biointerchange 0.2.2 → 1.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- 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.
|
222
|
-
(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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