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
@@ -9,1032 +9,1032 @@ class GOXRef:
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def AGI_LocusCode(cls):
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"""Returns the link-out URI for objects of "Arabidopsis Genome Initiative".
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"""
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cls.Namespace("http://arabidopsis.org/servlets/TairObject?type=locus&name=")
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@classmethod
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def ApiDB_PlasmoDB(cls):
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"""Returns the link-out URI for objects of "PlasmoDB Plasmodium Genome Resource".
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"""
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cls.Namespace("http://www.plasmodb.org/gene/")
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@classmethod
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def AraCyc(cls):
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"""Returns the link-out URI for objects of "AraCyc metabolic pathway database for Arabidopsis thaliana".
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"""
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cls.Namespace("http://www.arabidopsis.org:1555/ARA/NEW-IMAGE?type=NIL&object=")
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@classmethod
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def ASAP(cls):
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"""Returns the link-out URI for objects of "A Systematic Annotation Package for Community Analysis of Genomes".
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"""
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cls.Namespace("https://asap.ahabs.wisc.edu/annotation/php/feature_info.php?FeatureID=")
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@classmethod
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def AspGD(cls):
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"""Returns the link-out URI for objects of "Aspergillus Genome Database".
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"""
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cls.Namespace("http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=")
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@classmethod
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def AspGD_LOCUS(cls):
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"""Returns the link-out URI for objects of "Aspergillus Genome Database".
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"""
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cls.Namespace("http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=")
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@classmethod
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def AspGD_REF(cls):
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"""Returns the link-out URI for objects of "Aspergillus Genome Database".
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"""
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cls.Namespace("http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=")
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@classmethod
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def BFO(cls):
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"""Returns the link-out URI for objects of "Basic Formal Ontology".
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"""
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cls.Namespace("http://purl.obolibrary.org/obo/BFO_")
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@classmethod
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def BioCyc(cls):
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"""Returns the link-out URI for objects of "BioCyc collection of metabolic pathway databases".
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"""
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cls.Namespace("http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=")
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@classmethod
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def BIOMD(cls):
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"""Returns the link-out URI for objects of "BioModels Database".
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"""
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cls.Namespace("http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=")
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@classmethod
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def BRENDA(cls):
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"""Returns the link-out URI for objects of "BRENDA, The Comprehensive Enzyme Information System".
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"""
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cls.Namespace("http://www.brenda-enzymes.info/php/result_flat.php4?ecno=")
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@classmethod
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def Broad_MGG(cls):
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"""Returns the link-out URI for objects of "Magnaporthe grisea Database".
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"""
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cls.Namespace("http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/GeneLocus.html?sp=S")
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@classmethod
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def CASGEN(cls):
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"""Returns the link-out URI for objects of "Catalog of Fishes genus database".
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"""
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cls.Namespace("http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Genus&id=")
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@classmethod
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def CASREF(cls):
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"""Returns the link-out URI for objects of "Catalog of Fishes publications database".
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"""
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cls.Namespace("http://research.calacademy.org/research/ichthyology/catalog/getref.asp?id=")
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@classmethod
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def CASSPC(cls):
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"""Returns the link-out URI for objects of "Catalog of Fishes species database".
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"""
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cls.Namespace("http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Species&id=1979")
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@classmethod
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def CDD(cls):
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"""Returns the link-out URI for objects of "Conserved Domain Database at NCBI".
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"""
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cls.Namespace("http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=")
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@classmethod
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def CGD(cls):
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"""Returns the link-out URI for objects of "Candida Genome Database".
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"""
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cls.Namespace("http://www.candidagenome.org/cgi-bin/locus.pl?dbid=")
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@classmethod
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def CGD_LOCUS(cls):
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"""Returns the link-out URI for objects of "Candida Genome Database".
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"""
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cls.Namespace("http://www.candidagenome.org/cgi-bin/locus.pl?locus=")
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@classmethod
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def CGD_REF(cls):
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"""Returns the link-out URI for objects of "Candida Genome Database".
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"""
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cls.Namespace("http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=")
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@classmethod
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def CHEBI(cls):
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"""Returns the link-out URI for objects of "Chemical Entities of Biological Interest".
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"""
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cls.Namespace("http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:")
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@classmethod
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def CL(cls):
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"""Returns the link-out URI for objects of "Cell Type Ontology".
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"""
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cls.Namespace("http://purl.obolibrary.org/obo/CL_")
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@classmethod
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def COG_Cluster(cls):
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"""Returns the link-out URI for objects of "NCBI COG cluster".
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"""
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cls.Namespace("http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=")
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@classmethod
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def COG_Function(cls):
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"""Returns the link-out URI for objects of "NCBI COG function".
