biointerchange 0.2.2 → 1.0.0
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- data/Gemfile +1 -0
- data/README.md +269 -19
- data/VERSION +1 -1
- data/examples/bininda_emonds_mammals.new +1 -0
- data/examples/rdfization.rb +17 -0
- data/examples/tree1.new +1 -0
- data/examples/tree2.new +1 -0
- data/examples/vocabulary.rb +26 -5
- data/generators/javaify.rb +12 -18
- data/generators/make_supplement_releases.rb +2 -0
- data/generators/pythonify.rb +21 -8
- data/generators/rdfxml.rb +15 -1
- data/lib/biointerchange/cdao.rb +2014 -0
- data/lib/biointerchange/core.rb +70 -77
- data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +16 -0
- data/lib/biointerchange/genomics/gff3_reader.rb +18 -4
- data/lib/biointerchange/genomics/gvf_reader.rb +14 -0
- data/lib/biointerchange/phylogenetics/cdao_rdf_ntriples.rb +108 -0
- data/lib/biointerchange/phylogenetics/newick_reader.rb +81 -0
- data/lib/biointerchange/phylogenetics/tree_set.rb +50 -0
- data/lib/biointerchange/registry.rb +50 -8
- data/lib/biointerchange/so.rb +150 -0
- data/lib/biointerchange/textmining/pdfx_xml_reader.rb +21 -2
- data/lib/biointerchange/textmining/pubannos_json_reader.rb +24 -1
- data/lib/biointerchange/textmining/text_mining_rdf_ntriples.rb +9 -0
- data/lib/biointerchange/textmining/text_mining_reader.rb +5 -5
- data/spec/phylogenetics_spec.rb +79 -0
- data/supplemental/java/biointerchange/pom.xml +1 -1
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/CDAO.java +2602 -0
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/FALDO.java +30 -28
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GFF3O.java +136 -104
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GVF1O.java +367 -278
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SIO.java +4388 -3127
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SO.java +5970 -4351
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SOFA.java +733 -544
- data/supplemental/java/biointerchange/src/test/java/org/biointerchange/AppTest.java +3 -1
- data/supplemental/python/biointerchange/cdao.py +2021 -0
- data/supplemental/python/biointerchange/faldo.py +37 -38
- data/supplemental/python/biointerchange/gff3o.py +156 -157
- data/supplemental/python/biointerchange/goxref.py +172 -172
- data/supplemental/python/biointerchange/gvf1o.py +428 -429
- data/supplemental/python/biointerchange/sio.py +3133 -3134
- data/supplemental/python/biointerchange/so.py +6626 -6527
- data/supplemental/python/biointerchange/sofa.py +790 -791
- data/supplemental/python/example.py +23 -5
- data/supplemental/python/setup.py +2 -2
- data/web/about.html +1 -0
- data/web/api.html +223 -15
- data/web/biointerchange.js +27 -6
- data/web/cli.html +8 -3
- data/web/index.html +6 -2
- data/web/ontologies.html +3 -0
- data/web/service/rdfizer.fcgi +7 -15
- data/web/webservices.html +6 -2
- metadata +30 -3
@@ -7,1820 +7,1820 @@ class SOFA:
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@classmethod
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def adjacent_to(cls):
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return _namespace_SOFA('http_//purl.org/obo/owl:adjacent_to')
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return cls._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('http_//purl.org/obo/owl:complete_evidence_for_feature')
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return cls._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('http_//purl.org/obo/owl:contained_by')
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return cls._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('http_//purl.org/obo/owl:contains')
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return cls._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('http_//purl.org/obo/owl:derives_from')
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return cls._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('http_//purl.org/obo/owl:evidence_for_feature')
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return cls._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('http_//purl.org/obo/owl:has_integral_part')
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return cls._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('http_//purl.org/obo/owl:has_part')
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return cls._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('http_//purl.org/obo/owl:homologous_to')
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return cls._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('http_//purl.org/obo/owl:integral_part_of')
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return cls._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('http_//purl.org/obo/owl:member_of')
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return cls._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('http_//purl.org/obo/owl:non_functional_homolog_of')
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return cls._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('http_//purl.org/obo/owl:orthologous_to')
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return cls._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('http_//purl.org/obo/owl:paralogous_to')
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return cls._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('http_//purl.org/obo/owl:part_of')
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return cls._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('http_//purl.org/obo/owl:partial_evidence_for_feature')
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return cls._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('http_//purl.org/obo/owl:similar_to')
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return cls._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('SO_0000000')
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return cls._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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(http://purl.obolibrary.org/obo/SO_0000001)
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"""
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return _namespace_SOFA('SO_0000001')
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return cls._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('SO_0000004')
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return cls._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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(http://purl.obolibrary.org/obo/SO_0000005)
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"""
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return _namespace_SOFA('SO_0000005')
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return cls._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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(http://purl.obolibrary.org/obo/SO_0000006)
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"""
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return _namespace_SOFA('SO_0000006')
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return cls._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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(http://purl.obolibrary.org/obo/SO_0000007)
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"""
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return _namespace_SOFA('SO_0000007')
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return cls._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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(SO_0000013)
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(http://purl.obolibrary.org/obo/SO_0000013)
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"""
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return _namespace_SOFA('SO_0000013')
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return cls._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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(SO_0000038)
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(http://purl.obolibrary.org/obo/SO_0000038)
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"""
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return _namespace_SOFA('SO_0000038')
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return cls._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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(SO_0000039)
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(http://purl.obolibrary.org/obo/SO_0000039)
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"""
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return _namespace_SOFA('SO_0000039')
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return cls._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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(SO_0000050)
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(http://purl.obolibrary.org/obo/SO_0000050)
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"""
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return _namespace_SOFA('SO_0000050')
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return cls._namespace_SOFA('SO_0000050')
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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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(SO_0000057)
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(http://purl.obolibrary.org/obo/SO_0000057)
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"""
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return _namespace_SOFA('SO_0000057')
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return cls._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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(SO_0000059)
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(http://purl.obolibrary.org/obo/SO_0000059)
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"""
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return _namespace_SOFA('SO_0000059')
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return cls._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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(SO_0000101)
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(http://purl.obolibrary.org/obo/SO_0000101)
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"""
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return _namespace_SOFA('SO_0000101')
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return cls._namespace_SOFA('SO_0000101')
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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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(SO_0000102)
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(http://purl.obolibrary.org/obo/SO_0000102)
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"""
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return _namespace_SOFA('SO_0000102')
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return cls._namespace_SOFA('SO_0000102')
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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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(SO_0000103)
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(http://purl.obolibrary.org/obo/SO_0000103)
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"""
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return _namespace_SOFA('SO_0000103')
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return cls._namespace_SOFA('SO_0000103')
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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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(SO_0000104)
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(http://purl.obolibrary.org/obo/SO_0000104)
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"""
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return _namespace_SOFA('SO_0000104')
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return cls._namespace_SOFA('SO_0000104')
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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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(SO_0000109)
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(http://purl.obolibrary.org/obo/SO_0000109)
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"""
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return _namespace_SOFA('SO_0000109')
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return cls._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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(SO_0000110)
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(http://purl.obolibrary.org/obo/SO_0000110)
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"""
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return _namespace_SOFA('SO_0000110')
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return cls._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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(SO_0000112)
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(http://purl.obolibrary.org/obo/SO_0000112)
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"""
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return _namespace_SOFA('SO_0000112')
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return cls._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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(SO_0000113)
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(http://purl.obolibrary.org/obo/SO_0000113)
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"""
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return _namespace_SOFA('SO_0000113')
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return cls._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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(http://purl.obolibrary.org/obo/SO_0000114)
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"""
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return _namespace_SOFA('SO_0000114')
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return cls._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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(SO_0000120)
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(http://purl.obolibrary.org/obo/SO_0000120)
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"""
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return _namespace_SOFA('SO_0000120')
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return cls._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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(http://purl.obolibrary.org/obo/SO_0000139)
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"""
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|
-
return _namespace_SOFA('SO_0000139')
|
229
|
+
return cls._namespace_SOFA('SO_0000139')
|
230
230
|
|
231
231
|
@classmethod
|
232
232
|
def attenuator(cls):
|
233
233
|
"""A sequence segment located within the five prime end of an mRNA that causes premature termination of translation. (cls, SO:as)
|
234
|
-
(SO_0000140)
|
234
|
+
(http://purl.obolibrary.org/obo/SO_0000140)
|
235
235
|
"""
|
236
|
-
return _namespace_SOFA('SO_0000140')
|
236
|
+
return cls._namespace_SOFA('SO_0000140')
|
237
237
|
|
238
238
|
@classmethod
|
239
239
|
def terminator(cls):
|
240
240
|
"""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)
|
241
|
-
(SO_0000141)
|
241
|
+
(http://purl.obolibrary.org/obo/SO_0000141)
|
242
242
|
"""
|
243
|
-
return _namespace_SOFA('SO_0000141')
|
243
|
+
return cls._namespace_SOFA('SO_0000141')
|
244
244
|
|
245
245
|
@classmethod
|
246
246
|
def assembly_component(cls):
|
247
247
|
"""A region of known length which may be used to manufacture a longer region. (cls, SO:ke)
|
248
|
-
(SO_0000143)
|
248
|
+
(http://purl.obolibrary.org/obo/SO_0000143)
|
249
249
|
"""
|
250
|
-
return _namespace_SOFA('SO_0000143')
|
250
|
+
return cls._namespace_SOFA('SO_0000143')
|
251
251
|
|
252
252
|
@classmethod
|
253
253
|
def exon(cls):
|
254
254
|
"""A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing. (cls, SO:ke)
|
255
|
-
(SO_0000147)
|
255
|
+
(http://purl.obolibrary.org/obo/SO_0000147)
|
256
256
|
"""
|
257
|
-
return _namespace_SOFA('SO_0000147')
|
257
|
+
return cls._namespace_SOFA('SO_0000147')
|
258
258
|
|
259
259
|
@classmethod
|
260
260
|
def supercontig(cls):
|
261
261
|
"""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)
|
262
|
-
(SO_0000148)
|
262
|
+
(http://purl.obolibrary.org/obo/SO_0000148)
|
263
263
|
"""
|
264
|
-
return _namespace_SOFA('SO_0000148')
|
264
|
+
return cls._namespace_SOFA('SO_0000148')
|
265
265
|
|
266
266
|
@classmethod
|
267
267
|
