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
@@ -9,955 +9,955 @@ class GVF1O:
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def seqid(cls):
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"""Either:
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Establishes the landmark (cls, e.g. a chromosome) on which a feature is located.
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(GVF1_0004)
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+
(http://www.biointerchange.org/gvf1o#GVF1_0004)
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Or:
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Link to the landmark that establishes the coordinate system for the breakpoint.
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(GVF1_0072)
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(http://www.biointerchange.org/gvf1o#GVF1_0072)
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"""
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return [ _namespace_GVF1O('GVF1_0004'), _namespace_GVF1O('GVF1_0072') ]
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return [ cls._namespace_GVF1O('GVF1_0004'), cls._namespace_GVF1O('GVF1_0072') ]
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@classmethod
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def strand(cls):
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"""Either:
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Strand of the feature.
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(cls, GVF1_0010)
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(cls, http://www.biointerchange.org/gvf1o#GVF1_0010)
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Or:
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Strand of the breakpoint.
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(GVF1_0083)
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(http://www.biointerchange.org/gvf1o#GVF1_0083)
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Or:
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Strand of a target -- if applicable.
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(GVF1_0091)
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(http://www.biointerchange.org/gvf1o#GVF1_0091)
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"""
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return [ _namespace_GVF1O('GVF1_0010'), _namespace_GVF1O('GVF1_0083'), _namespace_GVF1O('GVF1_0091') ]
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return [ cls._namespace_GVF1O('GVF1_0010'), cls._namespace_GVF1O('GVF1_0083'), cls._namespace_GVF1O('GVF1_0091') ]
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@classmethod
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def attributes(cls):
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"""Either:
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Tag name/value pair attributes of a feature.
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(cls, GVF1_0012)
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(cls, http://www.biointerchange.org/gvf1o#GVF1_0012)
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Or:
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Tag name/value pair attributes that are not captured by the GVF specification.
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(GVF1_0152)
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(http://www.biointerchange.org/gvf1o#GVF1_0152)
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"""
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return [ _namespace_GVF1O('GVF1_0012'), _namespace_GVF1O('GVF1_0152') ]
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return [ cls._namespace_GVF1O('GVF1_0012'), cls._namespace_GVF1O('GVF1_0152') ]
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@classmethod
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def parent(cls):
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"""Link out to the parent feature.
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(cls, GVF1_0014)
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(cls, http://www.biointerchange.org/gvf1o#GVF1_0014)
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"""
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return _namespace_GVF1O('GVF1_0014')
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return cls._namespace_GVF1O('GVF1_0014')
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@classmethod
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def contains(cls):
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"""Relationship that describes which features belong to a feature set.
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(cls, GVF1_0015)
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(cls, http://www.biointerchange.org/gvf1o#GVF1_0015)
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"""
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return _namespace_GVF1O('GVF1_0015')
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return cls._namespace_GVF1O('GVF1_0015')
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@classmethod
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def region(cls):
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"""Either:
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FALDO "Region" instance replacement for a feature's start, stop, strand properties.
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(cls, GVF1_0021)
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(cls, http://www.biointerchange.org/gvf1o#GVF1_0021)
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Or:
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FALDO "Region" instance replacement for a breakpoint's start, stop, strand properties.
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(GVF1_0079)
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(http://www.biointerchange.org/gvf1o#GVF1_0079)
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Or:
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FALDO "Region" instance replacement for a target's start, stop, strand properties.
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(GVF1_0090)
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(http://www.biointerchange.org/gvf1o#GVF1_0090)
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"""
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return [ _namespace_GVF1O('GVF1_0021'), _namespace_GVF1O('GVF1_0079'), _namespace_GVF1O('GVF1_0090') ]
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return [ cls._namespace_GVF1O('GVF1_0021'), cls._namespace_GVF1O('GVF1_0079'), cls._namespace_GVF1O('GVF1_0090') ]
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@classmethod
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def species(cls):
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"""NCBI Taxonomy Ontology "NCBITaxon_1" (cls, or sub-classes) instance that denotes the species for a feature set.
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(GVF1_0023)
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(http://www.biointerchange.org/gvf1o#GVF1_0023)
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"""
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return _namespace_GVF1O('GVF1_0023')
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return cls._namespace_GVF1O('GVF1_0023')
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@classmethod
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def variant(cls):
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"""Specific information about the variant(cls, s) of a feature.
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(GVF1_0034)
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(http://www.biointerchange.org/gvf1o#GVF1_0034)
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"""
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return _namespace_GVF1O('GVF1_0034')
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return cls._namespace_GVF1O('GVF1_0034')
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@classmethod
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def individual(cls):
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"""Links to information about an individual.
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(cls, GVF1_0036)
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(cls, http://www.biointerchange.org/gvf1o#GVF1_0036)
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"""
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return _namespace_GVF1O('GVF1_0036')
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return cls._namespace_GVF1O('GVF1_0036')
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@classmethod
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def zygosity(cls):
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"""Zygosity of a variant.
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(cls, GVF1_0038)
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(cls, http://www.biointerchange.org/gvf1o#GVF1_0038)
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"""
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return _namespace_GVF1O('GVF1_0038')
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return cls._namespace_GVF1O('GVF1_0038')
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@classmethod
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def effect(cls):
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"""An effect of a particular feature variant.
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(cls, GVF1_0041)
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(cls, http://www.biointerchange.org/gvf1o#GVF1_0041)
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"""
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return _namespace_GVF1O('GVF1_0041')
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return cls._namespace_GVF1O('GVF1_0041')
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@classmethod
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def sequence_variant(cls):
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"""Effect of a sequence alteration on a sequence feature.
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(cls, GVF1_0042)
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(cls, http://www.biointerchange.org/gvf1o#GVF1_0042)
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"""
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return _namespace_GVF1O('GVF1_0042')
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return cls._namespace_GVF1O('GVF1_0042')
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@classmethod
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def feature_type(cls):
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"""A term that is describing the sequence feature that is being affected.
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(cls, GVF1_0043)
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(cls, http://www.biointerchange.org/gvf1o#GVF1_0043)
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"""
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return _namespace_GVF1O('GVF1_0043')
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return cls._namespace_GVF1O('GVF1_0043')
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@classmethod
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def start_range(cls):
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"""A coordinate range for ambiguous start coordinates.
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(cls, GVF1_0046)
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(cls, http://www.biointerchange.org/gvf1o#GVF1_0046)
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"""
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return _namespace_GVF1O('GVF1_0046')
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return cls._namespace_GVF1O('GVF1_0046')
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@classmethod
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def end_range(cls):
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"""A coordinate range for ambiguous start coordinates.
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(cls, GVF1_0047)
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(cls, http://www.biointerchange.org/gvf1o#GVF1_0047)
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"""
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return _namespace_GVF1O('GVF1_0047')
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return cls._namespace_GVF1O('GVF1_0047')
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@classmethod
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def chromosome(cls):
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"""Denotes abstract chromosome representations for capturing variants that appear on the same chromosome of a polyploid organism.
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(cls, GVF1_0051)
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(cls, http://www.biointerchange.org/gvf1o#GVF1_0051)
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"""
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return _namespace_GVF1O('GVF1_0051')
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return cls._namespace_GVF1O('GVF1_0051')
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@classmethod
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def genotype(cls):
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"""Determines the genotype as observed in an individual.
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(cls, GVF1_0053)
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(cls, http://www.biointerchange.org/gvf1o#GVF1_0053)
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"""
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return _namespace_GVF1O('GVF1_0053')
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return cls._namespace_GVF1O('GVF1_0053')
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@classmethod
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def feature_properties(cls):
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"""Either:
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Properties that are directly associated with Feature class instances.
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(cls, GVF1_0066)
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(cls, http://www.biointerchange.org/gvf1o#GVF1_0066)
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Or:
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Properties that are directly associated with Feature class instances.
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(GVF1_0059)
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(http://www.biointerchange.org/gvf1o#GVF1_0059)
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"""
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return [ _namespace_GVF1O('GVF1_0066'), _namespace_GVF1O('GVF1_0059') ]
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return [ cls._namespace_GVF1O('GVF1_0066'), cls._namespace_GVF1O('GVF1_0059') ]
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@classmethod
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def sequencedindividual_properties(cls):
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"""Either:
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Properties that are directly associated with SequencedIndividual class instances.
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(cls, GVF1_0067)
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(cls, http://www.biointerchange.org/gvf1o#GVF1_0067)
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Or:
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Properties that are directly associated with SequencedIndividual class instances.
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(GVF1_0065)
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+
(http://www.biointerchange.org/gvf1o#GVF1_0065)
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"""
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return [ _namespace_GVF1O('GVF1_0067'), _namespace_GVF1O('GVF1_0065') ]
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return [ cls._namespace_GVF1O('GVF1_0067'), cls._namespace_GVF1O('GVF1_0065') ]
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@classmethod
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def set_properties(cls):
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"""Either:
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Properties that are directly associated with Set class instances.
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(cls, GVF1_0068)
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(cls, http://www.biointerchange.org/gvf1o#GVF1_0068)
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Or:
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Properties that are directly associated with Set class instances.
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(GVF1_0063)
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(http://www.biointerchange.org/gvf1o#GVF1_0063)
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"""
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return [ _namespace_GVF1O('GVF1_0068'), _namespace_GVF1O('GVF1_0063') ]
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return [ cls._namespace_GVF1O('GVF1_0068'), cls._namespace_GVF1O('GVF1_0063') ]
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@classmethod
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def variant_properties(cls):
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"""Either:
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Properties that are directly associated with Variant class instances.
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(cls, GVF1_0069)
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(cls, http://www.biointerchange.org/gvf1o#GVF1_0069)
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Or:
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Properties that are directly associated with Variant class instances.
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-
(GVF1_0060)
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+
(http://www.biointerchange.org/gvf1o#GVF1_0060)
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"""
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return [ _namespace_GVF1O('GVF1_0069'), _namespace_GVF1O('GVF1_0060') ]
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return [ cls._namespace_GVF1O('GVF1_0069'), cls._namespace_GVF1O('GVF1_0060') ]
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@classmethod
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def effect_properties(cls):
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"""Either:
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Properties that are directly associated with Effect class instances.
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(cls, GVF1_0070)
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(cls, http://www.biointerchange.org/gvf1o#GVF1_0070)
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Or:
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Properties that are directly associated with Effect class instances.
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-
(GVF1_0158)
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(http://www.biointerchange.org/gvf1o#GVF1_0158)
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"""
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return [ _namespace_GVF1O('GVF1_0070'), _namespace_GVF1O('GVF1_0158') ]
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return [ cls._namespace_GVF1O('GVF1_0070'), cls._namespace_GVF1O('GVF1_0158') ]
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@classmethod
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def breakpoint_properties(cls):
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"""Either:
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Properties that are directly associated with Breakpoint class instances.
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-
(cls, GVF1_0075)
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(cls, http://www.biointerchange.org/gvf1o#GVF1_0075)
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Or:
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Properties that are directly associated with Breakpoint class instances.
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-
(GVF1_0071)
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+
(http://www.biointerchange.org/gvf1o#GVF1_0071)
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"""
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return [ _namespace_GVF1O('GVF1_0075'), _namespace_GVF1O('GVF1_0071') ]
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return [ cls._namespace_GVF1O('GVF1_0075'), cls._namespace_GVF1O('GVF1_0071') ]
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@classmethod
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def dbxref(cls):
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"""Either:
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A database cross-reference to associate a sequence alteration to its representation in another database.
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-
(cls, GVF1_0078)
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(cls, http://www.biointerchange.org/gvf1o#GVF1_0078)
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Or:
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A database cross-reference to associate a structured pragma to a representation in another database.