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"""
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cls.Namespace("http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=")
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@classmethod
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def COG_Pathway(cls):
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"""Returns the link-out URI for objects of "NCBI COG pathway".
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"""
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cls.Namespace("http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=")
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@classmethod
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def CORUM(cls):
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"""Returns the link-out URI for objects of "CORUM - the Comprehensive Resource of Mammalian protein complexes".
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"""
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cls.Namespace("http://mips.gsf.de/genre/proj/corum/complexdetails.html?id=")
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@classmethod
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def dbSNP(cls):
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"""Returns the link-out URI for objects of "NCBI dbSNP".
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"""
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cls.Namespace("http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=")
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@classmethod
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def DDBJ(cls):
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"""Returns the link-out URI for objects of "DNA Databank of Japan".
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"""
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cls.Namespace("http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch?KeyWord=")
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@classmethod
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def dictyBase(cls):
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"""Returns the link-out URI for objects of "dictyBase".
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"""
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cls.Namespace("http://dictybase.org/gene/")
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@classmethod
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def dictyBase_gene_name(cls):
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"""Returns the link-out URI for objects of "dictyBase".
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"""
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cls.Namespace("http://dictybase.org/gene/")
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@classmethod
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def dictyBase_REF(cls):
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"""Returns the link-out URI for objects of "dictyBase literature references".
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"""
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cls.Namespace("http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo=")
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@classmethod
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def DOI(cls):
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"""Returns the link-out URI for objects of "Digital Object Identifier".
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"""
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cls.Namespace("http://dx.doi.org/DOI:")
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@classmethod
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def EC(cls):
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"""Returns the link-out URI for objects of "Enzyme Commission".
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"""
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cls.Namespace("http://www.expasy.org/enzyme/")
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@classmethod
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def EchoBASE(cls):
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"""Returns the link-out URI for objects of "EchoBASE post-genomic database for Escherichia coli".
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"""
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cls.Namespace("http://www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID=")
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@classmethod
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def ECK(cls):
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"""Returns the link-out URI for objects of "EcoGene Database of Escherichia coli Sequence and Function".
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"""
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cls.Namespace("http://www.ecogene.org/geneInfo.php?eck_id=")
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@classmethod
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def EcoCyc(cls):
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"""Returns the link-out URI for objects of "Encyclopedia of E. coli metabolism".
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"""
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cls.Namespace("http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=")
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@classmethod
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def EcoCyc_REF(cls):
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"""Returns the link-out URI for objects of "Encyclopedia of E. coli metabolism".
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"""
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cls.Namespace("http://biocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object=")
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@classmethod
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def ECOGENE(cls):
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"""Returns the link-out URI for objects of "EcoGene Database of Escherichia coli Sequence and Function".
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"""
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cls.Namespace("http://www.ecogene.org/geneInfo.php?eg_id=")
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@classmethod
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def EMBL(cls):
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"""Returns the link-out URI for objects of "EMBL Nucleotide Sequence Database".
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"""
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cls.Namespace("http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=")
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@classmethod
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def ENA(cls):
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"""Returns the link-out URI for objects of "European Nucleotide Archive".
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"""
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cls.Namespace("http://www.ebi.ac.uk/ena/data/view/")
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@classmethod
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def ENSEMBL(cls):
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"""Returns the link-out URI for objects of "Ensembl database of automatically annotated genomic data".
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"""
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cls.Namespace("http://www.ensembl.org/id/")
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@classmethod
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def ENSEMBL_GeneID(cls):
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"""Returns the link-out URI for objects of "Ensembl database of automatically annotated genomic data".
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"""
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cls.Namespace("http://www.ensembl.org/id/")
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@classmethod
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def ENSEMBL_ProteinID(cls):
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"""Returns the link-out URI for objects of "Ensembl database of automatically annotated genomic data".
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"""
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cls.Namespace("http://www.ensembl.org/id/")
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@classmethod
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def ENSEMBL_TranscriptID(cls):
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"""Returns the link-out URI for objects of "Ensembl database of automatically annotated genomic data".
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"""
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cls.Namespace("http://www.ensembl.org/id/")
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@classmethod
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def ENZYME(cls):
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"""Returns the link-out URI for objects of "Swiss Institute of Bioinformatics enzyme database".
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"""
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cls.Namespace("http://www.expasy.ch/cgi-bin/nicezyme.pl?")
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@classmethod
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def FBbt(cls):
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"""Returns the link-out URI for objects of "Drosophila gross anatomy".
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"""
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cls.Namespace("http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:")
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@classmethod
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def GDB(cls):
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"""Returns the link-out URI for objects of "Human Genome Database".