def contig(cls):
|
268
268
|
"""A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. (cls, SO:ls)
|
269
|
-
(SO_0000149)
|
269
|
+
(http://purl.obolibrary.org/obo/SO_0000149)
|
270
270
|
"""
|
271
|
-
return _namespace_SOFA('SO_0000149')
|
271
|
+
return cls._namespace_SOFA('SO_0000149')
|
272
272
|
|
273
273
|
@classmethod
|
274
274
|
def read(cls):
|
275
275
|
"""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)
|
276
|
-
(SO_0000150)
|
276
|
+
(http://purl.obolibrary.org/obo/SO_0000150)
|
277
277
|
"""
|
278
|
-
return _namespace_SOFA('SO_0000150')
|
278
|
+
return cls._namespace_SOFA('SO_0000150')
|
279
279
|
|
280
280
|
@classmethod
|
281
|
-
def
|
281
|
+
def _clone_(cls):
|
282
282
|
"""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)
|
283
|
-
(SO_0000151)
|
283
|
+
(http://purl.obolibrary.org/obo/SO_0000151)
|
284
284
|
"""
|
285
|
-
return _namespace_SOFA('SO_0000151')
|
285
|
+
return cls._namespace_SOFA('SO_0000151')
|
286
286
|
|
287
287
|
@classmethod
|
288
288
|
def deletion(cls):
|
289
289
|
"""The point at which one or more contiguous nucleotides were excised. (cls, SO:ke)
|
290
|
-
(SO_0000159)
|
290
|
+
(http://purl.obolibrary.org/obo/SO_0000159)
|
291
291
|
"""
|
292
|
-
return _namespace_SOFA('SO_0000159')
|
292
|
+
return cls._namespace_SOFA('SO_0000159')
|
293
293
|
|
294
294
|
@classmethod
|
295
295
|
def methylated_A(cls):
|
296
296
|
"""A modified RNA base in which adenine has been methylated. (cls, SO:ke)
|
297
|
-
(SO_0000161)
|
297
|
+
(http://purl.obolibrary.org/obo/SO_0000161)
|
298
298
|
"""
|
299
|
-
return _namespace_SOFA('SO_0000161')
|
299
|
+
return cls._namespace_SOFA('SO_0000161')
|
300
300
|
|
301
301
|
@classmethod
|
302
302
|
def splice_site(cls):
|
303
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)
|
304
|
-
(SO_0000162)
|
304
|
+
(http://purl.obolibrary.org/obo/SO_0000162)
|
305
305
|
"""
|
306
|
-
return _namespace_SOFA('SO_0000162')
|
306
|
+
return cls._namespace_SOFA('SO_0000162')
|
307
307
|
|
308
308
|
@classmethod
|
309
309
|
def five_prime_cis_splice_site(cls):
|
310
310
|
"""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)
|
311
|
-
(SO_0000163)
|
311
|
+
(http://purl.obolibrary.org/obo/SO_0000163)
|
312
312
|
"""
|
313
|
-
return _namespace_SOFA('SO_0000163')
|
313
|
+
return cls._namespace_SOFA('SO_0000163')
|
314
314
|
|
315
315
|
@classmethod
|
316
316
|
def three_prime_cis_splice_site(cls):
|
317
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)
|
318
|
-
(SO_0000164)
|
318
|
+
(http://purl.obolibrary.org/obo/SO_0000164)
|
319
319
|
"""
|
320
|
-
return _namespace_SOFA('SO_0000164')
|
320
|
+
return cls._namespace_SOFA('SO_0000164')
|
321
321
|
|
322
322
|
@classmethod
|
323
323
|
def enhancer(cls):
|
324
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)
|
325
|
-
(SO_0000165)
|
325
|
+
(http://purl.obolibrary.org/obo/SO_0000165)
|
326
326
|
"""
|
327
|
-
return _namespace_SOFA('SO_0000165')
|
327
|
+
return cls._namespace_SOFA('SO_0000165')
|
328
328
|
|
329
329
|
@classmethod
|
330
330
|
def promoter(cls):
|
331
331
|
"""A regulatory_region composed of the TSS(cls, s) and binding sites for TF_complexes of the basal transcription machinery. (SO:regcreative)
|
332
|
-
(SO_0000167)
|
332
|
+
(http://purl.obolibrary.org/obo/SO_0000167)
|
333
333
|
"""
|
334
|
-
return _namespace_SOFA('SO_0000167')
|
334
|
+
return cls._namespace_SOFA('SO_0000167')
|
335
335
|
|
336
336
|
@classmethod
|
337
337
|
def cross_genome_match(cls):
|
338
338
|
"""A nucleotide match against a sequence from another organism. (cls, SO:ma)
|
339
|
-
(SO_0000177)
|
339
|
+
(http://purl.obolibrary.org/obo/SO_0000177)
|
340
340
|
"""
|
341
|
-
return _namespace_SOFA('SO_0000177')
|
341
|
+
return cls._namespace_SOFA('SO_0000177')
|
342
342
|
|
343
343
|
@classmethod
|
344
344
|
def operon(cls):
|
345
345
|
"""A group of contiguous genes transcribed as a single (cls, polycistronic) mRNA from a single regulatory region. (SO:ma)
|
346
|
-
(SO_0000178)
|
346
|
+
(http://purl.obolibrary.org/obo/SO_0000178)
|
347
347
|
"""
|
348
|
-
return _namespace_SOFA('SO_0000178')
|
348
|
+
return cls._namespace_SOFA('SO_0000178')
|
349
349
|
|
350
350
|
@classmethod
|
351
351
|
def clone_insert_start(cls):
|
352
352
|
"""The start of the clone insert. (cls, SO:ke)
|
353
|
-
(SO_0000179)
|
353
|
+
(http://purl.obolibrary.org/obo/SO_0000179)
|
354
354
|
"""
|
355
|
-
return _namespace_SOFA('SO_0000179')
|
355
|
+
return cls._namespace_SOFA('SO_0000179')
|
356
356
|
|
357
357
|
@classmethod
|
358
358
|
def translated_nucleotide_match(cls):
|
359
359
|
"""A match against a translated sequence. (cls, SO:ke)
|
360
|
-
(SO_0000181)
|
360
|
+
(http://purl.obolibrary.org/obo/SO_0000181)
|
361
361
|
"""
|
362
|
-
return _namespace_SOFA('SO_0000181')
|
362
|
+
return cls._namespace_SOFA('SO_0000181')
|
363
363
|
|
364
364
|
@classmethod
|
365
365
|
def non_transcribed_region(cls):
|
366
366
|
"""A region of the gene which is not transcribed. (cls, SO:ke)
|
367
|
-
(SO_0000183)
|
367
|
+
(http://purl.obolibrary.org/obo/SO_0000183)
|
368
368
|
"""
|
369
|
-
return _namespace_SOFA('SO_0000183')
|
369
|
+
return cls._namespace_SOFA('SO_0000183')
|
370
370
|
|
371
371
|
@classmethod
|
372
372
|
def primary_transcript(cls):
|
373
373
|
"""A transcript that in its initial state requires modification to be functional. (cls, SO:ma)
|
374
|
-
(SO_0000185)
|
374
|
+
(http://purl.obolibrary.org/obo/SO_0000185)
|
375
375
|
"""
|
376
|
-
return _namespace_SOFA('SO_0000185')
|
376
|
+
return cls._namespace_SOFA('SO_0000185')
|
377
377
|
|
378
378
|
@classmethod
|
379
379
|
def repeat_family(cls):
|
380
380
|
"""A group of characterized repeat sequences. (cls, SO:ke)
|
381
|
-
(SO_0000187)
|
381
|
+
(http://purl.obolibrary.org/obo/SO_0000187)
|
382
382
|
"""
|
383
|
-
return _namespace_SOFA('SO_0000187')
|
383
|
+
return cls._namespace_SOFA('SO_0000187')
|
384
384
|
|
385
385
|
@classmethod
|
386
386
|
def intron(cls):
|
387
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)
|
388
|
-
(SO_0000188)
|
388
|
+
(http://purl.obolibrary.org/obo/SO_0000188)
|
389
389
|
"""
|
390
|
-
return _namespace_SOFA('SO_0000188')
|
390
|
+
return cls._namespace_SOFA('SO_0000188')
|
391
391
|
|
392
392
|
@classmethod
|
393
393
|
def RFLP_fragment(cls):
|
394
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)
|
395
|
-
(SO_0000193)
|
395
|
+
(http://purl.obolibrary.org/obo/SO_0000193)
|
396
396
|
"""
|
397
|
-
return _namespace_SOFA('SO_0000193')
|
397
|
+
return cls._namespace_SOFA('SO_0000193')
|
398
398
|
|
399
399
|
@classmethod
|
400
400
|
def coding_exon(cls):
|
401
401
|
"""An exon whereby at least one base is part of a codon (cls, here, 'codon' is inclusive of the stop_codon). (SO:ke)
|
402
|
-
(SO_0000195)
|
402
|
+
(http://purl.obolibrary.org/obo/SO_0000195)
|
403
403
|
"""
|
404
|
-
return _namespace_SOFA('SO_0000195')
|
404
|
+
return cls._namespace_SOFA('SO_0000195')
|
405
405
|
|
406
406
|
@classmethod
|
407
407
|
def five_prime_coding_exon_coding_region(cls):
|
408
408
|
"""The sequence of the five_prime_coding_exon that codes for protein. (cls, SO:cjm)
|
409
|
-
(SO_0000196)
|
409
|
+
(http://purl.obolibrary.org/obo/SO_0000196)
|
410
410
|
"""
|
411
|
-
return _namespace_SOFA('SO_0000196')
|
411
|
+
return cls._namespace_SOFA('SO_0000196')
|
412
412
|
|
413
413
|
@classmethod
|
414
414
|
def three_prime_coding_exon_coding_region(cls):
|
415
415
|
"""The sequence of the three_prime_coding_exon that codes for protein. (cls, SO:cjm)
|
416
|
-
(SO_0000197)
|
416
|
+
(http://purl.obolibrary.org/obo/SO_0000197)
|
417
417
|
"""
|
418
|
-
return _namespace_SOFA('SO_0000197')
|
418
|
+
return cls._namespace_SOFA('SO_0000197')
|
419
419
|
|
420
420
|
@classmethod
|
421
421
|
def noncoding_exon(cls):
|
422
422
|
"""An exon that does not contain any codons. (cls, SO:ke)
|
423
|
-
(SO_0000198)
|
423
|
+
(http://purl.obolibrary.org/obo/SO_0000198)
|
424
424
|
"""
|
425
|
-
return _namespace_SOFA('SO_0000198')
|
425
|
+
return cls._namespace_SOFA('SO_0000198')
|
426
426
|
|
427
427
|
@classmethod
|
428
428
|
def five_prime_coding_exon(cls):
|
429
429
|
"""The 5' most coding exon. (cls, SO:ke)
|
430
|
-
(SO_0000200)
|
430
|
+
(http://purl.obolibrary.org/obo/SO_0000200)
|
431
431
|
"""
|
432
|
-
return _namespace_SOFA('SO_0000200')
|
432
|
+
return cls._namespace_SOFA('SO_0000200')
|
433
433
|
|
434
434
|
@classmethod
|
435
435
|
def UTR(cls):
|
436
436
|
"""Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated. (cls, SO:ke)
|
437
|
-
(SO_0000203)
|
437
|
+
(http://purl.obolibrary.org/obo/SO_0000203)
|
438
438
|
"""
|
439
|
-
return _namespace_SOFA('SO_0000203')
|
439
|
+
return cls._namespace_SOFA('SO_0000203')
|
440
440
|
|
441
441
|
@classmethod
|
442
442
|
def five_prime_UTR(cls):
|
443
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)
|
444
|
-
(SO_0000204)
|
444
|
+
(http://purl.obolibrary.org/obo/SO_0000204)
|
445
445
|
"""
|
446
|
-
return _namespace_SOFA('SO_0000204')
|
446
|
+
return cls._namespace_SOFA('SO_0000204')
|
447
447
|
|
448
448
|
@classmethod
|
449
449
|
def three_prime_UTR(cls):
|
450
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)
|
451
|
-
(SO_0000205)
|
451
|
+
(http://purl.obolibrary.org/obo/SO_0000205)
|
452
452
|
"""
|
453
|
-
return _namespace_SOFA('SO_0000205')
|
453
|
+
return cls._namespace_SOFA('SO_0000205')
|
454
454
|
|
455
455
|
@classmethod
|
456
456
|
def rRNA_primary_transcript(cls):
|
457
457
|
"""A primary transcript encoding a ribosomal RNA. (cls, SO:ke)
|
458
|
-
(SO_0000209)
|
458
|
+
(http://purl.obolibrary.org/obo/SO_0000209)
|
459
459
|
"""
|
460
|
-
return _namespace_SOFA('SO_0000209')
|
460
|
+
return cls._namespace_SOFA('SO_0000209')
|
461
461
|
|
462
462
|
@classmethod
|
463
463
|
def mature_transcript(cls):
|
464
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)
|
465
|
-
(SO_0000233)
|
465
|
+
(http://purl.obolibrary.org/obo/SO_0000233)
|
466
466
|
"""
|
467
|
-
return _namespace_SOFA('SO_0000233')
|
467
|
+
return cls._namespace_SOFA('SO_0000233')
|
468
468
|
|
469
469
|
@classmethod
|
470
470
|
def mRNA(cls):
|
471
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)
|
472
|
-
(SO_0000234)
|
472
|
+
(http://purl.obolibrary.org/obo/SO_0000234)
|
473
473
|
"""
|
474
|
-
return _namespace_SOFA('SO_0000234')
|
474
|
+
return cls._namespace_SOFA('SO_0000234')
|
475
475
|
|
476
476
|
@classmethod
|
477
477
|
def TF_binding_site(cls):
|
478
478
|
"""A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]. (cls, SO:ke)
|
479
|
-
(SO_0000235)
|
479
|
+
(http://purl.obolibrary.org/obo/SO_0000235)
|
480
480
|
"""
|
481
|
-
return _namespace_SOFA('SO_0000235')
|
481
|
+
return cls._namespace_SOFA('SO_0000235')
|
482
482
|
|
483
483
|
@classmethod
|
484
484
|
def ORF(cls):
|
485
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)
|
486
|
-
(SO_0000236)
|
486
|
+
(http://purl.obolibrary.org/obo/SO_0000236)
|
487
487
|
"""
|
488
|
-
return _namespace_SOFA('SO_0000236')
|
488
|
+
return cls._namespace_SOFA('SO_0000236')
|
489
489
|
|
490
490
|
@classmethod
|
491
491
|
def flanking_region(cls):
|
492
492
|
"""The sequences extending on either side of a specific region. (cls, SO:ke)
|
493
|
-
(SO_0000239)
|
493
|
+
(http://purl.obolibrary.org/obo/SO_0000239)
|
494
494
|
"""
|
495
|
-
return _namespace_SOFA('SO_0000239')
|
495
|
+
return cls._namespace_SOFA('SO_0000239')
|
496
496
|
|
497
497
|
@classmethod
|
498
498
|
def rRNA(cls):
|
499
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)
|
500
|
-
(SO_0000252)
|
500
|
+
(http://purl.obolibrary.org/obo/SO_0000252)
|
501
501
|
"""
|
502
|
-
return _namespace_SOFA('SO_0000252')
|
502
|
+
return cls._namespace_SOFA('SO_0000252')
|
503
503
|
|
504
504
|
@classmethod
|
505
505
|
def tRNA(cls):
|
506
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)
|
507
|
-
(SO_0000253)
|
507
|
+
(http://purl.obolibrary.org/obo/SO_0000253)
|
508
508
|
"""
|
509
|
-
return _namespace_SOFA('SO_0000253')
|
509
|
+
return cls._namespace_SOFA('SO_0000253')
|
510
510
|
|
511
511
|
@classmethod
|
512
512
|
def snRNA(cls):
|
513
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)
|
514
|
-
(SO_0000274)
|
514
|
+
(http://purl.obolibrary.org/obo/SO_0000274)
|
515
515
|
"""
|
516
|
-
return _namespace_SOFA('SO_0000274')
|
516
|
+
return cls._namespace_SOFA('SO_0000274')
|
517
517
|
|
518
518
|
@classmethod
|
519
519
|
def snoRNA(cls):
|
520
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)
|
521
|
-
(SO_0000275)
|
521
|
+
(http://purl.obolibrary.org/obo/SO_0000275)
|
522
522
|
"""
|
523
|
-
return _namespace_SOFA('SO_0000275')
|
523
|
+
return cls._namespace_SOFA('SO_0000275')
|
524
524
|
|
525
525
|
@classmethod
|
526
526
|
def miRNA(cls):
|
527
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)
|
528
|
-
(SO_0000276)
|
528
|
+
(http://purl.obolibrary.org/obo/SO_0000276)
|
529
529
|
"""
|
530
|
-
return _namespace_SOFA('SO_0000276')
|
530
|
+
return cls._namespace_SOFA('SO_0000276')
|
531
531
|
|
532
532
|
@classmethod
|
533
533
|
def microsatellite(cls):
|
534
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)
|
535
|
-
(SO_0000289)
|
535
|
+
(http://purl.obolibrary.org/obo/SO_0000289)
|
536
536
|
"""
|
537
|
-
return _namespace_SOFA('SO_0000289')
|
537
|
+
return cls._namespace_SOFA('SO_0000289')
|
538
538
|
|
539
539
|
@classmethod
|
540
540
|
def inverted_repeat(cls):
|
541
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)
|
542
|
-
(SO_0000294)
|
542
|
+
(http://purl.obolibrary.org/obo/SO_0000294)
|
543
543
|
"""
|
544
|
-
return _namespace_SOFA('SO_0000294')
|
544
|
+
return cls._namespace_SOFA('SO_0000294')
|
545
545
|
|
546
546
|
@classmethod
|
547
547
|
def origin_of_replication(cls):
|
548
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)
|
549
|
-
(SO_0000296)
|
549
|
+
(http://purl.obolibrary.org/obo/SO_0000296)
|
550
550
|
"""
|
551
|
-
return _namespace_SOFA('SO_0000296')
|
551
|
+
return cls._namespace_SOFA('SO_0000296')
|
552
552
|
|
553
553
|
@classmethod
|
554
554
|
def clip(cls):
|
555
555
|
"""Part of the primary transcript that is clipped off during processing. (cls, SO:ke)
|
556
|
-
(SO_0000303)
|
556
|
+
(http://purl.obolibrary.org/obo/SO_0000303)
|
557
557
|
"""
|
558
|
-
return _namespace_SOFA('SO_0000303')
|
558
|
+
return cls._namespace_SOFA('SO_0000303')
|
559
559
|
|
560
560
|
@classmethod
|
561
561
|
def modified_base(cls):
|
562
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)
|
563
|
-
(SO_0000305)
|
563
|
+
(http://purl.obolibrary.org/obo/SO_0000305)
|
564
564
|
"""
|
565
|
-
return _namespace_SOFA('SO_0000305')
|
565
|
+
return cls._namespace_SOFA('SO_0000305')
|
566
566
|
|
567
567
|
@classmethod
|
568
568
|
def methylated_base_feature(cls):
|
569
569
|
"""A nucleotide modified by methylation. (cls, SO:ke)
|
570
|
-
(SO_0000306)
|
570
|
+
(http://purl.obolibrary.org/obo/SO_0000306)
|
571
571
|
"""
|
572
|
-
return _namespace_SOFA('SO_0000306')
|
572
|
+
return cls._namespace_SOFA('SO_0000306')
|
573
573
|
|
574
574
|
@classmethod
|
575
575
|
def CpG_island(cls):
|
576
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)
|
577
|
-
(SO_0000307)
|
577
|
+
(http://purl.obolibrary.org/obo/SO_0000307)
|
578
578
|
"""
|
579
|
-
return _namespace_SOFA('SO_0000307')
|
579
|
+
return cls._namespace_SOFA('SO_0000307')
|
580
580
|
|
581
581
|
@classmethod
|
582
582
|
def direct_repeat(cls):
|
583
583
|
"""A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA. (cls, SO:ke)
|
584
|
-
(SO_0000314)
|
584
|
+
(http://purl.obolibrary.org/obo/SO_0000314)
|
585
585
|
"""
|
586
|
-
return _namespace_SOFA('SO_0000314')
|
586
|
+
return cls._namespace_SOFA('SO_0000314')
|
587
587
|
|
588
588
|
@classmethod
|
589
589
|
def TSS(cls):
|
590
590
|
"""The first base where RNA polymerase begins to synthesize the RNA transcript. (cls, SO:ke)
|
591
|
-
(SO_0000315)
|
591
|
+
(http://purl.obolibrary.org/obo/SO_0000315)
|
592
592
|
"""
|
593
|
-
return _namespace_SOFA('SO_0000315')
|
593
|
+
return cls._namespace_SOFA('SO_0000315')
|
594
594
|
|
595
595
|
@classmethod
|
596
596
|
def CDS(cls):
|
597
597
|
"""A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon. (cls, SO:ma)
|
598
|
-
(SO_0000316)
|
598
|
+
(http://purl.obolibrary.org/obo/SO_0000316)
|
599
599
|
"""
|
600
|
-
return _namespace_SOFA('SO_0000316')
|
600
|
+
return cls._namespace_SOFA('SO_0000316')
|
601
601
|
|
602
602
|
@classmethod
|
603
603
|
def start_codon(cls):
|
604
604
|
"""First codon to be translated by a ribosome. (cls, SO:ke)
|
605
|
-
(SO_0000318)
|
605
|
+
(http://purl.obolibrary.org/obo/SO_0000318)
|
606
606
|
"""
|
607
|
-
return _namespace_SOFA('SO_0000318')
|
607
|
+
return cls._namespace_SOFA('SO_0000318')
|
608
608
|
|
609
609
|
@classmethod
|
610
610
|
def stop_codon(cls):
|
611
611
|
"""In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis. (cls, SO:ke)
|
612
|
-
(SO_0000319)
|
612
|
+
(http://purl.obolibrary.org/obo/SO_0000319)
|
613
613
|
"""
