
1915
|
+
if uri == _namespace_SOFA('SO_0000110'):
|
1920
1916
|
return True
|
1921
|
-
if uri == _namespace_SOFA('
|
1917
|
+
if uri == _namespace_SOFA('SO_0000112'):
|
1922
1918
|
return True
|
1923
|
-
if uri == _namespace_SOFA('
|
1919
|
+
if uri == _namespace_SOFA('SO_0000113'):
|
1924
1920
|
return True
|
1925
|
-
if uri == _namespace_SOFA('
|
1921
|
+
if uri == _namespace_SOFA('SO_0000114'):
|
1926
1922
|
return True
|
1927
|
-
if uri == _namespace_SOFA('
|
1923
|
+
if uri == _namespace_SOFA('SO_0000120'):
|
1928
1924
|
return True
|
1929
|
-
if uri == _namespace_SOFA('
|
1925
|
+
if uri == _namespace_SOFA('SO_0000139'):
|
1930
1926
|
return True
|
1931
|
-
if uri == _namespace_SOFA('
|
1927
|
+
if uri == _namespace_SOFA('SO_0000140'):
|
1932
1928
|
return True
|
1933
|
-
if uri == _namespace_SOFA('
|
1929
|
+
if uri == _namespace_SOFA('SO_0000141'):
|
1934
1930
|
return True
|
1935
|
-
if uri == _namespace_SOFA('
|
1931
|
+
if uri == _namespace_SOFA('SO_0000143'):
|
1936
1932
|
return True
|
1937
|
-
if uri == _namespace_SOFA('
|
1933
|
+
if uri == _namespace_SOFA('SO_0000147'):
|
1938
1934
|
return True
|
1939
|
-
if uri == _namespace_SOFA('
|
1935
|
+
if uri == _namespace_SOFA('SO_0000148'):
|
1940
1936
|
return True
|
1941
|
-
if uri == _namespace_SOFA('
|
1937
|
+
if uri == _namespace_SOFA('SO_0000149'):
|
1942
1938
|
return True
|
1943
|
-
if uri == _namespace_SOFA('
|
1939
|
+
if uri == _namespace_SOFA('SO_0000150'):
|
1944
1940
|
return True
|
1945
|
-
if uri == _namespace_SOFA('
|
1941
|
+
if uri == _namespace_SOFA('SO_0000151'):
|
1946
1942
|
return True
|
1947
|
-
if uri == _namespace_SOFA('
|
1943
|
+
if uri == _namespace_SOFA('SO_0000159'):
|
1948
1944
|
return True
|
1949
|
-
if uri == _namespace_SOFA('
|
1945
|
+
if uri == _namespace_SOFA('SO_0000161'):
|
1950
1946
|
return True
|
1951
|
-
if uri == _namespace_SOFA('
|
1947
|
+
if uri == _namespace_SOFA('SO_0000162'):
|
1952
1948
|
return True
|
1953
|
-
if uri == _namespace_SOFA('
|
1949
|
+
if uri == _namespace_SOFA('SO_0000163'):
|
1954
1950
|
return True
|
1955
|
-
if uri == _namespace_SOFA('
|
1951
|
+
if uri == _namespace_SOFA('SO_0000164'):
|
1956
1952
|
return True
|
1957
|
-
if uri == _namespace_SOFA('
|
1953
|
+
if uri == _namespace_SOFA('SO_0000165'):
|
1958
1954
|
return True
|
1959
|
-
if uri == _namespace_SOFA('
|
1955
|
+
if uri == _namespace_SOFA('SO_0000167'):
|
1960
1956
|
return True
|
1961
|
-
if uri == _namespace_SOFA('
|
1957
|
+
if uri == _namespace_SOFA('SO_0000177'):
|
1962
1958
|
return True
|
1963
|
-
if uri == _namespace_SOFA('
|
1959
|
+
if uri == _namespace_SOFA('SO_0000178'):
|
1964
1960
|
return True
|
1965
|
-
if uri == _namespace_SOFA('
|
1961
|
+
if uri == _namespace_SOFA('SO_0000179'):
|
1966
1962
|
return True
|
1967
|
-
if uri == _namespace_SOFA('
|
1963
|
+
if uri == _namespace_SOFA('SO_0000181'):
|
1968
1964
|
return True
|
1969
|
-
if uri == _namespace_SOFA('
|
1965
|
+
if uri == _namespace_SOFA('SO_0000183'):
|
1970
1966
|
return True
|
1971
|
-
if uri == _namespace_SOFA('
|
1967
|
+
if uri == _namespace_SOFA('SO_0000185'):
|
1972
1968
|
return True
|
1973
|
-
if uri == _namespace_SOFA('
|
1969
|
+
if uri == _namespace_SOFA('SO_0000187'):
|
1974
1970
|
return True
|
1975
|
-
if uri == _namespace_SOFA('
|
1971
|
+
if uri == _namespace_SOFA('SO_0000188'):
|
1976
1972
|
return True
|
1977
|
-
if uri == _namespace_SOFA('
|
1973
|
+
if uri == _namespace_SOFA('SO_0000193'):
|
1978
1974
|
return True
|
1979
|
-
if uri == _namespace_SOFA('
|
1975
|
+
if uri == _namespace_SOFA('SO_0000195'):
|
1980
1976
|
return True
|
1981
|
-
if uri == _namespace_SOFA('
|
1977
|
+
if uri == _namespace_SOFA('SO_0000196'):
|
1982
1978
|
return True
|
1983
|
-
if uri == _namespace_SOFA('
|
1979
|
+
if uri == _namespace_SOFA('SO_0000197'):
|
1984
1980
|
return True
|
1985
|
-
if uri == _namespace_SOFA('
|
1981
|
+
if uri == _namespace_SOFA('SO_0000198'):
|
1986
1982
|
return True
|
1987
|
-
if uri == _namespace_SOFA('
|
1983
|
+
if uri == _namespace_SOFA('SO_0000200'):
|
1988
1984
|
return True
|
1989
|
-
if uri == _namespace_SOFA('
|
1985
|
+
if uri == _namespace_SOFA('SO_0000203'):
|
1990
1986
|
return True
|
1991
|
-
if uri == _namespace_SOFA('
|
1987
|
+
if uri == _namespace_SOFA('SO_0000204'):
|
1992
1988
|
return True
|
1993
|
-
if uri == _namespace_SOFA('
|
1989
|
+
if uri == _namespace_SOFA('SO_0000205'):
|
1994
1990
|
return True
|
1995
|
-
if uri == _namespace_SOFA('
|
1991
|
+
if uri == _namespace_SOFA('SO_0000209'):
|
1996
1992
|
return True
|
1997
|
-
if uri == _namespace_SOFA('
|
1993
|
+
if uri == _namespace_SOFA('SO_0000233'):
|
1998
1994
|
return True
|
1999
|
-
if uri == _namespace_SOFA('
|
1995
|
+
if uri == _namespace_SOFA('SO_0000234'):
|
2000
1996
|
return True
|
2001
|
-
if uri == _namespace_SOFA('
|
1997
|
+
if uri == _namespace_SOFA('SO_0000235'):
|
2002
1998
|
return True
|
2003
|
-
if uri == _namespace_SOFA('
|
1999
|
+
if uri == _namespace_SOFA('SO_0000236'):
|
2004
2000
|
return True
|
2005
|
-
if uri == _namespace_SOFA('
|
2001
|
+
if uri == _namespace_SOFA('SO_0000239'):
|
2006
2002
|
return True
|
2007
|
-
if uri == _namespace_SOFA('
|
2003
|
+
if uri == _namespace_SOFA('SO_0000252'):
|
2008
2004
|
return True
|
2009
|
-
if uri == _namespace_SOFA('
|
2005
|
+
if uri == _namespace_SOFA('SO_0000253'):
|
2010
2006
|
return True
|
2011
|
-
if uri == _namespace_SOFA('
|
2007
|
+
if uri == _namespace_SOFA('SO_0000274'):
|
2012
2008
|
return True
|
2013
|
-
if uri == _namespace_SOFA('
|
2009
|
+
if uri == _namespace_SOFA('SO_0000275'):
|
2014
2010
|
return True
|
2015
|
-
if uri == _namespace_SOFA('
|
2011
|
+
if uri == _namespace_SOFA('SO_0000276'):
|
2016
2012
|
return True
|
2017
|
-
if uri == _namespace_SOFA('
|
2013
|
+
if uri == _namespace_SOFA('SO_0000289'):
|
2018
2014
|
return True
|
2019
|
-
if uri == _namespace_SOFA('
|
2015
|
+
if uri == _namespace_SOFA('SO_0000294'):
|
2020
2016
|
return True
|
2021
|
-
if uri == _namespace_SOFA('
|
2017
|
+
if uri == _namespace_SOFA('SO_0000296'):
|
2022
2018
|
return True
|
2023
|
-
if uri == _namespace_SOFA('
|
2019
|
+
if uri == _namespace_SOFA('SO_0000303'):
|
2024
2020
|
return True
|
2025
|
-
if uri == _namespace_SOFA('
|
2021
|
+
if uri == _namespace_SOFA('SO_0000305'):
|
2026
2022
|
return True
|
2027
|
-
if uri == _namespace_SOFA('
|
2023
|
+
if uri == _namespace_SOFA('SO_0000306'):
|
2028
2024
|
return True
|
2029
|
-
if uri == _namespace_SOFA('
|
2025
|
+
if uri == _namespace_SOFA('SO_0000307'):
|
2030
2026
|
return True
|
2031
|
-
if uri == _namespace_SOFA('
|
2027
|
+
if uri == _namespace_SOFA('SO_0000314'):
|
2032
2028
|
return True
|
2033
|
-
if uri == _namespace_SOFA('
|
2029
|
+
if uri == _namespace_SOFA('SO_0000315'):
|
2034
2030
|
return True
|
2035
|
-
if uri == _namespace_SOFA('
|
2031
|
+
if uri == _namespace_SOFA('SO_0000316'):
|
2036
2032
|
return True
|
2037
|
-
if uri == _namespace_SOFA('
|
2033
|
+
if uri == _namespace_SOFA('SO_0000318'):
|
2038
2034
|
return True
|
2039
|
-
if uri == _namespace_SOFA('
|
2035
|
+
if uri == _namespace_SOFA('SO_0000319'):
|
2040
2036
|
return True
|
2041
|
-
if uri == _namespace_SOFA('
|
2037
|
+
if uri == _namespace_SOFA('SO_0000324'):
|
2042
2038
|
return True
|
2043
|
-
if uri == _namespace_SOFA('
|
2039
|
+
if uri == _namespace_SOFA('SO_0000325'):
|
2044
2040
|
return True
|
2045
|
-
if uri == _namespace_SOFA('
|
2041
|
+
if uri == _namespace_SOFA('SO_0000326'):
|
2046
2042
|
return True
|
2047
|
-
if uri == _namespace_SOFA('
|
2043
|
+
if uri == _namespace_SOFA('SO_0000330'):
|
2048
2044
|
return True
|
2049
|
-
if uri == _namespace_SOFA('
|
2045
|
+
if uri == _namespace_SOFA('SO_0000331'):
|
2050
2046
|
return True
|
2051
|
-
if uri == _namespace_SOFA('
|
2047
|
+
if uri == _namespace_SOFA('SO_0000332'):
|
2052
2048
|
return True
|
2053
|
-
if uri == _namespace_SOFA('
|
2049
|
+
if uri == _namespace_SOFA('SO_0000333'):
|
2054
2050
|
return True
|
2055
|
-
if uri == _namespace_SOFA('
|
2051
|
+
if uri == _namespace_SOFA('SO_0000334'):
|
2056
2052
|
return True
|
2057
|
-
if uri == _namespace_SOFA('
|
2053
|
+
if uri == _namespace_SOFA('SO_0000336'):
|
2058
2054
|
return True
|
2059
|
-
if uri == _namespace_SOFA('
|
2055
|
+
if uri == _namespace_SOFA('SO_0000337'):
|
2060
2056
|
return True