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"""
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cls.Namespace("http://www.gdb.org/gdb-bin/genera/accno?accessionNum=GDB:")
|
283
283
|
|
284
284
|
@classmethod
|
285
285
|
def GenBank(cls):
|
286
286
|
"""Returns the link-out URI for objects of "GenBank".
|
287
287
|
"""
|
288
|
-
|
288
|
+
cls.Namespace("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=")
|
289
289
|
|
290
290
|
@classmethod
|
291
291
|
def Gene3D(cls):
|
292
292
|
"""Returns the link-out URI for objects of "Domain Architecture Classification".
|
293
293
|
"""
|
294
|
-
|
294
|
+
cls.Namespace("http://gene3d.biochem.ucl.ac.uk/superfamily/?accession=")
|
295
295
|
|
296
296
|
@classmethod
|
297
297
|
def GeneDB_Gmorsitans(cls):
|
298
298
|
"""Returns the link-out URI for objects of "Glossina morsitans GeneDB".
|
299
299
|
"""
|
300
|
-
|
300
|
+
cls.Namespace("http://www.genedb.org/genedb/Search?organism=glossina&name=")
|
301
301
|
|
302
302
|
@classmethod
|
303
303
|
def GeneDB_Lmajor(cls):
|
304
304
|
"""Returns the link-out URI for objects of "Leishmania major GeneDB".
|
305
305
|
"""
|
306
|
-
|
306
|
+
cls.Namespace("http://www.genedb.org/genedb/Search?organism=leish&name=")
|
307
307
|
|
308
308
|
@classmethod
|
309
309
|
def GeneDB_Pfalciparum(cls):
|
310
310
|
"""Returns the link-out URI for objects of "Plasmodium falciparum GeneDB".
|
311
311
|
"""
|
312
|
-
|
312
|
+
cls.Namespace("http://www.genedb.org/genedb/Search?organism=malaria&name=")
|
313
313
|
|
314
314
|
@classmethod
|
315
315
|
def GeneDB_Spombe(cls):
|
316
316
|
"""Returns the link-out URI for objects of "Schizosaccharomyces pombe GeneDB".
|
317
317
|
"""
|
318
|
-
|
318
|
+
cls.Namespace("http://old.genedb.org/genedb/Search?organism=pombe&name=")
|
319
319
|
|
320
320
|
@classmethod
|
321
321
|
def GeneDB_Tbrucei(cls):
|
322
322
|
"""Returns the link-out URI for objects of "Trypanosoma brucei GeneDB".
|
323
323
|
"""
|
324
|
-
|
324
|
+
cls.Namespace("http://www.genedb.org/genedb/Search?organism=tryp&name=")
|
325
325
|
|
326
326
|
@classmethod
|
327
327
|
def GEO(cls):
|
328
328
|
"""Returns the link-out URI for objects of "NCBI Gene Expression Omnibus".
|
329
329
|
"""
|
330
|
-
|
330
|
+
cls.Namespace("http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=")
|
331
331
|
|
332
332
|
@classmethod
|
333
333
|
def GO(cls):
|
334
334
|
"""Returns the link-out URI for objects of "Gene Ontology Database".
|
335
335
|
"""
|
336
|
-
|
336
|
+
cls.Namespace("http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:")
|
337
337
|
|
338
338
|
@classmethod
|
339
339
|
def GO_REF(cls):
|
340
340
|
"""Returns the link-out URI for objects of "Gene Ontology Database references".
|
341
341
|
"""
|
342
|
-
|
342
|
+
cls.Namespace("http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:")
|
343
343
|
|
344
344
|
@classmethod
|
345
345
|
def GONUTS(cls):
|
346
346
|
"""Returns the link-out URI for objects of "Gene Ontology Normal Usage Tracking System (cls, GONUTS)".
|
347
347
|
"""
|
348
|
-
|
348
|
+
cls.Namespace("http://gowiki.tamu.edu/wiki/index.php/")
|
349
349
|
|
350
350
|
@classmethod
|
351
351
|
def GR(cls):
|
352
352
|
"""Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains".
|
353
353
|
"""
|
354
|
-
|
354
|
+
cls.Namespace("http://www.gramene.org/db/searches/browser?search_type=All&RGN=on&query=")
|
355
355
|
|
356
356
|
@classmethod
|
357
357
|
def GR_GENE(cls):
|
358
358
|
"""Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains".
|
359
359
|
"""
|
360
|
-
|
360
|
+
cls.Namespace("http://www.gramene.org/db/genes/search_gene?acc=")
|
361
361
|
|
362
362
|
@classmethod
|
363
363
|
def GR_PROTEIN(cls):
|
364
364
|
"""Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains".