|
614
|
-
return _namespace_SOFA('SO_0000319')
|
614
|
+
return cls._namespace_SOFA('SO_0000319')
|
615
615
|
|
616
616
|
@classmethod
|
617
617
|
def tag(cls):
|
618
618
|
"""A nucleotide sequence that may be used to identify a larger sequence. (cls, SO:ke)
|
619
|
-
(SO_0000324)
|
619
|
+
(http://purl.obolibrary.org/obo/SO_0000324)
|
620
620
|
"""
|
621
|
-
return _namespace_SOFA('SO_0000324')
|
621
|
+
return cls._namespace_SOFA('SO_0000324')
|
622
622
|
|
623
623
|
@classmethod
|
624
624
|
def rRNA_large_subunit_primary_transcript(cls):
|
625
625
|
"""A primary transcript encoding a large ribosomal subunit RNA. (cls, SO:ke)
|
626
|
-
(SO_0000325)
|
626
|
+
(http://purl.obolibrary.org/obo/SO_0000325)
|
627
627
|
"""
|
628
|
-
return _namespace_SOFA('SO_0000325')
|
628
|
+
return cls._namespace_SOFA('SO_0000325')
|
629
629
|
|
630
630
|
@classmethod
|
631
631
|
def SAGE_tag(cls):
|
632
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)
|
633
|
-
(SO_0000326)
|
633
|
+
(http://purl.obolibrary.org/obo/SO_0000326)
|
634
634
|
"""
|
635
|
-
return _namespace_SOFA('SO_0000326')
|
635
|
+
return cls._namespace_SOFA('SO_0000326')
|
636
636
|
|
637
637
|
@classmethod
|
638
638
|
def conserved_region(cls):
|
639
639
|
"""Region of sequence similarity by descent from a common ancestor. (cls, SO:ke)
|
640
|
-
(SO_0000330)
|
640
|
+
(http://purl.obolibrary.org/obo/SO_0000330)
|
641
641
|
"""
|
642
|
-
return _namespace_SOFA('SO_0000330')
|
642
|
+
return cls._namespace_SOFA('SO_0000330')
|
643
643
|
|
644
644
|
@classmethod
|
645
645
|
def STS(cls):
|
646
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)
|
647
|
-
(SO_0000331)
|
647
|
+
(http://purl.obolibrary.org/obo/SO_0000331)
|
648
648
|
"""
|
649
|
-
return _namespace_SOFA('SO_0000331')
|
649
|
+
return cls._namespace_SOFA('SO_0000331')
|
650
650
|
|
651
651
|
@classmethod
|
652
652
|
def coding_conserved_region(cls):
|
653
653
|
"""Coding region of sequence similarity by descent from a common ancestor. (cls, SO:ke)
|
654
|
-
(SO_0000332)
|
654
|
+
(http://purl.obolibrary.org/obo/SO_0000332)
|
655
655
|
"""
|
656
|
-
return _namespace_SOFA('SO_0000332')
|
656
|
+
return cls._namespace_SOFA('SO_0000332')
|
657
657
|
|
658
658
|
@classmethod
|
659
659
|
def exon_junction(cls):
|
660
660
|
"""The boundary between two exons in a processed transcript. (cls, SO:ke)
|
661
|
-
(SO_0000333)
|
661
|
+
(http://purl.obolibrary.org/obo/SO_0000333)
|
662
662
|
"""
|
663
|
-
return _namespace_SOFA('SO_0000333')
|
663
|
+
return cls._namespace_SOFA('SO_0000333')
|
664
664
|
|
665
665
|
@classmethod
|
666
666
|
def nc_conserved_region(cls):
|
667
667
|
"""Non-coding region of sequence similarity by descent from a common ancestor. (cls, SO:ke)
|
668
|
-
(SO_0000334)
|
668
|
+
(http://purl.obolibrary.org/obo/SO_0000334)
|
669
669
|
"""
|
670
|
-
return _namespace_SOFA('SO_0000334')
|
670
|
+
return cls._namespace_SOFA('SO_0000334')
|
671
671
|
|
672
672
|
@classmethod
|
673
673
|
def pseudogene(cls):
|
674
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)
|
675
|
-
(SO_0000336)
|
675
|
+
(http://purl.obolibrary.org/obo/SO_0000336)
|
676
676
|
"""
|
677
|
-
return _namespace_SOFA('SO_0000336')
|
677
|
+
return cls._namespace_SOFA('SO_0000336')
|
678
678
|
|
679
679
|
@classmethod
|
680
680
|
def RNAi_reagent(cls):
|
681
681
|
"""A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference. (cls, SO:rd)
|
682
|
-
(SO_0000337)
|
682
|
+
(http://purl.obolibrary.org/obo/SO_0000337)
|
683
683
|
"""
|
684
|
-
return _namespace_SOFA('SO_0000337')
|
684
|
+
return cls._namespace_SOFA('SO_0000337')
|
685
685
|
|
686
686
|
@classmethod
|
687
687
|
def chromosome(cls):
|
688
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)
|
689
|
-
(SO_0000340)
|
689
|
+
(http://purl.obolibrary.org/obo/SO_0000340)
|
690
690
|
"""
|
691
|
-
return _namespace_SOFA('SO_0000340')
|
691
|
+
return cls._namespace_SOFA('SO_0000340')
|
692
692
|
|
693
693
|
@classmethod
|
694
694
|
def chromosome_band(cls):
|
695
695
|
"""A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark. (cls, SO:ma)
|
696
|
-
(SO_0000341)
|
696
|
+
(http://purl.obolibrary.org/obo/SO_0000341)
|
697
697
|
"""
|
698
|
-
return _namespace_SOFA('SO_0000341')
|
698
|
+
return cls._namespace_SOFA('SO_0000341')
|
699
699
|
|
700
700
|
@classmethod
|
701
701
|
def match(cls):
|
702
702
|
"""A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. (cls, SO:ke)
|
703
|
-
(SO_0000343)
|
703
|
+
(http://purl.obolibrary.org/obo/SO_0000343)
|
704
704
|
"""
|
705
|
-
return _namespace_SOFA('SO_0000343')
|
705
|
+
return cls._namespace_SOFA('SO_0000343')
|
706
706
|
|
707
707
|
@classmethod
|
708
708
|
def splice_enhancer(cls):
|
709
709
|
"""Region of a transcript that regulates splicing. (cls, SO:ke)
|
710
|
-
(SO_0000344)
|
710
|
+
(http://purl.obolibrary.org/obo/SO_0000344)
|
711
711
|
"""
|
712
|
-
return _namespace_SOFA('SO_0000344')
|
712
|
+
return cls._namespace_SOFA('SO_0000344')
|
713
713
|
|
714
714
|
@classmethod
|
715
715
|
def EST(cls):
|
716
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)
|
717
|
-
(SO_0000345)
|
717
|
+
(http://purl.obolibrary.org/obo/SO_0000345)
|
718
718
|
"""
|
719
|
-
return _namespace_SOFA('SO_0000345')
|
719
|
+
return cls._namespace_SOFA('SO_0000345')
|
720
720
|
|
721
721
|
@classmethod
|
722
722
|
def nucleotide_match(cls):
|
723
723
|
"""A match against a nucleotide sequence. (cls, SO:ke)
|
724
|
-
(SO_0000347)
|
724
|
+
(http://purl.obolibrary.org/obo/SO_0000347)
|
725
725
|
"""
|
726
|
-
return _namespace_SOFA('SO_0000347')
|
726
|
+
return cls._namespace_SOFA('SO_0000347')
|
727
727
|
|
728
728
|
@classmethod
|
729
729
|
def protein_match(cls):
|
730
730
|
"""A match against a protein sequence. (cls, SO:ke)
|
731
|
-
(SO_0000349)
|
731
|
+
(http://purl.obolibrary.org/obo/SO_0000349)
|
732
732
|
"""
|
733
|
-
return _namespace_SOFA('SO_0000349')
|
733
|
+
return cls._namespace_SOFA('SO_0000349')
|
734
734
|
|
735
735
|
@classmethod
|
736
736
|
def sequence_assembly(cls):
|
737
737
|
"""A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. (cls, SO:ma)
|
738
|
-
(SO_0000353)
|
738
|
+
(http://purl.obolibrary.org/obo/SO_0000353)
|
739
739
|
"""
|
740
|
-
return _namespace_SOFA('SO_0000353')
|
740
|
+
return cls._namespace_SOFA('SO_0000353')
|
741
741
|
|
742
742
|
@classmethod
|
743
743
|
def codon(cls):
|
744
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)
|
745
|
-
(SO_0000360)
|
745
|
+
(http://purl.obolibrary.org/obo/SO_0000360)
|
746
746
|
"""
|
747
|
-
return _namespace_SOFA('SO_0000360')
|
747
|
+
return cls._namespace_SOFA('SO_0000360')
|
748
748
|
|
749
749
|
@classmethod
|
750
750
|
def insertion_site(cls):
|
751
751
|
"""The junction where an insertion occurred. (cls, SO:ke)
|
752
|
-
(SO_0000366)
|
752
|
+
(http://purl.obolibrary.org/obo/SO_0000366)
|
753
753
|
"""
|
754
|
-
return _namespace_SOFA('SO_0000366')
|
754
|
+
return cls._namespace_SOFA('SO_0000366')
|
755
755
|
|
756
756
|
@classmethod
|
757
757
|
def transposable_element_insertion_site(cls):
|
758
758
|
"""The junction in a genome where a transposable_element has inserted. (cls, SO:ke)
|
759
|
-
(SO_0000368)
|
759
|
+
(http://purl.obolibrary.org/obo/SO_0000368)
|
760
760
|
"""
|
761
|
-
return _namespace_SOFA('SO_0000368')
|
761
|
+
return cls._namespace_SOFA('SO_0000368')
|
762
762
|
|
763
763
|
@classmethod
|
764
764
|
def small_regulatory_ncRNA(cls):
|
765
765
|
"""A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression. (cls, SO:ma)
|
766
|
-
(SO_0000370)
|
766
|
+
(http://purl.obolibrary.org/obo/SO_0000370)
|
767
767
|
"""
|
768
|
-
return _namespace_SOFA('SO_0000370')
|
768
|
+
return cls._namespace_SOFA('SO_0000370')
|
769
769
|
|
770
770
|
@classmethod
|
771
771
|
def enzymatic_RNA(cls):
|
772
772
|
"""An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein. (cls, RSC:cb)
|
773
|
-
(SO_0000372)
|
773
|
+
(http://purl.obolibrary.org/obo/SO_0000372)
|
774
774
|
"""
|
775
|
-
return _namespace_SOFA('SO_0000372')
|
775
|
+
return cls._namespace_SOFA('SO_0000372')
|
776
776
|
|
777
777
|
@classmethod
|
778
778
|
def ribozyme(cls):
|
779
779
|
"""An RNA with catalytic activity. (cls, SO:ma)
|
780
|
-
(SO_0000374)
|
780
|
+
(http://purl.obolibrary.org/obo/SO_0000374)
|
781
781
|
"""
|
782
|
-
return _namespace_SOFA('SO_0000374')
|
782
|
+
return cls._namespace_SOFA('SO_0000374')
|
783
783
|
|
784
784
|
@classmethod
|
785
785
|
def rRNA_5_8S(cls):
|
786
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)
|
787
|
-
(SO_0000375)
|
787
|
+
(http://purl.obolibrary.org/obo/SO_0000375)
|
788
788
|
"""
|
789
|
-
return _namespace_SOFA('SO_0000375')
|
789
|
+
return cls._namespace_SOFA('SO_0000375')
|
790
790
|
|
791
791
|
@classmethod
|
792
792
|
def hammerhead_ribozyme(cls):
|
793
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)
|
794
|
-
(SO_0000380)
|
794
|
+
(http://purl.obolibrary.org/obo/SO_0000380)
|
795
795
|
"""
|
796
|
-
return _namespace_SOFA('SO_0000380')
|
796
|
+
return cls._namespace_SOFA('SO_0000380')
|
797
797
|
|
798
798
|
@classmethod
|
799
799
|
def RNase_MRP_RNA(cls):
|
800
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)
|
801
|
-
(SO_0000385)
|
801
|
+
(http://purl.obolibrary.org/obo/SO_0000385)
|
802
802
|
"""
|
803
|
-
return _namespace_SOFA('SO_0000385')
|
803
|
+
return cls._namespace_SOFA('SO_0000385')
|
804
804
|
|
805
805
|
@classmethod
|
806
806
|
def RNase_P_RNA(cls):
|
807
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)
|
808
|
-
(SO_0000386)
|
808
|
+
(http://purl.obolibrary.org/obo/SO_0000386)
|
809
809
|
"""
|
810
|
-
return _namespace_SOFA('SO_0000386')
|
810
|
+
return cls._namespace_SOFA('SO_0000386')
|
811
811
|
|
812
812
|
@classmethod
|
813
813
|
def telomerase_RNA(cls):
|
814
814
|
"""The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA. (cls, http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025)
|
815
|
-
(SO_0000390)
|
815
|
+
(http://purl.obolibrary.org/obo/SO_0000390)
|
816
816
|
"""
|
817
|
-
return _namespace_SOFA('SO_0000390')
|
817
|
+
return cls._namespace_SOFA('SO_0000390')
|
818
818
|
|
819
819
|
@classmethod
|
820
820
|
def U1_snRNA(cls):
|
821
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)
|
822
|
-
(SO_0000391)
|
822
|
+
(http://purl.obolibrary.org/obo/SO_0000391)
|
823
823
|
"""
|
824
|
-
return _namespace_SOFA('SO_0000391')
|
824
|
+
return cls._namespace_SOFA('SO_0000391')
|
825
825
|
|
826
826
|
@classmethod
|
827
827
|
def U2_snRNA(cls):
|
828
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)
|
829
|
-
(SO_0000392)
|
829
|
+
(http://purl.obolibrary.org/obo/SO_0000392)
|
830
830
|
"""
|
831
|
-
return _namespace_SOFA('SO_0000392')
|
831
|
+
return cls._namespace_SOFA('SO_0000392')
|
832
832
|
|
833
833
|
@classmethod
|
834
834
|
def U4_snRNA(cls):
|
835
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)
|
836
|
-
(SO_0000393)
|
836
|
+
(http://purl.obolibrary.org/obo/SO_0000393)
|
837
837
|
"""
|
838
|
-
return _namespace_SOFA('SO_0000393')
|
838
|
+
return cls._namespace_SOFA('SO_0000393')
|
839
839
|
|
840
840
|
@classmethod
|
841
841
|
def U4atac_snRNA(cls):
|
842
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)
|
843
|
-
(SO_0000394)
|
843
|
+
(http://purl.obolibrary.org/obo/SO_0000394)
|
844
844
|
"""
|
845
|
-
return _namespace_SOFA('SO_0000394')
|
845
|
+
return cls._namespace_SOFA('SO_0000394')
|
846
846
|
|
847
847
|
@classmethod
|
848
848
|
def U5_snRNA(cls):
|
849
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)
|
850
|
-
(SO_0000395)
|
850
|
+
(http://purl.obolibrary.org/obo/SO_0000395)
|
851
851
|
"""
|
852
|
-
return _namespace_SOFA('SO_0000395')
|
852
|
+
return cls._namespace_SOFA('SO_0000395')
|
853
853
|
|
854
854
|
@classmethod
|
855
855
|
def U6_snRNA(cls):
|
856
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)
|
857
|
-
(SO_0000396)
|
857
|
+
(http://purl.obolibrary.org/obo/SO_0000396)
|
858
858
|
"""
|
859
|
-
return _namespace_SOFA('SO_0000396')
|
859
|
+
return cls._namespace_SOFA('SO_0000396')
|
860
860
|
|
861
861
|
@classmethod
|
862
862
|
def U6atac_snRNA(cls):
|
863
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)
|
864
|
-
(SO_0000397)
|
864
|
+
(http://purl.obolibrary.org/obo/SO_0000397)
|
865
865
|
"""
|
866
|
-
return _namespace_SOFA('SO_0000397')
|
866
|
+
return cls._namespace_SOFA('SO_0000397')
|
867
867
|
|
868
868
|
@classmethod
|
869
869
|
def U11_snRNA(cls):
|
870
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)
|
871
|
-
(SO_0000398)
|
871
|
+
(http://purl.obolibrary.org/obo/SO_0000398)
|
872
872
|
"""
|
873
|
-
return _namespace_SOFA('SO_0000398')
|
873
|
+
return cls._namespace_SOFA('SO_0000398')
|
874
874
|
|
875
875
|
@classmethod
|
876
876
|
def U12_snRNA(cls):
|
877
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)
|
878
|
-
(SO_0000399)
|
878
|
+
(http://purl.obolibrary.org/obo/SO_0000399)
|
879
879
|
"""
|
880
|
-
return _namespace_SOFA('SO_0000399')
|
880
|
+
return cls._namespace_SOFA('SO_0000399')
|
881
881
|
|
882
882
|
@classmethod
|
883
883
|
def U14_snoRNA(cls):
|
884
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)
|
885
|
-
(SO_0000403)
|
885
|
+
(http://purl.obolibrary.org/obo/SO_0000403)
|
886
886
|
"""
|
887
|
-
return _namespace_SOFA('SO_0000403')
|
887
|
+
return cls._namespace_SOFA('SO_0000403')
|
888
888
|
|
889
889
|
@classmethod
|
890
890
|
def vault_RNA(cls):
|
891
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)
|
892
|
-
(SO_0000404)
|
892
|
+
(http://purl.obolibrary.org/obo/SO_0000404)
|
893
893
|
"""
|
894
|
-
return _namespace_SOFA('SO_0000404')
|
894
|
+
return cls._namespace_SOFA('SO_0000404')
|
895
895
|
|
896
896
|
@classmethod
|
897
897
|
def Y_RNA(cls):
|
898
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)
|
899
|
-
(SO_0000405)
|
899
|
+
(http://purl.obolibrary.org/obo/SO_0000405)
|
900
900
|
"""
|
901
|
-
return _namespace_SOFA('SO_0000405')
|
901
|
+
return cls._namespace_SOFA('SO_0000405')
|
902
902
|
|
903
903
|
@classmethod
|
904
904
|
def rRNA_18S(cls):
|
905
905
|
"""A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome. (cls, SO:ke)
|
906
|
-
(SO_0000407)
|
906
|
+
(http://purl.obolibrary.org/obo/SO_0000407)
|
907
907
|
"""
|
908
|
-
return _namespace_SOFA('SO_0000407')
|
908
|
+
return cls._namespace_SOFA('SO_0000407')
|
909
909
|
|
910
910
|
@classmethod
|
911
911
|
def binding_site(cls):
|
912
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)
|
913
|
-
(SO_0000409)
|
913
|
+
(http://purl.obolibrary.org/obo/SO_0000409)
|
914
914
|
"""
|
915
|
-
return _namespace_SOFA('SO_0000409')
|
915
|
+
return cls._namespace_SOFA('SO_0000409')
|
916
916
|
|
917
917
|
@classmethod
|
918
918
|
def protein_binding_site(cls):
|
919
919
|
"""A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules. (cls, SO:ke)
|
920
|
-
(SO_0000410)
|
920
|
+
(http://purl.obolibrary.org/obo/SO_0000410)
|
921
921
|
"""
|
922
|
-
return _namespace_SOFA('SO_0000410')
|
922
|
+
return cls._namespace_SOFA('SO_0000410')
|
923
923
|
|
924
924
|
@classmethod
|
925
925
|
def restriction_fragment(cls):
|
926
926
|
"""A region of polynucleotide sequence produced by digestion with a restriction endonuclease. (cls, SO:ke)
|
927
|
-
(SO_0000412)
|
927
|
+
(http://purl.obolibrary.org/obo/SO_0000412)
|
928
928
|
"""
|
929
|
-
return _namespace_SOFA('SO_0000412')
|
929
|
+
return cls._namespace_SOFA('SO_0000412')
|
930
930
|
|
931
931
|
@classmethod
|
932
932
|
def sequence_difference(cls):
|
933
933
|
"""A region where the sequence differs from that of a specified sequence. (cls, SO:ke)
|
934
|
-
(SO_0000413)
|
934
|
+
(http://purl.obolibrary.org/obo/SO_0000413)
|
935
935
|
"""
|
936
|
-
return _namespace_SOFA('SO_0000413')
|
936
|
+
return cls._namespace_SOFA('SO_0000413')
|
937
937
|
|
938
938
|
@classmethod
|
939
939
|
def signal_peptide(cls):
|
940
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)
|
941
|
-
(SO_0000418)
|
941
|
+
(http://purl.obolibrary.org/obo/SO_0000418)
|
942
942
|
"""
|
943
|
-
return _namespace_SOFA('SO_0000418')
|
943
|
+
return cls._namespace_SOFA('SO_0000418')
|
944
944
|
|
945
945
|
@classmethod
|
946
946
|
def mature_protein_region(cls):
|
947
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)
|
948
|
-
(SO_0000419)
|
948
|
+
(http://purl.obolibrary.org/obo/SO_0000419)
|
949
949
|
"""
|
950
|
-
return _namespace_SOFA('SO_0000419')
|
950
|
+
return cls._namespace_SOFA('SO_0000419')
|
951
951
|
|
952
952
|
@classmethod
|
953
953
|
def ARS(cls):
|
954
954
|
"""A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host. (cls, SO:ma)
|
955
|
-
(SO_0000436)
|
955
|
+
(http://purl.obolibrary.org/obo/SO_0000436)
|
956
956
|
"""
|
957
|
-
return _namespace_SOFA('SO_0000436')
|
957
|
+
return cls._namespace_SOFA('SO_0000436')
|
958
958
|
|
959
959
|
@classmethod
|
960
960
|
def ss_oligo(cls):
|
961
961
|
"""A single stranded oligonucleotide. (cls, SO:ke)
|
962
|
-
(SO_0000441)
|
962
|
+
(http://purl.obolibrary.org/obo/SO_0000441)