|
2061
|
-
if uri == _namespace_SOFA('
|
2057
|
+
if uri == _namespace_SOFA('SO_0000340'):
|
2062
2058
|
return True
|
2063
|
-
if uri == _namespace_SOFA('
|
2059
|
+
if uri == _namespace_SOFA('SO_0000341'):
|
2064
2060
|
return True
|
2065
|
-
if uri == _namespace_SOFA('
|
2061
|
+
if uri == _namespace_SOFA('SO_0000343'):
|
2066
2062
|
return True
|
2067
|
-
if uri == _namespace_SOFA('
|
2063
|
+
if uri == _namespace_SOFA('SO_0000344'):
|
2068
2064
|
return True
|
2069
|
-
if uri == _namespace_SOFA('
|
2065
|
+
if uri == _namespace_SOFA('SO_0000345'):
|
2070
2066
|
return True
|
2071
|
-
if uri == _namespace_SOFA('
|
2067
|
+
if uri == _namespace_SOFA('SO_0000347'):
|
2072
2068
|
return True
|
2073
|
-
if uri == _namespace_SOFA('
|
2069
|
+
if uri == _namespace_SOFA('SO_0000349'):
|
2074
2070
|
return True
|
2075
|
-
if uri == _namespace_SOFA('
|
2071
|
+
if uri == _namespace_SOFA('SO_0000353'):
|
2076
2072
|
return True
|
2077
|
-
if uri == _namespace_SOFA('
|
2073
|
+
if uri == _namespace_SOFA('SO_0000360'):
|
2078
2074
|
return True
|
2079
|
-
if uri == _namespace_SOFA('
|
2075
|
+
if uri == _namespace_SOFA('SO_0000366'):
|
2080
2076
|
return True
|
2081
|
-
if uri == _namespace_SOFA('
|
2077
|
+
if uri == _namespace_SOFA('SO_0000368'):
|
2082
2078
|
return True
|
2083
|
-
if uri == _namespace_SOFA('
|
2079
|
+
if uri == _namespace_SOFA('SO_0000370'):
|
2084
2080
|
return True
|
2085
|
-
if uri == _namespace_SOFA('
|
2081
|
+
if uri == _namespace_SOFA('SO_0000372'):
|
2086
2082
|
return True
|
2087
|
-
if uri == _namespace_SOFA('
|
2083
|
+
if uri == _namespace_SOFA('SO_0000374'):
|
2088
2084
|
return True
|
2089
|
-
if uri == _namespace_SOFA('
|
2085
|
+
if uri == _namespace_SOFA('SO_0000375'):
|
2090
2086
|
return True
|
2091
|
-
if uri == _namespace_SOFA('
|
2087
|
+
if uri == _namespace_SOFA('SO_0000380'):
|
2092
2088
|
return True
|
2093
|
-
if uri == _namespace_SOFA('
|
2089
|
+
if uri == _namespace_SOFA('SO_0000385'):
|
2094
2090
|
return True
|
2095
|
-
if uri == _namespace_SOFA('
|
2091
|
+
if uri == _namespace_SOFA('SO_0000386'):
|
2096
2092
|
return True
|
2097
|
-
if uri == _namespace_SOFA('
|
2093
|
+
if uri == _namespace_SOFA('SO_0000390'):
|
2098
2094
|
return True
|
2099
|
-
if uri == _namespace_SOFA('
|
2095
|
+
if uri == _namespace_SOFA('SO_0000391'):
|
2100
2096
|
return True
|
2101
|
-
if uri == _namespace_SOFA('
|
2097
|
+
if uri == _namespace_SOFA('SO_0000392'):
|
2102
2098
|
return True
|
2103
|
-
if uri == _namespace_SOFA('
|
2099
|
+
if uri == _namespace_SOFA('SO_0000393'):
|
2104
2100
|
return True
|
2105
|
-
if uri == _namespace_SOFA('
|
2101
|
+
if uri == _namespace_SOFA('SO_0000394'):
|
2106
2102
|
return True
|
2107
|
-
if uri == _namespace_SOFA('
|
2103
|
+
if uri == _namespace_SOFA('SO_0000395'):
|
2108
2104
|
return True
|
2109
|
-
if uri == _namespace_SOFA('
|
2105
|
+
if uri == _namespace_SOFA('SO_0000396'):
|
2110
2106
|
return True
|
2111
|
-
if uri == _namespace_SOFA('
|
2107
|
+
if uri == _namespace_SOFA('SO_0000397'):
|
2112
2108
|
return True
|
2113
|
-
if uri == _namespace_SOFA('
|
2109
|
+
if uri == _namespace_SOFA('SO_0000398'):
|
2114
2110
|
return True
|
2115
|
-
if uri == _namespace_SOFA('
|
2111
|
+
if uri == _namespace_SOFA('SO_0000399'):
|
2116
2112
|
return True
|
2117
|
-
if uri == _namespace_SOFA('
|
2113
|
+
if uri == _namespace_SOFA('SO_0000403'):
|
2118
2114
|
return True
|
2119
|
-
if uri == _namespace_SOFA('
|
2115
|
+
if uri == _namespace_SOFA('SO_0000404'):
|
2120
2116
|
return True
|
2121
|
-
if uri == _namespace_SOFA('
|
2117
|
+
if uri == _namespace_SOFA('SO_0000405'):
|
2122
2118
|
return True
|
2123
|
-
if uri == _namespace_SOFA('
|
2119
|
+
if uri == _namespace_SOFA('SO_0000407'):
|
2124
2120
|
return True
|
2125
|
-
if uri == _namespace_SOFA('
|
2121
|
+
if uri == _namespace_SOFA('SO_0000409'):
|
2126
2122
|
return True
|
2127
|
-
if uri == _namespace_SOFA('
|
2123
|
+
if uri == _namespace_SOFA('SO_0000410'):
|
2128
2124
|
return True
|
2129
|
-
if uri == _namespace_SOFA('
|
2125
|
+
if uri == _namespace_SOFA('SO_0000412'):
|
2130
2126
|
return True
|
2131
|
-
if uri == _namespace_SOFA('
|
2127
|
+
if uri == _namespace_SOFA('SO_0000413'):
|
2132
2128
|
return True
|
2133
|
-
if uri == _namespace_SOFA('
|
2129
|
+
if uri == _namespace_SOFA('SO_0000418'):
|
2134
2130
|
return True
|
2135
|
-
if uri == _namespace_SOFA('
|
2131
|
+
if uri == _namespace_SOFA('SO_0000419'):
|
2136
2132
|
return True
|
2137
|
-
if uri == _namespace_SOFA('
|
2133
|
+
if uri == _namespace_SOFA('SO_0000436'):
|
2138
2134
|
return True
|
2139
|
-
if uri == _namespace_SOFA('
|
2135
|
+
if uri == _namespace_SOFA('SO_0000441'):
|
2140
2136
|
return True
|
2141
|
-
if uri == _namespace_SOFA('
|
2137
|
+
if uri == _namespace_SOFA('SO_0000442'):
|
2142
2138
|
return True
|
2143
|
-
if uri == _namespace_SOFA('
|
2139
|
+
if uri == _namespace_SOFA('SO_0000454'):
|
2144
2140
|
return True
|
2145
|
-
if uri == _namespace_SOFA('
|
2141
|
+
if uri == _namespace_SOFA('SO_0000462'):
|
2146
2142
|
return True
|
2147
|
-
if uri == _namespace_SOFA('
|
2143
|
+
if uri == _namespace_SOFA('SO_0000464'):
|
2148
2144
|
return True
|
2149
|
-
if uri == _namespace_SOFA('
|
2145
|
+
if uri == _namespace_SOFA('SO_0000468'):
|
2150
2146
|
return True
|
2151
|
-
if uri == _namespace_SOFA('
|
2147
|
+
if uri == _namespace_SOFA('SO_0000472'):
|
2152
2148
|
return True
|
2153
|
-
if uri == _namespace_SOFA('
|
2149
|
+
if uri == _namespace_SOFA('SO_0000474'):
|
2154
2150
|
return True
|
2155
|
-
if uri == _namespace_SOFA('
|
2151
|
+
if uri == _namespace_SOFA('SO_0000483'):
|
2156
2152
|
return True
|
2157
|
-
if uri == _namespace_SOFA('
|
2153
|
+
if uri == _namespace_SOFA('SO_0000484'):
|
2158
2154
|
return True
|
2159
|
-
if uri == _namespace_SOFA('
|
2155
|
+
if uri == _namespace_SOFA('SO_0000486'):
|
2160
2156
|
return True
|
2161
|
-
if uri == _namespace_SOFA('
|
2157
|
+
if uri == _namespace_SOFA('SO_0000499'):
|
2162
2158
|
return True
|
2163
|
-
if uri == _namespace_SOFA('
|
2159
|
+
if uri == _namespace_SOFA('SO_0000502'):
|
2164
2160
|
return True
|
2165
|
-
if uri == _namespace_SOFA('
|
2161
|
+
if uri == _namespace_SOFA('SO_0000551'):
|
2166
2162
|
return True
|
2167
|
-
if uri == _namespace_SOFA('
|
2163
|
+
if uri == _namespace_SOFA('SO_0000553'):
|
2168
2164
|
return True
|
2169
|
-
if uri == _namespace_SOFA('
|
2165
|
+
if uri == _namespace_SOFA('SO_0000577'):
|
2170
2166
|
return True
|
2171
|
-
if uri == _namespace_SOFA('
|
2167
|
+
if uri == _namespace_SOFA('SO_0000581'):
|
2172
2168
|
return True
|
2173
|
-
if uri == _namespace_SOFA('
|
2169
|
+
if uri == _namespace_SOFA('SO_0000587'):
|
2174
2170
|
return True
|
2175
|
-
if uri == _namespace_SOFA('
|
2171
|
+
if uri == _namespace_SOFA('SO_0000588'):
|
2176
2172
|
return True
|
2177
|
-
if uri == _namespace_SOFA('
|
2173
|
+
if uri == _namespace_SOFA('SO_0000590'):
|
2178
2174
|
return True
|
2179
|
-
if uri == _namespace_SOFA('
|
2175
|
+
if uri == _namespace_SOFA('SO_0000593'):
|
2180
2176
|
return True
|
2181
|
-
if uri == _namespace_SOFA('
|
2177
|
+
if uri == _namespace_SOFA('SO_0000602'):
|
2182
2178
|
return True
|
2183
|
-
if uri == _namespace_SOFA('
|
2179
|
+
if uri == _namespace_SOFA('SO_0000603'):
|
2184
2180
|
return True
|
2185
|
-
if uri == _namespace_SOFA('
|
2181
|
+
if uri == _namespace_SOFA('SO_0000605'):
|
2186
2182
|
return True
|
2187
|
-
if uri == _namespace_SOFA('
|
2183
|
+
if uri == _namespace_SOFA('SO_0000610'):
|
2188
2184
|
return True
|
2189
|
-
if uri == _namespace_SOFA('
|
2185
|
+
if uri == _namespace_SOFA('SO_0000611'):
|
2190
2186
|
return True
|
2191
|
-
if uri == _namespace_SOFA('
|
2187
|
+
if uri == _namespace_SOFA('SO_0000612'):
|
2192
2188
|
return True
|
2193
|
-
if uri == _namespace_SOFA('
|
2189
|
+
if uri == _namespace_SOFA('SO_0000616'):
|
2194
2190
|
return True
|
2195
|
-
if uri == _namespace_SOFA('
|
2191
|
+
if uri == _namespace_SOFA('SO_0000624'):
|
2196
2192
|
return True
|
2197
|
-
if uri == _namespace_SOFA('
|
2193
|
+
if uri == _namespace_SOFA('SO_0000625'):
|
2198
2194
|
return True
|
2199
|
-
if uri == _namespace_SOFA('
|
2195
|
+
if uri == _namespace_SOFA('SO_0000627'):
|
2200
2196
|
return True
|
2201
|
-
if uri == _namespace_SOFA('
|
2197
|
+
if uri == _namespace_SOFA('SO_0000628'):