|
365
365
|
"""
|
366
|
-
|
366
|
+
cls.Namespace("http://www.gramene.org/db/protein/protein_search?acc=")
|
367
367
|
|
368
368
|
@classmethod
|
369
369
|
def GR_QTL(cls):
|
370
370
|
"""Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains".
|
371
371
|
"""
|
372
|
-
|
372
|
+
cls.Namespace("http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=")
|
373
373
|
|
374
374
|
@classmethod
|
375
375
|
def GR_REF(cls):
|
376
376
|
"""Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains".
|
377
377
|
"""
|
378
|
-
|
378
|
+
cls.Namespace("http://www.gramene.org/db/literature/pub_search?ref_id=")
|
379
379
|
|
380
380
|
@classmethod
|
381
381
|
def H_invDB_cDNA(cls):
|
382
382
|
"""Returns the link-out URI for objects of "H-invitational Database".
|
383
383
|
"""
|
384
|
-
|
384
|
+
cls.Namespace("http://www.h-invitational.jp/hinv/spsoup/transcript_view?acc_id=")
|
385
385
|
|
386
386
|
@classmethod
|
387
387
|
def H_invDB_locus(cls):
|
388
388
|
"""Returns the link-out URI for objects of "H-invitational Database".
|
389
389
|
"""
|
390
|
-
|
390
|
+
cls.Namespace("http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=")
|
391
391
|
|
392
392
|
@classmethod
|
393
393
|
def HAMAP(cls):
|
394
394
|
"""Returns the link-out URI for objects of "High-quality Automated and Manual Annotation of microbial Proteomes".
|
395
395
|
"""
|
396
|
-
|
396
|
+
cls.Namespace("http://us.expasy.org/unirules/")
|
397
397
|
|
398
398
|
@classmethod
|
399
399
|
def HGNC(cls):
|
400
400
|
"""Returns the link-out URI for objects of "HUGO Gene Nomenclature Committee".
|
401
401
|
"""
|
402
|
-
|
402
|
+
cls.Namespace("http://www.genenames.org/data/hgnc_data.php?hgnc_id=HGNC:")
|
403
403
|
|
404
404
|
@classmethod
|
405
405
|
def HGNC_gene(cls):
|
406
406
|
"""Returns the link-out URI for objects of "HUGO Gene Nomenclature Committee".
|
407
407
|
"""
|
408
|
-
|
408
|
+
cls.Namespace("http://www.genenames.org/data/hgnc_data.php?app_sym=")
|
409
409
|
|
410
410
|
@classmethod
|
411
411
|
def HPA(cls):
|
412
412
|
"""Returns the link-out URI for objects of "Human Protein Atlas tissue profile information".
|
413
413
|
"""
|
414
|
-
|
414
|
+
cls.Namespace("http://www.proteinatlas.org/tissue_profile.php?antibody_id=")
|
415
415
|
|
416
416
|
@classmethod
|
417
417
|
def HPA_antibody(cls):
|
418
418
|
"""Returns the link-out URI for objects of "Human Protein Atlas antibody information".
|
419
419
|
"""
|
420
|
-
|
420
|
+
cls.Namespace("http://www.proteinatlas.org/antibody_info.php?antibody_id=")
|
421
421
|
|
422
422
|
@classmethod
|
423
423
|
def IMG(cls):
|
424
424
|
"""Returns the link-out URI for objects of "Integrated Microbial Genomes; JGI web site for genome annotation".
|
425
425
|
"""
|
426
|
-
|
426
|
+
cls.Namespace("http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=")
|
427
427
|
|
428
428
|
@classmethod
|
429
429
|
def IntAct(cls):
|
430
430
|
"""Returns the link-out URI for objects of "IntAct protein interaction database".
|
431
431
|
"""
|
432
|
-
|
432
|
+
cls.Namespace("http://www.ebi.ac.uk/intact/search/do/search?searchString=")
|
433
433
|
|
434
434
|
@classmethod
|
435
435
|
def InterPro(cls):
|
436
436
|
"""Returns the link-out URI for objects of "InterPro database of protein domains and motifs".
|
437
437
|
"""
|
438
|
-
|
438
|
+
cls.Namespace("http://www.ebi.ac.uk/interpro/IEntry?ac=")
|
439
439
|
|
440
440
|
@classmethod
|
441
441
|
def ISBN(cls):
|
442
442
|
"""Returns the link-out URI for objects of "International Standard Book Number".