|
963
963
|
"""
|
964
|
-
return _namespace_SOFA('SO_0000441')
|
964
|
+
return cls._namespace_SOFA('SO_0000441')
|
965
965
|
|
966
966
|
@classmethod
|
967
967
|
def ds_oligo(cls):
|
968
968
|
"""A double stranded oligonucleotide. (cls, SO:ke)
|
969
|
-
(SO_0000442)
|
969
|
+
(http://purl.obolibrary.org/obo/SO_0000442)
|
970
970
|
"""
|
971
|
-
return _namespace_SOFA('SO_0000442')
|
971
|
+
return cls._namespace_SOFA('SO_0000442')
|
972
972
|
|
973
973
|
@classmethod
|
974
974
|
def rasiRNA(cls):
|
975
975
|
"""A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements. (cls, http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284)
|
976
|
-
(SO_0000454)
|
976
|
+
(http://purl.obolibrary.org/obo/SO_0000454)
|
977
977
|
"""
|
978
|
-
return _namespace_SOFA('SO_0000454')
|
978
|
+
return cls._namespace_SOFA('SO_0000454')
|
979
979
|
|
980
980
|
@classmethod
|
981
981
|
def pseudogenic_region(cls):
|
982
982
|
"""A non-functional descendent of a functional entity. (cls, SO:cjm)
|
983
|
-
(SO_0000462)
|
983
|
+
(http://purl.obolibrary.org/obo/SO_0000462)
|
984
984
|
"""
|
985
|
-
return _namespace_SOFA('SO_0000462')
|
985
|
+
return cls._namespace_SOFA('SO_0000462')
|
986
986
|
|
987
987
|
@classmethod
|
988
988
|
def decayed_exon(cls):
|
989
989
|
"""A non-functional descendant of an exon. (cls, SO:ke)
|
990
|
-
(SO_0000464)
|
990
|
+
(http://purl.obolibrary.org/obo/SO_0000464)
|
991
991
|
"""
|
992
|
-
return _namespace_SOFA('SO_0000464')
|
992
|
+
return cls._namespace_SOFA('SO_0000464')
|
993
993
|
|
994
994
|
@classmethod
|
995
995
|
def golden_path_fragment(cls):
|
996
996
|
"""One of the pieces of sequence that make up a golden path. (cls, SO:rd)
|
997
|
-
(SO_0000468)
|
997
|
+
(http://purl.obolibrary.org/obo/SO_0000468)
|
998
998
|
"""
|
999
|
-
return _namespace_SOFA('SO_0000468')
|
999
|
+
return cls._namespace_SOFA('SO_0000468')
|
1000
1000
|
|
1001
1001
|
@classmethod
|
1002
1002
|
def tiling_path(cls):
|
1003
1003
|
"""A set of regions which overlap with minimal polymorphism to form a linear sequence. (cls, SO:cjm)
|
1004
|
-
(SO_0000472)
|
1004
|
+
(http://purl.obolibrary.org/obo/SO_0000472)
|
1005
1005
|
"""
|
1006
|
-
return _namespace_SOFA('SO_0000472')
|
1006
|
+
return cls._namespace_SOFA('SO_0000472')
|
1007
1007
|
|
1008
1008
|
@classmethod
|
1009
1009
|
def tiling_path_fragment(cls):
|
1010
1010
|
"""A piece of sequence that makes up a tiling_path (cls, SO:0000472). (SO:ke)
|
1011
|
-
(SO_0000474)
|
1011
|
+
(http://purl.obolibrary.org/obo/SO_0000474)
|
1012
1012
|
"""
|
1013
|
-
return _namespace_SOFA('SO_0000474')
|
1013
|
+
return cls._namespace_SOFA('SO_0000474')
|
1014
1014
|
|
1015
1015
|
@classmethod
|
1016
1016
|
def nc_primary_transcript(cls):
|
1017
1017
|
"""A primary transcript that is never translated into a protein. (cls, SO:ke)
|
1018
|
-
(SO_0000483)
|
1018
|
+
(http://purl.obolibrary.org/obo/SO_0000483)
|
1019
1019
|
"""
|
1020
|
-
return _namespace_SOFA('SO_0000483')
|
1020
|
+
return cls._namespace_SOFA('SO_0000483')
|
1021
1021
|
|
1022
1022
|
@classmethod
|
1023
1023
|
def three_prime_coding_exon_noncoding_region(cls):
|
1024
1024
|
"""The sequence of the 3' exon that is not coding. (cls, SO:ke)
|
1025
|
-
(SO_0000484)
|
1025
|
+
(http://purl.obolibrary.org/obo/SO_0000484)
|
1026
1026
|
"""
|
1027
|
-
return _namespace_SOFA('SO_0000484')
|
1027
|
+
return cls._namespace_SOFA('SO_0000484')
|
1028
1028
|
|
1029
1029
|
@classmethod
|
1030
1030
|
def five_prime_coding_exon_noncoding_region(cls):
|
1031
1031
|
"""The sequence of the 5' exon preceding the start codon. (cls, SO:ke)
|
1032
|
-
(SO_0000486)
|
1032
|
+
(http://purl.obolibrary.org/obo/SO_0000486)
|
1033
1033
|
"""
|
1034
|
-
return _namespace_SOFA('SO_0000486')
|
1034
|
+
return cls._namespace_SOFA('SO_0000486')
|
1035
1035
|
|
1036
1036
|
@classmethod
|
1037
1037
|
def virtual_sequence(cls):
|
1038
1038
|
"""A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database. (cls, SO:ke)
|
1039
|
-
(SO_0000499)
|
1039
|
+
(http://purl.obolibrary.org/obo/SO_0000499)
|
1040
1040
|
"""
|
1041
|
-
return _namespace_SOFA('SO_0000499')
|
1041
|
+
return cls._namespace_SOFA('SO_0000499')
|
1042
1042
|
|
1043
1043
|
@classmethod
|
1044
1044
|
def transcribed_region(cls):
|
1045
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)
|
1046
|
-
(SO_0000502)
|
1046
|
+
(http://purl.obolibrary.org/obo/SO_0000502)
|
1047
1047
|
"""
|
1048
|
-
return _namespace_SOFA('SO_0000502')
|
1048
|
+
return cls._namespace_SOFA('SO_0000502')
|
1049
1049
|
|
1050
1050
|
@classmethod
|
1051
1051
|
def polyA_signal_sequence(cls):
|
1052
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)
|
1053
|
-
(SO_0000551)
|
1053
|
+
(http://purl.obolibrary.org/obo/SO_0000551)
|
1054
1054
|
"""
|
1055
|
-
return _namespace_SOFA('SO_0000551')
|
1055
|
+
return cls._namespace_SOFA('SO_0000551')
|
1056
1056
|
|
1057
1057
|
@classmethod
|
1058
1058
|
def polyA_site(cls):
|
1059
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)
|
1060
|
-
(SO_0000553)
|
1060
|
+
(http://purl.obolibrary.org/obo/SO_0000553)
|
1061
1061
|
"""
|
1062
|
-
return _namespace_SOFA('SO_0000553')
|
1062
|
+
return cls._namespace_SOFA('SO_0000553')
|
1063
1063
|
|
1064
1064
|
@classmethod
|
1065
1065
|
def centromere(cls):
|
1066
1066
|
"""A region of chromosome where the spindle fibers attach during mitosis and meiosis. (cls, SO:ke)
|
1067
|
-
(SO_0000577)
|
1067
|
+
(http://purl.obolibrary.org/obo/SO_0000577)
|
1068
1068
|
"""
|
1069
|
-
return _namespace_SOFA('SO_0000577')
|
1069
|
+
return cls._namespace_SOFA('SO_0000577')
|
1070
1070
|
|
1071
1071
|
@classmethod
|
1072
1072
|
def cap(cls):
|
1073
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)
|
1074
|
-
(SO_0000581)
|
1074
|
+
(http://purl.obolibrary.org/obo/SO_0000581)
|
1075
1075
|
"""
|
1076
|
-
return _namespace_SOFA('SO_0000581')
|
1076
|
+
return cls._namespace_SOFA('SO_0000581')
|
1077
1077
|
|
1078
1078
|
@classmethod
|
1079
1079
|
def group_I_intron(cls):
|
1080
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)
|
1081
|
-
(SO_0000587)
|
1081
|
+
(http://purl.obolibrary.org/obo/SO_0000587)
|
1082
1082
|
"""
|
1083
|
-
return _namespace_SOFA('SO_0000587')
|
1083
|
+
return cls._namespace_SOFA('SO_0000587')
|
1084
1084
|
|
1085
1085
|
@classmethod
|
1086
1086
|
def autocatalytically_spliced_intron(cls):
|
1087
1087
|
"""A self spliced intron. (cls, SO:ke)
|
1088
|
-
(SO_0000588)
|
1088
|
+
(http://purl.obolibrary.org/obo/SO_0000588)
|
1089
1089
|
"""
|
1090
|
-
return _namespace_SOFA('SO_0000588')
|
1090
|
+
return cls._namespace_SOFA('SO_0000588')
|
1091
1091
|
|
1092
1092
|
@classmethod
|
1093
1093
|
def SRP_RNA(cls):
|
1094
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)
|
1095
|
-
(SO_0000590)
|
1095
|
+
(http://purl.obolibrary.org/obo/SO_0000590)
|
1096
1096
|
"""
|
1097
|
-
return _namespace_SOFA('SO_0000590')
|
1097
|
+
return cls._namespace_SOFA('SO_0000590')
|
1098
1098
|
|
1099
1099
|
@classmethod
|
1100
1100
|
def C_D_box_snoRNA(cls):
|
1101
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)
|
1102
|
-
(SO_0000593)
|
1102
|
+
(http://purl.obolibrary.org/obo/SO_0000593)
|
1103
1103
|
"""
|
1104
|
-
return _namespace_SOFA('SO_0000593')
|
1104
|
+
return cls._namespace_SOFA('SO_0000593')
|
1105
1105
|
|
1106
1106
|
@classmethod
|
1107
1107
|
def guide_RNA(cls):
|
1108
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)
|
1109
|
-
(SO_0000602)
|
1109
|
+
(http://purl.obolibrary.org/obo/SO_0000602)
|
1110
1110
|
"""
|
1111
|
-
return _namespace_SOFA('SO_0000602')
|
1111
|
+
return cls._namespace_SOFA('SO_0000602')
|
1112
1112
|
|
1113
1113
|
@classmethod
|
1114
1114
|
def group_II_intron(cls):
|
1115
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)
|
1116
|
-
(SO_0000603)
|
1116
|
+
(http://purl.obolibrary.org/obo/SO_0000603)
|
1117
1117
|
"""
|
1118
|
-
return _namespace_SOFA('SO_0000603')
|
1118
|
+
return cls._namespace_SOFA('SO_0000603')
|
1119
1119
|
|
1120
1120
|
@classmethod
|
1121
1121
|
def intergenic_region(cls):
|
1122
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)
|
1123
|
-
(SO_0000605)
|
1123
|
+
(http://purl.obolibrary.org/obo/SO_0000605)
|
1124
1124
|
"""
|
1125
|
-
return _namespace_SOFA('SO_0000605')
|
1125
|
+
return cls._namespace_SOFA('SO_0000605')
|
1126
1126
|
|
1127
1127
|
@classmethod
|
1128
1128
|
def polyA_sequence(cls):
|
1129
1129
|
"""Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs. (cls, SO:ke)
|
1130
|
-
(SO_0000610)
|
1130
|
+
(http://purl.obolibrary.org/obo/SO_0000610)
|
1131
1131
|
"""
|
1132
|
-
return _namespace_SOFA('SO_0000610')
|
1132
|
+
return cls._namespace_SOFA('SO_0000610')
|
1133
1133
|
|
1134
1134
|
@classmethod
|
1135
1135
|
def branch_site(cls):
|
1136
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)
|
1137
|
-
(SO_0000611)
|
1137
|
+
(http://purl.obolibrary.org/obo/SO_0000611)
|
1138
1138
|
"""
|
1139
|
-
return _namespace_SOFA('SO_0000611')
|
1139
|
+
return cls._namespace_SOFA('SO_0000611')
|
1140
1140
|
|
1141
1141
|
@classmethod
|
1142
1142
|
def polypyrimidine_tract(cls):
|
1143
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)
|
1144
|
-
(SO_0000612)
|
1144
|
+
(http://purl.obolibrary.org/obo/SO_0000612)
|
1145
1145
|
"""
|
1146
|
-
return _namespace_SOFA('SO_0000612')
|
1146
|
+
return cls._namespace_SOFA('SO_0000612')
|
1147
1147
|
|
1148
1148
|
@classmethod
|
1149
1149
|
def transcription_end_site(cls):
|
1150
1150
|
"""The base where transcription ends. (cls, SO:ke)
|
1151
|
-
(SO_0000616)
|
1151
|
+
(http://purl.obolibrary.org/obo/SO_0000616)
|
1152
1152
|
"""
|
1153
|
-
return _namespace_SOFA('SO_0000616')
|
1153
|
+
return cls._namespace_SOFA('SO_0000616')
|
1154
1154
|
|
1155
1155
|
@classmethod
|
1156
1156
|
def telomere(cls):
|
1157
1157
|
"""A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end. (cls, SO:ma)
|
1158
|
-
(SO_0000624)
|
1158
|
+
(http://purl.obolibrary.org/obo/SO_0000624)
|
1159
1159
|
"""
|
1160
|
-
return _namespace_SOFA('SO_0000624')
|
1160
|
+
return cls._namespace_SOFA('SO_0000624')
|
1161
1161
|
|
1162
1162
|
@classmethod
|
1163
1163
|
def silencer(cls):
|
1164
1164
|
"""A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control. (cls, SO:ke)
|
1165
|
-
(SO_0000625)
|
1165
|
+
(http://purl.obolibrary.org/obo/SO_0000625)
|
1166
1166
|
"""
|
1167
|
-
return _namespace_SOFA('SO_0000625')
|
1167
|
+
return cls._namespace_SOFA('SO_0000625')
|
1168
1168
|
|
1169
1169
|
@classmethod
|
1170
1170
|
def insulator(cls):
|
1171
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)
|
1172
|
-
(SO_0000627)
|
1172
|
+
(http://purl.obolibrary.org/obo/SO_0000627)
|
1173
1173
|
"""
|
1174
|
-
return _namespace_SOFA('SO_0000627')
|
1174
|
+
return cls._namespace_SOFA('SO_0000627')
|
1175
1175
|
|
1176
1176
|
@classmethod
|
1177
1177
|
def chromosomal_structural_element(cls):
|
1178
|
-
return _namespace_SOFA('SO_0000628')
|
1178
|
+
return cls._namespace_SOFA('SO_0000628')
|
1179
1179
|
|
1180
1180
|
@classmethod
|
1181
1181
|
def minisatellite(cls):
|
1182
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)
|
1183
|
-
(SO_0000643)
|
1183
|
+
(http://purl.obolibrary.org/obo/SO_0000643)
|
1184
1184
|
"""
|
1185
|
-
return _namespace_SOFA('SO_0000643')
|
1185
|
+
return cls._namespace_SOFA('SO_0000643')
|
1186
1186
|
|
1187
1187
|
@classmethod
|
1188
1188
|
def antisense_RNA(cls):
|
1189
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)
|
1190
|
-
(SO_0000644)
|
1190
|
+
(http://purl.obolibrary.org/obo/SO_0000644)
|
1191
1191
|
"""
|
1192
|
-
return _namespace_SOFA('SO_0000644')
|
1192
|
+
return cls._namespace_SOFA('SO_0000644')
|
1193
1193
|
|
1194
1194
|
@classmethod
|
1195
1195
|
def antisense_primary_transcript(cls):
|
1196
1196
|
"""The reverse complement of the primary transcript. (cls, SO:ke)
|
1197
|
-
(SO_0000645)
|
1197
|
+
(http://purl.obolibrary.org/obo/SO_0000645)
|
1198
1198
|
"""
|
1199
|
-
return _namespace_SOFA('SO_0000645')
|
1199
|
+
return cls._namespace_SOFA('SO_0000645')
|
1200
1200
|
|
1201
1201
|
@classmethod
|
1202
1202
|
def siRNA(cls):
|
1203
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)
|
1204
|
-
(SO_0000646)
|
1204
|
+
(http://purl.obolibrary.org/obo/SO_0000646)
|
1205
1205
|
"""
|
1206
|
-
return _namespace_SOFA('SO_0000646')
|
1206
|
+
return cls._namespace_SOFA('SO_0000646')
|
1207
1207
|
|
1208
1208
|
@classmethod
|
1209
1209
|
def stRNA(cls):
|
1210
1210
|
"""Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans. (cls, PMID:11081512)
|
1211
|
-
(SO_0000649)
|
1211
|
+
(http://purl.obolibrary.org/obo/SO_0000649)
|
1212
1212
|
"""
|
1213
|
-
return _namespace_SOFA('SO_0000649')
|
1213
|
+
return cls._namespace_SOFA('SO_0000649')
|
1214
1214
|
|
1215
1215
|
@classmethod
|
1216
1216
|
def small_subunit_rRNA(cls):
|
1217
1217
|
"""Ribosomal RNA transcript that structures the small subunit of the ribosome. (cls, SO:ke)
|
1218
|
-
(SO_0000650)
|
1218
|
+
(http://purl.obolibrary.org/obo/SO_0000650)
|
1219
1219
|
"""
|
1220
|
-
return _namespace_SOFA('SO_0000650')
|
1220
|
+
return cls._namespace_SOFA('SO_0000650')
|
1221
1221
|
|
1222
1222
|
@classmethod
|
1223
1223
|
def large_subunit_rRNA(cls):
|
1224
1224
|
"""Ribosomal RNA transcript that structures the large subunit of the ribosome. (cls, SO:ke)
|
1225
|
-
(SO_0000651)
|
1225
|
+
(http://purl.obolibrary.org/obo/SO_0000651)
|
1226
1226
|
"""
|
1227
|
-
return _namespace_SOFA('SO_0000651')
|
1227
|
+
return cls._namespace_SOFA('SO_0000651')
|
1228
1228
|
|
1229
1229
|
@classmethod
|
1230
1230
|
def rRNA_5S(cls):
|
1231
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)
|
1232
|
-
(SO_0000652)
|
1232
|
+
(http://purl.obolibrary.org/obo/SO_0000652)
|
1233
1233
|
"""
|
1234
|
-
return _namespace_SOFA('SO_0000652')
|
1234
|
+
return cls._namespace_SOFA('SO_0000652')
|
1235
1235
|
|
1236
1236
|
@classmethod
|
1237
1237
|
def rRNA_28S(cls):
|
1238
1238
|
"""A component of the large ribosomal subunit. (cls, SO:ke)
|
1239
|
-
(SO_0000653)
|
1239
|
+
(http://purl.obolibrary.org/obo/SO_0000653)
|
1240
1240
|
"""
|
1241
|
-
return _namespace_SOFA('SO_0000653')
|
1241
|
+
return cls._namespace_SOFA('SO_0000653')
|
1242
1242
|
|
1243
1243
|
@classmethod
|
1244
1244
|
def ncRNA(cls):
|
1245
1245
|
"""An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product. (cls, SO:ke)
|
1246
|
-
(SO_0000655)
|
1246
|
+
(http://purl.obolibrary.org/obo/SO_0000655)
|
1247
1247
|
"""
|
1248
|
-
return _namespace_SOFA('SO_0000655')
|
1248
|
+
return cls._namespace_SOFA('SO_0000655')
|
1249
1249
|
|
1250
1250
|
@classmethod
|
1251
1251
|
def repeat_region(cls):
|
1252
1252
|
"""A region of sequence containing one or more repeat units. (cls, SO:ke)
|
1253
|
-
(SO_0000657)
|
1253
|
+
(http://purl.obolibrary.org/obo/SO_0000657)
|
1254
1254
|
"""
|
1255
|
-
return _namespace_SOFA('SO_0000657')
|
1255
|
+
return cls._namespace_SOFA('SO_0000657')
|
1256
1256
|
|
1257
1257
|
@classmethod
|
1258
1258
|
def dispersed_repeat(cls):
|
1259
1259
|
"""A repeat that is located at dispersed sites in the genome. (cls, SO:ke)
|
1260
|
-
(SO_0000658)
|
1260
|
+
(http://purl.obolibrary.org/obo/SO_0000658)
|
1261
1261
|
"""
|
1262
|
-
return _namespace_SOFA('SO_0000658')
|
1262
|
+
return cls._namespace_SOFA('SO_0000658')
|
1263
1263
|
|
1264
1264
|
@classmethod
|
1265
1265
|
def spliceosomal_intron(cls):
|
1266
1266
|
"""An intron which is spliced by the spliceosome. (cls, SO:ke)
|
1267
|
-
(SO_0000662)
|
1267
|
+
(http://purl.obolibrary.org/obo/SO_0000662)
|
1268
1268
|
"""
|
1269
|
-
return _namespace_SOFA('SO_0000662')
|
1269
|
+
return cls._namespace_SOFA('SO_0000662')
|
1270
1270
|
|
1271
1271
|
@classmethod
|
1272
1272
|
def insertion(cls):
|
1273
1273
|
"""The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence. (cls, SO:ke)
|
1274
|
-
(SO_0000667)
|
1274
|
+
(http://purl.obolibrary.org/obo/SO_0000667)
|
1275
1275
|
"""
|
1276
|
-
return _namespace_SOFA('SO_0000667')
|
1276
|
+
return cls._namespace_SOFA('SO_0000667')
|
1277
1277
|
|
1278
1278
|
@classmethod
|
1279
1279
|
def EST_match(cls):
|
1280
1280
|
"""A match against an EST sequence. (cls, SO:ke)
|
1281
|
-
(SO_0000668)
|
1281
|
+
(http://purl.obolibrary.org/obo/SO_0000668)
|
1282
1282
|
"""
|
1283
|
-
return _namespace_SOFA('SO_0000668')
|
1283
|
+
return cls._namespace_SOFA('SO_0000668')
|
1284
1284
|
|
1285
1285
|
@classmethod
|
1286
1286
|
def transcript(cls):
|
1287
1287
|
"""An RNA synthesized on a DNA or RNA template by an RNA polymerase. (cls, SO:ma)
|
1288
|
-
(SO_0000673)
|
1288
|
+
(http://purl.obolibrary.org/obo/SO_0000673)
|
1289
1289
|
"""
|
1290
|
-
return _namespace_SOFA('SO_0000673')
|
1290
|
+
return cls._namespace_SOFA('SO_0000673')
|
1291
1291
|
|
1292
1292
|
@classmethod
|
1293
1293
|
def nuclease_sensitive_site(cls):
|
1294
1294
|
"""A region of nucleotide sequence targeted by a nuclease enzyme. (cls, SO:ma)
|
1295
|
-
(SO_0000684)
|
1295
|
+
(http://purl.obolibrary.org/obo/SO_0000684)