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-
(GVF1_0104)
|
222
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0104)
|
223
223
|
"""
|
224
|
-
return [ _namespace_GVF1O('GVF1_0078'), _namespace_GVF1O('GVF1_0104') ]
|
224
|
+
return [ cls._namespace_GVF1O('GVF1_0078'), cls._namespace_GVF1O('GVF1_0104') ]
|
225
225
|
|
226
226
|
@classmethod
|
227
227
|
def breakpoint(cls):
|
228
228
|
"""Potential source or destination of zero-length sequence alterations.
|
229
|
-
(cls, GVF1_0080)
|
229
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0080)
|
230
230
|
"""
|
231
|
-
return _namespace_GVF1O('GVF1_0080')
|
231
|
+
return cls._namespace_GVF1O('GVF1_0080')
|
232
232
|
|
233
233
|
@classmethod
|
234
234
|
def target_properties(cls):
|
235
235
|
"""Either:
|
236
236
|
Properties that are directly associated with Target class instances.
|
237
|
-
(cls, GVF1_0089)
|
237
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0089)
|
238
238
|
Or:
|
239
239
|
Properties that are directly associated with Target class instances.
|
240
|
-
(GVF1_0092)
|
240
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0092)
|
241
241
|
"""
|
242
|
-
return [ _namespace_GVF1O('GVF1_0089'), _namespace_GVF1O('GVF1_0092') ]
|
242
|
+
return [ cls._namespace_GVF1O('GVF1_0089'), cls._namespace_GVF1O('GVF1_0092') ]
|
243
243
|
|
244
244
|
@classmethod
|
245
245
|
def technologyplatform_properties(cls):
|
246
246
|
"""Either:
|
247
247
|
Properties that are directly associated with TechnologyPlatform class instances.
|
248
|
-
(cls, GVF1_0102)
|
248
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0102)
|
249
249
|
Or:
|
250
250
|
Properties that are directly associated with TechnologyPlatform class instances.
|
251
|
-
(GVF1_0107)
|
251
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0107)
|
252
252
|
"""
|
253
|
-
return [ _namespace_GVF1O('GVF1_0102'), _namespace_GVF1O('GVF1_0107') ]
|
253
|
+
return [ cls._namespace_GVF1O('GVF1_0102'), cls._namespace_GVF1O('GVF1_0107') ]
|
254
254
|
|
255
255
|
@classmethod
|
256
256
|
def datasource_properties(cls):
|
257
257
|
"""Properties that are directly associated with DataSource class instances.
|
258
|
-
(cls, GVF1_0103)
|
258
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0103)
|
259
259
|
"""
|
260
|
-
return _namespace_GVF1O('GVF1_0103')
|
260
|
+
return cls._namespace_GVF1O('GVF1_0103')
|
261
261
|
|
262
262
|
@classmethod
|
263
263
|
def structuredpragma_properties(cls):
|
264
264
|
"""Either:
|
265
265
|
Properties describing structured pragma properties.
|
266
|
-
(cls, GVF1_0112)
|
266
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0112)
|
267
267
|
Or:
|
268
268
|
Properties describing structured pragma properties.
|
269
|
-
(GVF1_0113)
|
269
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0113)
|
270
270
|
"""
|
271
|
-
return [ _namespace_GVF1O('GVF1_0112'), _namespace_GVF1O('GVF1_0113') ]
|
271
|
+
return [ cls._namespace_GVF1O('GVF1_0112'), cls._namespace_GVF1O('GVF1_0113') ]
|
272
272
|
|
273
273
|
@classmethod
|
274
274
|
def read_type(cls):
|
275
275
|
"""Types of reads produced by the platform.
|
276
|
-
(cls, GVF1_0119)
|
276
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0119)
|
277
277
|
"""
|
278
|
-
return _namespace_GVF1O('GVF1_0119')
|
278
|
+
return cls._namespace_GVF1O('GVF1_0119')
|
279
279
|
|
280
280
|
@classmethod
|
281
281
|
def data_type(cls):
|
282
282
|
"""Datatype of this data source.
|
283
|
-
(cls, GVF1_0120)
|
283
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0120)
|
284
284
|
"""
|
285
|
-
return _namespace_GVF1O('GVF1_0120')
|
285
|
+
return cls._namespace_GVF1O('GVF1_0120')
|
286
286
|
|
287
287
|
@classmethod
|
288
288
|
def technology_platform(cls):
|
289
289
|
"""Technology platform that was used to derive the feature.
|
290
|
-
(cls, GVF1_0121)
|
290
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0121)
|
291
291
|
"""
|
292
|
-
return _namespace_GVF1O('GVF1_0121')
|
292
|
+
return cls._namespace_GVF1O('GVF1_0121')
|
293
293
|
|
294
294
|
@classmethod
|
295
295
|
def data_source(cls):
|
296
296
|
"""Data source origin of the feature.
|
297
|
-
(cls, GVF1_0122)
|
297
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0122)
|
298
298
|
"""
|
299
|
-
return _namespace_GVF1O('GVF1_0122')
|
299
|
+
return cls._namespace_GVF1O('GVF1_0122')
|
300
300
|
|
301
301
|
@classmethod
|
302
302
|
def score_method(cls):
|
303
303
|
"""Used scoring method.
|
304
|
-
(cls, GVF1_0123)
|
304
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0123)
|
305
305
|
"""
|
306
|
-
return _namespace_GVF1O('GVF1_0123')
|
306
|
+
return cls._namespace_GVF1O('GVF1_0123')
|
307
307
|
|
308
308
|
@classmethod
|
309
309
|
def source_method(cls):
|
310
310
|
"""Further information about the algorithm/methodologies used.
|
311
|
-
(cls, GVF1_0124)
|
311
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0124)
|
312
312
|
"""
|
313
|
-
return _namespace_GVF1O('GVF1_0124')
|
313
|
+
return cls._namespace_GVF1O('GVF1_0124')
|
314
314
|
|
315
315
|
@classmethod
|
316
316
|
def phenotype_description(cls):
|
317
317
|
"""Further information about an individual's phenotype. Applies only to single individual sets.
|
318
|
-
(cls, GVF1_0125)
|
318
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0125)
|
319
319
|
"""
|
320
|
-
return _namespace_GVF1O('GVF1_0125')
|
320
|
+
return cls._namespace_GVF1O('GVF1_0125')
|
321
321
|
|
322
322
|
@classmethod
|
323
323
|
def attribute_method(cls):
|
324
324
|
"""Either:
|
325
325
|
Further information about the associated attribute(cls, s).
|
326
|
-
(GVF1_0126)
|
326
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0126)
|
327
327
|
Or:
|
328
328
|
Further information about the associated attribute(s).
|
329
|
-
(GVF1_0127)
|
329
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0127)
|
330
330
|
Or:
|
331
331
|
Further information about the associated attribute(s).
|
332
|
-
(GVF1_0129)
|
332
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0129)
|
333
333
|
Or:
|
334
334
|
Further information about the associated attribute(s).
|
335
|
-
(GVF1_0130)
|
335
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0130)
|
336
336
|
Or:
|
337
337
|
Further information about the associated attribute(s).
|
338
|
-
(GVF1_0131)
|
338
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0131)
|
339
339
|
"""
|
340
|
-
return [ _namespace_GVF1O('GVF1_0126'), _namespace_GVF1O('GVF1_0127'), _namespace_GVF1O('GVF1_0129'), _namespace_GVF1O('GVF1_0130'), _namespace_GVF1O('GVF1_0131') ]
|
340
|
+
return [ cls._namespace_GVF1O('GVF1_0126'), cls._namespace_GVF1O('GVF1_0127'), cls._namespace_GVF1O('GVF1_0129'), cls._namespace_GVF1O('GVF1_0130'), cls._namespace_GVF1O('GVF1_0131') ]
|
341
341
|
|
342
342
|
@classmethod
|
343
343
|
def attribute_properties(cls):
|
344
344
|
"""Either:
|
345
345
|
Properties about Attribute instances.
|
346
|
-
(cls, GVF1_0128)
|
346
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0128)
|
347
347
|
Or:
|
348
348
|
Properties that are directly associated with Attribute class instances.
|
349
|
-
(GVF1_0064)
|
349
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0064)
|
350
350
|
"""
|
351
|
-
return [ _namespace_GVF1O('GVF1_0128'), _namespace_GVF1O('GVF1_0064') ]
|
351
|
+
return [ cls._namespace_GVF1O('GVF1_0128'), cls._namespace_GVF1O('GVF1_0064') ]
|
352
352
|
|
353
353
|
@classmethod
|
354
354
|
def sex(cls):
|
355
355
|
"""Denotes the sex of the sequenced individual for single-individual sets.
|
356
|
-
(cls, GVF1_0147)
|
356
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0147)
|
357
357
|
"""
|
358
|
-
return _namespace_GVF1O('GVF1_0147')
|
358
|
+
return cls._namespace_GVF1O('GVF1_0147')
|
359
359
|
|
360
360
|
@classmethod
|
361
361
|
def genomic_source(cls):
|
362
362
|
"""Denotes the source of genomic data (cls, on a cell-type level).
|
363
|
-
(GVF1_0148)
|
363
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0148)
|
364
364
|
"""
|
365
|
-
return _namespace_GVF1O('GVF1_0148')
|
365
|
+
return cls._namespace_GVF1O('GVF1_0148')
|
366
366
|
|
367
367
|
@classmethod
|
368
368
|
def feature_ontology(cls):
|
369
369
|
"""Explicit link-out to one or more ontologies that have been used for describing features. This is a meta comment about the URIs that link out to SO/SOFA or other ontologies.
|
370
|
-
(cls, GVF1_0150)
|
370
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0150)
|
371
371
|
"""
|
372
|
-
return _namespace_GVF1O('GVF1_0150')
|
372
|
+
return cls._namespace_GVF1O('GVF1_0150')
|
373
373
|
|
374
374
|
@classmethod
|
375
375
|
def target(cls):
|
376
376
|
"""Identifies the target that the features aligns to.
|
377
|
-
(cls, GVF1_0155)
|
377
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0155)
|
378
378
|
"""
|
379
|
-
return _namespace_GVF1O('GVF1_0155')
|
379
|
+
return cls._namespace_GVF1O('GVF1_0155')
|
380
380
|
|
381
381
|
@classmethod
|
382
382
|
def source(cls):
|
383
383
|
"""A free text qualifier that describes the algorithm or operating procedure that generated this feature. For example, the name of the software that generated this feature or a database name.
|
384
|
-
(cls, GVF1_0005)
|
384
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0005)
|
385
385
|
"""
|
386
|
-
return _namespace_GVF1O('GVF1_0005')
|
386
|
+
return cls._namespace_GVF1O('GVF1_0005')
|
387
387
|
|
388
388
|
@classmethod
|
389
389
|
def type(cls):
|
390
390
|
"""Type of the feature, which is either an entry the "lite" version of the Sequence Ontology (cls, SOFA) or a child entry of sequence_feature (SO:0000110) of the full Sequence Ontology (SO).
|
391
|
-
(GVF1_0006)
|
391
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0006)
|
392
392
|
"""
|
393
|
-
return _namespace_GVF1O('GVF1_0006')
|
393
|
+
return cls._namespace_GVF1O('GVF1_0006')
|
394
394
|
|
395
395
|
@classmethod
|
396
396
|
def start(cls):
|
397
397
|
"""Either:
|
398
398
|
Start coordinate of the feature on the seqid landmark.
|
399
|
-
(cls, GVF1_0007)
|
399
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0007)
|
400
400
|
Or:
|
401
401
|
A coordinate that defines the start of an ambiguous coordinate range.
|
402
|
-
(GVF1_0048)
|
402
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0048)
|
403
403
|
Or:
|
404
404
|
Start coordinate of the feature on the seqid landmark.
|
405
|
-
(GVF1_0073)
|
405
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0073)
|
406
406
|
Or:
|
407
407
|
Start coordinate of the target.
|
408
|
-
(GVF1_0094)
|
408
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0094)
|
409
409
|
Or:
|
410
410
|
Genomic start coordinate of the landmark.