|
443
443
|
"""
|
444
|
-
|
444
|
+
cls.Namespace("http://my.linkbaton.com/get?lbCC=q&nC=q&genre=book&item=")
|
445
445
|
|
446
446
|
@classmethod
|
447
447
|
def IUPHAR_GPCR(cls):
|
448
448
|
"""Returns the link-out URI for objects of "International Union of Pharmacology".
|
449
449
|
"""
|
450
|
-
|
450
|
+
cls.Namespace("http://www.iuphar-db.org/DATABASE/FamilyMenuForward?familyId=")
|
451
451
|
|
452
452
|
@classmethod
|
453
453
|
def IUPHAR_RECEPTOR(cls):
|
454
454
|
"""Returns the link-out URI for objects of "International Union of Pharmacology".
|
455
455
|
"""
|
456
|
-
|
456
|
+
cls.Namespace("http://www.iuphar-db.org/DATABASE/ObjectDisplayForward?objectId=")
|
457
457
|
|
458
458
|
@classmethod
|
459
459
|
def JCVI_CMR(cls):
|
460
460
|
"""Returns the link-out URI for objects of "Comprehensive Microbial Resource at the J. Craig Venter Institute".
|
461
461
|
"""
|
462
|
-
|
462
|
+
cls.Namespace("http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=")
|
463
463
|
|
464
464
|
@classmethod
|
465
465
|
def JCVI_EGAD(cls):
|
466
466
|
"""Returns the link-out URI for objects of "Comprehensive Microbial Resource at the J. Craig Venter Institute".
|
467
467
|
"""
|
468
|
-
|
468
|
+
cls.Namespace("http://cmr.jcvi.org/cgi-bin/CMR/EgadSearch.cgi?search_string=")
|
469
469
|
|
470
470
|
@classmethod
|
471
471
|
def JCVI_GenProp(cls):
|
472
472
|
"""Returns the link-out URI for objects of "Genome Properties database at the J. Craig Venter Institute".
|
473
473
|
"""
|
474
|
-
|
474
|
+
cls.Namespace("http://cmr.jcvi.org/cgi-bin/CMR/shared/GenomePropDefinition.cgi?prop_acc=")
|
475
475
|
|
476
476
|
@classmethod
|
477
477
|
def JCVI_Medtr(cls):
|
478
478
|
"""Returns the link-out URI for objects of "Medicago truncatula genome database at the J. Craig Venter Institute ".
|
479
479
|
"""
|
480
|
-
|
480
|
+
cls.Namespace("http://medicago.jcvi.org/cgi-bin/medicago/search/shared/ORF_infopage.cgi?orf=")
|
481
481
|
|
482
482
|
@classmethod
|
483
483
|
def JCVI_TIGRFAMS(cls):
|
484
484
|
"""Returns the link-out URI for objects of "TIGRFAMs HMM collection at the J. Craig Venter Institute".
|
485
485
|
"""
|
486
|
-
|
486
|
+
cls.Namespace("http://search.jcvi.org/search?p&q=")
|
487
487
|
|
488
488
|
@classmethod
|
489
489
|
def JSTOR(cls):
|
490
490
|
"""Returns the link-out URI for objects of "Digital archive of scholarly articles".
|
491
491
|
"""
|
492
|
-
|
492
|
+
cls.Namespace("http://www.jstor.org/stable/")
|
493
493
|
|
494
494
|
@classmethod
|
495
495
|
def KEGG_ENZYME(cls):
|
496
496
|
"""Returns the link-out URI for objects of "KEGG Enzyme Database".
|
497
497
|
"""
|
498
|
-
|
498
|
+
cls.Namespace("http://www.genome.jp/dbget-bin/www_bget?ec:")
|
499
499
|
|
500
500
|
@classmethod
|
501
501
|
def KEGG_LIGAND(cls):
|
502
502
|
"""Returns the link-out URI for objects of "KEGG LIGAND Database".
|
503
503
|
"""
|
504
|
-
|
504
|
+
cls.Namespace("http://www.genome.jp/dbget-bin/www_bget?cpd:")
|
505
505
|
|
506
506
|
@classmethod
|
507
507
|
def KEGG_PATHWAY(cls):
|
508
508
|
"""Returns the link-out URI for objects of "KEGG Pathways Database".
|
509
509
|
"""
|
510
|
-
|
510
|
+
cls.Namespace("http://www.genome.jp/dbget-bin/www_bget?path:")
|
511
511
|
|
512
512
|
@classmethod
|
513
513
|
def KEGG_REACTION(cls):
|
514
514
|
"""Returns the link-out URI for objects of "KEGG Reaction Database".
|
515
515
|
"""
|
516
|
-
|
516
|
+
cls.Namespace("http://www.genome.jp/dbget-bin/www_bget?rn:")
|
517
517
|
|
518
518
|
@classmethod
|
519
519
|
def LIFEdb(cls):
|
520
520
|
"""Returns the link-out URI for objects of "LifeDB".