|
1296
1296
|
"""
|
1297
|
-
return _namespace_SOFA('SO_0000684')
|
1297
|
+
return cls._namespace_SOFA('SO_0000684')
|
1298
1298
|
|
1299
1299
|
@classmethod
|
1300
1300
|
def deletion_junction(cls):
|
1301
1301
|
"""The space between two bases in a sequence which marks the position where a deletion has occurred. (cls, SO:ke)
|
1302
|
-
(SO_0000687)
|
1302
|
+
(http://purl.obolibrary.org/obo/SO_0000687)
|
1303
1303
|
"""
|
1304
|
-
return _namespace_SOFA('SO_0000687')
|
1304
|
+
return cls._namespace_SOFA('SO_0000687')
|
1305
1305
|
|
1306
1306
|
@classmethod
|
1307
1307
|
def golden_path(cls):
|
1308
1308
|
"""A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence. (cls, SO:ls)
|
1309
|
-
(SO_0000688)
|
1309
|
+
(http://purl.obolibrary.org/obo/SO_0000688)
|
1310
1310
|
"""
|
1311
|
-
return _namespace_SOFA('SO_0000688')
|
1311
|
+
return cls._namespace_SOFA('SO_0000688')
|
1312
1312
|
|
1313
1313
|
@classmethod
|
1314
1314
|
def cDNA_match(cls):
|
1315
1315
|
"""A match against cDNA sequence. (cls, SO:ke)
|
1316
|
-
(SO_0000689)
|
1316
|
+
(http://purl.obolibrary.org/obo/SO_0000689)
|
1317
1317
|
"""
|
1318
|
-
return _namespace_SOFA('SO_0000689')
|
1318
|
+
return cls._namespace_SOFA('SO_0000689')
|
1319
1319
|
|
1320
1320
|
@classmethod
|
1321
1321
|
def SNP(cls):
|
1322
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)
|
1323
|
-
(SO_0000694)
|
1323
|
+
(http://purl.obolibrary.org/obo/SO_0000694)
|
1324
1324
|
"""
|
1325
|
-
return _namespace_SOFA('SO_0000694')
|
1325
|
+
return cls._namespace_SOFA('SO_0000694')
|
1326
1326
|
|
1327
1327
|
@classmethod
|
1328
1328
|
def reagent(cls):
|
1329
1329
|
"""A sequence used in experiment. (cls, SO:ke)
|
1330
|
-
(SO_0000695)
|
1330
|
+
(http://purl.obolibrary.org/obo/SO_0000695)
|
1331
1331
|
"""
|
1332
|
-
return _namespace_SOFA('SO_0000695')
|
1332
|
+
return cls._namespace_SOFA('SO_0000695')
|
1333
1333
|
|
1334
1334
|
@classmethod
|
1335
1335
|
def oligo(cls):
|
1336
1336
|
"""A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. (cls, SO:ma)
|
1337
|
-
(SO_0000696)
|
1337
|
+
(http://purl.obolibrary.org/obo/SO_0000696)
|
1338
1338
|
"""
|
1339
|
-
return _namespace_SOFA('SO_0000696')
|
1339
|
+
return cls._namespace_SOFA('SO_0000696')
|
1340
1340
|
|
1341
1341
|
@classmethod
|
1342
1342
|
def junction(cls):
|
1343
1343
|
"""A sequence_feature with an extent of zero. (cls, SO:ke)
|
1344
|
-
(SO_0000699)
|
1344
|
+
(http://purl.obolibrary.org/obo/SO_0000699)
|
1345
1345
|
"""
|
1346
|
-
return _namespace_SOFA('SO_0000699')
|
1346
|
+
return cls._namespace_SOFA('SO_0000699')
|
1347
1347
|
|
1348
1348
|
@classmethod
|
1349
1349
|
def remark(cls):
|
1350
1350
|
"""A comment about the sequence. (cls, SO:ke)
|
1351
|
-
(SO_0000700)
|
1351
|
+
(http://purl.obolibrary.org/obo/SO_0000700)
|
1352
1352
|
"""
|
1353
|
-
return _namespace_SOFA('SO_0000700')
|
1353
|
+
return cls._namespace_SOFA('SO_0000700')
|
1354
1354
|
|
1355
1355
|
@classmethod
|
1356
1356
|
def possible_base_call_error(cls):
|
1357
1357
|
"""A region of sequence where the validity of the base calling is questionable. (cls, SO:ke)
|
1358
|
-
(SO_0000701)
|
1358
|
+
(http://purl.obolibrary.org/obo/SO_0000701)
|
1359
1359
|
"""
|
1360
|
-
return _namespace_SOFA('SO_0000701')
|
1360
|
+
return cls._namespace_SOFA('SO_0000701')
|
1361
1361
|
|
1362
1362
|
@classmethod
|
1363
1363
|
def possible_assembly_error(cls):
|
1364
1364
|
"""A region of sequence where there may have been an error in the assembly. (cls, SO:ke)
|
1365
|
-
(SO_0000702)
|
1365
|
+
(http://purl.obolibrary.org/obo/SO_0000702)
|
1366
1366
|
"""
|
1367
|
-
return _namespace_SOFA('SO_0000702')
|
1367
|
+
return cls._namespace_SOFA('SO_0000702')
|
1368
1368
|
|
1369
1369
|
@classmethod
|
1370
1370
|
def experimental_result_region(cls):
|
1371
1371
|
"""A region of sequence implicated in an experimental result. (cls, SO:ke)
|
1372
|
-
(SO_0000703)
|
1372
|
+
(http://purl.obolibrary.org/obo/SO_0000703)
|
1373
1373
|
"""
|
1374
|
-
return _namespace_SOFA('SO_0000703')
|
1374
|
+
return cls._namespace_SOFA('SO_0000703')
|
1375
1375
|
|
1376
1376
|
@classmethod
|
1377
1377
|
def gene(cls):
|
1378
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)
|
1379
|
-
(SO_0000704)
|
1379
|
+
(http://purl.obolibrary.org/obo/SO_0000704)
|
1380
1380
|
"""
|
1381
|
-
return _namespace_SOFA('SO_0000704')
|
1381
|
+
return cls._namespace_SOFA('SO_0000704')
|
1382
1382
|
|
1383
1383
|
@classmethod
|
1384
1384
|
def tandem_repeat(cls):
|
1385
1385
|
"""Two or more adjcent copies of a region (cls, of length greater than 1). (SO:ke)
|
1386
|
-
(SO_0000705)
|
1386
|
+
(http://purl.obolibrary.org/obo/SO_0000705)
|
1387
1387
|
"""
|
1388
|
-
return _namespace_SOFA('SO_0000705')
|
1388
|
+
return cls._namespace_SOFA('SO_0000705')
|
1389
1389
|
|
1390
1390
|
@classmethod
|
1391
1391
|
def trans_splice_acceptor_site(cls):
|
1392
1392
|
"""The 3' splice site of the acceptor primary transcript. (cls, SO:ke)
|
1393
|
-
(SO_0000706)
|
1393
|
+
(http://purl.obolibrary.org/obo/SO_0000706)
|
1394
1394
|
"""
|
1395
|
-
return _namespace_SOFA('SO_0000706')
|
1395
|
+
return cls._namespace_SOFA('SO_0000706')
|
1396
1396
|
|
1397
1397
|
@classmethod
|
1398
1398
|
def nucleotide_motif(cls):
|
1399
1399
|
"""A region of nucleotide sequence corresponding to a known motif. (cls, SO:ke)
|
1400
|
-
(SO_0000714)
|
1400
|
+
(http://purl.obolibrary.org/obo/SO_0000714)
|
1401
1401
|
"""
|
1402
|
-
return _namespace_SOFA('SO_0000714')
|
1402
|
+
return cls._namespace_SOFA('SO_0000714')
|
1403
1403
|
|
1404
1404
|
@classmethod
|
1405
1405
|
def RNA_motif(cls):
|
1406
1406
|
"""A motif that is active in RNA sequence. (cls, SO:ke)
|
1407
|
-
(SO_0000715)
|
1407
|
+
(http://purl.obolibrary.org/obo/SO_0000715)
|
1408
1408
|
"""
|
1409
|
-
return _namespace_SOFA('SO_0000715')
|
1409
|
+
return cls._namespace_SOFA('SO_0000715')
|
1410
1410
|
|
1411
1411
|
@classmethod
|
1412
1412
|
def reading_frame(cls):
|
1413
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)
|
1414
|
-
(SO_0000717)
|
1414
|
+
(http://purl.obolibrary.org/obo/SO_0000717)
|
1415
1415
|
"""
|
1416
|
-
return _namespace_SOFA('SO_0000717')
|
1416
|
+
return cls._namespace_SOFA('SO_0000717')
|
1417
1417
|
|
1418
1418
|
@classmethod
|
1419
1419
|
def ultracontig(cls):
|
1420
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)
|
1421
|
-
(SO_0000719)
|
1421
|
+
(http://purl.obolibrary.org/obo/SO_0000719)
|
1422
1422
|
"""
|
1423
|
-
return _namespace_SOFA('SO_0000719')
|
1423
|
+
return cls._namespace_SOFA('SO_0000719')
|
1424
1424
|
|
1425
1425
|
@classmethod
|
1426
1426
|
def oriT(cls):
|
1427
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)
|
1428
|
-
(SO_0000724)
|
1428
|
+
(http://purl.obolibrary.org/obo/SO_0000724)
|
1429
1429
|
"""
|
1430
|
-
return _namespace_SOFA('SO_0000724')
|
1430
|
+
return cls._namespace_SOFA('SO_0000724')
|
1431
1431
|
|
1432
1432
|
@classmethod
|
1433
1433
|
def transit_peptide(cls):
|
1434
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)
|
1435
|
-
(SO_0000725)
|
1435
|
+
(http://purl.obolibrary.org/obo/SO_0000725)
|
1436
1436
|
"""
|
1437
|
-
return _namespace_SOFA('SO_0000725')
|
1437
|
+
return cls._namespace_SOFA('SO_0000725')
|
1438
1438
|
|
1439
1439
|
@classmethod
|
1440
1440
|
def CRM(cls):
|
1441
1441
|
"""A regulatory_region where more than 1 TF_binding_site together are regulatorily active. (cls, SO:SG)
|
1442
|
-
(SO_0000727)
|
1442
|
+
(http://purl.obolibrary.org/obo/SO_0000727)
|
1443
1443
|
"""
|
1444
|
-
return _namespace_SOFA('SO_0000727')
|
1444
|
+
return cls._namespace_SOFA('SO_0000727')
|
1445
1445
|
|
1446
1446
|
@classmethod
|
1447
1447
|
def gap(cls):
|
1448
1448
|
"""A gap in the sequence of known length. The unknown bases are filled in with N's. (cls, SO:ke)
|
1449
|
-
(SO_0000730)
|
1449
|
+
(http://purl.obolibrary.org/obo/SO_0000730)
|
1450
1450
|
"""
|
1451
|
-
return _namespace_SOFA('SO_0000730')
|
1451
|
+
return cls._namespace_SOFA('SO_0000730')
|
1452
1452
|
|
1453
1453
|
@classmethod
|
1454
1454
|
def gene_group_regulatory_region(cls):
|
1455
|
-
return _namespace_SOFA('SO_0000752')
|
1455
|
+
return cls._namespace_SOFA('SO_0000752')
|
1456
1456
|
|
1457
1457
|
@classmethod
|
1458
1458
|
def clone_insert(cls):
|
1459
1459
|
"""The region of sequence that has been inserted and is being propagated by the clone. (cls, SO:ke)
|
1460
|
-
(SO_0000753)
|
1460
|
+
(http://purl.obolibrary.org/obo/SO_0000753)
|
1461
1461
|
"""
|
1462
|
-
return _namespace_SOFA('SO_0000753')
|
1462
|
+
return cls._namespace_SOFA('SO_0000753')
|
1463
1463
|
|
1464
1464
|
@classmethod
|
1465
1465
|
def pseudogenic_rRNA(cls):
|
1466
1466
|
"""A non functional descendent of an rRNA. (cls, SO:ke)
|
1467
|
-
(SO_0000777)
|
1467
|
+
(http://purl.obolibrary.org/obo/SO_0000777)
|
1468
1468
|
"""
|
1469
|
-
return _namespace_SOFA('SO_0000777')
|
1469
|
+
return cls._namespace_SOFA('SO_0000777')
|
1470
1470
|
|
1471
1471
|
@classmethod
|
1472
1472
|
def pseudogenic_tRNA(cls):
|
1473
1473
|
"""A non functional descendent of a tRNA. (cls, SO:ke)
|
1474
|
-
(SO_0000778)
|
1474
|
+
(http://purl.obolibrary.org/obo/SO_0000778)
|
1475
1475
|
"""
|
1476
|
-
return _namespace_SOFA('SO_0000778')
|
1476
|
+
return cls._namespace_SOFA('SO_0000778')
|
1477
1477
|
|
1478
1478
|
@classmethod
|
1479
1479
|
def chromosome_part(cls):
|
1480
1480
|
"""A region of a chromosome. (cls, SO:ke)
|
1481
|
-
(SO_0000830)
|
1481
|
+
(http://purl.obolibrary.org/obo/SO_0000830)
|
1482
1482
|
"""
|
1483
|
-
return _namespace_SOFA('SO_0000830')
|
1483
|
+
return cls._namespace_SOFA('SO_0000830')
|
1484
1484
|
|
1485
1485
|
@classmethod
|
1486
1486
|
def gene_member_region(cls):
|
1487
1487
|
"""A region of a gene. (cls, SO:ke)
|
1488
|
-
(SO_0000831)
|
1488
|
+
(http://purl.obolibrary.org/obo/SO_0000831)
|
1489
1489
|
"""
|
1490
|
-
return _namespace_SOFA('SO_0000831')
|
1490
|
+
return cls._namespace_SOFA('SO_0000831')
|
1491
1491
|
|
1492
1492
|
@classmethod
|
1493
1493
|
def transcript_region(cls):
|
1494
1494
|
"""A region of a transcript. (cls, SO:ke)
|
1495
|
-
(SO_0000833)
|
1495
|
+
(http://purl.obolibrary.org/obo/SO_0000833)
|
1496
1496
|
"""
|
1497
|
-
return _namespace_SOFA('SO_0000833')
|
1497
|
+
return cls._namespace_SOFA('SO_0000833')
|
1498
1498
|
|
1499
1499
|
@classmethod
|
1500
1500
|
def mature_transcript_region(cls):
|
1501
1501
|
"""A region of a mature transcript. (cls, SO:ke)
|
1502
|
-
(SO_0000834)
|
1502
|
+
(http://purl.obolibrary.org/obo/SO_0000834)
|
1503
1503
|
"""
|
1504
|
-
return _namespace_SOFA('SO_0000834')
|
1504
|
+
return cls._namespace_SOFA('SO_0000834')
|
1505
1505
|
|
1506
1506
|
@classmethod
|
1507
1507
|
def primary_transcript_region(cls):
|
1508
1508
|
"""A part of a primary transcript. (cls, SO:ke)
|
1509
|
-
(SO_0000835)
|
1509
|
+
(http://purl.obolibrary.org/obo/SO_0000835)
|
1510
1510
|
"""
|
1511
|
-
return _namespace_SOFA('SO_0000835')
|
1511
|
+
return cls._namespace_SOFA('SO_0000835')
|
1512
1512
|
|
1513
1513
|
@classmethod
|
1514
1514
|
def mRNA_region(cls):
|
1515
1515
|
"""A region of an mRNA. (cls, SO:cb)
|
1516
|
-
(SO_0000836)
|
1516
|
+
(http://purl.obolibrary.org/obo/SO_0000836)
|
1517
1517
|
"""
|
1518
|
-
return _namespace_SOFA('SO_0000836')
|
1518
|
+
return cls._namespace_SOFA('SO_0000836')
|
1519
1519
|
|
1520
1520
|
@classmethod
|
1521
1521
|
def UTR_region(cls):
|
1522
1522
|
"""A region of UTR. (cls, SO:ke)
|
1523
|
-
(SO_0000837)
|
1523
|
+
(http://purl.obolibrary.org/obo/SO_0000837)
|
1524
1524
|
"""
|
1525
|
-
return _namespace_SOFA('SO_0000837')
|
1525
|
+
return cls._namespace_SOFA('SO_0000837')
|
1526
1526
|
|
1527
1527
|
@classmethod
|
1528
1528
|
def polypeptide_region(cls):
|
1529
1529
|
"""Biological sequence region that can be assigned to a specific subsequence of a polypeptide. (cls, SO:GAR, SO:ke)
|
1530
|
-
(SO_0000839)
|
1530
|
+
(http://purl.obolibrary.org/obo/SO_0000839)
|
1531
1531
|
"""
|
1532
|
-
return _namespace_SOFA('SO_0000839')
|
1532
|
+
return cls._namespace_SOFA('SO_0000839')
|
1533
1533
|
|
1534
1534
|
@classmethod
|
1535
1535
|
def spliceosomal_intron_region(cls):
|
1536
1536
|
"""A region within an intron. (cls, SO:ke)
|
1537
|
-
(SO_0000841)
|
1537
|
+
(http://purl.obolibrary.org/obo/SO_0000841)
|
1538
1538
|
"""
|
1539
|
-
return _namespace_SOFA('SO_0000841')
|
1539
|
+
return cls._namespace_SOFA('SO_0000841')
|
1540
1540
|
|
1541
1541
|
@classmethod
|
1542
1542
|
def gene_component_region(cls):
|
1543
|
-
return _namespace_SOFA('SO_0000842')
|
1543
|
+
return cls._namespace_SOFA('SO_0000842')
|
1544
1544
|
|
1545
1545
|
@classmethod
|
1546
1546
|
def CDS_region(cls):
|
1547
1547
|
"""A region of a CDS. (cls, SO:cb)
|
1548
|
-
(SO_0000851)
|
1548
|
+
(http://purl.obolibrary.org/obo/SO_0000851)
|
1549
1549
|
"""
|
1550
|
-
return _namespace_SOFA('SO_0000851')
|
1550
|
+
return cls._namespace_SOFA('SO_0000851')
|
1551
1551
|
|
1552
1552
|
@classmethod
|
1553
1553
|
def exon_region(cls):
|
1554
1554
|
"""A region of an exon. (cls, RSC:cb)
|
1555
|
-
(SO_0000852)
|
1555
|
+
(http://purl.obolibrary.org/obo/SO_0000852)
|
1556
1556
|
"""
|
1557
|
-
return _namespace_SOFA('SO_0000852')
|
1557
|
+
return cls._namespace_SOFA('SO_0000852')
|
1558
1558
|
|
1559
1559
|
@classmethod
|
1560
1560
|
def rRNA_16S(cls):
|
1561
1561
|
"""A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome. (cls, SO:ke)
|
1562
|
-
(SO_0001000)
|
1562
|
+
(http://purl.obolibrary.org/obo/SO_0001000)
|
1563
1563
|
"""
|
1564
|
-
return _namespace_SOFA('SO_0001000')
|
1564
|
+
return cls._namespace_SOFA('SO_0001000')
|
1565
1565
|
|
1566
1566
|
@classmethod
|
1567
1567
|
def rRNA_23S(cls):
|
1568
1568
|
"""A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome. (cls, SO:ke)
|
1569
|
-
(SO_0001001)
|
1569
|
+
(http://purl.obolibrary.org/obo/SO_0001001)
|
1570
1570
|
"""
|
1571
|
-
return _namespace_SOFA('SO_0001001')
|
1571
|
+
return cls._namespace_SOFA('SO_0001001')
|
1572
1572
|
|
1573
1573
|
@classmethod
|
1574
1574
|
def rRNA_25S(cls):
|
1575
1575
|
"""A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes. (cls, RSC:cb)
|
1576
|
-
(SO_0001002)
|
1576
|
+
(http://purl.obolibrary.org/obo/SO_0001002)
|
1577
1577
|
"""
|
1578
|
-
return _namespace_SOFA('SO_0001002')
|
1578
|
+
return cls._namespace_SOFA('SO_0001002')
|
1579
1579
|
|
1580
1580
|
@classmethod
|
1581
1581
|
def copy_number_variation(cls):
|
1582
1582
|
"""A variation that increases or decreases the copy number of a given region. (cls, SO:ke)
|
1583
|
-
(SO_0001019)
|
1583
|
+
(http://purl.obolibrary.org/obo/SO_0001019)
|
1584
1584
|
"""
|
1585
|
-
return _namespace_SOFA('SO_0001019')
|
1585
|
+
return cls._namespace_SOFA('SO_0001019')
|
1586
1586
|
|
1587
1587
|
@classmethod
|
1588
1588
|
def mobile_genetic_element(cls):
|
1589
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)
|
1590
|
-
(SO_0001037)
|
1590
|
+
(http://purl.obolibrary.org/obo/SO_0001037)
|
1591
1591
|
"""
|
1592
|
-
return _namespace_SOFA('SO_0001037')
|
1592
|
+
return cls._namespace_SOFA('SO_0001037')
|
1593
1593
|
|
1594
1594
|
@classmethod
|
1595
1595
|
def integrated_mobile_genetic_element(cls):
|
1596
1596
|
"""An MGE that is integrated into the host chromosome. (cls, SO:ke)
|
1597
|
-
(SO_0001039)
|
1597
|
+
(http://purl.obolibrary.org/obo/SO_0001039)
|
1598
1598
|
"""
|
1599
|
-
return _namespace_SOFA('SO_0001039')
|
1599
|
+
return cls._namespace_SOFA('SO_0001039')
|
1600
1600
|
|
1601
1601
|
@classmethod
|
1602
1602
|
def transcriptional_cis_regulatory_region(cls):
|
1603
1603
|
"""A regulatory_region that modulates the transcription of a gene or genes. (cls, SO:regcreative)
|
1604
|
-
(SO_0001055)
|
1604
|
+
(http://purl.obolibrary.org/obo/SO_0001055)
|
1605
1605
|
"""
|
1606
|
-
return _namespace_SOFA('SO_0001055')
|
1606
|
+
return cls._namespace_SOFA('SO_0001055')
|
1607
1607
|
|
1608
1608
|
@classmethod
|
1609
1609
|
def splicing_regulatory_region(cls):
|
1610
1610
|
"""A regulatory_region that modulates splicing. (cls, SO:ke)
|
1611
|
-
(SO_0001056)
|
1611
|
+
(http://purl.obolibrary.org/obo/SO_0001056)
|
1612
1612
|
"""
|
1613
|
-
return _namespace_SOFA('SO_0001056')
|
1613
|
+
return cls._namespace_SOFA('SO_0001056')
|
1614
1614
|
|
1615
1615
|
@classmethod
|
1616
1616
|
def sequence_alteration(cls):
|
1617
1617
|
"""A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. (cls, SO:ke)
|
1618
|
-
(SO_0001059)
|
1618
|
+
(http://purl.obolibrary.org/obo/SO_0001059)
|
1619
1619
|
"""
|
1620
|
-
return _namespace_SOFA('SO_0001059')
|
1620
|
+
return cls._namespace_SOFA('SO_0001059')
|
1621
1621
|
|
1622
1622
|
@classmethod
|
1623
1623
|
def immature_peptide_region(cls):
|
1624
1624
|
"""An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs. (cls, EBIBS:GAR)
|
1625
|
-
(SO_0001063)
|
1625
|
+
(http://purl.obolibrary.org/obo/SO_0001063)
|
1626
1626
|
"""
|
1627
|
-
return _namespace_SOFA('SO_0001063')
|
1627
|
+