|
411
|
-
(GVF1_0138)
|
411
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0138)
|
412
412
|
"""
|
413
|
-
return [ _namespace_GVF1O('GVF1_0007'), _namespace_GVF1O('GVF1_0048'), _namespace_GVF1O('GVF1_0073'), _namespace_GVF1O('GVF1_0094'), _namespace_GVF1O('GVF1_0138') ]
|
413
|
+
return [ cls._namespace_GVF1O('GVF1_0007'), cls._namespace_GVF1O('GVF1_0048'), cls._namespace_GVF1O('GVF1_0073'), cls._namespace_GVF1O('GVF1_0094'), cls._namespace_GVF1O('GVF1_0138') ]
|
414
414
|
|
415
415
|
@classmethod
|
416
416
|
def end(cls):
|
417
417
|
"""Either:
|
418
418
|
End coordinate of the feature on the seqid landmark.
|
419
|
-
(cls, GVF1_0008)
|
419
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0008)
|
420
420
|
Or:
|
421
421
|
A coordinate that defines the end of an ambiguous coordinate range.
|
422
|
-
(GVF1_0049)
|
422
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0049)
|
423
423
|
Or:
|
424
424
|
End coordinate of the feature on the seqid landmark.
|
425
|
-
(GVF1_0074)
|
425
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0074)
|
426
426
|
Or:
|
427
427
|
End coordinate of the target.
|
428
|
-
(GVF1_0095)
|
428
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0095)
|
429
429
|
Or:
|
430
430
|
Genomic end coordinate of the landmark.
|
431
|
-
(GVF1_0139)
|
431
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0139)
|
432
432
|
"""
|
433
|
-
return [ _namespace_GVF1O('GVF1_0008'), _namespace_GVF1O('GVF1_0049'), _namespace_GVF1O('GVF1_0074'), _namespace_GVF1O('GVF1_0095'), _namespace_GVF1O('GVF1_0139') ]
|
433
|
+
return [ cls._namespace_GVF1O('GVF1_0008'), cls._namespace_GVF1O('GVF1_0049'), cls._namespace_GVF1O('GVF1_0074'), cls._namespace_GVF1O('GVF1_0095'), cls._namespace_GVF1O('GVF1_0139') ]
|
434
434
|
|
435
435
|
@classmethod
|
436
436
|
def score(cls):
|
437
437
|
"""Score of the feature. For example, an E-value for sequence similarity features or a P-value for ab initio gene prediction features.
|
438
|
-
(cls, GVF1_0009)
|
438
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0009)
|
439
439
|
"""
|
440
|
-
return _namespace_GVF1O('GVF1_0009')
|
440
|
+
return cls._namespace_GVF1O('GVF1_0009')
|
441
441
|
|
442
442
|
@classmethod
|
443
443
|
def tag(cls):
|
444
444
|
"""Either:
|
445
445
|
Tag name of a feature attribute.
|
446
|
-
(cls, GVF1_0013)
|
446
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0013)
|
447
447
|
Or:
|
448
448
|
Tag name of an user defined structured attribute.
|
449
|
-
(GVF1_0154)
|
449
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0154)
|
450
450
|
"""
|
451
|
-
return [ _namespace_GVF1O('GVF1_0013'), _namespace_GVF1O('GVF1_0154') ]
|
451
|
+
return [ cls._namespace_GVF1O('GVF1_0013'), cls._namespace_GVF1O('GVF1_0154') ]
|
452
452
|
|
453
453
|
@classmethod
|
454
454
|
def gvf_version(cls):
|
455
455
|
"""Version of the GVF specification that defines the feature set contents.
|
456
|
-
(cls, GVF1_0022)
|
456
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0022)
|
457
457
|
"""
|
458
|
-
return _namespace_GVF1O('GVF1_0022')
|
458
|
+
return cls._namespace_GVF1O('GVF1_0022')
|
459
459
|
|
460
460
|
@classmethod
|
461
461
|
def build(cls):
|
462
462
|
"""Name of a genome assembly build that denotes the provenance of features in a feature set. For example, 'NCBI 36' or 'FlyBase r4.1'.
|
463
|
-
(cls, GVF1_0024)
|
463
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0024)
|
464
464
|
"""
|
465
|
-
return _namespace_GVF1O('GVF1_0024')
|
465
|
+
return cls._namespace_GVF1O('GVF1_0024')
|
466
466
|
|
467
467
|
@classmethod
|
468
468
|
def variant_seq(cls):
|
469
469
|
"""All sequence variations at a locus -- including the reference sequence when appropriate (cls, for example, when the locus is heterozygous). If the feature is on the minus strand, then the sequence is the reverse-compliment of the reference genome for these coordinates.
|
470
|
-
(GVF1_0025)
|
470
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0025)
|
471
471
|
"""
|
472
|
-
return _namespace_GVF1O('GVF1_0025')
|
472
|
+
return cls._namespace_GVF1O('GVF1_0025')
|
473
473
|
|
474
474
|
@classmethod
|
475
475
|
def id(cls):
|
476
476
|
"""Either:
|
477
477
|
A unique identifier for the feature within the feature set.
|
478
|
-
(cls, GVF1_0026)
|
478
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0026)
|
479
479
|
Or:
|
480
480
|
ID that uniquely establishes the Landmark's identity within a Set.
|
481
|
-
(GVF1_0137)
|
481
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0137)
|
482
482
|
"""
|
483
|
-
return [ _namespace_GVF1O('GVF1_0026'), _namespace_GVF1O('GVF1_0137') ]
|
483
|
+
return [ cls._namespace_GVF1O('GVF1_0026'), cls._namespace_GVF1O('GVF1_0137') ]
|
484
484
|
|
485
485
|
@classmethod
|
486
486
|
def alias(cls):
|
487
487
|
"""Secondary name of a feature, which can be HGVS/ISCN nomenclature names, but not cross-references to databases (cls, e.g. dbSNP, OMIM) which should use the dbxref property.
|
488
|
-
(GVF1_0027)
|
488
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0027)
|
489
489
|
"""
|
490
|
-
return _namespace_GVF1O('GVF1_0027')
|
490
|
+
return cls._namespace_GVF1O('GVF1_0027')
|
491
491
|
|
492
492
|
@classmethod
|
493
493
|
def reference_seq(cls):
|
494
494
|
"""Sequence from the reference genome.
|
495
|
-
(cls, GVF1_0031)
|
495
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0031)
|
496
496
|
"""
|
497
|
-
return _namespace_GVF1O('GVF1_0031')
|
497
|
+
return cls._namespace_GVF1O('GVF1_0031')
|
498
498
|
|
499
499
|
@classmethod
|
500
500
|
def variant_reads(cls):
|
501
501
|
"""Number of reads that are supporting this variant.
|
502
|
-
(cls, GVF1_0032)
|
502
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0032)
|
503
503
|
"""
|
504
|
-
return _namespace_GVF1O('GVF1_0032')
|
504
|
+
return cls._namespace_GVF1O('GVF1_0032')
|
505
505
|
|
506
506
|
@classmethod
|
507
507
|
def total_reads(cls):
|
508
508
|
"""Total number of reads.
|
509
|
-
(cls, GVF1_0037)
|
509
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0037)
|
510
510
|
"""
|
511
|
-
return _namespace_GVF1O('GVF1_0037')
|
511
|
+
return cls._namespace_GVF1O('GVF1_0037')
|
512
512
|
|
513
513
|
@classmethod
|
514
514
|
def variant_freq(cls):
|
515
515
|
"""Frequency of a variant in a population.
|
516
|
-
(cls, GVF1_0039)
|
516
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0039)
|
517
517
|
"""
|
518
|
-
return _namespace_GVF1O('GVF1_0039')
|
518
|
+
return cls._namespace_GVF1O('GVF1_0039')
|
519
519
|
|
520
520
|
@classmethod
|
521
521
|
def feature(cls):
|
522
522
|
"""Features that are affected by this sequence alteration effect. This can be an external feature identifier, such as an Ensembl gene/transcript identifier.
|
523
|
-
(cls, GVF1_0044)
|
523
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0044)
|
524
524
|
"""
|
525
|
-
return _namespace_GVF1O('GVF1_0044')
|
525
|
+
return cls._namespace_GVF1O('GVF1_0044')
|
526
526
|
|
527
527
|
@classmethod
|
528
528
|
def phased(cls):
|
529
529
|
"""Either:
|
530
530
|
Unclear from GVF specification.
|
531
|
-
(cls, GVF1_0050)
|
531
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0050)
|
532
532
|
Or:
|
533
533
|
Indicates whether this particular is phased. Used to encode ##phased-genotypes statements.
|
534
|
-
(GVF1_0101)
|
534
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0101)
|
535
535
|
"""
|
536
|
-
return [ _namespace_GVF1O('GVF1_0050'), _namespace_GVF1O('GVF1_0101') ]
|
536
|
+
return [ cls._namespace_GVF1O('GVF1_0050'), cls._namespace_GVF1O('GVF1_0101') ]
|
537
537
|
|
538
538
|
@classmethod
|
539
539
|
def variant_codon(cls):
|
540
540
|
"""Describes the codon that overlaps this variant.
|
541
|
-
(cls, GVF1_0054)
|
541
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0054)
|
542
542
|
"""
|
543
|
-
return _namespace_GVF1O('GVF1_0054')
|
543
|
+
return cls._namespace_GVF1O('GVF1_0054')
|
544
544
|
|
545
545
|
@classmethod
|
546
546
|
def reference_codon(cls):
|
547
547
|
"""Describes the codon from the reference sequence whose coordinates overlap with this variant.
|
548
|
-
(cls, GVF1_0055)
|
548
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0055)
|
549
549
|
"""
|
550
|
-
return _namespace_GVF1O('GVF1_0055')
|
550
|
+
return cls._namespace_GVF1O('GVF1_0055')
|
551
551
|
|
552
552
|
@classmethod
|
553
553
|
def variant_aa(cls):
|
554
554
|
"""Amino acid that overlaps with the variant.
|
555
|
-
(cls, GVF1_0056)
|
555
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0056)
|
556
556
|
"""
|
557
|
-
return _namespace_GVF1O('GVF1_0056')
|
557
|
+
return cls._namespace_GVF1O('GVF1_0056')
|
558
558
|
|
559
559
|
@classmethod
|
560
560
|
def reference_aa(cls):
|
561
561
|
"""Amino acid in the reference genome that overlaps with a variant's genome coordinates.
|
562
|
-
(cls, GVF1_0057)
|
562
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0057)
|
563
563
|
"""
|
564
|
-
return _namespace_GVF1O('GVF1_0057')
|
564
|
+
return cls._namespace_GVF1O('GVF1_0057')
|
565
565
|
|
566
566
|
@classmethod
|
567
567
|
def range_properties(cls):
|
568
568
|
"""Properties that are directly associated with Range class instances.
|
569
|
-
(cls, GVF1_0061)
|
569
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0061)
|
570
570
|
"""
|
571
|
-
return _namespace_GVF1O('GVF1_0061')
|
571
|
+
return cls._namespace_GVF1O('GVF1_0061')
|
572
572
|
|
573
573
|
@classmethod
|
574
574
|
def a_context(cls):
|
575
575
|
"""Sequence context (cls, positive strand) of a feature on the 5' end.
|
576
|
-
(GVF1_0076)
|
576
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0076)
|
577
577
|
"""
|
578
|
-
return _namespace_GVF1O('GVF1_0076')
|
578
|
+
return cls._namespace_GVF1O('GVF1_0076')
|
579
579
|
|
580
580
|
@classmethod
|
581
581
|
def gff_version(cls):
|
582
582
|
"""Version of the GFF specification that defines the feature set contents apart from GVF related definitions.
|
583
|
-
(cls, GVF1_0081)
|
583
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0081)
|
584
584
|
"""
|
585
|
-
return _namespace_GVF1O('GVF1_0081')
|
585
|
+
return cls._namespace_GVF1O('GVF1_0081')
|
586
586
|
|
587
587
|
@classmethod
|
588
588
|
def file_date(cls):
|
589
589
|
"""Creation date of the GVF file that this set stems from.
|
590
|
-
(cls, GVF1_0082)
|
590
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0082)
|
591
591
|
"""
|
592
|
-
return _namespace_GVF1O('GVF1_0082')
|
592
|
+
return cls._namespace_GVF1O('GVF1_0082')
|
593
593
|
|
594
594
|
@classmethod
|
595
595
|
def target_id(cls):
|
596
596
|
"""ID or accession of the target alignment.