|
521
521
|
"""
|
522
|
-
|
522
|
+
cls.Namespace("http://www.dkfz.de/LIFEdb/LIFEdb.aspx?ID=")
|
523
523
|
|
524
524
|
@classmethod
|
525
525
|
def MA(cls):
|
526
526
|
"""Returns the link-out URI for objects of "Adult Mouse Anatomical Dictionary".
|
527
527
|
"""
|
528
|
-
|
528
|
+
cls.Namespace("http://www.informatics.jax.org/searches/AMA.cgi?id=MA:")
|
529
529
|
|
530
530
|
@classmethod
|
531
531
|
def MaizeGDB(cls):
|
532
532
|
"""Returns the link-out URI for objects of "MaizeGDB".
|
533
533
|
"""
|
534
|
-
|
534
|
+
cls.Namespace("http://www.maizegdb.org/cgi-bin/id_search.cgi?id=")
|
535
535
|
|
536
536
|
@classmethod
|
537
537
|
def MaizeGDB_Locus(cls):
|
538
538
|
"""Returns the link-out URI for objects of "MaizeGDB".
|
539
539
|
"""
|
540
|
-
|
540
|
+
cls.Namespace("http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=")
|
541
541
|
|
542
542
|
@classmethod
|
543
543
|
def MEROPS(cls):
|
544
544
|
"""Returns the link-out URI for objects of "MEROPS peptidase database".
|
545
545
|
"""
|
546
|
-
|
546
|
+
cls.Namespace("http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=")
|
547
547
|
|
548
548
|
@classmethod
|
549
549
|
def MEROPS_fam(cls):
|
550
550
|
"""Returns the link-out URI for objects of "MEROPS peptidase database".
|
551
551
|
"""
|
552
|
-
|
552
|
+
cls.Namespace("http://merops.sanger.ac.uk/cgi-bin/famsum?family=")
|
553
553
|
|
554
554
|
@classmethod
|
555
555
|
def MeSH(cls):
|
556
556
|
"""Returns the link-out URI for objects of "Medical Subject Headings".
|
557
557
|
"""
|
558
|
-
|
558
|
+
cls.Namespace("http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=")
|
559
559
|
|
560
560
|
@classmethod
|
561
561
|
def MetaCyc(cls):
|
562
562
|
"""Returns the link-out URI for objects of "Metabolic Encyclopedia of metabolic and other pathways".
|
563
563
|
"""
|
564
|
-
|
564
|
+
cls.Namespace("http://biocyc.org/META/NEW-IMAGE?type=NIL&object=")
|
565
565
|
|
566
566
|
@classmethod
|
567
567
|
def MGI(cls):
|
568
568
|
"""Returns the link-out URI for objects of "Mouse Genome Informatics".
|
569
569
|
"""
|
570
|
-
|
570
|
+
cls.Namespace("http://www.informatics.jax.org/accession/")
|
571
571
|
|
572
572
|
@classmethod
|
573
573
|
def MIPS_funcat(cls):
|
574
574
|
"""Returns the link-out URI for objects of "MIPS Functional Catalogue".
|
575
575
|
"""
|
576
|
-
|
576
|
+
cls.Namespace("http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=")
|
577
577
|
|
578
578
|
@classmethod
|
579
579
|
def MO(cls):
|
580
580
|
"""Returns the link-out URI for objects of "MGED Ontology".
|
581
581
|
"""
|
582
|
-
|
582
|
+
cls.Namespace("http://mged.sourceforge.net/ontologies/MGEDontology.php#")
|
583
583
|
|
584
584
|
@classmethod
|
585
585
|
def ModBase(cls):
|
586
586
|
"""Returns the link-out URI for objects of "ModBase comprehensive Database of Comparative Protein Structure Models".
|
587
587
|
"""
|
588
|
-
|
588
|
+
cls.Namespace("http://salilab.org/modbase/searchbyid?databaseID=")
|
589
589
|
|
590
590
|
@classmethod
|
591
591
|
def NASC_code(cls):
|
592
592
|
"""Returns the link-out URI for objects of "Nottingham Arabidopsis Stock Centre Seeds Database".
|
593
593
|
"""
|
594
|
-
|
594
|
+
cls.Namespace("http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=")
|
595
595
|
|
596
596
|
@classmethod
|
597
597
|
def NCBI_Gene(cls):
|
598
598
|
"""Returns the link-out URI for objects of "NCBI Gene".