|
2202
2198
|
return True
|
2203
|
-
if uri == _namespace_SOFA('
|
2199
|
+
if uri == _namespace_SOFA('SO_0000643'):
|
2204
2200
|
return True
|
2205
|
-
if uri == _namespace_SOFA('
|
2201
|
+
if uri == _namespace_SOFA('SO_0000644'):
|
2206
2202
|
return True
|
2207
|
-
if uri == _namespace_SOFA('
|
2203
|
+
if uri == _namespace_SOFA('SO_0000645'):
|
2208
2204
|
return True
|
2209
|
-
if uri == _namespace_SOFA('
|
2205
|
+
if uri == _namespace_SOFA('SO_0000646'):
|
2210
2206
|
return True
|
2211
|
-
if uri == _namespace_SOFA('
|
2207
|
+
if uri == _namespace_SOFA('SO_0000649'):
|
2212
2208
|
return True
|
2213
|
-
if uri == _namespace_SOFA('
|
2209
|
+
if uri == _namespace_SOFA('SO_0000650'):
|
2214
2210
|
return True
|
2215
|
-
if uri == _namespace_SOFA('
|
2211
|
+
if uri == _namespace_SOFA('SO_0000651'):
|
2216
2212
|
return True
|
2217
|
-
if uri == _namespace_SOFA('
|
2213
|
+
if uri == _namespace_SOFA('SO_0000652'):
|
2218
2214
|
return True
|
2219
|
-
if uri == _namespace_SOFA('
|
2215
|
+
if uri == _namespace_SOFA('SO_0000653'):
|
2220
2216
|
return True
|
2221
|
-
if uri == _namespace_SOFA('
|
2217
|
+
if uri == _namespace_SOFA('SO_0000655'):
|
2222
2218
|
return True
|
2223
|
-
if uri == _namespace_SOFA('
|
2219
|
+
if uri == _namespace_SOFA('SO_0000657'):
|
2224
2220
|
return True
|
2225
|
-
if uri == _namespace_SOFA('
|
2221
|
+
if uri == _namespace_SOFA('SO_0000658'):
|
2226
2222
|
return True
|
2227
|
-
if uri == _namespace_SOFA('
|
2223
|
+
if uri == _namespace_SOFA('SO_0000662'):
|
2228
2224
|
return True
|
2229
|
-
if uri == _namespace_SOFA('
|
2225
|
+
if uri == _namespace_SOFA('SO_0000667'):
|
2230
2226
|
return True
|
2231
|
-
if uri == _namespace_SOFA('
|
2227
|
+
if uri == _namespace_SOFA('SO_0000668'):
|
2232
2228
|
return True
|
2233
|
-
if uri == _namespace_SOFA('
|
2229
|
+
if uri == _namespace_SOFA('SO_0000673'):
|
2234
2230
|
return True
|
2235
|
-
if uri == _namespace_SOFA('
|
2231
|
+
if uri == _namespace_SOFA('SO_0000684'):
|
2236
2232
|
return True
|
2237
|
-
if uri == _namespace_SOFA('
|
2233
|
+
if uri == _namespace_SOFA('SO_0000687'):
|
2238
2234
|
return True
|
2239
|
-
if uri == _namespace_SOFA('
|
2235
|
+
if uri == _namespace_SOFA('SO_0000688'):
|
2240
2236
|
return True
|
2241
|
-
if uri == _namespace_SOFA('
|
2237
|
+
if uri == _namespace_SOFA('SO_0000689'):
|
2242
2238
|
return True
|
2243
|
-
if uri == _namespace_SOFA('
|
2239
|
+
if uri == _namespace_SOFA('SO_0000694'):
|
2244
2240
|
return True
|
2245
|
-
if uri == _namespace_SOFA('
|
2241
|
+
if uri == _namespace_SOFA('SO_0000695'):
|
2246
2242
|
return True
|
2247
|
-
if uri == _namespace_SOFA('
|
2243
|
+
if uri == _namespace_SOFA('SO_0000696'):
|
2248
2244
|
return True
|
2249
|
-
if uri == _namespace_SOFA('
|
2245
|
+
if uri == _namespace_SOFA('SO_0000699'):
|
2250
2246
|
return True
|
2251
|
-
if uri == _namespace_SOFA('
|
2247
|
+
if uri == _namespace_SOFA('SO_0000700'):
|
2252
2248
|
return True
|
2253
|
-
if uri == _namespace_SOFA('
|
2249
|
+
if uri == _namespace_SOFA('SO_0000701'):
|
2254
2250
|
return True
|
2255
|
-
if uri == _namespace_SOFA('
|
2251
|
+
if uri == _namespace_SOFA('SO_0000702'):
|
2256
2252
|
return True
|
2257
|
-
if uri == _namespace_SOFA('
|
2253
|
+
if uri == _namespace_SOFA('SO_0000703'):
|
2258
2254
|
return True
|
2259
|
-
if uri == _namespace_SOFA('
|
2255
|
+
if uri == _namespace_SOFA('SO_0000704'):
|
2260
2256
|
return True
|
2261
|
-
if uri == _namespace_SOFA('
|
2257
|
+
if uri == _namespace_SOFA('SO_0000705'):
|
2262
2258
|
return True
|
2263
|
-
if uri == _namespace_SOFA('
|
2259
|
+
if uri == _namespace_SOFA('SO_0000706'):
|
2264
2260
|
return True
|
2265
|
-
if uri == _namespace_SOFA('
|
2261
|
+
if uri == _namespace_SOFA('SO_0000714'):
|
2266
2262
|
return True
|
2267
|
-
if uri == _namespace_SOFA('
|
2263
|
+
if uri == _namespace_SOFA('SO_0000715'):
|
2268
2264
|
return True
|
2269
|
-
if uri == _namespace_SOFA('
|
2265
|
+
if uri == _namespace_SOFA('SO_0000717'):
|
2270
2266
|
return True
|
2271
|
-
if uri == _namespace_SOFA('
|
2267
|
+
if uri == _namespace_SOFA('SO_0000719'):
|
2272
2268
|
return True
|
2273
|
-
if uri == _namespace_SOFA('
|
2269
|
+
if uri == _namespace_SOFA('SO_0000724'):
|
2274
2270
|
return True
|
2275
|
-
if uri == _namespace_SOFA('
|
2271
|
+
if uri == _namespace_SOFA('SO_0000725'):
|
2276
2272
|
return True
|
2277
|
-
if uri == _namespace_SOFA('
|
2273
|
+
if uri == _namespace_SOFA('SO_0000727'):
|
2278
2274
|
return True
|
2279
|
-
if uri == _namespace_SOFA('
|
2275
|
+
if uri == _namespace_SOFA('SO_0000730'):
|
2280
2276
|
return True
|
2281
|
-
if uri == _namespace_SOFA('
|
2277
|
+
if uri == _namespace_SOFA('SO_0000752'):
|
2282
2278
|
return True
|
2283
|
-
if uri == _namespace_SOFA('
|
2279
|
+
if uri == _namespace_SOFA('SO_0000753'):
|
2284
2280
|
return True
|
2285
|
-
if uri == _namespace_SOFA('
|
2281
|
+
if uri == _namespace_SOFA('SO_0000777'):
|
2286
2282
|
return True
|
2287
|
-
if uri == _namespace_SOFA('
|
2283
|
+
if uri == _namespace_SOFA('SO_0000778'):
|
2288
2284
|
return True
|
2289
|
-
if uri == _namespace_SOFA('
|
2285
|
+
if uri == _namespace_SOFA('SO_0000830'):
|
2290
2286
|
return True
|
2291
|
-
if uri == _namespace_SOFA('
|
2287
|
+
if uri == _namespace_SOFA('SO_0000831'):
|
2292
2288
|
return True
|
2293
|
-
if uri == _namespace_SOFA('
|
2289
|
+
if uri == _namespace_SOFA('SO_0000833'):
|
2294
2290
|
return True
|
2295
|
-
if uri == _namespace_SOFA('
|
2291
|
+
if uri == _namespace_SOFA('SO_0000834'):
|
2296
2292
|
return True
|
2297
|
-
if uri == _namespace_SOFA('
|
2293
|
+
if uri == _namespace_SOFA('SO_0000835'):
|
2298
2294
|
return True
|
2299
|
-
if uri == _namespace_SOFA('
|
2295
|
+
if uri == _namespace_SOFA('SO_0000836'):
|
2300
2296
|
return True
|
2301
|
-
if uri == _namespace_SOFA('
|
2297
|
+
if uri == _namespace_SOFA('SO_0000837'):
|
2302
2298
|
return True
|
2303
|
-
if uri == _namespace_SOFA('
|
2299
|
+
if uri == _namespace_SOFA('SO_0000839'):
|
2304
2300
|
return True
|
2305
|
-
if uri == _namespace_SOFA('
|
2301
|
+
if uri == _namespace_SOFA('SO_0000841'):
|
2306
2302
|
return True
|
2307
|
-
if uri == _namespace_SOFA('
|
2303
|
+
if uri == _namespace_SOFA('SO_0000842'):
|
2308
2304
|
return True
|
2309
|
-
if uri == _namespace_SOFA('
|
2305
|
+
if uri == _namespace_SOFA('SO_0000851'):
|
2310
2306
|
return True
|
2311
|
-
if uri == _namespace_SOFA('
|
2307
|
+
if uri == _namespace_SOFA('SO_0000852'):
|
2312
2308
|
return True
|
2313
|
-
if uri == _namespace_SOFA('
|
2309
|
+
if uri == _namespace_SOFA('SO_0001000'):
|
2314
2310
|
return True
|
2315
|
-
if uri == _namespace_SOFA('
|
2311
|
+
if uri == _namespace_SOFA('SO_0001001'):
|
2316
2312
|
return True
|
2317
|
-
if uri == _namespace_SOFA('
|
2313
|
+
if uri == _namespace_SOFA('SO_0001002'):
|
2318
2314
|
return True
|
2319
|
-
if uri == _namespace_SOFA('
|
2315
|
+
if uri == _namespace_SOFA('SO_0001019'):
|
2320
2316
|
return True
|
2321
|
-
if uri == _namespace_SOFA('
|
2317
|
+
if uri == _namespace_SOFA('SO_0001037'):
|
2322
2318
|
return True
|
2323
|
-
if uri == _namespace_SOFA('
|
2319
|
+
if uri == _namespace_SOFA('SO_0001039'):
|
2324
2320
|
return True
|
2325
|
-
if uri == _namespace_SOFA('
|
2321
|
+
if uri == _namespace_SOFA('SO_0001055'):
|
2326
2322
|
return True
|
2327
|
-
if uri == _namespace_SOFA('
|
2323
|
+
if uri == _namespace_SOFA('SO_0001056'):
|
2328
2324
|
return True
|
2329
|
-
if uri == _namespace_SOFA('
|
2325
|
+
if uri == _namespace_SOFA('SO_0001059'):
|
2330
2326
|
return True
|
2331
|
-
if uri == _namespace_SOFA('
|
2327
|
+
if uri == _namespace_SOFA('SO_0001063'):
|
2332
2328
|
return True
|
2333
|
-
if uri == _namespace_SOFA('
|
2329
|
+
if uri == _namespace_SOFA('SO_0001214'):
|
2334
2330
|
return True
|
2335
|
-
if uri == _namespace_SOFA('
|
2331
|
+
if uri == _namespace_SOFA('SO_0001215'):
|
2336
2332
|
return True
|
2337
|
-
if uri == _namespace_SOFA('
|
2333
|
+
if uri == _namespace_SOFA('SO_0001235'):
|
2338
2334
|
return True
|
2339
|
-
if uri == _namespace_SOFA('
|
2335
|
+
if uri == _namespace_SOFA('SO_0001236'):
|
2340
2336
|
return True
|
2341
|
-
if uri == _namespace_SOFA('
|
2337
|
+
if uri == _namespace_SOFA('SO_0001248'):
|
2342
2338
|
return True
|
2343
|
-
if uri == _namespace_SOFA('