return cls._namespace_SOFA('SO_0001063')
|
1628
1628
|
|
1629
1629
|
@classmethod
|
1630
1630
|
def noncoding_region_of_exon(cls):
|
1631
1631
|
"""The maximal intersection of exon and UTR. (cls, SO:ke)
|
1632
|
-
(SO_0001214)
|
1632
|
+
(http://purl.obolibrary.org/obo/SO_0001214)
|
1633
1633
|
"""
|
1634
|
-
return _namespace_SOFA('SO_0001214')
|
1634
|
+
return cls._namespace_SOFA('SO_0001214')
|
1635
1635
|
|
1636
1636
|
@classmethod
|
1637
1637
|
def coding_region_of_exon(cls):
|
1638
1638
|
"""The region of an exon that encodes for protein sequence. (cls, SO:ke)
|
1639
|
-
(SO_0001215)
|
1639
|
+
(http://purl.obolibrary.org/obo/SO_0001215)
|
1640
1640
|
"""
|
1641
|
-
return _namespace_SOFA('SO_0001215')
|
1641
|
+
return cls._namespace_SOFA('SO_0001215')
|
1642
1642
|
|
1643
1643
|
@classmethod
|
1644
1644
|
def replicon(cls):
|
1645
1645
|
"""A region containing at least one unique origin of replication and a unique termination site. (cls, ISBN:0716719207)
|
1646
|
-
(SO_0001235)
|
1646
|
+
(http://purl.obolibrary.org/obo/SO_0001235)
|
1647
1647
|
"""
|
1648
|
-
return _namespace_SOFA('SO_0001235')
|
1648
|
+
return cls._namespace_SOFA('SO_0001235')
|
1649
1649
|
|
1650
1650
|
@classmethod
|
1651
1651
|
def base(cls):
|
1652
1652
|
"""A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. (cls, SO:ke)
|
1653
|
-
(SO_0001236)
|
1653
|
+
(http://purl.obolibrary.org/obo/SO_0001236)
|
1654
1654
|
"""
|
1655
|
-
return _namespace_SOFA('SO_0001236')
|
1655
|
+
return cls._namespace_SOFA('SO_0001236')
|
1656
1656
|
|
1657
1657
|
@classmethod
|
1658
1658
|
def assembly(cls):
|
1659
1659
|
"""A region of the genome of known length that is composed by ordering and aligning two or more different regions. (cls, SO:ke)
|
1660
|
-
(SO_0001248)
|
1660
|
+
(http://purl.obolibrary.org/obo/SO_0001248)
|
1661
1661
|
"""
|
1662
|
-
return _namespace_SOFA('SO_0001248')
|
1662
|
+
return cls._namespace_SOFA('SO_0001248')
|
1663
1663
|
|
1664
1664
|
@classmethod
|
1665
1665
|
def biomaterial_region(cls):
|
1666
1666
|
"""A region which is intended for use in an experiment. (cls, SO:cb)
|
1667
|
-
(SO_0001409)
|
1667
|
+
(http://purl.obolibrary.org/obo/SO_0001409)
|
1668
1668
|
"""
|
1669
|
-
return _namespace_SOFA('SO_0001409')
|
1669
|
+
return cls._namespace_SOFA('SO_0001409')
|
1670
1670
|
|
1671
1671
|
@classmethod
|
1672
1672
|
def experimental_feature(cls):
|
1673
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)
|
1674
|
-
(SO_0001410)
|
1674
|
+
(http://purl.obolibrary.org/obo/SO_0001410)
|
1675
1675
|
"""
|
1676
|
-
return _namespace_SOFA('SO_0001410')
|
1676
|
+
return cls._namespace_SOFA('SO_0001410')
|
1677
1677
|
|
1678
1678
|
@classmethod
|
1679
1679
|
def biological_region(cls):
|
1680
1680
|
"""A region defined by its disposition to be involved in a biological process. (cls, SO:cb)
|
1681
|
-
(SO_0001411)
|
1681
|
+
(http://purl.obolibrary.org/obo/SO_0001411)
|
1682
1682
|
"""
|
1683
|
-
return _namespace_SOFA('SO_0001411')
|
1683
|
+
return cls._namespace_SOFA('SO_0001411')
|
1684
1684
|
|
1685
1685
|
@classmethod
|
1686
1686
|
def topologically_defined_region(cls):
|
1687
1687
|
"""A region that is defined according to its relations with other regions within the same sequence. (cls, SO:cb)
|
1688
|
-
(SO_0001412)
|
1688
|
+
(http://purl.obolibrary.org/obo/SO_0001412)
|
1689
1689
|
"""
|
1690
|
-
return _namespace_SOFA('SO_0001412')
|
1690
|
+
return cls._namespace_SOFA('SO_0001412')
|
1691
1691
|
|
1692
1692
|
@classmethod
|
1693
1693
|
def cis_splice_site(cls):
|
1694
1694
|
"""Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron. (cls, SO:cjm, SO:ke)
|
1695
|
-
(SO_0001419)
|
1695
|
+
(http://purl.obolibrary.org/obo/SO_0001419)
|
1696
1696
|
"""
|
1697
|
-
return _namespace_SOFA('SO_0001419')
|
1697
|
+
return cls._namespace_SOFA('SO_0001419')
|
1698
1698
|
|
1699
1699
|
@classmethod
|
1700
1700
|
def trans_splice_site(cls):
|
1701
1701
|
"""Primary transcript region bordering trans-splice junction. (cls, SO:ke)
|
1702
|
-
(SO_0001420)
|
1702
|
+
(http://purl.obolibrary.org/obo/SO_0001420)
|
1703
1703
|
"""
|
1704
|
-
return _namespace_SOFA('SO_0001420')
|
1704
|
+
return cls._namespace_SOFA('SO_0001420')
|
1705
1705
|
|
1706
1706
|
@classmethod
|
1707
1707
|
def SNV(cls):
|
1708
1708
|
"""SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist. (cls, SO:bm)
|
1709
|
-
(SO_0001483)
|
1709
|
+
(http://purl.obolibrary.org/obo/SO_0001483)
|
1710
1710
|
"""
|
1711
|
-
return _namespace_SOFA('SO_0001483')
|
1711
|
+
return cls._namespace_SOFA('SO_0001483')
|
1712
1712
|
|
1713
1713
|
@classmethod
|
1714
1714
|
def peptide_localization_signal(cls):
|
1715
1715
|
"""A region of peptide sequence used to target the polypeptide molecule to a specific organelle. (cls, SO:ke)
|
1716
|
-
(SO_0001527)
|
1716
|
+
(http://purl.obolibrary.org/obo/SO_0001527)
|
1717
1717
|
"""
|
1718
|
-
return _namespace_SOFA('SO_0001527')
|
1718
|
+
return cls._namespace_SOFA('SO_0001527')
|
1719
1719
|
|
1720
1720
|
@classmethod
|
1721
1721
|
def kozak_sequence(cls):
|
1722
1722
|
"""A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence. (cls, SO:ke)
|
1723
|
-
(SO_0001647)
|
1723
|
+
(http://purl.obolibrary.org/obo/SO_0001647)
|
1724
1724
|
"""
|
1725
|
-
return _namespace_SOFA('SO_0001647')
|
1725
|
+
return cls._namespace_SOFA('SO_0001647')
|
1726
1726
|
|
1727
1727
|
@classmethod
|
1728
1728
|
def nucleotide_to_protein_binding_site(cls):
|
1729
1729
|
"""A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues. (cls, SO:ke)
|
1730
|
-
(SO_0001654)
|
1730
|
+
(http://purl.obolibrary.org/obo/SO_0001654)
|
1731
1731
|
"""
|
1732
|
-
return _namespace_SOFA('SO_0001654')
|
1732
|
+
return cls._namespace_SOFA('SO_0001654')
|
1733
1733
|
|
1734
1734
|
@classmethod
|
1735
1735
|
def transcription_regulatory_region(cls):
|
1736
1736
|
"""A regulatory region that is involved in the control of the process of transcription. (cls, SO:ke)
|
1737
|
-
(SO_0001679)
|
1737
|
+
(http://purl.obolibrary.org/obo/SO_0001679)
|
1738
1738
|
"""
|
1739
|
-
return _namespace_SOFA('SO_0001679')
|
1739
|
+
return cls._namespace_SOFA('SO_0001679')
|
1740
1740
|
|
1741
1741
|
@classmethod
|
1742
1742
|
def sequence_motif(cls):
|
1743
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)
|
1744
|
-
(SO_0001683)
|
1744
|
+
(http://purl.obolibrary.org/obo/SO_0001683)
|
1745
1745
|
"""
|
1746
|
-
return _namespace_SOFA('SO_0001683')
|
1746
|
+
return cls._namespace_SOFA('SO_0001683')
|
1747
1747
|
|
1748
1748
|
@classmethod
|
1749
1749
|
def epigenetically_modified_region(cls):
|
1750
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)
|
1751
|
-
(SO_0001720)
|
1751
|
+
(http://purl.obolibrary.org/obo/SO_0001720)
|
1752
1752
|
"""
|
1753
|
-
return _namespace_SOFA('SO_0001720')
|
1753
|
+
return cls._namespace_SOFA('SO_0001720')
|
1754
1754
|
|
1755
1755
|
@classmethod
|
1756
1756
|
def paired_end_fragment(cls):
|
1757
1757
|
"""An assembly region that has been sequenced from both ends resulting in a read_pair (cls, mate_pair). (SO:ke)
|
1758
|
-
(SO_0001790)
|
1758
|
+
(http://purl.obolibrary.org/obo/SO_0001790)
|
1759
1759
|
"""
|
1760
|
-
return _namespace_SOFA('SO_0001790')
|
1760
|
+
return cls._namespace_SOFA('SO_0001790')
|
1761
1761
|
|
1762
1762
|
@classmethod
|
1763
1763
|
def regulatory_region(cls):
|
1764
1764
|
"""A region of sequence that is involved in the control of a biological process. (cls, SO:ke)
|
1765
|
-
(SO_0005836)
|
1765
|
+
(http://purl.obolibrary.org/obo/SO_0005836)
|
1766
1766
|
"""
|
1767
|
-
return _namespace_SOFA('SO_0005836')
|
1767
|
+
return cls._namespace_SOFA('SO_0005836')
|
1768
1768
|
|
1769
1769
|
@classmethod
|
1770
1770
|
def gene_group(cls):
|
1771
1771
|
"""A collection of related genes. (cls, SO:ma)
|
1772
|
-
(SO_0005855)
|
1772
|
+
(http://purl.obolibrary.org/obo/SO_0005855)
|
1773
1773
|
"""
|
1774
|
-
return _namespace_SOFA('SO_0005855')
|
1774
|
+
return cls._namespace_SOFA('SO_0005855')
|
1775
1775
|
|
1776
1776
|
@classmethod
|
1777
1777
|
def cleaved_peptide_region(cls):
|
1778
1778
|
"""The cleaved_peptide_regon is the a region of peptide sequence that is cleaved during maturation. (cls, EBIBS:GAR)
|
1779
|
-
(SO_0100011)
|
1779
|
+
(http://purl.obolibrary.org/obo/SO_0100011)
|
1780
1780
|
"""
|
1781
|
-
return _namespace_SOFA('SO_0100011')
|
1781
|
+
return cls._namespace_SOFA('SO_0100011')
|
1782
1782
|
|
1783
1783
|
@classmethod
|
1784
1784
|
def substitution(cls):
|
1785
1785
|
"""A sequence alteration where the length of the change in the variant is the same as that of the reference. (cls, SO:ke)
|
1786
|
-
(SO_1000002)
|
1786
|
+
(http://purl.obolibrary.org/obo/SO_1000002)
|
1787
1787
|
"""
|
1788
|
-
return _namespace_SOFA('SO_1000002')
|
1788
|
+
return cls._namespace_SOFA('SO_1000002')
|
1789
1789
|
|
1790
1790
|
@classmethod
|
1791
1791
|
def complex_substitution(cls):
|
1792
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)
|
1793
|
-
(SO_1000005)
|
1793
|
+
(http://purl.obolibrary.org/obo/SO_1000005)
|
1794
1794
|
"""
|
1795
|
-
return _namespace_SOFA('SO_1000005')
|
1795
|
+
return cls._namespace_SOFA('SO_1000005')
|
1796
1796
|
|
1797
1797
|
@classmethod
|
1798
1798
|
def point_mutation(cls):
|
1799
1799
|
"""A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. (cls, SO:immuno_workshop)
|
1800
|
-
(SO_1000008)
|
1800
|
+
(http://purl.obolibrary.org/obo/SO_1000008)
|
1801
1801
|
"""
|
1802
|
-
return _namespace_SOFA('SO_1000008')
|
1802
|
+
return cls._namespace_SOFA('SO_1000008')
|
1803
1803
|
|
1804
1804
|
@classmethod
|
1805
1805
|
def inversion(cls):
|
1806
1806
|
"""A continuous nucleotide sequence is inverted in the same position. (cls, EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html)
|
1807
|
-
(SO_1000036)
|
1807
|
+
(http://purl.obolibrary.org/obo/SO_1000036)
|
1808
1808
|
"""
|
1809
|
-
return _namespace_SOFA('SO_1000036')
|
1809
|
+
return cls._namespace_SOFA('SO_1000036')
|
1810
1810
|
|
1811
1811
|
@classmethod
|
1812
1812
|
def regulon(cls):
|
1813
1813
|
"""A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal. (cls, ISBN:0198506732)
|
1814
|
-
(SO_1001284)
|
1814
|
+
(http://purl.obolibrary.org/obo/SO_1001284)
|
1815
1815
|
"""
|
1816
|
-
return _namespace_SOFA('SO_1001284')
|
1816
|
+
return cls._namespace_SOFA('SO_1001284')
|
1817
1817
|
|
1818
1818
|
@classmethod
|
1819
1819
|
def databank_entry(cls):
|
1820
1820
|
"""The sequence referred to by an entry in a databank such as Genbank or SwissProt. (cls, SO:ke)
|
1821
|
-
(SO_2000061)
|
1821
|
+
(http://purl.obolibrary.org/obo/SO_2000061)
|
1822
1822
|
"""
|
1823
|
-
return _namespace_SOFA('SO_2000061')
|
1823
|
+
return cls._namespace_SOFA('SO_2000061')
|
1824
1824
|
|
1825
1825
|
@classmethod
|
1826
1826
|
def is_object_property(cls, uri):
|
@@ -1828,39 +1828,39 @@ class SOFA:
|
|
1828
1828
|
|
1829
1829
|
uri -- URI that is tested for being an object property
|
1830
1830
|
"""
|
1831
|
-
if uri == _namespace_SOFA('http_//purl.org/obo/owl:adjacent_to'):
|
1831
|
+
if uri == cls._namespace_SOFA('http_//purl.org/obo/owl:adjacent_to'):
|
1832
1832
|
return True
|
1833
|
-
if uri == _namespace_SOFA('http_//purl.org/obo/owl:complete_evidence_for_feature'):
|
1833
|
+
if uri == cls._namespace_SOFA('http_//purl.org/obo/owl:complete_evidence_for_feature'):
|
1834
1834
|
return True
|
1835
|
-
if uri == _namespace_SOFA('http_//purl.org/obo/owl:contained_by'):
|
1835
|
+
if uri == cls._namespace_SOFA('http_//purl.org/obo/owl:contained_by'):
|
1836
1836
|
return True
|
1837
|
-
if uri == _namespace_SOFA('http_//purl.org/obo/owl:contains'):
|
1837
|
+
if uri == cls._namespace_SOFA('http_//purl.org/obo/owl:contains'):
|
1838
1838
|
return True
|
1839
|
-
if uri == _namespace_SOFA('http_//purl.org/obo/owl:derives_from'):
|
1839
|
+
if uri == cls._namespace_SOFA('http_//purl.org/obo/owl:derives_from'):
|
1840
1840
|
return True
|
1841
|
-
if uri == _namespace_SOFA('http_//purl.org/obo/owl:evidence_for_feature'):
|
1841
|
+
if uri == cls._namespace_SOFA('http_//purl.org/obo/owl:evidence_for_feature'):
|
1842
1842
|
return True
|
1843
|
-
if uri == _namespace_SOFA('http_//purl.org/obo/owl:has_integral_part'):
|
1843
|
+
if uri == cls._namespace_SOFA('http_//purl.org/obo/owl:has_integral_part'):
|
1844
1844
|
return True
|
1845
|
-
if uri == _namespace_SOFA('http_//purl.org/obo/owl:has_part'):
|
1845
|
+
if uri == cls._namespace_SOFA('http_//purl.org/obo/owl:has_part'):
|
1846
1846
|
return True
|
1847
|
-
if uri == _namespace_SOFA('http_//purl.org/obo/owl:homologous_to'):
|
1847
|
+
if uri == cls._namespace_SOFA('http_//purl.org/obo/owl:homologous_to'):
|
1848
1848
|
return True
|
1849
|
-
if uri == _namespace_SOFA('http_//purl.org/obo/owl:integral_part_of'):
|
1849
|
+
if uri == cls._namespace_SOFA('http_//purl.org/obo/owl:integral_part_of'):
|
1850
1850
|
return True
|
1851
|
-
if uri == _namespace_SOFA('http_//purl.org/obo/owl:member_of'):
|
1851
|
+
if uri == cls._namespace_SOFA('http_//purl.org/obo/owl:member_of'):
|
1852
1852
|
return True
|
1853
|
-
if uri == _namespace_SOFA('http_//purl.org/obo/owl:non_functional_homolog_of'):
|
1853
|
+
if uri == cls._namespace_SOFA('http_//purl.org/obo/owl:non_functional_homolog_of'):
|
1854
1854
|
return True
|
1855
|
-
if uri == _namespace_SOFA('http_//purl.org/obo/owl:orthologous_to'):
|
1855
|
+
if uri == cls._namespace_SOFA('http_//purl.org/obo/owl:orthologous_to'):
|
1856
1856
|
return True
|
1857
|
-
if uri == _namespace_SOFA('http_//purl.org/obo/owl:paralogous_to'):
|
1857
|
+
if uri == cls._namespace_SOFA('http_//purl.org/obo/owl:paralogous_to'):
|
1858
1858
|
return True
|
1859
|
-
if uri == _namespace_SOFA('http_//purl.org/obo/owl:part_of'):
|
1859
|
+
if uri == cls._namespace_SOFA('http_//purl.org/obo/owl:part_of'):
|
1860
1860
|
return True
|
1861
|
-
if uri == _namespace_SOFA('http_//purl.org/obo/owl:partial_evidence_for_feature'):
|
1861
|
+
if uri == cls._namespace_SOFA('http_//purl.org/obo/owl:partial_evidence_for_feature'):
|
1862
1862
|
return True
|
1863
|
-
if uri == _namespace_SOFA('http_//purl.org/obo/owl:similar_to'):
|
1863
|
+
if uri == cls._namespace_SOFA('http_//purl.org/obo/owl:similar_to'):
|
1864
1864
|
return True
|
1865
1865
|
return False
|
1866
1866
|
|
@@ -1878,509 +1878,509 @@ class SOFA:
|
|
1878
1878
|
|
1879
1879
|
uri -- URI that is tested for being a class
|
1880
1880
|
"""
|
1881
|
-
if uri == _namespace_SOFA('SO_0000000'):
|
1881
|
+
if uri == cls._namespace_SOFA('SO_0000000'):
|
1882
1882
|
return True
|
1883
|
-
if uri == _namespace_SOFA('SO_0000001'):
|
1883
|
+
if uri == cls._namespace_SOFA('SO_0000001'):
|
1884
1884
|
return True
|
1885
|
-
if uri == _namespace_SOFA('SO_0000004'):
|
1885
|
+
if uri == cls._namespace_SOFA('SO_0000004'):
|
1886
1886
|
return True
|
1887
|
-
if uri == _namespace_SOFA('SO_0000005'):
|
1887
|
+
if uri == cls._namespace_SOFA('SO_0000005'):
|
1888
1888
|
return True
|
1889
|
-
if uri == _namespace_SOFA('SO_0000006'):
|
1889
|
+
if uri == cls._namespace_SOFA('SO_0000006'):
|
1890
1890
|
return True
|
1891
|
-
if uri == _namespace_SOFA('SO_0000007'):
|
1891
|
+
if uri == cls._namespace_SOFA('SO_0000007'):
|
1892
1892
|
return True
|
1893
|
-
if uri == _namespace_SOFA('SO_0000013'):
|
1893
|
+
if uri == cls._namespace_SOFA('SO_0000013'):
|
1894
1894
|
return True
|
1895
|
-
if uri == _namespace_SOFA('SO_0000038'):
|
1895
|
+
if uri == cls._namespace_SOFA('SO_0000038'):
|
1896
1896
|
return True
|
1897
|
-
if uri == _namespace_SOFA('SO_0000039'):
|
1897
|
+
if uri == cls._namespace_SOFA('SO_0000039'):
|
1898
1898
|
return True
|
1899
|
-
if uri == _namespace_SOFA('SO_0000050'):
|
1899
|
+
if uri == cls._namespace_SOFA('SO_0000050'):
|
1900
1900
|
return True
|
1901
|
-
if uri == _namespace_SOFA('SO_0000057'):
|
1901
|
+
if uri == cls._namespace_SOFA('SO_0000057'):
|
1902
1902
|
return True
|
1903
|
-
if uri == _namespace_SOFA('SO_0000059'):
|
1903
|
+
if uri == cls._namespace_SOFA('SO_0000059'):
|
1904
1904
|
return True
|
1905
|
-
if uri == _namespace_SOFA('SO_0000101'):
|
1905
|
+
if uri == cls._namespace_SOFA('SO_0000101'):
|
1906
1906
|
return True
|
1907
|
-
if uri == _namespace_SOFA('SO_0000102'):
|
1907
|
+
if uri == cls._namespace_SOFA('SO_0000102'):
|
1908
1908
|
return True
|
1909
|
-
if uri == _namespace_SOFA('SO_0000103'):
|
1909
|
+
if uri == cls._namespace_SOFA('SO_0000103'):
|
1910
1910
|
return True
|
1911
|
-
if uri == _namespace_SOFA('SO_0000104'):
|
1911
|
+
if uri == cls._namespace_SOFA('SO_0000104'):
|
1912
1912
|
return True
|
1913
|
-
if uri == _namespace_SOFA('SO_0000109'):
|
1913
|
+
if uri == cls._namespace_SOFA('SO_0000109'):
|
1914
1914
|
return True
|
1915
|
-
if uri == _namespace_SOFA('SO_0000110'):
|
1915
|
+
if uri == cls._namespace_SOFA('SO_0000110'):
|
1916
1916
|
return True
|
1917
|
-
if uri == _namespace_SOFA('SO_0000112'):
|
1917
|
+
if uri == cls._namespace_SOFA('SO_0000112'):
|
1918
1918
|
return True
|
1919
|
-