|
599
599
|
"""
|
600
|
-
|
600
|
+
cls.Namespace("http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=gene&list_uids=")
|
601
601
|
|
602
602
|
@classmethod
|
603
603
|
def NCBI_gi(cls):
|
604
604
|
"""Returns the link-out URI for objects of "NCBI databases".
|
605
605
|
"""
|
606
|
-
|
606
|
+
cls.Namespace("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=")
|
607
607
|
|
608
608
|
@classmethod
|
609
609
|
def NCBI_GP(cls):
|
610
610
|
"""Returns the link-out URI for objects of "NCBI GenPept".
|
611
611
|
"""
|
612
|
-
|
612
|
+
cls.Namespace("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=")
|
613
613
|
|
614
614
|
@classmethod
|
615
615
|
def NIF_Subcellular(cls):
|
616
616
|
"""Returns the link-out URI for objects of "Neuroscience Information Framework standard ontology, subcellular hierarchy".
|
617
617
|
"""
|
618
|
-
|
618
|
+
cls.Namespace("http://www.neurolex.org/wiki/")
|
619
619
|
|
620
620
|
@classmethod
|
621
621
|
def NMPDR(cls):
|
622
622
|
"""Returns the link-out URI for objects of "National Microbial Pathogen Data Resource".
|
623
623
|
"""
|
624
|
-
|
624
|
+
cls.Namespace("http://www.nmpdr.org/linkin.cgi?id=")
|
625
625
|
|
626
626
|
@classmethod
|
627
627
|
def OMIM(cls):
|
628
628
|
"""Returns the link-out URI for objects of "Mendelian Inheritance in Man".
|
629
629
|
"""
|
630
|
-
|
630
|
+
cls.Namespace("http://omim.org/entry/")
|
631
631
|
|
632
632
|
@classmethod
|
633
633
|
def PAMGO_GAT(cls):
|
634
634
|
"""Returns the link-out URI for objects of "Genome Annotation Tool (cls, Agrobacterium tumefaciens C58); PAMGO Interest Group".
|
635
635
|
"""
|
636
|
-
|
636
|
+
cls.Namespace("http://agro.vbi.vt.edu/public/servlet/GeneEdit?&Search=Search&level=2&genename=")
|
637
637
|
|
638
638
|
@classmethod
|
639
639
|
def PAMGO_MGG(cls):
|
640
640
|
"""Returns the link-out URI for objects of "Magnaporthe grisea database".
|
641
641
|
"""
|
642
|
-
|
642
|
+
cls.Namespace("http://scotland.fgl.ncsu.edu/cgi-bin/adHocQuery.cgi?adHocQuery_dbName=smeng_goannotation&Action=Data&QueryName=Functional+Categorization+of+MGG+GO+Annotation&P_KeyWord=")
|
643
643
|
|
644
644
|
@classmethod
|
645
645
|
def PAMGO_VMD(cls):
|
646
646
|
"""Returns the link-out URI for objects of "Virginia Bioinformatics Institute Microbial Database".
|
647
647
|
"""
|
648
|
-
|
648
|
+
cls.Namespace("http://vmd.vbi.vt.edu/cgi-bin/browse/go_detail.cgi?gene_id=")
|
649
649
|
|
650
650
|
@classmethod
|
651
651
|
def PANTHER(cls):
|
652
652
|
"""Returns the link-out URI for objects of "Protein ANalysis THrough Evolutionary Relationships".
|
653
653
|
"""
|
654
|
-
|
654
|
+
cls.Namespace("http://pantree.org/node/annotationNode.jsp?id=")
|
655
655
|
|
656
656
|
@classmethod
|
657
657
|
def PATRIC(cls):
|
658
658
|
"""Returns the link-out URI for objects of "PathoSystems Resource Integration Center".
|
659
659
|
"""
|
660
|
-
|
660
|
+
cls.Namespace("http://patric.vbi.vt.edu/gene/overview.php?fid=")
|
661
661
|
|
662
662
|
@classmethod
|
663
663
|
def PDB(cls):
|
664
664
|
"""Returns the link-out URI for objects of "Protein Data Bank".
|
665
665
|
"""
|
666
|
-
|
666
|
+
cls.Namespace("http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=")
|
667
667
|
|
668
668
|
@classmethod
|
669
669
|
def Pfam(cls):
|
670
670
|
"""Returns the link-out URI for objects of "Pfam database of protein families".
|
671
671
|
"""
|
672
|
-
|
672
|
+
cls.Namespace("http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?")
|
673
673
|
|
674
674
|
@classmethod
|
675
675
|
def PharmGKB(cls):
|
676
676
|
"""Returns the link-out URI for objects of "Pharmacogenetics and Pharmacogenomics Knowledge Base".