|
2339
|
+
if uri == _namespace_SOFA('SO_0001409'):
|
2344
2340
|
return True
|
2345
|
-
if uri == _namespace_SOFA('
|
2341
|
+
if uri == _namespace_SOFA('SO_0001410'):
|
2346
2342
|
return True
|
2347
|
-
if uri == _namespace_SOFA('
|
2343
|
+
if uri == _namespace_SOFA('SO_0001411'):
|
2348
2344
|
return True
|
2349
|
-
if uri == _namespace_SOFA('
|
2345
|
+
if uri == _namespace_SOFA('SO_0001412'):
|
2350
2346
|
return True
|
2351
|
-
if uri == _namespace_SOFA('
|
2347
|
+
if uri == _namespace_SOFA('SO_0001419'):
|
2352
2348
|
return True
|
2353
|
-
if uri == _namespace_SOFA('
|
2349
|
+
if uri == _namespace_SOFA('SO_0001420'):
|
2354
2350
|
return True
|
2355
|
-
if uri == _namespace_SOFA('
|
2351
|
+
if uri == _namespace_SOFA('SO_0001483'):
|
2356
2352
|
return True
|
2357
|
-
if uri == _namespace_SOFA('
|
2353
|
+
if uri == _namespace_SOFA('SO_0001527'):
|
2358
2354
|
return True
|
2359
|
-
if uri == _namespace_SOFA('
|
2355
|
+
if uri == _namespace_SOFA('SO_0001647'):
|
2360
2356
|
return True
|
2361
|
-
if uri == _namespace_SOFA('
|
2357
|
+
if uri == _namespace_SOFA('SO_0001654'):
|
2362
2358
|
return True
|
2363
|
-
if uri == _namespace_SOFA('
|
2359
|
+
if uri == _namespace_SOFA('SO_0001679'):
|
2364
2360
|
return True
|
2365
|
-
if uri == _namespace_SOFA('
|
2361
|
+
if uri == _namespace_SOFA('SO_0001683'):
|
2366
2362
|
return True
|
2367
|
-
if uri == _namespace_SOFA('
|
2363
|
+
if uri == _namespace_SOFA('SO_0001720'):
|
2368
2364
|
return True
|
2369
|
-
if uri == _namespace_SOFA('
|
2365
|
+
if uri == _namespace_SOFA('SO_0001790'):
|
2370
2366
|
return True
|
2371
|
-
if uri == _namespace_SOFA('
|
2367
|
+
if uri == _namespace_SOFA('SO_0005836'):
|
2372
2368
|
return True
|
2373
|
-
if uri == _namespace_SOFA('
|
2369
|
+
if uri == _namespace_SOFA('SO_0005855'):
|
2374
2370
|
return True
|
2375
|
-
if uri == _namespace_SOFA('
|
2371
|
+
if uri == _namespace_SOFA('SO_0100011'):
|
2376
2372
|
return True
|
2377
|
-
if uri == _namespace_SOFA('
|
2373
|
+
if uri == _namespace_SOFA('SO_1000002'):
|
2378
2374
|
return True
|
2379
|
-
if uri == _namespace_SOFA('
|
2375
|
+
if uri == _namespace_SOFA('SO_1000005'):
|
2380
2376
|
return True
|
2381
|
-
if uri == _namespace_SOFA('
|
2377
|
+
if uri == _namespace_SOFA('SO_1000008'):
|
2382
2378
|
return True
|
2383
|
-
if uri == _namespace_SOFA('
|
2379
|
+
if uri == _namespace_SOFA('SO_1000036'):
|
2384
2380
|
return True
|
2385
|
-
if uri == _namespace_SOFA('
|
2381
|
+
if uri == _namespace_SOFA('SO_1001284'):
|
2386
2382
|
return True
|
2387
|
-
if uri == _namespace_SOFA('
|
2383
|
+
if uri == _namespace_SOFA('SO_2000061'):
|
2388
2384
|
return True
|
2389
2385
|
return False
|
2390
2386
|
|
@@ -2418,5 +2414,11 @@ class SOFA:
|
|
2418
2414
|
return cls.has_parent(cls.__parent_properties[uri], parent)
|
2419
2415
|
return False
|
2420
2416
|
|
2421
|
-
__parent_properties = { _namespace_SOFA('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:complete_evidence_for_feature') : _namespace_SOFA('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:evidence_for_feature') , _namespace_SOFA('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:has_integral_part') : _namespace_SOFA('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:has_part') , _namespace_SOFA('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:homologous_to') : _namespace_SOFA('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:similar_to') , _namespace_SOFA('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:integral_part_of') : _namespace_SOFA('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:part_of') , _namespace_SOFA('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:member_of') : _namespace_SOFA('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:part_of') , _namespace_SOFA('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:non_functional_homolog_of') : _namespace_SOFA('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:homologous_to') , _namespace_SOFA('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:orthologous_to') : _namespace_SOFA('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:homologous_to') , _namespace_SOFA('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:paralogous_to') : _namespace_SOFA('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:homologous_to') , _namespace_SOFA('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:partial_evidence_for_feature') : _namespace_SOFA('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:evidence_for_feature') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000001') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000110') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000004') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000195') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000005') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000705') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000006') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000695') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000057') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000752') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000059') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001654') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000101') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001039') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000102') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000347') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000112') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000441') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000113') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001039') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000114') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000306') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000120') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000185') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000139') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000836') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000143') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001410') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000147') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000833') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000151') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000695') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000159') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001411') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000161') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000306') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000162') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000835') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000163') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001419') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000164') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001419') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000165') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000727') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000167') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001055') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000177') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000347') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000178') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0005855') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000181') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000347') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000183') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000842') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000185') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000673') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000188') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000835') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000193') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000412') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000195') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000147') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000198') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000147') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000200') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000195') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000203') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000836') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000204') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000203') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000205') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000203') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000209') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000483') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000234') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000233') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000235') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001679') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000236') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000717') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000239') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001412') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000289') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000005') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000294') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000657') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000303') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000835') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000305') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001720') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000306') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000305') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000307') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001411') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000314') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000657') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000315') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000835') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000316') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000836') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000318') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000360') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000319') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000360') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000324') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000696') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000325') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000209') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000326') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000324') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000330') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001410') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000331') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000324') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000332') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000330') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000334') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000330') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000337') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000442') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000340') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001235') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000341') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000830') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000343') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001410') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000344') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001056') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000347') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000343') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000349') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000343') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000353') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001248') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000360') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000851') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000366') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000699') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000368') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000366') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000370') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000655') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000372') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000673') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000374') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000372') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000375') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000651') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000380') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000715') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000385') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000655') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000386') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000655') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000390') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000655') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000391') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000274') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000392') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000274') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000393') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000274') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000394') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000274') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000395') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000274') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000396') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000274') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000397') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000274') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000398') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000274') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000399') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000274') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000403') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000593') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000404') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000655') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000405') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000655') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000407') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000650') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000409') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001411') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000410') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000409') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000412') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000143') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000413') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000700') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000436') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000296') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000441') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000696') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000442') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000696') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