if uri == _namespace_SOFA('SO_0000113'):
|
1919
|
+
if uri == cls._namespace_SOFA('SO_0000113'):
|
1920
1920
|
return True
|
1921
|
-
if uri == _namespace_SOFA('SO_0000114'):
|
1921
|
+
if uri == cls._namespace_SOFA('SO_0000114'):
|
1922
1922
|
return True
|
1923
|
-
if uri == _namespace_SOFA('SO_0000120'):
|
1923
|
+
if uri == cls._namespace_SOFA('SO_0000120'):
|
1924
1924
|
return True
|
1925
|
-
if uri == _namespace_SOFA('SO_0000139'):
|
1925
|
+
if uri == cls._namespace_SOFA('SO_0000139'):
|
1926
1926
|
return True
|
1927
|
-
if uri == _namespace_SOFA('SO_0000140'):
|
1927
|
+
if uri == cls._namespace_SOFA('SO_0000140'):
|
1928
1928
|
return True
|
1929
|
-
if uri == _namespace_SOFA('SO_0000141'):
|
1929
|
+
if uri == cls._namespace_SOFA('SO_0000141'):
|
1930
1930
|
return True
|
1931
|
-
if uri == _namespace_SOFA('SO_0000143'):
|
1931
|
+
if uri == cls._namespace_SOFA('SO_0000143'):
|
1932
1932
|
return True
|
1933
|
-
if uri == _namespace_SOFA('SO_0000147'):
|
1933
|
+
if uri == cls._namespace_SOFA('SO_0000147'):
|
1934
1934
|
return True
|
1935
|
-
if uri == _namespace_SOFA('SO_0000148'):
|
1935
|
+
if uri == cls._namespace_SOFA('SO_0000148'):
|
1936
1936
|
return True
|
1937
|
-
if uri == _namespace_SOFA('SO_0000149'):
|
1937
|
+
if uri == cls._namespace_SOFA('SO_0000149'):
|
1938
1938
|
return True
|
1939
|
-
if uri == _namespace_SOFA('SO_0000150'):
|
1939
|
+
if uri == cls._namespace_SOFA('SO_0000150'):
|
1940
1940
|
return True
|
1941
|
-
if uri == _namespace_SOFA('SO_0000151'):
|
1941
|
+
if uri == cls._namespace_SOFA('SO_0000151'):
|
1942
1942
|
return True
|
1943
|
-
if uri == _namespace_SOFA('SO_0000159'):
|
1943
|
+
if uri == cls._namespace_SOFA('SO_0000159'):
|
1944
1944
|
return True
|
1945
|
-
if uri == _namespace_SOFA('SO_0000161'):
|
1945
|
+
if uri == cls._namespace_SOFA('SO_0000161'):
|
1946
1946
|
return True
|
1947
|
-
if uri == _namespace_SOFA('SO_0000162'):
|
1947
|
+
if uri == cls._namespace_SOFA('SO_0000162'):
|
1948
1948
|
return True
|
1949
|
-
if uri == _namespace_SOFA('SO_0000163'):
|
1949
|
+
if uri == cls._namespace_SOFA('SO_0000163'):
|
1950
1950
|
return True
|
1951
|
-
if uri == _namespace_SOFA('SO_0000164'):
|
1951
|
+
if uri == cls._namespace_SOFA('SO_0000164'):
|
1952
1952
|
return True
|
1953
|
-
if uri == _namespace_SOFA('SO_0000165'):
|
1953
|
+
if uri == cls._namespace_SOFA('SO_0000165'):
|
1954
1954
|
return True
|
1955
|
-
if uri == _namespace_SOFA('SO_0000167'):
|
1955
|
+
if uri == cls._namespace_SOFA('SO_0000167'):
|
1956
1956
|
return True
|
1957
|
-
if uri == _namespace_SOFA('SO_0000177'):
|
1957
|
+
if uri == cls._namespace_SOFA('SO_0000177'):
|
1958
1958
|
return True
|
1959
|
-
if uri == _namespace_SOFA('SO_0000178'):
|
1959
|
+
if uri == cls._namespace_SOFA('SO_0000178'):
|
1960
1960
|
return True
|
1961
|
-
if uri == _namespace_SOFA('SO_0000179'):
|
1961
|
+
if uri == cls._namespace_SOFA('SO_0000179'):
|
1962
1962
|
return True
|
1963
|
-
if uri == _namespace_SOFA('SO_0000181'):
|
1963
|
+
if uri == cls._namespace_SOFA('SO_0000181'):
|
1964
1964
|
return True
|
1965
|
-
if uri == _namespace_SOFA('SO_0000183'):
|
1965
|
+
if uri == cls._namespace_SOFA('SO_0000183'):
|
1966
1966
|
return True
|
1967
|
-
if uri == _namespace_SOFA('SO_0000185'):
|
1967
|
+
if uri == cls._namespace_SOFA('SO_0000185'):
|
1968
1968
|
return True
|
1969
|
-
if uri == _namespace_SOFA('SO_0000187'):
|
1969
|
+
if uri == cls._namespace_SOFA('SO_0000187'):
|
1970
1970
|
return True
|
1971
|
-
if uri == _namespace_SOFA('SO_0000188'):
|
1971
|
+
if uri == cls._namespace_SOFA('SO_0000188'):
|
1972
1972
|
return True
|
1973
|
-
if uri == _namespace_SOFA('SO_0000193'):
|
1973
|
+
if uri == cls._namespace_SOFA('SO_0000193'):
|
1974
1974
|
return True
|
1975
|
-
if uri == _namespace_SOFA('SO_0000195'):
|
1975
|
+
if uri == cls._namespace_SOFA('SO_0000195'):
|
1976
1976
|
return True
|
1977
|
-
if uri == _namespace_SOFA('SO_0000196'):
|
1977
|
+
if uri == cls._namespace_SOFA('SO_0000196'):
|
1978
1978
|
return True
|
1979
|
-
if uri == _namespace_SOFA('SO_0000197'):
|
1979
|
+
if uri == cls._namespace_SOFA('SO_0000197'):
|
1980
1980
|
return True
|
1981
|
-
if uri == _namespace_SOFA('SO_0000198'):
|
1981
|
+
if uri == cls._namespace_SOFA('SO_0000198'):
|
1982
1982
|
return True
|
1983
|
-
if uri == _namespace_SOFA('SO_0000200'):
|
1983
|
+
if uri == cls._namespace_SOFA('SO_0000200'):
|
1984
1984
|
return True
|
1985
|
-
if uri == _namespace_SOFA('SO_0000203'):
|
1985
|
+
if uri == cls._namespace_SOFA('SO_0000203'):
|
1986
1986
|
return True
|
1987
|
-
if uri == _namespace_SOFA('SO_0000204'):
|
1987
|
+
if uri == cls._namespace_SOFA('SO_0000204'):
|
1988
1988
|
return True
|
1989
|
-
if uri == _namespace_SOFA('SO_0000205'):
|
1989
|
+
if uri == cls._namespace_SOFA('SO_0000205'):
|
1990
1990
|
return True
|
1991
|
-
if uri == _namespace_SOFA('SO_0000209'):
|
1991
|
+
if uri == cls._namespace_SOFA('SO_0000209'):
|
1992
1992
|
return True
|
1993
|
-
if uri == _namespace_SOFA('SO_0000233'):
|
1993
|
+
if uri == cls._namespace_SOFA('SO_0000233'):
|
1994
1994
|
return True
|
1995
|
-
if uri == _namespace_SOFA('SO_0000234'):
|
1995
|
+
if uri == cls._namespace_SOFA('SO_0000234'):
|
1996
1996
|
return True
|
1997
|
-
if uri == _namespace_SOFA('SO_0000235'):
|
1997
|
+
if uri == cls._namespace_SOFA('SO_0000235'):
|
1998
1998
|
return True
|
1999
|
-
if uri == _namespace_SOFA('SO_0000236'):
|
1999
|
+
if uri == cls._namespace_SOFA('SO_0000236'):
|
2000
2000
|
return True
|
2001
|
-
if uri == _namespace_SOFA('SO_0000239'):
|
2001
|
+
if uri == cls._namespace_SOFA('SO_0000239'):
|
2002
2002
|
return True
|
2003
|
-
if uri == _namespace_SOFA('SO_0000252'):
|
2003
|
+
if uri == cls._namespace_SOFA('SO_0000252'):
|
2004
2004
|
return True
|
2005
|
-
if uri == _namespace_SOFA('SO_0000253'):
|
2005
|
+
if uri == cls._namespace_SOFA('SO_0000253'):
|
2006
2006
|
return True
|
2007
|
-
if uri == _namespace_SOFA('SO_0000274'):
|
2007
|
+
if uri == cls._namespace_SOFA('SO_0000274'):
|
2008
2008
|
return True
|
2009
|
-
if uri == _namespace_SOFA('SO_0000275'):
|
2009
|
+
if uri == cls._namespace_SOFA('SO_0000275'):
|
2010
2010
|
return True
|
2011
|
-
if uri == _namespace_SOFA('SO_0000276'):
|
2011
|
+
if uri == cls._namespace_SOFA('SO_0000276'):
|
2012
2012
|
return True
|
2013
|
-
if uri == _namespace_SOFA('SO_0000289'):
|
2013
|
+
if uri == cls._namespace_SOFA('SO_0000289'):
|
2014
2014
|
return True
|
2015
|
-
if uri == _namespace_SOFA('SO_0000294'):
|
2015
|
+
if uri == cls._namespace_SOFA('SO_0000294'):
|
2016
2016
|
return True
|
2017
|
-
if uri == _namespace_SOFA('SO_0000296'):
|
2017
|
+
if uri == cls._namespace_SOFA('SO_0000296'):
|
2018
2018
|
return True
|
2019
|
-
if uri == _namespace_SOFA('SO_0000303'):
|
2019
|
+
if uri == cls._namespace_SOFA('SO_0000303'):
|
2020
2020
|
return True
|
2021
|
-
if uri == _namespace_SOFA('SO_0000305'):
|
2021
|
+
if uri == cls._namespace_SOFA('SO_0000305'):
|
2022
2022
|
return True
|
2023
|
-
if uri == _namespace_SOFA('SO_0000306'):
|
2023
|
+
if uri == cls._namespace_SOFA('SO_0000306'):
|
2024
2024
|
return True
|
2025
|
-
if uri == _namespace_SOFA('SO_0000307'):
|
2025
|
+
if uri == cls._namespace_SOFA('SO_0000307'):
|
2026
2026
|
return True
|
2027
|
-
if uri == _namespace_SOFA('SO_0000314'):
|
2027
|
+
if uri == cls._namespace_SOFA('SO_0000314'):
|
2028
2028
|
return True
|
2029
|
-
if uri == _namespace_SOFA('SO_0000315'):
|
2029
|
+
if uri == cls._namespace_SOFA('SO_0000315'):
|
2030
2030
|
return True
|
2031
|
-
if uri == _namespace_SOFA('SO_0000316'):
|
2031
|
+
if uri == cls._namespace_SOFA('SO_0000316'):
|
2032
2032
|
return True
|
2033
|
-
if uri == _namespace_SOFA('SO_0000318'):
|
2033
|
+
if uri == cls._namespace_SOFA('SO_0000318'):
|
2034
2034
|
return True
|
2035
|
-
if uri == _namespace_SOFA('SO_0000319'):
|
2035
|
+
if uri == cls._namespace_SOFA('SO_0000319'):
|
2036
2036
|
return True
|
2037
|
-
if uri == _namespace_SOFA('SO_0000324'):
|
2037
|
+
if uri == cls._namespace_SOFA('SO_0000324'):
|
2038
2038
|
return True
|
2039
|
-
if uri == _namespace_SOFA('SO_0000325'):
|
2039
|
+
if uri == cls._namespace_SOFA('SO_0000325'):
|
2040
2040
|
return True
|
2041
|
-
if uri == _namespace_SOFA('SO_0000326'):
|
2041
|
+
if uri == cls._namespace_SOFA('SO_0000326'):
|
2042
2042
|
return True
|
2043
|
-
if uri == _namespace_SOFA('SO_0000330'):
|
2043
|
+
if uri == cls._namespace_SOFA('SO_0000330'):
|
2044
2044
|
return True
|
2045
|
-
if uri == _namespace_SOFA('SO_0000331'):
|
2045
|
+
if uri == cls._namespace_SOFA('SO_0000331'):
|
2046
2046
|
return True
|
2047
|
-
if uri == _namespace_SOFA('SO_0000332'):
|
2047
|
+
if uri == cls._namespace_SOFA('SO_0000332'):
|
2048
2048
|
return True
|
2049
|
-
if uri == _namespace_SOFA('SO_0000333'):
|
2049
|
+
if uri == cls._namespace_SOFA('SO_0000333'):
|
2050
2050
|
return True
|
2051
|
-
if uri == _namespace_SOFA('SO_0000334'):
|
2051
|
+
if uri == cls._namespace_SOFA('SO_0000334'):
|
2052
2052
|
return True
|
2053
|
-
if uri == _namespace_SOFA('SO_0000336'):
|
2053
|
+
if uri == cls._namespace_SOFA('SO_0000336'):
|
2054
2054
|
return True
|
2055
|
-
if uri == _namespace_SOFA('SO_0000337'):
|
2055
|
+
if uri == cls._namespace_SOFA('SO_0000337'):
|
2056
2056
|
return True
|
2057
|
-
if uri == _namespace_SOFA('SO_0000340'):
|
2057
|
+
if uri == cls._namespace_SOFA('SO_0000340'):
|
2058
2058
|
return True
|
2059
|
-
if uri == _namespace_SOFA('SO_0000341'):
|
2059
|
+
if uri == cls._namespace_SOFA('SO_0000341'):
|
2060
2060
|
return True
|
2061
|
-
if uri == _namespace_SOFA('SO_0000343'):
|
2061
|
+
if uri == cls._namespace_SOFA('SO_0000343'):
|
2062
2062
|
return True
|
2063
|
-
if uri == _namespace_SOFA('SO_0000344'):
|
2063
|
+
if uri == cls._namespace_SOFA('SO_0000344'):
|
2064
2064
|
return True
|
2065
|
-
if uri == _namespace_SOFA('SO_0000345'):
|
2065
|
+
if uri == cls._namespace_SOFA('SO_0000345'):
|
2066
2066
|
return True
|
2067
|
-
if uri == _namespace_SOFA('SO_0000347'):
|
2067
|
+
if uri == cls._namespace_SOFA('SO_0000347'):
|
2068
2068
|
return True
|
2069
|
-
if uri == _namespace_SOFA('SO_0000349'):
|
2069
|
+
if uri == cls._namespace_SOFA('SO_0000349'):
|
2070
2070
|
return True
|
2071
|
-
if uri == _namespace_SOFA('SO_0000353'):
|
2071
|
+
if uri == cls._namespace_SOFA('SO_0000353'):
|
2072
2072
|
return True
|
2073
|
-
if uri == _namespace_SOFA('SO_0000360'):
|
2073
|
+
if uri == cls._namespace_SOFA('SO_0000360'):
|
2074
2074
|
return True
|
2075
|
-
if uri == _namespace_SOFA('SO_0000366'):
|
2075
|
+
if uri == cls._namespace_SOFA('SO_0000366'):
|
2076
2076
|
return True
|
2077
|
-
if uri == _namespace_SOFA('SO_0000368'):
|
2077
|
+
if uri == cls._namespace_SOFA('SO_0000368'):
|
2078
2078
|
return True
|
2079
|
-
if uri == _namespace_SOFA('SO_0000370'):
|
2079
|
+
if uri == cls._namespace_SOFA('SO_0000370'):
|
2080
2080
|
return True
|
2081
|
-
if uri == _namespace_SOFA('SO_0000372'):
|
2081
|
+
if uri == cls._namespace_SOFA('SO_0000372'):
|
2082
2082
|
return True
|
2083
|
-
if uri == _namespace_SOFA('SO_0000374'):
|
2083
|
+
if uri == cls._namespace_SOFA('SO_0000374'):
|
2084
2084
|
return True
|
2085
|
-
if uri == _namespace_SOFA('SO_0000375'):
|
2085
|
+
if uri == cls._namespace_SOFA('SO_0000375'):
|
2086
2086
|
return True
|
2087
|
-
if uri == _namespace_SOFA('SO_0000380'):
|
2087
|
+
if uri == cls._namespace_SOFA('SO_0000380'):
|
2088
2088
|
return True
|
2089
|
-
if uri == _namespace_SOFA('SO_0000385'):
|
2089
|
+
if uri == cls._namespace_SOFA('SO_0000385'):
|
2090
2090
|
return True
|
2091
|
-
if uri == _namespace_SOFA('SO_0000386'):
|
2091
|
+
if uri == cls._namespace_SOFA('SO_0000386'):
|
2092
2092
|
return True
|
2093
|
-
if uri == _namespace_SOFA('SO_0000390'):
|
2093
|
+
if uri == cls._namespace_SOFA('SO_0000390'):
|
2094
2094
|
return True
|
2095
|
-
if uri == _namespace_SOFA('SO_0000391'):
|
2095
|
+
if uri == cls._namespace_SOFA('SO_0000391'):
|
2096
2096
|
return True
|
2097
|
-
if uri == _namespace_SOFA('SO_0000392'):
|
2097
|
+
if uri == cls._namespace_SOFA('SO_0000392'):
|
2098
2098
|
return True
|
2099
|
-
if uri == _namespace_SOFA('SO_0000393'):
|
2099
|
+
if uri == cls._namespace_SOFA('SO_0000393'):
|
2100
2100
|
return True
|
2101
|
-
if uri == _namespace_SOFA('SO_0000394'):
|
2101
|
+
if uri == cls._namespace_SOFA('SO_0000394'):
|
2102
2102
|
return True
|
2103
|
-
if uri == _namespace_SOFA('SO_0000395'):
|
2103
|
+
if uri == cls._namespace_SOFA('SO_0000395'):
|
2104
2104
|
return True
|
2105
|
-
if uri == _namespace_SOFA('SO_0000396'):
|
2105
|
+
if uri == cls._namespace_SOFA('SO_0000396'):
|
2106
2106
|
return True
|
2107
|
-
if uri == _namespace_SOFA('SO_0000397'):
|
2107
|
+
if uri == cls._namespace_SOFA('SO_0000397'):
|
2108
2108
|
return True
|
2109
|
-
if uri == _namespace_SOFA('SO_0000398'):
|
2109
|
+
if uri == cls._namespace_SOFA('SO_0000398'):
|
2110
2110
|
return True
|
2111
|
-
if uri == _namespace_SOFA('SO_0000399'):
|
2111
|
+
if uri == cls._namespace_SOFA('SO_0000399'):
|
2112
2112
|
return True
|
2113
|
-
if uri == _namespace_SOFA('SO_0000403'):
|
2113
|
+
if uri == cls._namespace_SOFA('SO_0000403'):
|
2114
2114
|
return True
|
2115
|
-
if uri == _namespace_SOFA('SO_0000404'):
|
2115
|
+
if uri == cls._namespace_SOFA('SO_0000404'):
|
2116
2116
|
return True
|
2117
|
-
if uri == _namespace_SOFA('SO_0000405'):
|
2117
|
+
if uri == cls._namespace_SOFA('SO_0000405'):
|
2118
2118
|
return True
|
2119
|
-
if uri == _namespace_SOFA('SO_0000407'):
|
2119
|
+
if uri == cls._namespace_SOFA('SO_0000407'):
|
2120
2120
|
return True
|
2121
|
-
if uri == _namespace_SOFA('SO_0000409'):
|
2121
|
+
if uri == cls._namespace_SOFA('SO_0000409'):
|
2122
2122
|
return True
|
2123
|
-
if uri == _namespace_SOFA('SO_0000410'):
|
2123
|
+
if uri == cls._namespace_SOFA('SO_0000410'):
|
2124
2124
|
return True
|
2125
|
-
if uri == _namespace_SOFA('SO_0000412'):
|
2125
|
+
if uri == cls._namespace_SOFA('SO_0000412'):
|
2126
2126
|
return True
|
2127
|
-
if uri == _namespace_SOFA('SO_0000413'):
|
2127
|
+
if uri == cls._namespace_SOFA('SO_0000413'):
|
2128
2128
|
return True
|
2129
|
-
if uri == _namespace_SOFA('SO_0000418'):
|
2129
|
+
if uri == cls._namespace_SOFA('SO_0000418'):
|
2130
2130
|
return True
|
2131
|
-
if uri == _namespace_SOFA('SO_0000419'):
|
2131
|
+
if uri == cls._namespace_SOFA('SO_0000419'):
|
2132
2132
|
return True
|
2133
|
-
if uri == _namespace_SOFA('SO_0000436'):
|
2133
|
+
if uri == cls._namespace_SOFA('SO_0000436'):
|
2134
2134
|
return True
|
2135
|
-
if uri == _namespace_SOFA('SO_0000441'):
|
2135
|
+
if uri == cls._namespace_SOFA('SO_0000441'):
|
2136
2136
|
return True
|
2137
|
-
if uri == _namespace_SOFA('SO_0000442'):
|
2137
|
+
if uri == cls._namespace_SOFA('SO_0000442'):
|
2138
2138
|
return True
|
2139
|
-
if uri == _namespace_SOFA('SO_0000454'):
|
2139
|
+
if uri == cls._namespace_SOFA('SO_0000454'):
|
2140
2140
|
return True
|
2141
|
-
if uri == _namespace_SOFA('SO_0000462'):
|
2141
|
+
if uri == cls._namespace_SOFA('SO_0000462'):
|
2142
2142
|
return True
|
2143
|
-
if uri == _namespace_SOFA('SO_0000464'):
|
2143
|
+
if uri == cls._namespace_SOFA('SO_0000464'):
|
2144
2144
|
return True
|
2145
|
-
if uri == _namespace_SOFA('SO_0000468'):
|
2145
|
+
if uri == cls._namespace_SOFA('SO_0000468'):
|
2146
2146
|
return True
|
2147
|
-
if uri == _namespace_SOFA('SO_0000472'):
|
2147
|
+
if uri == cls._namespace_SOFA('SO_0000472'):
|
2148
2148
|
return True
|
2149
|
-
if uri == _namespace_SOFA('SO_0000474'):
|
2149
|
+
if uri == cls._namespace_SOFA('SO_0000474'):
|
2150
2150
|
return True
|
2151
|
-
if uri == _namespace_SOFA('SO_0000483'):
|
2151
|
+
if uri == cls._namespace_SOFA('SO_0000483'):
|
2152
2152
|
return True
|
2153
|
-
if uri == _namespace_SOFA('SO_0000484'):
|
2153
|
+
if uri == cls._namespace_SOFA('SO_0000484'):
|
2154
2154
|
return True
|
2155
|
-
if uri == _namespace_SOFA('SO_0000486'):
|
2155
|
+
if uri == cls._namespace_SOFA('SO_0000486'):
|
2156
2156
|
return True
|
2157
|
-
if uri == _namespace_SOFA('SO_0000499'):
|
2157
|
+
if uri == cls._namespace_SOFA('SO_0000499'):
|
2158
2158
|
return True
|
2159
|
-
if uri == _namespace_SOFA('SO_0000502'):
|
2159
|
+
if uri == cls._namespace_SOFA('SO_0000502'):
|
2160
2160
|
return True
|
2161
|
-
if uri == _namespace_SOFA('SO_0000551'):
|
2161
|
+
if uri == cls._namespace_SOFA('SO_0000551'):
|
2162
2162
|
return True
|
2163
|
-
if uri == _namespace_SOFA('SO_0000553'):
|
2163
|
+
if uri == cls._namespace_SOFA('SO_0000553'):
|
2164
2164
|
return True
|
2165
|
-
if uri == _namespace_SOFA('SO_0000577'):
|
2165
|
+
if uri == cls._namespace_SOFA('SO_0000577'):
|
2166
2166
|
return True
|
2167
|
-
if uri == _namespace_SOFA('SO_0000581'):
|
2167
|
+
if uri == cls._namespace_SOFA('SO_0000581'):
|
2168
2168
|
return True
|
2169
|
-
if uri == _namespace_SOFA('SO_0000587'):
|
2169
|
+
if uri == cls._namespace_SOFA('SO_0000587'):
|
2170
2170
|
return True
|
2171
|
-