|
597
|
-
(cls, GVF1_0093)
|
597
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0093)
|
598
598
|
"""
|
599
|
-
return _namespace_GVF1O('GVF1_0093')
|
599
|
+
return cls._namespace_GVF1O('GVF1_0093')
|
600
600
|
|
601
601
|
@classmethod
|
602
602
|
def ontology_term(cls):
|
603
603
|
"""A cross-reference to an ontology term that is associated with a feature.
|
604
|
-
(cls, GVF1_0096)
|
604
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0096)
|
605
605
|
"""
|
606
|
-
return _namespace_GVF1O('GVF1_0096')
|
606
|
+
return cls._namespace_GVF1O('GVF1_0096')
|
607
607
|
|
608
608
|
@classmethod
|
609
609
|
def comment(cls):
|
610
610
|
"""An arbitrary comment. Free text.
|
611
|
-
(cls, GVF1_0105)
|
611
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0105)
|
612
612
|
"""
|
613
|
-
return _namespace_GVF1O('GVF1_0105')
|
613
|
+
return cls._namespace_GVF1O('GVF1_0105')
|
614
614
|
|
615
615
|
@classmethod
|
616
616
|
def platform_class(cls):
|
617
617
|
"""Type of technology used to gather the variant data. Unrestricted range due to open specification.
|
618
|
-
(cls, GVF1_0106)
|
618
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0106)
|
619
619
|
"""
|
620
|
-
return _namespace_GVF1O('GVF1_0106')
|
620
|
+
return cls._namespace_GVF1O('GVF1_0106')
|
621
621
|
|
622
622
|
@classmethod
|
623
623
|
def platform_name(cls):
|
624
624
|
"""Sequencer or other machine used to collect the variant data. Unrestricted range due to open specification.
|
625
|
-
(cls, GVF1_0108)
|
625
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0108)
|
626
626
|
"""
|
627
|
-
return _namespace_GVF1O('GVF1_0108')
|
627
|
+
return cls._namespace_GVF1O('GVF1_0108')
|
628
628
|
|
629
629
|
@classmethod
|
630
630
|
def read_length(cls):
|
631
631
|
"""Undocumented in GVF specification.
|
632
|
-
(cls, GVF1_0132)
|
632
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0132)
|
633
633
|
"""
|
634
|
-
return _namespace_GVF1O('GVF1_0132')
|
634
|
+
return cls._namespace_GVF1O('GVF1_0132')
|
635
635
|
|
636
636
|
@classmethod
|
637
637
|
def read_pair_span(cls):
|
638
638
|
"""Undocumented in GVF specification.
|
639
|
-
(cls, GVF1_0133)
|
639
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0133)
|
640
640
|
"""
|
641
|
-
return _namespace_GVF1O('GVF1_0133')
|
641
|
+
return cls._namespace_GVF1O('GVF1_0133')
|
642
642
|
|
643
643
|
@classmethod
|
644
644
|
def average_coverage(cls):
|
645
645
|
"""Undocumented in GVF specification.
|
646
|
-
(cls, GVF1_0134)
|
646
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0134)
|
647
647
|
"""
|
648
|
-
return _namespace_GVF1O('GVF1_0134')
|
648
|
+
return cls._namespace_GVF1O('GVF1_0134')
|
649
649
|
|
650
650
|
@classmethod
|
651
651
|
def landmark_properties(cls):
|
652
652
|
"""Properties that are directly associated with Landmark class instances.
|
653
|
-
(cls, GVF1_0136)
|
653
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0136)
|
654
654
|
"""
|
655
|
-
return _namespace_GVF1O('GVF1_0136')
|
655
|
+
return cls._namespace_GVF1O('GVF1_0136')
|
656
656
|
|
657
657
|
@classmethod
|
658
658
|
def file_version(cls):
|
659
659
|
"""Version of the GVF file that this set stems from.
|
660
|
-
(cls, GVF1_0149)
|
660
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0149)
|
661
661
|
"""
|
662
|
-
return _namespace_GVF1O('GVF1_0149')
|
662
|
+
return cls._namespace_GVF1O('GVF1_0149')
|
663
663
|
|
664
664
|
@classmethod
|
665
665
|
def structuredattribute_properties(cls):
|
666
666
|
"""Properties that are directly associated with StructuredAttribute class instances.
|
667
|
-
(cls, GVF1_0153)
|
667
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0153)
|
668
668
|
"""
|
669
|
-
return _namespace_GVF1O('GVF1_0153')
|
669
|
+
return cls._namespace_GVF1O('GVF1_0153')
|
670
670
|
|
671
671
|
@classmethod
|
672
672
|
def sequence(cls):
|
673
673
|
"""Either:
|
674
674
|
Sequence associated with this feature, if it has been specified using a FASTA string.
|
675
|
-
(cls, GVF1_0156)
|
675
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0156)
|
676
676
|
Or:
|
677
677
|
Sequence associated with this feature, if it has been specified using a FASTA string.
|
678
|
-
(GVF1_0157)
|
678
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0157)
|
679
679
|
"""
|
680
|
-
return [ _namespace_GVF1O('GVF1_0156'), _namespace_GVF1O('GVF1_0157') ]
|
680
|
+
return [ cls._namespace_GVF1O('GVF1_0156'), cls._namespace_GVF1O('GVF1_0157') ]
|
681
681
|
|
682
682
|
@classmethod
|
683
683
|
def Set(cls):
|
684
684
|
"""Set of genomic sequence features, whose identifiers are unique within the set.
|
685
|
-
(cls, GVF1_0001)
|
685
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0001)
|
686
686
|
"""
|
687
|
-
return _namespace_GVF1O('GVF1_0001')
|
687
|
+
return cls._namespace_GVF1O('GVF1_0001')
|
688
688
|
|
689
689
|
@classmethod
|
690
690
|
def Feature(cls):
|
691
691
|
"""A genomic sequence feature.
|
692
|
-
(cls, GVF1_0002)
|
692
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0002)
|
693
693
|
"""
|
694
|
-
return _namespace_GVF1O('GVF1_0002')
|
694
|
+
return cls._namespace_GVF1O('GVF1_0002')
|
695
695
|
|
696
696
|
@classmethod
|
697
697
|
def Attribute(cls):
|
698
698
|
"""Representation of attribute tag/value pairs that are not covered by specific classes such as Effect or Variant.
|
699
|
-
(cls, GVF1_0003)
|
699
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0003)
|
700
700
|
"""
|
701
|
-
return _namespace_GVF1O('GVF1_0003')
|
701
|
+
return cls._namespace_GVF1O('GVF1_0003')
|
702
702
|
|
703
703
|
@classmethod
|
704
704
|
def Strand(cls):
|
705
705
|
"""Class describing a genomic strand. Instances of the class (cls, individuals) are used to denote forward-/reverse-strands, etc.
|
706
|
-
(GVF1_0016)
|
706
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0016)
|
707
707
|
"""
|
708
|
-
return _namespace_GVF1O('GVF1_0016')
|
708
|
+
return cls._namespace_GVF1O('GVF1_0016')
|
709
709
|
|
710
710
|
@classmethod
|
711
711
|
def Variant(cls):
|
712
712
|
"""Describing specific alterations of a feature.
|
713
|
-
(cls, GVF1_0033)
|
713
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0033)
|
714
714
|
"""
|
715
|
-
return _namespace_GVF1O('GVF1_0033')
|
715
|
+
return cls._namespace_GVF1O('GVF1_0033')
|
716
716
|
|
717
717
|
@classmethod
|
718
718
|
def SequencedIndividual(cls):
|
719
719
|
"""Aggregated sequencing information for a particular individual.
|
720
|
-
(cls, GVF1_0035)
|
720
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0035)
|
721
721
|
"""
|
722
|
-
return _namespace_GVF1O('GVF1_0035')
|
722
|
+
return cls._namespace_GVF1O('GVF1_0035')
|
723
723
|
|
724
724
|
@classmethod
|
725
725
|
def Effect(cls):
|
726
726
|
"""Describing the effect of a feature variant.
|
727
|
-
(cls, GVF1_0040)
|
727
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0040)
|
728
728
|
"""
|
729
|
-
return _namespace_GVF1O('GVF1_0040')
|
729
|
+
return cls._namespace_GVF1O('GVF1_0040')
|
730
730
|
|
731
731
|
@classmethod
|
732
732
|
def Range(cls):
|
733
733
|
"""Describe ambiguity in either start or end coordinates.
|
734
|
-
(cls, GVF1_0045)
|
734
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0045)
|
735
735
|
"""
|
736
|
-
return _namespace_GVF1O('GVF1_0045')
|
736
|
+
return cls._namespace_GVF1O('GVF1_0045')
|
737
737
|
|
738
738
|
@classmethod
|
739
739
|
def Chromosome(cls):
|
740
740
|
"""An abstract representation of a chromosome to represent ploidy.
|
741
|
-
(cls, GVF1_0052)
|
741
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0052)
|
742
742
|
"""
|
743
|
-
return _namespace_GVF1O('GVF1_0052')
|
743
|
+
return cls._namespace_GVF1O('GVF1_0052')
|
744
744
|
|
745
745
|
@classmethod
|
746
746
|
def Breakpoint(cls):
|
747
747
|
"""Describes the source or destination of a zero-length sequence alteration.
|
748
|
-
(cls, GVF1_0058)
|
748
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0058)
|
749
749
|
"""
|
750
|
-
return _namespace_GVF1O('GVF1_0058')
|
750
|
+
return cls._namespace_GVF1O('GVF1_0058')
|
751
751
|
|
752
752
|
@classmethod
|
753
753
|
def Zygosity(cls):
|
754
754
|
"""Denotes the zygosity of alleles.
|
755
|
-
(cls, GVF1_0084)
|
755
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0084)
|
756
756
|
"""
|
757
|
-
return _namespace_GVF1O('GVF1_0084')
|
757
|
+
return cls._namespace_GVF1O('GVF1_0084')
|
758
758
|
|
759
759
|
@classmethod
|
760
760
|
def Target(cls):
|
761
761
|
"""Indicates a feature's "target" of a nucleotide-to-nucleotide or protein-to-nucleotide alignment.
|
762
|
-
(cls, GVF1_0088)
|
762
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0088)
|
763
763
|
"""
|
764
|
-
return _namespace_GVF1O('GVF1_0088')
|
764
|
+
return cls._namespace_GVF1O('GVF1_0088')
|
765
765
|
|
766
766
|
@classmethod
|
767
767
|
def TechnologyPlatform(cls):
|
768
768
|
"""Details about the sequencing/microarray technology used to gather the data in a set.
|
769
|
-
(cls, GVF1_0097)
|
769
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0097)
|
770
770
|
"""
|
771
|
-
return _namespace_GVF1O('GVF1_0097')
|
771
|
+
return cls._namespace_GVF1O('GVF1_0097')
|
772
772
|
|
773
773
|
@classmethod
|
774
774
|
def DataSource(cls):
|
775
775
|
"""Provides information about the source of the data. For example, it can link out to actual sequences associated with the Feature individuals in a Set.
|
776
|
-
(cls, GVF1_0098)
|
776
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0098)
|
777
777
|
"""
|
778
|
-
return _namespace_GVF1O('GVF1_0098')
|
778
|
+
return cls._namespace_GVF1O('GVF1_0098')
|
779
779
|
|
780
780
|
@classmethod
|
781
781
|
def Method(cls):
|
782
782
|
"""Information about the used scoring algorithm or method.
|
783
|
-
(cls, GVF1_0099)
|
783
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0099)
|
784
784
|
"""
|
785
|
-
return _namespace_GVF1O('GVF1_0099')
|
785
|
+
return cls._namespace_GVF1O('GVF1_0099')
|
786
786
|
|
787
787
|
@classmethod
|
788
788
|
def PhenotypeDescription(cls):
|
789
789
|
"""Additional information about an individual's phenotype.