000454') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000655') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000462') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001411') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000472') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000353') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000483') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000185') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000499') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000353') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000551') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001679') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000577') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000628') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000581') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001411') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000587') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000588') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000588') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000188') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000593') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000275') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000602') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000655') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000603') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000588') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000605') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001411') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000611') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000841') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000612') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000841') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000616') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000835') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000624') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000628') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000625') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000727') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000627') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001055') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000628') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000830') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000643') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000005') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000645') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000185') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000646') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000655') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000649') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000655') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000650') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000252') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000652') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000651') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000653') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000651') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000655') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000233') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000658') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000657') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000662') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000188') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000667') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001411') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000668') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000102') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000673') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000831') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000684') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000059') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000687') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000699') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000688') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000353') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000689') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000102') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000694') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001483') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000695') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001409') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000696') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000695') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000699') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000110') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000700') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001410') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000701') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000413') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000702') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000413') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000703') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000700') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000705') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000657') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000706') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001420') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000714') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001683') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000715') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000714') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000717') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001410') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000719') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000353') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000724') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000296') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000725') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001527') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000777') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000462') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000778') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000462') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000834') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000833') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000837') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000836') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001000') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000650') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001001') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000651') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001002') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000651') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001019') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001059') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001037') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001411') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001039') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001037') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001055') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001679') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001056') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001679') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001059') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000110') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001063') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000839') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001214') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000852') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001215') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000852') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001235') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001411') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001236') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001411') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001248') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001410') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001409') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000001') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001410') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000001') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001411') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000001') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001412') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000001') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001419') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000162') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001420') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000162') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001483') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_1000002') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001527') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000839') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001647') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000139') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001654') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000410') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001679') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0005836') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001683') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001411') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001720') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001411') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001790') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000143') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0005836') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000831') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0005855') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001411') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_1000002') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001411') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_1000005') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_1000002') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_1000008') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001483') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_1000036') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0001411') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_1001284') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0005855') , _namespace_SOFA('http://purl.obolibrary.org/obo/SO_2000061') : _namespace_SOFA('http://purl.obolibrary.org/obo/SO_0000695') }
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__namespace_SOFA = Namespace('http://purl.obolibrary.org/obo/')
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2418
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+
|
2419
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+
def _namespace_SOFA(accession):
|
2420
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return __namespace_SOFA[accession]
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2421
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+
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2422
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+
__parent_properties = { _namespace_SOFA('http_//purl.org/obo/owl:complete_evidence_for_feature') : _namespace_SOFA('http_//purl.org/obo/owl:evidence_for_feature') , _namespace_SOFA('http_//purl.org/obo/owl:has_integral_part') : _namespace_SOFA('http_//purl.org/obo/owl:has_part') , _namespace_SOFA('http_//purl.org/obo/owl:homologous_to') : _namespace_SOFA('http_//purl.org/obo/owl:similar_to') , _namespace_SOFA('http_//purl.org/obo/owl:integral_part_of') : _namespace_SOFA('http_//purl.org/obo/owl:part_of') , _namespace_SOFA('http_//purl.org/obo/owl:member_of') : _namespace_SOFA('http_//purl.org/obo/owl:part_of') , _namespace_SOFA('http_//purl.org/obo/owl:non_functional_homolog_of') : _namespace_SOFA('http_//purl.org/obo/owl:homologous_to') , _namespace_SOFA('http_//purl.org/obo/owl:orthologous_to') : _namespace_SOFA('http_//purl.org/obo/owl:homologous_to') , _namespace_SOFA('http_//purl.org/obo/owl:paralogous_to') : _namespace_SOFA('http_//purl.org/obo/owl:homologous_to') , _namespace_SOFA('http_//purl.org/obo/owl:partial_evidence_for_feature') : _namespace_SOFA('http_//purl.org/obo/owl:evidence_for_feature') , _namespace_SOFA('SO_0000001') : _namespace_SOFA('SO_0000110') , _namespace_SOFA('SO_0000004') : _namespace_SOFA('SO_0000195') , _namespace_SOFA('SO_0000005') : _namespace_SOFA('SO_0000705') , _namespace_SOFA('SO_0000006') : _namespace_SOFA('SO_0000695') , _namespace_SOFA('SO_0000057') : _namespace_SOFA('SO_0000752') , _namespace_SOFA('SO_0000059') : _namespace_SOFA('SO_0001654') , _namespace_SOFA('SO_0000101') : _namespace_SOFA('SO_0001039') , _namespace_SOFA('SO_0000102') : _namespace_SOFA('SO_0000347') , _namespace_SOFA('SO_0000112') : _namespace_SOFA('SO_0000441') , _namespace_SOFA('SO_0000113') : _namespace_SOFA('SO_0001039') , _namespace_SOFA('SO_0000114') : _namespace_SOFA('SO_0000306') , _namespace_SOFA('SO_0000120') : _namespace_SOFA('SO_0000185') , _namespace_SOFA('SO_0000139') : _namespace_SOFA('SO_0000836') , _namespace_SOFA('SO_0000143') : _namespace_SOFA('SO_0001410') , _namespace_SOFA('SO_0000147') : _namespace_SOFA('SO_0000833') , _namespace_SOFA('SO_0000151') : _namespace_SOFA('SO_0000695') , _namespace_SOFA('SO_0000159') : _namespace_SOFA('SO_0001411') , _namespace_SOFA('SO_0000161') : _namespace_SOFA('SO_0000306') , _namespace_SOFA('SO_0000162') : _namespace_SOFA('SO_0000835') , _namespace_SOFA('SO_0000163') : _namespace_SOFA('SO_0001419') , _namespace_SOFA('SO_0000164') : _namespace_SOFA('SO_0001419') , _namespace_SOFA('SO_0000165') : _namespace_SOFA('SO_0000727') , _namespace_SOFA('SO_0000167') : _namespace_SOFA('SO_0001055') , _namespace_SOFA('SO_0000177') : _namespace_SOFA('SO_0000347') , _namespace_SOFA('SO_0000178') : _namespace_SOFA('SO_0005855') , _namespace_SOFA('SO_0000181') : _namespace_SOFA('SO_0000347') , _namespace_SOFA('SO_0000183') : _namespace_SOFA('SO_0000842') , _namespace_SOFA('SO_0000185') : _namespace_SOFA('SO_0000673') , _namespace_SOFA('SO_0000188') : _namespace_SOFA('SO_0000835') , _namespace_SOFA('SO_0000193') : _namespace_SOFA('SO_0000412') , _namespace_SOFA('SO_0000195') : _namespace_SOFA('SO_0000147') , _namespace_SOFA('SO_0000198') : _namespace_SOFA('SO_0000147') , _namespace_SOFA('SO_0000200') : _namespace_SOFA('SO_0000195') , _namespace_SOFA('SO_0000203') : _namespace_SOFA('SO_0000836') , _namespace_SOFA('SO_0000204') : _namespace_SOFA('SO_0000203') , _namespace_SOFA('SO_0000205') : _namespace_SOFA('SO_0000203') , _namespace_SOFA('SO_0000209') : _namespace_SOFA('SO_0000483') , _namespace_SOFA('SO_0000234') : _namespace_SOFA('SO_0000233') , _namespace_SOFA('SO_0000235') : _namespace_SOFA('SO_0001679') , _namespace_SOFA('SO_0000236') : _namespace_SOFA('SO_0000717') , _namespace_SOFA('SO_0000239') : _namespace_SOFA('SO_0001412') , _namespace_SOFA('SO_0000289') : _namespace_SOFA('SO_0000005') , _namespace_SOFA('SO_0000294') : _namespace_SOFA('SO_0000657') , _namespace_SOFA('SO_0000303') : _namespace_SOFA('SO_0000835') , _namespace_SOFA('SO_0000305') : _namespace_SOFA('SO_0001720') , _namespace_SOFA('SO_0000306') : _namespace_SOFA('SO_0000305') , _namespace_SOFA('SO_0000307') : _namespace_SOFA('SO_0001411') , _namespace_SOFA('SO_0000314') : _namespace_SOFA('SO_0000657') , _namespace_SOFA('SO_0000315') : _namespace_SOFA('SO_0000835') , _namespace_SOFA('SO_0000316') : _namespace_SOFA('SO_0000836') , _namespace_SOFA('SO_0000318') : _namespace_SOFA('SO_0000360') , _namespace_SOFA('SO_0000319') : _namespace_SOFA('SO_0000360') , _namespace_SOFA('SO_0000324') : _namespace_SOFA('SO_0000696') , _namespace_SOFA('SO_0000325') : _namespace_SOFA('SO_0000209') , _namespace_SOFA('SO_0000326') : _namespace_SOFA('SO_0000324') , _namespace_SOFA('SO_0000330') : _namespace_SOFA('SO_0001410') , _namespace_SOFA('SO_0000331') : _namespace_SOFA('SO_0000324') , _namespace_SOFA('SO_0000332') : _namespace_SOFA('SO_0000330') , _namespace_SOFA('SO_0000334') : _namespace_SOFA('SO_0000330') , _namespace_SOFA('SO_0000337') : 