if uri == _namespace_SOFA('SO_0000588'):
|
2171
|
+
if uri == cls._namespace_SOFA('SO_0000588'):
|
2172
2172
|
return True
|
2173
|
-
if uri == _namespace_SOFA('SO_0000590'):
|
2173
|
+
if uri == cls._namespace_SOFA('SO_0000590'):
|
2174
2174
|
return True
|
2175
|
-
if uri == _namespace_SOFA('SO_0000593'):
|
2175
|
+
if uri == cls._namespace_SOFA('SO_0000593'):
|
2176
2176
|
return True
|
2177
|
-
if uri == _namespace_SOFA('SO_0000602'):
|
2177
|
+
if uri == cls._namespace_SOFA('SO_0000602'):
|
2178
2178
|
return True
|
2179
|
-
if uri == _namespace_SOFA('SO_0000603'):
|
2179
|
+
if uri == cls._namespace_SOFA('SO_0000603'):
|
2180
2180
|
return True
|
2181
|
-
if uri == _namespace_SOFA('SO_0000605'):
|
2181
|
+
if uri == cls._namespace_SOFA('SO_0000605'):
|
2182
2182
|
return True
|
2183
|
-
if uri == _namespace_SOFA('SO_0000610'):
|
2183
|
+
if uri == cls._namespace_SOFA('SO_0000610'):
|
2184
2184
|
return True
|
2185
|
-
if uri == _namespace_SOFA('SO_0000611'):
|
2185
|
+
if uri == cls._namespace_SOFA('SO_0000611'):
|
2186
2186
|
return True
|
2187
|
-
if uri == _namespace_SOFA('SO_0000612'):
|
2187
|
+
if uri == cls._namespace_SOFA('SO_0000612'):
|
2188
2188
|
return True
|
2189
|
-
if uri == _namespace_SOFA('SO_0000616'):
|
2189
|
+
if uri == cls._namespace_SOFA('SO_0000616'):
|
2190
2190
|
return True
|
2191
|
-
if uri == _namespace_SOFA('SO_0000624'):
|
2191
|
+
if uri == cls._namespace_SOFA('SO_0000624'):
|
2192
2192
|
return True
|
2193
|
-
if uri == _namespace_SOFA('SO_0000625'):
|
2193
|
+
if uri == cls._namespace_SOFA('SO_0000625'):
|
2194
2194
|
return True
|
2195
|
-
if uri == _namespace_SOFA('SO_0000627'):
|
2195
|
+
if uri == cls._namespace_SOFA('SO_0000627'):
|
2196
2196
|
return True
|
2197
|
-
if uri == _namespace_SOFA('SO_0000628'):
|
2197
|
+
if uri == cls._namespace_SOFA('SO_0000628'):
|
2198
2198
|
return True
|
2199
|
-
if uri == _namespace_SOFA('SO_0000643'):
|
2199
|
+
if uri == cls._namespace_SOFA('SO_0000643'):
|
2200
2200
|
return True
|
2201
|
-
if uri == _namespace_SOFA('SO_0000644'):
|
2201
|
+
if uri == cls._namespace_SOFA('SO_0000644'):
|
2202
2202
|
return True
|
2203
|
-
if uri == _namespace_SOFA('SO_0000645'):
|
2203
|
+
if uri == cls._namespace_SOFA('SO_0000645'):
|
2204
2204
|
return True
|
2205
|
-
if uri == _namespace_SOFA('SO_0000646'):
|
2205
|
+
if uri == cls._namespace_SOFA('SO_0000646'):
|
2206
2206
|
return True
|
2207
|
-
if uri == _namespace_SOFA('SO_0000649'):
|
2207
|
+
if uri == cls._namespace_SOFA('SO_0000649'):
|
2208
2208
|
return True
|
2209
|
-
if uri == _namespace_SOFA('SO_0000650'):
|
2209
|
+
if uri == cls._namespace_SOFA('SO_0000650'):
|
2210
2210
|
return True
|
2211
|
-
if uri == _namespace_SOFA('SO_0000651'):
|
2211
|
+
if uri == cls._namespace_SOFA('SO_0000651'):
|
2212
2212
|
return True
|
2213
|
-
if uri == _namespace_SOFA('SO_0000652'):
|
2213
|
+
if uri == cls._namespace_SOFA('SO_0000652'):
|
2214
2214
|
return True
|
2215
|
-
if uri == _namespace_SOFA('SO_0000653'):
|
2215
|
+
if uri == cls._namespace_SOFA('SO_0000653'):
|
2216
2216
|
return True
|
2217
|
-
if uri == _namespace_SOFA('SO_0000655'):
|
2217
|
+
if uri == cls._namespace_SOFA('SO_0000655'):
|
2218
2218
|
return True
|
2219
|
-
if uri == _namespace_SOFA('SO_0000657'):
|
2219
|
+
if uri == cls._namespace_SOFA('SO_0000657'):
|
2220
2220
|
return True
|
2221
|
-
if uri == _namespace_SOFA('SO_0000658'):
|
2221
|
+
if uri == cls._namespace_SOFA('SO_0000658'):
|
2222
2222
|
return True
|
2223
|
-
if uri == _namespace_SOFA('SO_0000662'):
|
2223
|
+
if uri == cls._namespace_SOFA('SO_0000662'):
|
2224
2224
|
return True
|
2225
|
-
if uri == _namespace_SOFA('SO_0000667'):
|
2225
|
+
if uri == cls._namespace_SOFA('SO_0000667'):
|
2226
2226
|
return True
|
2227
|
-
if uri == _namespace_SOFA('SO_0000668'):
|
2227
|
+
if uri == cls._namespace_SOFA('SO_0000668'):
|
2228
2228
|
return True
|
2229
|
-
if uri == _namespace_SOFA('SO_0000673'):
|
2229
|
+
if uri == cls._namespace_SOFA('SO_0000673'):
|
2230
2230
|
return True
|
2231
|
-
if uri == _namespace_SOFA('SO_0000684'):
|
2231
|
+
if uri == cls._namespace_SOFA('SO_0000684'):
|
2232
2232
|
return True
|
2233
|
-
if uri == _namespace_SOFA('SO_0000687'):
|
2233
|
+
if uri == cls._namespace_SOFA('SO_0000687'):
|
2234
2234
|
return True
|
2235
|
-
if uri == _namespace_SOFA('SO_0000688'):
|
2235
|
+
if uri == cls._namespace_SOFA('SO_0000688'):
|
2236
2236
|
return True
|
2237
|
-
if uri == _namespace_SOFA('SO_0000689'):
|
2237
|
+
if uri == cls._namespace_SOFA('SO_0000689'):
|
2238
2238
|
return True
|
2239
|
-
if uri == _namespace_SOFA('SO_0000694'):
|
2239
|
+
if uri == cls._namespace_SOFA('SO_0000694'):
|
2240
2240
|
return True
|
2241
|
-
if uri == _namespace_SOFA('SO_0000695'):
|
2241
|
+
if uri == cls._namespace_SOFA('SO_0000695'):
|
2242
2242
|
return True
|
2243
|
-
if uri == _namespace_SOFA('SO_0000696'):
|
2243
|
+
if uri == cls._namespace_SOFA('SO_0000696'):
|
2244
2244
|
return True
|
2245
|
-
if uri == _namespace_SOFA('SO_0000699'):
|
2245
|
+
if uri == cls._namespace_SOFA('SO_0000699'):
|
2246
2246
|
return True
|
2247
|
-
if uri == _namespace_SOFA('SO_0000700'):
|
2247
|
+
if uri == cls._namespace_SOFA('SO_0000700'):
|
2248
2248
|
return True
|
2249
|
-
if uri == _namespace_SOFA('SO_0000701'):
|
2249
|
+
if uri == cls._namespace_SOFA('SO_0000701'):
|
2250
2250
|
return True
|
2251
|
-
if uri == _namespace_SOFA('SO_0000702'):
|
2251
|
+
if uri == cls._namespace_SOFA('SO_0000702'):
|
2252
2252
|
return True
|
2253
|
-
if uri == _namespace_SOFA('SO_0000703'):
|
2253
|
+
if uri == cls._namespace_SOFA('SO_0000703'):
|
2254
2254
|
return True
|
2255
|
-
if uri == _namespace_SOFA('SO_0000704'):
|
2255
|
+
if uri == cls._namespace_SOFA('SO_0000704'):
|
2256
2256
|
return True
|
2257
|
-
if uri == _namespace_SOFA('SO_0000705'):
|
2257
|
+
if uri == cls._namespace_SOFA('SO_0000705'):
|
2258
2258
|
return True
|
2259
|
-
if uri == _namespace_SOFA('SO_0000706'):
|
2259
|
+
if uri == cls._namespace_SOFA('SO_0000706'):
|
2260
2260
|
return True
|
2261
|
-
if uri == _namespace_SOFA('SO_0000714'):
|
2261
|
+
if uri == cls._namespace_SOFA('SO_0000714'):
|
2262
2262
|
return True
|
2263
|
-
if uri == _namespace_SOFA('SO_0000715'):
|
2263
|
+
if uri == cls._namespace_SOFA('SO_0000715'):
|
2264
2264
|
return True
|
2265
|
-
if uri == _namespace_SOFA('SO_0000717'):
|
2265
|
+
if uri == cls._namespace_SOFA('SO_0000717'):
|
2266
2266
|
return True
|
2267
|
-
if uri == _namespace_SOFA('SO_0000719'):
|
2267
|
+
if uri == cls._namespace_SOFA('SO_0000719'):
|
2268
2268
|
return True
|
2269
|
-
if uri == _namespace_SOFA('SO_0000724'):
|
2269
|
+
if uri == cls._namespace_SOFA('SO_0000724'):
|
2270
2270
|
return True
|
2271
|
-
if uri == _namespace_SOFA('SO_0000725'):
|
2271
|
+
if uri == cls._namespace_SOFA('SO_0000725'):
|
2272
2272
|
return True
|
2273
|
-
if uri == _namespace_SOFA('SO_0000727'):
|
2273
|
+
if uri == cls._namespace_SOFA('SO_0000727'):
|
2274
2274
|
return True
|
2275
|
-
if uri == _namespace_SOFA('SO_0000730'):
|
2275
|
+
if uri == cls._namespace_SOFA('SO_0000730'):
|
2276
2276
|
return True
|
2277
|
-
if uri == _namespace_SOFA('SO_0000752'):
|
2277
|
+
if uri == cls._namespace_SOFA('SO_0000752'):
|
2278
2278
|
return True
|
2279
|
-
if uri == _namespace_SOFA('SO_0000753'):
|
2279
|
+
if uri == cls._namespace_SOFA('SO_0000753'):
|
2280
2280
|
return True
|
2281
|
-
if uri == _namespace_SOFA('SO_0000777'):
|
2281
|
+
if uri == cls._namespace_SOFA('SO_0000777'):
|
2282
2282
|
return True
|
2283
|
-
if uri == _namespace_SOFA('SO_0000778'):
|
2283
|
+
if uri == cls._namespace_SOFA('SO_0000778'):
|
2284
2284
|
return True
|
2285
|
-
if uri == _namespace_SOFA('SO_0000830'):
|
2285
|
+
if uri == cls._namespace_SOFA('SO_0000830'):
|
2286
2286
|
return True
|
2287
|
-
if uri == _namespace_SOFA('SO_0000831'):
|
2287
|
+
if uri == cls._namespace_SOFA('SO_0000831'):
|
2288
2288
|
return True
|
2289
|
-
if uri == _namespace_SOFA('SO_0000833'):
|
2289
|
+
if uri == cls._namespace_SOFA('SO_0000833'):
|
2290
2290
|
return True
|
2291
|
-
if uri == _namespace_SOFA('SO_0000834'):
|
2291
|
+
if uri == cls._namespace_SOFA('SO_0000834'):
|
2292
2292
|
return True
|
2293
|
-
if uri == _namespace_SOFA('SO_0000835'):
|
2293
|
+
if uri == cls._namespace_SOFA('SO_0000835'):
|
2294
2294
|
return True
|
2295
|
-
if uri == _namespace_SOFA('SO_0000836'):
|
2295
|
+
if uri == cls._namespace_SOFA('SO_0000836'):
|
2296
2296
|
return True
|
2297
|
-
if uri == _namespace_SOFA('SO_0000837'):
|
2297
|
+
if uri == cls._namespace_SOFA('SO_0000837'):
|
2298
2298
|
return True
|
2299
|
-
if uri == _namespace_SOFA('SO_0000839'):
|
2299
|
+
if uri == cls._namespace_SOFA('SO_0000839'):
|
2300
2300
|
return True
|
2301
|
-
if uri == _namespace_SOFA('SO_0000841'):
|
2301
|
+
if uri == cls._namespace_SOFA('SO_0000841'):
|
2302
2302
|
return True
|
2303
|
-
if uri == _namespace_SOFA('SO_0000842'):
|
2303
|
+
if uri == cls._namespace_SOFA('SO_0000842'):
|
2304
2304
|
return True
|
2305
|
-
if uri == _namespace_SOFA('SO_0000851'):
|
2305
|
+
if uri == cls._namespace_SOFA('SO_0000851'):
|
2306
2306
|
return True
|
2307
|
-
if uri == _namespace_SOFA('SO_0000852'):
|
2307
|
+
if uri == cls._namespace_SOFA('SO_0000852'):
|
2308
2308
|
return True
|
2309
|
-
if uri == _namespace_SOFA('SO_0001000'):
|
2309
|
+
if uri == cls._namespace_SOFA('SO_0001000'):
|
2310
2310
|
return True
|
2311
|
-
if uri == _namespace_SOFA('SO_0001001'):
|
2311
|
+
if uri == cls._namespace_SOFA('SO_0001001'):
|
2312
2312
|
return True
|
2313
|
-
if uri == _namespace_SOFA('SO_0001002'):
|
2313
|
+
if uri == cls._namespace_SOFA('SO_0001002'):
|
2314
2314
|
return True
|
2315
|
-
if uri == _namespace_SOFA('SO_0001019'):
|
2315
|
+
if uri == cls._namespace_SOFA('SO_0001019'):
|
2316
2316
|
return True
|
2317
|
-
if uri == _namespace_SOFA('SO_0001037'):
|
2317
|
+
if uri == cls._namespace_SOFA('SO_0001037'):
|
2318
2318
|
return True
|
2319
|
-
if uri == _namespace_SOFA('SO_0001039'):
|
2319
|
+
if uri == cls._namespace_SOFA('SO_0001039'):
|
2320
2320
|
return True
|
2321
|
-
if uri == _namespace_SOFA('SO_0001055'):
|
2321
|
+
if uri == cls._namespace_SOFA('SO_0001055'):
|
2322
2322
|
return True
|
2323
|
-
if uri == _namespace_SOFA('SO_0001056'):
|
2323
|
+
if uri == cls._namespace_SOFA('SO_0001056'):
|
2324
2324
|
return True
|
2325
|
-
if uri == _namespace_SOFA('SO_0001059'):
|
2325
|
+
if uri == cls._namespace_SOFA('SO_0001059'):
|
2326
2326
|
return True
|
2327
|
-
if uri == _namespace_SOFA('SO_0001063'):
|
2327
|
+
if uri == cls._namespace_SOFA('SO_0001063'):
|
2328
2328
|
return True
|
2329
|
-
if uri == _namespace_SOFA('SO_0001214'):
|
2329
|
+
if uri == cls._namespace_SOFA('SO_0001214'):
|
2330
2330
|
return True
|
2331
|
-
if uri == _namespace_SOFA('SO_0001215'):
|
2331
|
+
if uri == cls._namespace_SOFA('SO_0001215'):
|
2332
2332
|
return True
|
2333
|
-
if uri == _namespace_SOFA('SO_0001235'):
|
2333
|
+
if uri == cls._namespace_SOFA('SO_0001235'):
|
2334
2334
|
return True
|
2335
|
-
if uri == _namespace_SOFA('SO_0001236'):
|
2335
|
+
if uri == cls._namespace_SOFA('SO_0001236'):
|
2336
2336
|
return True
|
2337
|
-
if uri == _namespace_SOFA('SO_0001248'):
|
2337
|
+
if uri == cls._namespace_SOFA('SO_0001248'):
|
2338
2338
|
return True
|
2339
|
-
if uri == _namespace_SOFA('SO_0001409'):
|
2339
|
+
if uri == cls._namespace_SOFA('SO_0001409'):
|
2340
2340
|
return True
|
2341
|
-
if uri == _namespace_SOFA('SO_0001410'):
|
2341
|
+
if uri == cls._namespace_SOFA('SO_0001410'):
|
2342
2342
|
return True
|
2343
|
-
if uri == _namespace_SOFA('SO_0001411'):
|
2343
|
+
if uri == cls._namespace_SOFA('SO_0001411'):
|
2344
2344
|
return True
|
2345
|
-
if uri == _namespace_SOFA('SO_0001412'):
|
2345
|
+
if uri == cls._namespace_SOFA('SO_0001412'):
|
2346
2346
|
return True
|
2347
|
-
if uri == _namespace_SOFA('SO_0001419'):
|
2347
|
+
if uri == cls._namespace_SOFA('SO_0001419'):
|
2348
2348
|
return True
|
2349
|
-
if uri == _namespace_SOFA('SO_0001420'):
|
2349
|
+
if uri == cls._namespace_SOFA('SO_0001420'):
|
2350
2350
|
return True
|
2351
|
-
if uri == _namespace_SOFA('SO_0001483'):
|
2351
|
+
if uri == cls._namespace_SOFA('SO_0001483'):
|
2352
2352
|
return True
|
2353
|
-
if uri == _namespace_SOFA('SO_0001527'):
|
2353
|
+
if uri == cls._namespace_SOFA('SO_0001527'):
|
2354
2354
|
return True
|
2355
|
-
if uri == _namespace_SOFA('SO_0001647'):
|
2355
|
+
if uri == cls._namespace_SOFA('SO_0001647'):
|
2356
2356
|
return True
|
2357
|
-
if uri == _namespace_SOFA('SO_0001654'):
|
2357
|
+
if uri == cls._namespace_SOFA('SO_0001654'):
|
2358
2358
|
return True
|
2359
|
-
if uri == _namespace_SOFA('SO_0001679'):
|
2359
|
+
if uri == cls._namespace_SOFA('SO_0001679'):
|
2360
2360
|
return True
|
2361
|
-
if uri == _namespace_SOFA('SO_0001683'):
|
2361
|
+
if uri == cls._namespace_SOFA('SO_0001683'):
|
2362
2362
|
return True
|
2363
|
-
if uri == _namespace_SOFA('SO_0001720'):
|
2363
|
+
if uri == cls._namespace_SOFA('SO_0001720'):
|
2364
2364
|
return True
|
2365
|
-
if uri == _namespace_SOFA('SO_0001790'):
|
2365
|
+
if uri == cls._namespace_SOFA('SO_0001790'):
|
2366
2366
|
return True
|
2367
|
-
if uri == _namespace_SOFA('SO_0005836'):
|
2367
|
+
if uri == cls._namespace_SOFA('SO_0005836'):
|
2368
2368
|
return True
|
2369
|
-
if uri == _namespace_SOFA('SO_0005855'):
|
2369
|
+
if uri == cls._namespace_SOFA('SO_0005855'):
|
2370
2370
|
return True
|
2371
|
-
if uri == _namespace_SOFA('SO_0100011'):
|
2371
|
+
if uri == cls._namespace_SOFA('SO_0100011'):
|
2372
2372
|
return True
|
2373
|
-
if uri == _namespace_SOFA('SO_1000002'):
|
2373
|
+
if uri == cls._namespace_SOFA('SO_1000002'):
|
2374
2374
|
return True
|
2375
|
-
if uri == _namespace_SOFA('SO_1000005'):
|
2375
|
+
if uri == cls._namespace_SOFA('SO_1000005'):
|
2376
2376
|
return True
|
2377
|
-
if uri == _namespace_SOFA('SO_1000008'):
|
2377
|
+
if uri == cls._namespace_SOFA('SO_1000008'):
|
2378
2378
|
return True
|
2379
|
-
if uri == _namespace_SOFA('SO_1000036'):
|
2379
|
+
if uri == cls._namespace_SOFA('SO_1000036'):
|
2380
2380
|
return True
|
2381
|
-
if uri == _namespace_SOFA('SO_1001284'):
|
2381
|
+
if uri == cls._namespace_SOFA('SO_1001284'):
|
2382
2382
|
return True
|
2383
|
-
if uri == _namespace_SOFA('SO_2000061'):
|
2383
|
+
if uri == cls._namespace_SOFA('SO_2000061'):
|
2384
2384
|
return True
|
2385
2385
|
return False
|
2386
2386
|
|
@@ -2414,11 +2414,10 @@ class SOFA:
|
|
2414
2414
|
return cls.has_parent(cls.__parent_properties[uri], parent)
|
2415
2415
|
return False
|
2416
2416
|
|
2417
|
-
|
2418
|
-
|
2419
|
-
|
2420
|
-
return __namespace_SOFA[accession]
|
2417
|
+
@classmethod
|
2418
|
+
def _namespace_SOFA(cls, accession):
|
2419
|
+
return Namespace('http://purl.obolibrary.org/obo/')[accession]
|
2421
2420
|
|
2422
|
-
__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') : _namespace_SOFA('SO_0000442') , _namespace_SOFA('SO_0000340') : _namespace_SOFA('SO_0001235') , _namespace_SOFA('SO_0000341') : _namespace_SOFA('SO_0000830') , _namespace_SOFA('SO_0000343') : _namespace_SOFA('SO_0001410') , _namespace_SOFA('SO_0000344') : _namespace_SOFA('SO_0001056') , _namespace_SOFA('SO_0000347') : _namespace_SOFA('SO_0000343') , _namespace_SOFA('SO_0000349') : _namespace_SOFA('SO_0000343') , _namespace_SOFA('SO_0000353') : _namespace_SOFA('SO_0001248') , _namespace_SOFA('SO_0000360') : _namespace_SOFA('SO_0000851') , _namespace_SOFA('SO_0000366') : _namespace_SOFA('SO_0000699') , _namespace_SOFA('SO_0000368') : _namespace_SOFA('SO_0000366') , _namespace_SOFA('SO_0000370') : _namespace_SOFA('SO_0000655') , _namespace_SOFA('SO_0000372') : _namespace_SOFA('SO_0000673') , _namespace_SOFA('SO_0000374') : _namespace_SOFA('SO_0000372') , _namespace_SOFA('SO_0000375') : _namespace_SOFA('SO_0000651') , _namespace_SOFA('SO_0000380') : _namespace_SOFA('SO_0000715') , _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') }
|
2421
|
+
__parent_properties = { Namespace('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:complete_evidence_for_feature') : Namespace('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:evidence_for_feature') , Namespace('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:has_integral_part') : Namespace('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:has_part') , Namespace('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:homologous_to') : Namespace('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:similar_to') , Namespace('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:integral_part_of') : Namespace('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:part_of') , Namespace('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:member_of') : Namespace('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:part_of') , Namespace('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:non_functional_homolog_of') : 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