|
790
|
-
(cls, GVF1_0100)
|
790
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0100)
|
791
791
|
"""
|
792
|
-
return _namespace_GVF1O('GVF1_0100')
|
792
|
+
return cls._namespace_GVF1O('GVF1_0100')
|
793
793
|
|
794
794
|
@classmethod
|
795
795
|
def ReadType(cls):
|
796
796
|
"""Type of reads obtained for a given technology platform.
|
797
|
-
(cls, GVF1_0109)
|
797
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0109)
|
798
798
|
"""
|
799
|
-
return _namespace_GVF1O('GVF1_0109')
|
799
|
+
return cls._namespace_GVF1O('GVF1_0109')
|
800
800
|
|
801
801
|
@classmethod
|
802
802
|
def DataType(cls):
|
803
803
|
"""Determines the datatype of a variant sequence.
|
804
|
-
(cls, GVF1_0114)
|
804
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0114)
|
805
805
|
"""
|
806
|
-
return _namespace_GVF1O('GVF1_0114')
|
806
|
+
return cls._namespace_GVF1O('GVF1_0114')
|
807
807
|
|
808
808
|
@classmethod
|
809
809
|
def Landmark(cls):
|
810
810
|
"""A landmark that establishes the coordinate system for features.
|
811
|
-
(cls, GVF1_0135)
|
811
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0135)
|
812
812
|
"""
|
813
|
-
return _namespace_GVF1O('GVF1_0135')
|
813
|
+
return cls._namespace_GVF1O('GVF1_0135')
|
814
814
|
|
815
815
|
@classmethod
|
816
816
|
def Sex(cls):
|
817
817
|
"""For single individual sets, the Sex class' OWL-individuals can be used to specify the sex of the sequenced (cls, real-life) individuals.
|
818
|
-
(GVF1_0140)
|
818
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0140)
|
819
819
|
"""
|
820
|
-
return _namespace_GVF1O('GVF1_0140')
|
820
|
+
return cls._namespace_GVF1O('GVF1_0140')
|
821
821
|
|
822
822
|
@classmethod
|
823
823
|
def GenomicSource(cls):
|
824
824
|
"""An enumerated class for determining the genomic source (cls, cell type) of sequenced data.
|
825
|
-
(GVF1_0141)
|
825
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0141)
|
826
826
|
"""
|
827
|
-
return _namespace_GVF1O('GVF1_0141')
|
827
|
+
return cls._namespace_GVF1O('GVF1_0141')
|
828
828
|
|
829
829
|
@classmethod
|
830
830
|
def StructuredAttribute(cls):
|
831
831
|
"""Representation of attribute tag/value pairs that are specific to particular structured attributes, but which are not covered by the GVF specification.
|
832
|
-
(cls, GVF1_0151)
|
832
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0151)
|
833
833
|
"""
|
834
|
-
return _namespace_GVF1O('GVF1_0151')
|
834
|
+
return cls._namespace_GVF1O('GVF1_0151')
|
835
835
|
|
836
836
|
@classmethod
|
837
837
|
def Positive(cls):
|
838
838
|
"""Location on the positive (cls, forward) strand.
|
839
|
-
(GVF1_0017)
|
839
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0017)
|
840
840
|
"""
|
841
|
-
return _namespace_GVF1O('GVF1_0017')
|
841
|
+
return cls._namespace_GVF1O('GVF1_0017')
|
842
842
|
|
843
843
|
@classmethod
|
844
844
|
def Negative(cls):
|
845
845
|
"""Location on the negative (cls, reverse) strand.
|
846
|
-
(GVF1_0018)
|
846
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0018)
|
847
847
|
"""
|
848
|
-
return _namespace_GVF1O('GVF1_0018')
|
848
|
+
return cls._namespace_GVF1O('GVF1_0018')
|
849
849
|
|
850
850
|
@classmethod
|
851
851
|
def UnknownStrand(cls):
|
852
852
|
"""Strand was not determined, which leaves it open whether the location is on the positive (cls, forward) or negative (reverse) strand.
|
853
|
-
(GVF1_0019)
|
853
|
+
(http://www.biointerchange.org/gvf1o#GVF1_0019)
|
854
854
|
"""
|
855
|
-
return _namespace_GVF1O('GVF1_0019')
|
855
|
+
return cls._namespace_GVF1O('GVF1_0019')
|
856
856
|
|
857
857
|
@classmethod
|
858
858
|
def NotStranded(cls):
|
859
859
|
"""Strand is not applicable.
|
860
|
-
(cls, GVF1_0020)
|
860
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0020)
|
861
861
|
"""
|
862
|
-
return _namespace_GVF1O('GVF1_0020')
|
862
|
+
return cls._namespace_GVF1O('GVF1_0020')
|
863
863
|
|
864
864
|
@classmethod
|
865
865
|
def Heterozygous(cls):
|
866
866
|
"""Denotes heterozygous alleles.
|
867
|
-
(cls, GVF1_0085)
|
867
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0085)
|
868
868
|
"""
|
869
|
-
return _namespace_GVF1O('GVF1_0085')
|
869
|
+
return cls._namespace_GVF1O('GVF1_0085')
|
870
870
|
|
871
871
|
@classmethod
|
872
872
|
def Homozygous(cls):
|
873
873
|
"""Denotes homozygous alleles.
|
874
|
-
(cls, GVF1_0086)
|
874
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0086)
|
875
875
|
"""
|
876
|
-
return _namespace_GVF1O('GVF1_0086')
|
876
|
+
return cls._namespace_GVF1O('GVF1_0086')
|
877
877
|
|
878
878
|
@classmethod
|
879
879
|
def Hemizygous(cls):
|
880
880
|
"""Denotes hemizygous alleles.
|
881
|
-
(cls, GVF1_0087)
|
881
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0087)
|
882
882
|
"""
|
883
|
-
return _namespace_GVF1O('GVF1_0087')
|
883
|
+
return cls._namespace_GVF1O('GVF1_0087')
|
884
884
|
|
885
885
|
@classmethod
|
886
886
|
def Fragment(cls):
|
887
887
|
"""Denotes reads that are fragments.
|
888
|
-
(cls, GVF1_0110)
|
888
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0110)
|
889
889
|
"""
|
890
|
-
return _namespace_GVF1O('GVF1_0110')
|
890
|
+
return cls._namespace_GVF1O('GVF1_0110')
|
891
891
|
|
892
892
|
@classmethod
|
893
893
|
def Pair(cls):
|
894
894
|
"""Denotes reads that are pairs.
|
895
|
-
(cls, GVF1_0111)
|
895
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0111)
|
896
896
|
"""
|
897
|
-
return _namespace_GVF1O('GVF1_0111')
|
897
|
+
return cls._namespace_GVF1O('GVF1_0111')
|
898
898
|
|
899
899
|
@classmethod
|
900
900
|
def DNASequence(cls):
|
901
901
|
"""Denotes a DNA sequence.
|
902
|
-
(cls, GVF1_0115)
|
902
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0115)
|
903
903
|
"""
|
904
|
-
return _namespace_GVF1O('GVF1_0115')
|
904
|
+
return cls._namespace_GVF1O('GVF1_0115')
|
905
905
|
|
906
906
|
@classmethod
|
907
907
|
def RNASequence(cls):
|
908
908
|
"""Denotes an RNA sequence.
|
909
|
-
(cls, GVF1_0116)
|
909
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0116)
|
910
910
|
"""
|
911
|
-
return _namespace_GVF1O('GVF1_0116')
|
911
|
+
return cls._namespace_GVF1O('GVF1_0116')
|
912
912
|
|
913
913
|
@classmethod
|
914
914
|
def DNAMicroarray(cls):
|
915
915
|
"""Denotes a DNA microarray probe.
|
916
|
-
(cls, GVF1_0117)
|
916
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0117)
|
917
917
|
"""
|
918
|
-
return _namespace_GVF1O('GVF1_0117')
|
918
|
+
return cls._namespace_GVF1O('GVF1_0117')
|
919
919
|
|
920
920
|
@classmethod
|
921
921
|
def ArrayComparativeGenomicHybridization(cls):
|
922
922
|
"""Denotes an array-comparative genomic hybridization.
|
923
|
-
(cls, GVF1_0118)
|
923
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0118)
|
924
924
|
"""
|
925
|
-
return _namespace_GVF1O('GVF1_0118')
|
925
|
+
return cls._namespace_GVF1O('GVF1_0118')
|
926
926
|
|
927
927
|
@classmethod
|
928
928
|
def Female(cls):
|
929
929
|
"""Denotes that a Set contains features of a female.
|
930
|
-
(cls, GVF1_0142)
|
930
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0142)
|
931
931
|
"""
|
932
|
-
return _namespace_GVF1O('GVF1_0142')
|
932
|
+
return cls._namespace_GVF1O('GVF1_0142')
|
933
933
|
|
934
934
|
@classmethod
|
935
935
|
def Male(cls):
|
936
936
|
"""Denotes that a Set contains features of a male.
|
937
|
-
(cls, GVF1_0143)
|
937
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0143)
|
938
938
|
"""
|
939
|
-
return _namespace_GVF1O('GVF1_0143')
|
939
|
+
return cls._namespace_GVF1O('GVF1_0143')
|
940
940
|
|
941
941
|
@classmethod
|
942
942
|
def Prenatal(cls):
|
943
943
|
"""Denotes that a set contains features of prenatal cells.
|
944
|
-
(cls, GVF1_0144)
|
944
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0144)
|
945
945
|
"""
|
946
|
-
return _namespace_GVF1O('GVF1_0144')
|
946
|
+
return cls._namespace_GVF1O('GVF1_0144')
|
947
947
|
|
948
948
|
@classmethod
|
949
949
|
def Germline(cls):
|
950
950
|
"""Denotes that a set contains features of germline cells.
|
951
|
-
(cls, GVF1_0145)
|
951
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0145)
|
952
952
|
"""
|
953
|
-
return _namespace_GVF1O('GVF1_0145')
|
953
|
+
return cls._namespace_GVF1O('GVF1_0145')
|
954
954
|
|
955
955
|
@classmethod
|
956
956
|
def Somatic(cls):
|
957
957
|
"""Denotes that a set contains features of somatic cells.