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_namespace_SOFA('SO_0000385') : _namespace_SOFA('SO_0000655') , _namespace_SOFA('SO_0000386') : _namespace_SOFA('SO_0000655') , _namespace_SOFA('SO_0000390') : _namespace_SOFA('SO_0000655') , _namespace_SOFA('SO_0000391') : _namespace_SOFA('SO_0000274') , _namespace_SOFA('SO_0000392') : _namespace_SOFA('SO_0000274') , _namespace_SOFA('SO_0000393') : _namespace_SOFA('SO_0000274') , _namespace_SOFA('SO_0000394') : _namespace_SOFA('SO_0000274') , _namespace_SOFA('SO_0000395') : _namespace_SOFA('SO_0000274') , _namespace_SOFA('SO_0000396') : _namespace_SOFA('SO_0000274') , _namespace_SOFA('SO_0000397') : _namespace_SOFA('SO_0000274') , _namespace_SOFA('SO_0000398') : _namespace_SOFA('SO_0000274') , _namespace_SOFA('SO_0000399') : _namespace_SOFA('SO_0000274') , _namespace_SOFA('SO_0000403') : _namespace_SOFA('SO_0000593') , _namespace_SOFA('SO_0000404') : _namespace_SOFA('SO_0000655') , _namespace_SOFA('SO_0000405') : _namespace_SOFA('SO_0000655') , _namespace_SOFA('SO_0000407') : _namespace_SOFA('SO_0000650') , _namespace_SOFA('SO_0000409') : _namespace_SOFA('SO_0001411') , _namespace_SOFA('SO_0000410') : _namespace_SOFA('SO_0000409') , _namespace_SOFA('SO_0000412') : _namespace_SOFA('SO_0000143') , _namespace_SOFA('SO_0000413') : _namespace_SOFA('SO_0000700') , _namespace_SOFA('SO_0000436') : _namespace_SOFA('SO_0000296') , _namespace_SOFA('SO_0000441') : _namespace_SOFA('SO_0000696') , _namespace_SOFA('SO_0000442') : _namespace_SOFA('SO_0000696') , _namespace_SOFA('SO_0000454') : _namespace_SOFA('SO_0000655') , _namespace_SOFA('SO_0000462') : _namespace_SOFA('SO_0001411') , _namespace_SOFA('SO_0000472') : _namespace_SOFA('SO_0000353') , _namespace_SOFA('SO_0000483') : _namespace_SOFA('SO_0000185') , _namespace_SOFA('SO_0000499') : _namespace_SOFA('SO_0000353') , _namespace_SOFA('SO_0000551') : _namespace_SOFA('SO_0001679') , _namespace_SOFA('SO_0000577') : _namespace_SOFA('SO_0000628') , _namespace_SOFA('SO_0000581') : _namespace_SOFA('SO_0001411') , _namespace_SOFA('SO_0000587') : _namespace_SOFA('SO_0000588') , _namespace_SOFA('SO_0000588') : _namespace_SOFA('SO_0000188') , _namespace_SOFA('SO_0000593') : _namespace_SOFA('SO_0000275') , _namespace_SOFA('SO_0000602') : _namespace_SOFA('SO_0000655') , _namespace_SOFA('SO_0000603') : _namespace_SOFA('SO_0000588') , _namespace_SOFA('SO_0000605') : _namespace_SOFA('SO_0001411') , _namespace_SOFA('SO_0000611') : _namespace_SOFA('SO_0000841') , _namespace_SOFA('SO_0000612') : _namespace_SOFA('SO_0000841') , _namespace_SOFA('SO_0000616') : _namespace_SOFA('SO_0000835') , _namespace_SOFA('SO_0000624') : _namespace_SOFA('SO_0000628') , _namespace_SOFA('SO_0000625') : _namespace_SOFA('SO_0000727') , _namespace_SOFA('SO_0000627') : _namespace_SOFA('SO_0001055') , _namespace_SOFA('SO_0000628') : _namespace_SOFA('SO_0000830') , _namespace_SOFA('SO_0000643') : _namespace_SOFA('SO_0000005') , _namespace_SOFA('SO_0000645') : _namespace_SOFA('SO_0000185') , _namespace_SOFA('SO_0000646') : _namespace_SOFA('SO_0000655') , _namespace_SOFA('SO_0000649') : _namespace_SOFA('SO_0000655') , _namespace_SOFA('SO_0000650') : _namespace_SOFA('SO_0000252') , _namespace_SOFA('SO_0000652') : _namespace_SOFA('SO_0000651') , _namespace_SOFA('SO_0000653') : _namespace_SOFA('SO_0000651') , _namespace_SOFA('SO_0000655') : _namespace_SOFA('SO_0000233') , _namespace_SOFA('SO_0000658') : _namespace_SOFA('SO_0000657') , _namespace_SOFA('SO_0000662') : _namespace_SOFA('SO_0000188') , _namespace_SOFA('SO_0000667') : _namespace_SOFA('SO_0001411') , _namespace_SOFA('SO_0000668') : _namespace_SOFA('SO_0000102') , _namespace_SOFA('SO_0000673') : _namespace_SOFA('SO_0000831') , _namespace_SOFA('SO_0000684') : _namespace_SOFA('SO_0000059') , _namespace_SOFA('SO_0000687') : _namespace_SOFA('SO_0000699') , _namespace_SOFA('SO_0000688') : _namespace_SOFA('SO_0000353') , _namespace_SOFA('SO_0000689') : _namespace_SOFA('SO_0000102') , _namespace_SOFA('SO_0000694') : _namespace_SOFA('SO_0001483') , _namespace_SOFA('SO_0000695') : _namespace_SOFA('SO_0001409') , _namespace_SOFA('SO_0000696') : _namespace_SOFA('SO_0000695') , _namespace_SOFA('SO_0000699') : _namespace_SOFA('SO_0000110') , _namespace_SOFA('SO_0000700') : _namespace_SOFA('SO_0001410') , _namespace_SOFA('SO_0000701') : _namespace_SOFA('SO_0000413') , _namespace_SOFA('SO_0000702') : _namespace_SOFA('SO_0000413') , _namespace_SOFA('SO_0000703') : _namespace_SOFA('SO_0000700') , _namespace_SOFA('SO_0000705') : _namespace_SOFA('SO_0000657') , _namespace_SOFA('SO_0000706') : _namespace_SOFA('SO_0001420') , _namespace_SOFA('SO_0000714') : _namespace_SOFA('SO_0001683') , _namespace_SOFA('SO_0000715') : _namespace_SOFA('SO_0000714') , _namespace_SOFA('SO_0000717') : _namespace_SOFA('SO_0001410') , _namespace_SOFA('SO_0000719') : _namespace_SOFA('SO_0000353') , _namespace_SOFA('SO_0000724') : _namespace_SOFA('SO_0000296') , _namespace_SOFA('SO_0000725') : _namespace_SOFA('SO_0001527') , _namespace_SOFA('SO_0000777') : _namespace_SOFA('SO_0000462') , _namespace_SOFA('SO_0000778') : _namespace_SOFA('SO_0000462') , _namespace_SOFA('SO_0000834') : _namespace_SOFA('SO_0000833') , _namespace_SOFA('SO_0000837') : _namespace_SOFA('SO_0000836') , _namespace_SOFA('SO_0001000') : _namespace_SOFA('SO_0000650') , _namespace_SOFA('SO_0001001') : _namespace_SOFA('SO_0000651') , _namespace_SOFA('SO_0001002') : _namespace_SOFA('SO_0000651') , _namespace_SOFA('SO_0001019') : _namespace_SOFA('SO_0001059') , _namespace_SOFA('SO_0001037') : _namespace_SOFA('SO_0001411') , _namespace_SOFA('SO_0001039') : _namespace_SOFA('SO_0001037') , _namespace_SOFA('SO_0001055') : _namespace_SOFA('SO_0001679') , _namespace_SOFA('SO_0001056') : _namespace_SOFA('SO_0001679') , _namespace_SOFA('SO_0001059') : _namespace_SOFA('SO_0000110') , _namespace_SOFA('SO_0001063') : _namespace_SOFA('SO_0000839') , _namespace_SOFA('SO_0001214') : _namespace_SOFA('SO_0000852') , _namespace_SOFA('SO_0001215') : _namespace_SOFA('SO_0000852') , _namespace_SOFA('SO_0001235') : _namespace_SOFA('SO_0001411') , _namespace_SOFA('SO_0001236') : _namespace_SOFA('SO_0001411') , _namespace_SOFA('SO_0001248') : _namespace_SOFA('SO_0001410') , _namespace_SOFA('SO_0001409') : _namespace_SOFA('SO_0000001') , _namespace_SOFA('SO_0001410') : _namespace_SOFA('SO_0000001') , _namespace_SOFA('SO_0001411') : _namespace_SOFA('SO_0000001') , _namespace_SOFA('SO_0001412') : _namespace_SOFA('SO_0000001') , _namespace_SOFA('SO_0001419') : _namespace_SOFA('SO_0000162') , _namespace_SOFA('SO_0001420') : _namespace_SOFA('SO_0000162') , _namespace_SOFA('SO_0001483') : _namespace_SOFA('SO_1000002') , _namespace_SOFA('SO_0001527') : _namespace_SOFA('SO_0000839') , _namespace_SOFA('SO_0001647') : _namespace_SOFA('SO_0000139') , _namespace_SOFA('SO_0001654') : _namespace_SOFA('SO_0000410') , _namespace_SOFA('SO_0001679') : _namespace_SOFA('SO_0005836') , _namespace_SOFA('SO_0001683') : _namespace_SOFA('SO_0001411') , _namespace_SOFA('SO_0001720') : _namespace_SOFA('SO_0001411') , _namespace_SOFA('SO_0001790') : _namespace_SOFA('SO_0000143') , _namespace_SOFA('SO_0005836') : _namespace_SOFA('SO_0000831') , _namespace_SOFA('SO_0005855') : _namespace_SOFA('SO_0001411') , _namespace_SOFA('SO_1000002') : _namespace_SOFA('SO_0001411') , _namespace_SOFA('SO_1000005') : _namespace_SOFA('SO_1000002') , _namespace_SOFA('SO_1000008') : _namespace_SOFA('SO_0001483') , _namespace_SOFA('SO_1000036') : _namespace_SOFA('SO_0001411') , _namespace_SOFA('SO_1001284') : _namespace_SOFA('SO_0005855') , _namespace_SOFA('SO_2000061') : _namespace_SOFA('SO_0000695') }
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