|
958
|
-
(cls, GVF1_0146)
|
958
|
+
(cls, http://www.biointerchange.org/gvf1o#GVF1_0146)
|
959
959
|
"""
|
960
|
-
return _namespace_GVF1O('GVF1_0146')
|
960
|
+
return cls._namespace_GVF1O('GVF1_0146')
|
961
961
|
|
962
962
|
@classmethod
|
963
963
|
def is_object_property(cls, uri):
|
@@ -965,111 +965,111 @@ class GVF1O:
|
|
965
965
|
|
966
966
|
uri -- URI that is tested for being an object property
|
967
967
|
"""
|
968
|
-
if uri == _namespace_GVF1O('GVF1_0004'):
|
968
|
+
if uri == cls._namespace_GVF1O('GVF1_0004'):
|
969
969
|
return True
|
970
|
-
if uri == _namespace_GVF1O('GVF1_0010'):
|
970
|
+
if uri == cls._namespace_GVF1O('GVF1_0010'):
|
971
971
|
return True
|
972
|
-
if uri == _namespace_GVF1O('GVF1_0012'):
|
972
|
+
if uri == cls._namespace_GVF1O('GVF1_0012'):
|
973
973
|
return True
|
974
|
-
if uri == _namespace_GVF1O('GVF1_0014'):
|
974
|
+
if uri == cls._namespace_GVF1O('GVF1_0014'):
|
975
975
|
return True
|
976
|
-
if uri == _namespace_GVF1O('GVF1_0015'):
|
976
|
+
if uri == cls._namespace_GVF1O('GVF1_0015'):
|
977
977
|
return True
|
978
|
-
if uri == _namespace_GVF1O('GVF1_0021'):
|
978
|
+
if uri == cls._namespace_GVF1O('GVF1_0021'):
|
979
979
|
return True
|
980
|
-
if uri == _namespace_GVF1O('GVF1_0023'):
|
980
|
+
if uri == cls._namespace_GVF1O('GVF1_0023'):
|
981
981
|
return True
|
982
|
-
if uri == _namespace_GVF1O('GVF1_0034'):
|
982
|
+
if uri == cls._namespace_GVF1O('GVF1_0034'):
|
983
983
|
return True
|
984
|
-
if uri == _namespace_GVF1O('GVF1_0036'):
|
984
|
+
if uri == cls._namespace_GVF1O('GVF1_0036'):
|
985
985
|
return True
|
986
|
-
if uri == _namespace_GVF1O('GVF1_0038'):
|
986
|
+
if uri == cls._namespace_GVF1O('GVF1_0038'):
|
987
987
|
return True
|
988
|
-
if uri == _namespace_GVF1O('GVF1_0041'):
|
988
|
+
if uri == cls._namespace_GVF1O('GVF1_0041'):
|
989
989
|
return True
|
990
|
-
if uri == _namespace_GVF1O('GVF1_0042'):
|
990
|
+
if uri == cls._namespace_GVF1O('GVF1_0042'):
|
991
991
|
return True
|
992
|
-
if uri == _namespace_GVF1O('GVF1_0043'):
|
992
|
+
if uri == cls._namespace_GVF1O('GVF1_0043'):
|
993
993
|
return True
|
994
|
-
if uri == _namespace_GVF1O('GVF1_0046'):
|
994
|
+
if uri == cls._namespace_GVF1O('GVF1_0046'):
|
995
995
|
return True
|
996
|
-
if uri == _namespace_GVF1O('GVF1_0047'):
|
996
|
+
if uri == cls._namespace_GVF1O('GVF1_0047'):
|
997
997
|
return True
|
998
|
-
if uri == _namespace_GVF1O('GVF1_0051'):
|
998
|
+
if uri == cls._namespace_GVF1O('GVF1_0051'):
|
999
999
|
return True
|
1000
|
-
if uri == _namespace_GVF1O('GVF1_0053'):
|
1000
|
+
if uri == cls._namespace_GVF1O('GVF1_0053'):
|
1001
1001
|
return True
|
1002
|
-
if uri == _namespace_GVF1O('GVF1_0066'):
|
1002
|
+
if uri == cls._namespace_GVF1O('GVF1_0066'):
|
1003
1003
|
return True
|
1004
|
-
if uri == _namespace_GVF1O('GVF1_0067'):
|
1004
|
+
if uri == cls._namespace_GVF1O('GVF1_0067'):
|
1005
1005
|
return True
|
1006
|
-
if uri == _namespace_GVF1O('GVF1_0068'):
|
1006
|
+
if uri == cls._namespace_GVF1O('GVF1_0068'):
|
1007
1007
|
return True
|
1008
|
-
if uri == _namespace_GVF1O('GVF1_0069'):
|
1008
|
+
if uri == cls._namespace_GVF1O('GVF1_0069'):
|
1009
1009
|
return True
|
1010
|
-
if uri == _namespace_GVF1O('GVF1_0070'):
|
1010
|
+
if uri == cls._namespace_GVF1O('GVF1_0070'):
|
1011
1011
|
return True
|
1012
|
-
if uri == _namespace_GVF1O('GVF1_0072'):
|
1012
|
+
if uri == cls._namespace_GVF1O('GVF1_0072'):
|
1013
1013
|
return True
|
1014
|
-
if uri == _namespace_GVF1O('GVF1_0075'):
|
1014
|
+
if uri == cls._namespace_GVF1O('GVF1_0075'):
|
1015
1015
|
return True
|
1016
|
-
if uri == _namespace_GVF1O('GVF1_0078'):
|
1016
|
+
if uri == cls._namespace_GVF1O('GVF1_0078'):
|
1017
1017
|
return True
|
1018
|
-
if uri == _namespace_GVF1O('GVF1_0079'):
|
1018
|
+
if uri == cls._namespace_GVF1O('GVF1_0079'):
|
1019
1019
|
return True
|
1020
|
-
if uri == _namespace_GVF1O('GVF1_0080'):
|
1020
|
+
if uri == cls._namespace_GVF1O('GVF1_0080'):
|
1021
1021
|
return True
|
1022
|
-
if uri == _namespace_GVF1O('GVF1_0083'):
|
1022
|
+
if uri == cls._namespace_GVF1O('GVF1_0083'):
|
1023
1023
|
return True
|
1024
|
-
if uri == _namespace_GVF1O('GVF1_0089'):
|
1024
|
+
if uri == cls._namespace_GVF1O('GVF1_0089'):
|
1025
1025
|
return True
|
1026
|
-
if uri == _namespace_GVF1O('GVF1_0090'):
|
1026
|
+
if uri == cls._namespace_GVF1O('GVF1_0090'):
|
1027
1027
|
return True
|
1028
|
-
if uri == _namespace_GVF1O('GVF1_0091'):
|
1028
|
+
if uri == cls._namespace_GVF1O('GVF1_0091'):
|
1029
1029
|
return True
|
1030
|
-
if uri == _namespace_GVF1O('GVF1_0102'):
|
1030
|
+
if uri == cls._namespace_GVF1O('GVF1_0102'):
|
1031
1031
|
return True
|
1032
|
-
if uri == _namespace_GVF1O('GVF1_0103'):
|
1032
|
+
if uri == cls._namespace_GVF1O('GVF1_0103'):
|
1033
1033
|
return True
|
1034
|
-
if uri == _namespace_GVF1O('GVF1_0104'):
|
1034
|
+
if uri == cls._namespace_GVF1O('GVF1_0104'):
|
1035
1035
|
return True
|
1036
|
-
if uri == _namespace_GVF1O('GVF1_0112'):
|
1036
|
+
if uri == cls._namespace_GVF1O('GVF1_0112'):
|
1037
1037
|
return True
|
1038
|
-
if uri == _namespace_GVF1O('GVF1_0119'):
|
1038
|
+
if uri == cls._namespace_GVF1O('GVF1_0119'):
|
1039
1039
|
return True
|
1040
|
-
if uri == _namespace_GVF1O('GVF1_0120'):
|
1040
|
+
if uri == cls._namespace_GVF1O('GVF1_0120'):
|
1041
1041
|
return True
|
1042
|
-
if uri == _namespace_GVF1O('GVF1_0121'):
|
1042
|
+
if uri == cls._namespace_GVF1O('GVF1_0121'):
|
1043
1043
|
return True
|
1044
|
-
if uri == _namespace_GVF1O('GVF1_0122'):
|
1044
|
+
if uri == cls._namespace_GVF1O('GVF1_0122'):
|
1045
1045
|
return True
|
1046
|
-
if uri == _namespace_GVF1O('GVF1_0123'):
|
1046
|
+
if uri == cls._namespace_GVF1O('GVF1_0123'):
|
1047
1047
|
return True
|
1048
|
-
if uri == _namespace_GVF1O('GVF1_0124'):
|
1048
|
+
if uri == cls._namespace_GVF1O('GVF1_0124'):
|
1049
1049
|
return True
|
1050
|
-
if uri == _namespace_GVF1O('GVF1_0125'):
|
1050
|
+
if uri == cls._namespace_GVF1O('GVF1_0125'):
|
1051
1051
|
return True
|
1052
|
-
if uri == _namespace_GVF1O('GVF1_0126'):
|
1052
|
+
if uri == cls._namespace_GVF1O('GVF1_0126'):
|
1053
1053
|
return True
|
1054
|
-
if uri == _namespace_GVF1O('GVF1_0127'):
|
1054
|
+
if uri == cls._namespace_GVF1O('GVF1_0127'):
|
1055
1055
|
return True
|
1056
|
-
if uri == _namespace_GVF1O('GVF1_0128'):
|
1056
|
+
if uri == cls._namespace_GVF1O('GVF1_0128'):
|
1057
1057
|
return True
|
1058
|
-
if uri == _namespace_GVF1O('GVF1_0129'):
|
1058
|
+
if uri == cls._namespace_GVF1O('GVF1_0129'):
|
1059
1059
|
return True
|
1060
|
-
if uri == _namespace_GVF1O('GVF1_0130'):
|
1060
|
+
if uri == cls._namespace_GVF1O('GVF1_0130'):
|
1061
1061
|
return True
|
1062
|
-
if uri == _namespace_GVF1O('GVF1_0131'):
|
1062
|
+
if uri == cls._namespace_GVF1O('GVF1_0131'):
|
1063
1063
|
return True
|
1064
|
-
if uri == _namespace_GVF1O('GVF1_0147'):
|
1064
|
+
if uri == cls._namespace_GVF1O('GVF1_0147'):
|
1065
1065
|
return True
|
1066
|
-
if uri == _namespace_GVF1O('GVF1_0148'):
|
1066
|
+
if uri == cls._namespace_GVF1O('GVF1_0148'):
|
1067
1067
|
return True
|
1068
|
-
if uri == _namespace_GVF1O('GVF1_0150'):
|
1068
|
+
if uri == cls._namespace_GVF1O('GVF1_0150'):
|
1069
1069
|
return True
|
1070
|
-
if uri == _namespace_GVF1O('GVF1_0152'):
|
1070
|
+
if uri == cls._namespace_GVF1O('GVF1_0152'):
|
1071
1071
|
return True
|
1072
|
-
if uri == _namespace_GVF1O('GVF1_0155'):
|
1072
|
+
if uri == cls._namespace_GVF1O('GVF1_0155'):
|
1073
1073
|
return True
|
1074
1074
|
return False
|
1075
1075
|
|
@@ -1079,125 +1079,125 @@ class GVF1O:
|
|
1079
1079
|
|
1080
1080
|
uri -- URI that is tested for being a datatype property
|
1081
1081
|
"""
|
1082
|
-
if uri == _namespace_GVF1O('GVF1_0005'):
|
1082
|
+
if uri == cls._namespace_GVF1O('GVF1_0005'):
|
1083
1083
|
return True
|
1084
|
-
if uri == _namespace_GVF1O('GVF1_0006'):
|
1084
|
+
if uri == cls._namespace_GVF1O('GVF1_0006'):
|
1085
1085
|
return True
|
1086
|
-
if uri == _namespace_GVF1O('GVF1_0007'):
|
1086
|
+
if uri == cls._namespace_GVF1O('GVF1_0007'):
|
1087
1087
|
return True
|
1088
|
-
if uri == _namespace_GVF1O('GVF1_0008'):
|
1088
|
+
if uri == cls._namespace_GVF1O('GVF1_0008'):
|
1089
1089
|
return True
|
1090
|
-
if uri == _namespace_GVF1O('GVF1_0009'):
|
1090
|
+
if uri == cls._namespace_GVF1O('GVF1_0009'):
|
1091
1091
|
return True
|
1092
|
-
if uri == _namespace_GVF1O('GVF1_0013'):
|
1092
|
+
if uri == cls._namespace_GVF1O('GVF1_0013'):
|
1093
1093
|
return True
|
1094
|
-
if uri == _namespace_GVF1O('GVF1_0022'):
|
1094
|
+
if uri == cls._namespace_GVF1O('GVF1_0022'):
|
1095
1095
|
return True
|
1096
|
-
if uri == _namespace_GVF1O('GVF1_0024'):
|
1096
|
+
if uri == cls._namespace_GVF1O('GVF1_0024'):
|
1097
1097
|
return True
|
1098
|
-
if uri == _namespace_GVF1O('GVF1_0025'):
|
1098
|
+
if uri == cls._namespace_GVF1O('GVF1_0025'):
|
1099
1099
|
return True
|
1100
|
-
if uri == _namespace_GVF1O('GVF1_0026'):
|
1100
|
+
if uri == cls._namespace_GVF1O('GVF1_0026'):
|
1101
1101
|
return True
|
1102
|
-
if uri == _namespace_GVF1O('GVF1_0027'):
|
1102
|
+
if uri == cls._namespace_GVF1O('GVF1_0027'):
|
1103
1103
|
return True
|
1104
|
-
if uri == _namespace_GVF1O('GVF1_0031'):
|
1104
|
+
if uri == cls._namespace_GVF1O('GVF1_0031'):
|
1105
1105
|
return True
|
1106
|
-
if uri == _namespace_GVF1O('GVF1_0032'):
|
1106
|
+
if uri == cls._namespace_GVF1O('GVF1_0032'):
|
1107
1107
|
return True
|
1108
|
-
if uri == _namespace_GVF1O('GVF1_0037'):
|
1108
|
+
if uri == cls._namespace_GVF1O('GVF1_0037'):
|
1109
1109
|
return True
|
1110
|
-
if uri == _namespace_GVF1O('GVF1_0039'):
|
1110
|
+
if uri == cls._namespace_GVF1O('GVF1_0039'):
|
1111
1111
|
return True
|
1112
|
-
if uri == _namespace_GVF1O('GVF1_0044'):
|
1112
|
+
if uri == cls._namespace_GVF1O('GVF1_0044'):
|
1113
1113
|
return True
|
1114
|
-
if uri == _namespace_GVF1O('GVF1_0048'):
|
1114
|
+
if uri == cls._namespace_GVF1O('GVF1_0048'):
|
1115
1115
|
return True
|
1116
|
-
if uri == _namespace_GVF1O('GVF1_0049'):
|
1116
|
+
if uri == cls._namespace_GVF1O('GVF1_0049'):
|
1117
1117
|
return True
|
1118
|
-
if uri == _namespace_GVF1O('GVF1_0050'):
|
1118
|
+
if uri == cls._namespace_GVF1O('GVF1_0050'):
|
1119
1119
|
return True
|
1120
|
-
if uri == _namespace_GVF1O('GVF1_0054'):
|
1120
|
+
if uri == cls._namespace_GVF1O('GVF1_0054'):
|
1121
1121
|
return True
|
1122
|
-
if uri == _namespace_GVF1O('GVF1_0055'):
|
1122
|
+
if uri == cls._namespace_GVF1O('GVF1_0055'):
|
1123
1123
|
return True
|
1124
|
-
if uri == _namespace_GVF1O('GVF1_0056'):
|
1124
|
+
if uri == cls._namespace_GVF1O('GVF1_0056'):
|
1125
1125
|
return True
|
1126
|
-
if uri == _namespace_GVF1O('GVF1_0057'):
|
1126
|
+
if uri == cls._namespace_GVF1O('GVF1_0057'):
|
1127
1127
|
return True
|
1128
|
-
if uri == _namespace_GVF1O('GVF1_0059'):
|
1128
|
+
if uri == cls._namespace_GVF1O('GVF1_0059'):
|
1129
1129
|
return True
|
1130
|
-
if uri == _namespace_GVF1O('GVF1_0060'):
|
1130
|
+
if uri == cls._namespace_GVF1O('GVF1_0060'):
|
1131
1131
|
return True
|
1132
|
-
if uri == _namespace_GVF1O('GVF1_0061'):
|
1132
|
+
if uri == cls._namespace_GVF1O('GVF1_0061'):
|
1133
1133
|
return True
|
1134
|
-
if uri == _namespace_GVF1O('GVF1_0063'):
|
1134
|
+
if uri == cls._namespace_GVF1O('GVF1_0063'):
|
1135
1135
|
return True
|
1136
|
-
if uri == _namespace_GVF1O('GVF1_0064'):
|
1136
|
+
if uri == cls._namespace_GVF1O('GVF1_0064'):
|
1137
1137
|
return True
|
1138
|
-
if uri == _namespace_GVF1O('GVF1_0065'):
|
1138
|
+
if uri == cls._namespace_GVF1O('GVF1_0065'):
|
1139
1139
|
return True
|
1140
|
-
if uri == _namespace_GVF1O('GVF1_0071'):
|
1140
|
+
if uri == cls._namespace_GVF1O('GVF1_0071'):
|
1141
1141
|
return True
|
1142
|
-
if uri == _namespace_GVF1O('GVF1_0073'):
|
1142
|
+
if uri == cls._namespace_GVF1O('GVF1_0073'):
|
1143
1143
|
return True
|
1144
|
-
if uri == _namespace_GVF1O('GVF1_0074'):
|
1144
|
+
if uri == cls._namespace_GVF1O('GVF1_0074'):
|
1145
1145
|
return True
|
1146
|
-
if uri == _namespace_GVF1O('GVF1_0076'):
|
1146
|
+
if uri == cls._namespace_GVF1O('GVF1_0076'):
|
1147
1147
|
return True
|
1148
|
-
if uri == _namespace_GVF1O('GVF1_0077'):
|
1148
|
+
if uri == cls._namespace_GVF1O('GVF1_0077'):
|
1149
1149
|
return True
|
1150
|
-
if uri == _namespace_GVF1O('GVF1_0081'):
|
1150
|
+
if uri == cls._namespace_GVF1O('GVF1_0081'):
|
1151
1151
|
return True
|
1152
|
-
if uri == _namespace_GVF1O('GVF1_0082'):
|
1152
|
+
if uri == cls._namespace_GVF1O('GVF1_0082'):
|
1153
1153
|
return True
|
1154
|
-
if uri == _namespace_GVF1O('GVF1_0092'):
|
1154
|
+
if uri == cls._namespace_GVF1O('GVF1_0092'):
|
1155
1155
|
return True
|
1156
|
-
if uri == _namespace_GVF1O('GVF1_0093'):
|
1156
|
+
if uri == cls._namespace_GVF1O('GVF1_0093'):
|
1157
1157
|
return True
|
1158
|
-
if uri == _namespace_GVF1O('GVF1_0094'):
|
1158
|
+
if uri == cls._namespace_GVF1O('GVF1_0094'):
|
1159
1159
|
return True
|
1160
|
-
if uri == _namespace_GVF1O('GVF1_0095'):
|
1160
|
+
if uri == cls._namespace_GVF1O('GVF1_0095'):
|
1161
1161
|
return True
|
1162
|
-
if uri == _namespace_GVF1O('GVF1_0096'):
|
1162
|
+
if uri == cls._namespace_GVF1O('GVF1_0096'):
|
1163
1163
|
return True
|
1164
|
-
if uri == _namespace_GVF1O('GVF1_0101'):
|
1164
|
+
if uri == cls._namespace_GVF1O('GVF1_0101'):
|
1165
1165
|
return True
|
1166
|
-
if uri == _namespace_GVF1O('GVF1_0105'):
|
1166
|
+
if uri == cls._namespace_GVF1O('GVF1_0105'):
|
1167
1167
|
return True
|
1168
|
-
if uri == _namespace_GVF1O('GVF1_0106'):
|
1168
|
+
if uri == cls._namespace_GVF1O('GVF1_0106'):
|
1169
1169
|
return True
|
1170
|
-
if uri == _namespace_GVF1O('GVF1_0107'):
|
1170
|
+
if uri == cls._namespace_GVF1O('GVF1_0107'):
|
1171
1171
|
return True
|
1172
|
-
if uri == _namespace_GVF1O('GVF1_0108'):
|
1172
|
+
if uri == cls._namespace_GVF1O('GVF1_0108'):
|
1173
1173
|
return True
|
1174
|
-
if uri == _namespace_GVF1O('GVF1_0113'):
|
1174
|
+
if uri == cls._namespace_GVF1O('GVF1_0113'):
|
1175
1175
|
return True
|
1176
|
-
if uri == _namespace_GVF1O('GVF1_0132'):
|
1176
|
+
if uri == cls._namespace_GVF1O('GVF1_0132'):
|
1177
1177
|
return True
|
1178
|
-
if uri == _namespace_GVF1O('GVF1_0133'):
|
1178
|
+
if uri == cls._namespace_GVF1O('GVF1_0133'):
|
1179
1179
|
return True
|
1180
|
-
if uri == _namespace_GVF1O('GVF1_0134'):
|
1180
|
+
if uri == cls._namespace_GVF1O('GVF1_0134'):
|
1181
1181
|
return True
|
1182
|
-
if uri == _namespace_GVF1O('GVF1_0136'):
|
1182
|
+
if uri == cls._namespace_GVF1O('GVF1_0136'):
|
1183
1183
|
return True
|
1184
|
-
if uri == _namespace_GVF1O('GVF1_0137'):
|
1184
|
+
if uri == cls._namespace_GVF1O('GVF1_0137'):
|
1185
1185
|
return True
|
1186
|
-
if uri == _namespace_GVF1O('GVF1_0138'):
|
1186
|
+
if uri == cls._namespace_GVF1O('GVF1_0138'):
|
1187
1187
|
return True
|
1188
|
-
if uri == _namespace_GVF1O('GVF1_0139'):
|
1188
|
+
if uri == cls._namespace_GVF1O('GVF1_0139'):
|
1189
1189
|
return True
|
1190
|
-
if uri == _namespace_GVF1O('GVF1_0149'):
|
1190
|
+
if uri == cls._namespace_GVF1O('GVF1_0149'):
|
1191
1191
|
return True
|
1192
|
-
if uri == _namespace_GVF1O('GVF1_0153'):
|
1192
|
+
if uri == cls._namespace_GVF1O('GVF1_0153'):
|
1193
1193
|
return True
|
1194
|
-
if uri == _namespace_GVF1O('GVF1_0154'):
|
1194
|
+
if uri == cls._namespace_GVF1O('GVF1_0154'):
|
1195
1195
|
return True
|
1196
|
-
if uri == _namespace_GVF1O('GVF1_0156'):
|
1196
|
+
if uri == cls._namespace_GVF1O('GVF1_0156'):
|
1197
1197
|
return True
|
1198
|
-
if uri == _namespace_GVF1O('GVF1_0157'):
|
1198
|
+
if uri == cls._namespace_GVF1O('GVF1_0157'):
|
1199
1199
|
return True
|
1200
|
-
if uri == _namespace_GVF1O('GVF1_0158'):
|
1200
|
+
if uri == cls._namespace_GVF1O('GVF1_0158'):
|
1201
1201
|
return True
|
1202
1202
|
return False
|
1203
1203
|
|
@@ -1207,49 +1207,49 @@ class GVF1O:
|
|
1207
1207
|
|
1208
1208
|
uri -- URI that is tested for being a class
|
1209
1209
|
"""
|
1210
|
-
if uri == _namespace_GVF1O('GVF1_0001'):
|
1210
|
+
if uri == cls._namespace_GVF1O('GVF1_0001'):
|
1211
1211
|
return True
|
1212
|
-
if uri == _namespace_GVF1O('GVF1_0002'):
|
1212
|
+
if uri == cls._namespace_GVF1O('GVF1_0002'):
|
1213
1213
|
return True
|
1214
|
-
if uri == _namespace_GVF1O('GVF1_0003'):
|
1214
|
+
if uri == cls._namespace_GVF1O('GVF1_0003'):
|
1215
1215
|
return True
|
1216
|
-
if uri == _namespace_GVF1O('GVF1_0016'):
|
1216
|
+
if uri == cls._namespace_GVF1O('GVF1_0016'):
|
1217
1217
|
return True
|
1218
|
-
if uri == _namespace_GVF1O('GVF1_0033'):
|
1218
|
+
if uri == cls._namespace_GVF1O('GVF1_0033'):
|
1219
1219
|
return True
|
1220
|
-
if uri == _namespace_GVF1O('GVF1_0035'):
|
1220
|
+
if uri == cls._namespace_GVF1O('GVF1_0035'):
|
1221
1221
|
return True
|
1222
|
-
if uri == _namespace_GVF1O('GVF1_0040'):
|
1222
|
+
if uri == cls._namespace_GVF1O('GVF1_0040'):
|
1223
1223
|
return True
|
1224
|
-
if uri == _namespace_GVF1O('GVF1_0045'):
|
1224
|
+
if uri == cls._namespace_GVF1O('GVF1_0045'):
|
1225
1225
|
return True
|
1226
|
-
if uri == _namespace_GVF1O('GVF1_0052'):
|
1226
|
+
if uri == cls._namespace_GVF1O('GVF1_0052'):
|
1227
1227
|
return True
|
1228
|
-
if uri == _namespace_GVF1O('GVF1_0058'):
|
1228
|
+
if uri == cls._namespace_GVF1O('GVF1_0058'):
|
1229
1229
|
return True
|
1230
|
-
if uri == _namespace_GVF1O('GVF1_0084'):
|
1230
|
+
if uri == cls._namespace_GVF1O('GVF1_0084'):
|
1231
1231
|
return True
|
1232
|
-
if uri == _namespace_GVF1O('GVF1_0088'):
|
1232
|
+
if uri == cls._namespace_GVF1O('GVF1_0088'):
|
1233
1233
|
return True
|
1234
|
-
if uri == _namespace_GVF1O('GVF1_0097'):
|
1234
|
+
if uri == cls._namespace_GVF1O('GVF1_0097'):
|
1235
1235
|
return True
|
1236
|
-
if uri == _namespace_GVF1O('GVF1_0098'):
|
1236
|
+
if uri == cls._namespace_GVF1O('GVF1_0098'):
|
1237
1237
|
return True
|
1238
|
-
if uri == _namespace_GVF1O('GVF1_0099'):
|
1238
|
+
if uri == cls._namespace_GVF1O('GVF1_0099'):
|
1239
1239
|
return True
|
1240
|
-
if uri == _namespace_GVF1O('GVF1_0100'):
|
1240
|
+
if uri == cls._namespace_GVF1O('GVF1_0100'):
|
1241
1241
|
return True
|
1242
|
-
if uri == _namespace_GVF1O('GVF1_0109'):
|
1242
|
+
if uri == cls._namespace_GVF1O('GVF1_0109'):
|
1243
1243
|
return True
|
1244
|
-
if uri == _namespace_GVF1O('GVF1_0114'):
|
1244
|
+
if uri == cls._namespace_GVF1O('GVF1_0114'):
|
1245
1245
|
return True
|
1246
|
-
if uri == _namespace_GVF1O('GVF1_0135'):
|
1246
|
+
if uri == cls._namespace_GVF1O('GVF1_0135'):
|
1247
1247
|
return True
|
1248
|
-
if uri == _namespace_GVF1O('GVF1_0140'):
|
1248
|
+
if uri == cls._namespace_GVF1O('GVF1_0140'):
|
1249
1249
|
return True
|
1250
|
-
if uri == _namespace_GVF1O('GVF1_0141'):
|
1250
|
+
if uri == cls._namespace_GVF1O('GVF1_0141'):
|
1251
1251
|
return True
|
1252
|
-
if uri == _namespace_GVF1O('GVF1_0151'):
|
1252
|
+
if uri == cls._namespace_GVF1O('GVF1_0151'):
|
1253
1253
|
return True
|
1254
1254
|
return False
|
1255
1255
|
|
@@ -1259,41 +1259,41 @@ class GVF1O:
|
|
1259
1259
|
|
1260
1260
|
uri -- URI that is tested for being a named individual
|
1261
1261
|
"""
|
1262
|
-
if uri == _namespace_GVF1O('GVF1_0017'):
|
1262
|
+
if uri == cls._namespace_GVF1O('GVF1_0017'):
|
1263
1263
|
return True
|
1264
|
-
if uri == _namespace_GVF1O('GVF1_0018'):
|
1264
|
+
if uri == cls._namespace_GVF1O('GVF1_0018'):
|
1265
1265
|
return True
|
1266
|
-
if uri == _namespace_GVF1O('GVF1_0019'):
|
1266
|
+
if uri == cls._namespace_GVF1O('GVF1_0019'):
|
1267
1267
|
return True
|
1268
|
-
if uri == _namespace_GVF1O('GVF1_0020'):
|
1268
|
+
if uri == cls._namespace_GVF1O('GVF1_0020'):
|
1269
1269
|
return True
|
1270
|
-
if uri == _namespace_GVF1O('GVF1_0085'):
|
1270
|
+
if uri == cls._namespace_GVF1O('GVF1_0085'):
|
1271
1271
|
return True
|
1272
|
-
if uri == _namespace_GVF1O('GVF1_0086'):
|
1272
|
+
if uri == cls._namespace_GVF1O('GVF1_0086'):
|
1273
1273
|
return True
|
1274
|
-
if uri == _namespace_GVF1O('GVF1_0087'):
|
1274
|
+
if uri == cls._namespace_GVF1O('GVF1_0087'):
|
1275
1275
|
return True
|
1276
|
-
if uri == _namespace_GVF1O('GVF1_0110'):
|
1276
|
+
if uri == cls._namespace_GVF1O('GVF1_0110'):
|
1277
1277
|
return True
|
1278
|
-
if uri == _namespace_GVF1O('GVF1_0111'):
|
1278
|
+
if uri == cls._namespace_GVF1O('GVF1_0111'):
|
1279
1279
|
return True
|
1280
|
-
if uri == _namespace_GVF1O('GVF1_0115'):
|
1280
|
+
if uri == cls._namespace_GVF1O('GVF1_0115'):
|
1281
1281
|
return True
|
1282
|
-
if uri == _namespace_GVF1O('GVF1_0116'):
|
1282
|
+
if uri == cls._namespace_GVF1O('GVF1_0116'):
|
1283
1283
|
return True
|
1284
|
-
if uri == _namespace_GVF1O('GVF1_0117'):
|
1284
|
+
if uri == cls._namespace_GVF1O('GVF1_0117'):
|
1285
1285
|
return True
|
1286
|
-
if uri == _namespace_GVF1O('GVF1_0118'):
|
1286
|
+
if uri == cls._namespace_GVF1O('GVF1_0118'):
|
1287
1287
|
return True
|
1288
|
-
if uri == _namespace_GVF1O('GVF1_0142'):
|
1288
|
+
if uri == cls._namespace_GVF1O('GVF1_0142'):
|
1289
1289
|
return True
|
1290
|
-
if uri == _namespace_GVF1O('GVF1_0143'):
|
1290
|
+
if uri == cls._namespace_GVF1O('GVF1_0143'):
|
1291
1291
|
return True
|
1292
|
-
if uri == _namespace_GVF1O('GVF1_0144'):
|
1292
|
+
if uri == cls._namespace_GVF1O('GVF1_0144'):
|
1293
1293
|
return True
|
1294
|
-
if uri == _namespace_GVF1O('GVF1_0145'):
|
1294
|
+
if uri == cls._namespace_GVF1O('GVF1_0145'):
|
1295
1295
|
return True
|
1296
|
-
if uri == _namespace_GVF1O('GVF1_0146'):
|
1296
|
+
if uri == cls._namespace_GVF1O('GVF1_0146'):
|
1297
1297
|
return True
|
1298
1298
|
return False
|
1299
1299
|
|
@@ -1319,11 +1319,10 @@ class GVF1O:
|
|
1319
1319
|
return cls.has_parent(cls.__parent_properties[uri], parent)
|
1320
1320
|
return False
|
1321
1321
|
|
1322
|
-
|
1323
|
-
|
1324
|
-
|
1325
|
-
return __namespace_GVF1O[accession]
|
1322
|
+
@classmethod
|
1323
|
+
def _namespace_GVF1O(cls, accession):
|
1324
|
+
return Namespace('http://www.biointerchange.org/gvf1o#')[accession]
|
1326
1325
|
|
1327
|
-
__parent_properties = { _namespace_GVF1O('GVF1_0004') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0010') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0012') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0014') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0015') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0021') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0023') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0034') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0036') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0038') : _namespace_GVF1O('GVF1_0069') , _namespace_GVF1O('GVF1_0041') : _namespace_GVF1O('GVF1_0069') , _namespace_GVF1O('GVF1_0042') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0043') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0046') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0047') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0051') : _namespace_GVF1O('GVF1_0067') , _namespace_GVF1O('GVF1_0053') : _namespace_GVF1O('GVF1_0069') , _namespace_GVF1O('GVF1_0072') : _namespace_GVF1O('GVF1_0075') , _namespace_GVF1O('GVF1_0078') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0079') : _namespace_GVF1O('GVF1_0075') , _namespace_GVF1O('GVF1_0080') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0083') : _namespace_GVF1O('GVF1_0075') , _namespace_GVF1O('GVF1_0090') : _namespace_GVF1O('GVF1_0089') , _namespace_GVF1O('GVF1_0091') : _namespace_GVF1O('GVF1_0089') , _namespace_GVF1O('GVF1_0102') : _namespace_GVF1O('GVF1_0112') , _namespace_GVF1O('GVF1_0103') : _namespace_GVF1O('GVF1_0112') , _namespace_GVF1O('GVF1_0104') : _namespace_GVF1O('GVF1_0112') , _namespace_GVF1O('GVF1_0119') : _namespace_GVF1O('GVF1_0102') , _namespace_GVF1O('GVF1_0120') : _namespace_GVF1O('GVF1_0103') , _namespace_GVF1O('GVF1_0121') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0122') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0123') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0124') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0125') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0126') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0127') : _namespace_GVF1O('GVF1_0075') , _namespace_GVF1O('GVF1_0129') : _namespace_GVF1O('GVF1_0128') , _namespace_GVF1O('GVF1_0130') : _namespace_GVF1O('GVF1_0089') , _namespace_GVF1O('GVF1_0131') : _namespace_GVF1O('GVF1_0069') , _namespace_GVF1O('GVF1_0147') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0148') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0150') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0152') : _namespace_GVF1O('GVF1_0112') , _namespace_GVF1O('GVF1_0155') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0005') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0006') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0007') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0008') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0009') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0013') : _namespace_GVF1O('GVF1_0064') , _namespace_GVF1O('GVF1_0022') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0024') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0025') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0026') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0027') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0031') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0032') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0037') : _namespace_GVF1O('GVF1_0065') , _namespace_GVF1O('GVF1_0039') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0044') : _namespace_GVF1O('GVF1_0158') , _namespace_GVF1O('GVF1_0048') : _namespace_GVF1O('GVF1_0061') , _namespace_GVF1O('GVF1_0049') : _namespace_GVF1O('GVF1_0061') , _namespace_GVF1O('GVF1_0050') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0054') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0055') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0056') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0057') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0073') : _namespace_GVF1O('GVF1_0071') , _namespace_GVF1O('GVF1_0074') : _namespace_GVF1O('GVF1_0071') , _namespace_GVF1O('GVF1_0076') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0077') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0081') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0082') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0093') : _namespace_GVF1O('GVF1_0092') , _namespace_GVF1O('GVF1_0094') : _namespace_GVF1O('GVF1_0092') , _namespace_GVF1O('GVF1_0095') : _namespace_GVF1O('GVF1_0092') , _namespace_GVF1O('GVF1_0096') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0101') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0105') : _namespace_GVF1O('GVF1_0113') , _namespace_GVF1O('GVF1_0106') : _namespace_GVF1O('GVF1_0107') , _namespace_GVF1O('GVF1_0107') : _namespace_GVF1O('GVF1_0113') , _namespace_GVF1O('GVF1_0108') : _namespace_GVF1O('GVF1_0107') , _namespace_GVF1O('GVF1_0132') : _namespace_GVF1O('GVF1_0107') , _namespace_GVF1O('GVF1_0133') : _namespace_GVF1O('GVF1_0107') , _namespace_GVF1O('GVF1_0134') : _namespace_GVF1O('GVF1_0107') , _namespace_GVF1O('GVF1_0137') : _namespace_GVF1O('GVF1_0136') , _namespace_GVF1O('GVF1_0138') : _namespace_GVF1O('GVF1_0136') , _namespace_GVF1O('GVF1_0139') : _namespace_GVF1O('GVF1_0136') , _namespace_GVF1O('GVF1_0149') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0154') : _namespace_GVF1O('GVF1_0153') , _namespace_GVF1O('GVF1_0156') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0157') : _namespace_GVF1O('GVF1_0136') , _namespace_GVF1O('GVF1_0088') : _namespace_GVF1O('http://www.w3.org/2002/07/owl#Thing') , _namespace_GVF1O('GVF1_0151') : _namespace_GVF1O('http://www.w3.org/2002/07/owl#Thing') }
|
1326
|
+
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