|
677
677
|
"""
|
678
|
-
|
678
|
+
cls.Namespace("http://www.pharmgkb.org/do/serve?objId=")
|
679
679
|
|
680
680
|
@classmethod
|
681
681
|
def PIR(cls):
|
682
682
|
"""Returns the link-out URI for objects of "Protein Information Resource".
|
683
683
|
"""
|
684
|
-
|
684
|
+
cls.Namespace("http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?uid=")
|
685
685
|
|
686
686
|
@classmethod
|
687
687
|
def PIRSF(cls):
|
688
688
|
"""Returns the link-out URI for objects of "PIR Superfamily Classification System".
|
689
689
|
"""
|
690
|
-
|
690
|
+
cls.Namespace("http://pir.georgetown.edu/cgi-bin/ipcSF?id=")
|
691
691
|
|
692
692
|
@classmethod
|
693
693
|
def PMCID(cls):
|
694
694
|
"""Returns the link-out URI for objects of "Pubmed Central".
|
695
695
|
"""
|
696
|
-
|
696
|
+
cls.Namespace("http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term=")
|
697
697
|
|
698
698
|
@classmethod
|
699
699
|
def PMID(cls):
|
700
700
|
"""Returns the link-out URI for objects of "PubMed".
|
701
701
|
"""
|
702
|
-
|
702
|
+
cls.Namespace("http://www.ncbi.nlm.nih.gov/pubmed/")
|
703
703
|
|
704
704
|
@classmethod
|
705
705
|
def PO(cls):
|
706
706
|
"""Returns the link-out URI for objects of "Plant Ontology Consortium Database".
|
707
707
|
"""
|
708
|
-
|
708
|
+
cls.Namespace("http://www.plantontology.org/amigo/go.cgi?action=query&view=query&search_constraint=terms&query=PO:")
|
709
709
|
|
710
710
|
@classmethod
|
711
711
|
def PO_REF(cls):
|
712
712
|
"""Returns the link-out URI for objects of "Plant Ontology custom references".
|
713
713
|
"""
|
714
|
-
|
714
|
+
cls.Namespace("http://wiki.plantontology.org:8080/index.php/PO_REF:")
|
715
715
|
|
716
716
|
@classmethod
|
717
717
|
def PomBase(cls):
|
718
718
|
"""Returns the link-out URI for objects of "PomBase".
|
719
719
|
"""
|
720
|
-
|
720
|
+
cls.Namespace("http://www.pombase.org/spombe/result/")
|
721
721
|
|
722
722
|
@classmethod
|
723
723
|
def PR(cls):
|
724
724
|
"""Returns the link-out URI for objects of "Protein Ontology".
|
725
725
|
"""
|
726
|
-
|
726
|
+
cls.Namespace("http://www.proconsortium.org/cgi-bin/pro/entry_pro?id=PR:")
|
727
727
|
|
728
728
|
@classmethod
|
729
729
|
def PRINTS(cls):
|
730
730
|
"""Returns the link-out URI for objects of "PRINTS compendium of protein fingerprints".
|
731
731
|
"""
|
732
|
-
|
732
|
+
cls.Namespace("http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=False®expr=off&prints_accn=")
|
733
733
|
|
734
734
|
@classmethod
|
735
735
|
def ProDom(cls):
|
736
736
|
"""Returns the link-out URI for objects of "ProDom protein domain families".
|
737
737
|
"""
|
738
|
-
|
738
|
+
cls.Namespace("http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=")
|
739
739
|
|
740
740
|
@classmethod
|
741
741
|
def Prosite(cls):
|
742
742
|
"""Returns the link-out URI for objects of "Prosite database of protein families and domains".
|
743
743
|
"""
|
744
|
-
|
744
|
+
cls.Namespace("http://www.expasy.ch/cgi-bin/prosite-search-ac?")
|
745
745
|
|
746
746
|
@classmethod
|
747
747
|
def PseudoCAP(cls):
|
748
748
|
"""Returns the link-out URI for objects of "Pseudomonas Genome Project".
|
749
749
|
"""
|
750
|
-
|
750
|
+
cls.Namespace("http://v2.pseudomonas.com/getAnnotation.do?locusID=")
|
751
751
|
|
752
752
|
@classmethod
|
753
753
|
def PSI_MOD(cls):
|
754
754
|
"""Returns the link-out URI for objects of "Proteomics Standards Initiative protein modification ontology".
|
755
755
|
"""
|
756
|
-
|
756
|
+
cls.Namespace("http://www.ebi.ac.uk/ontology-lookup/?termId=MOD:")
|
757
757
|
|
758
758
|
@classmethod
|
759
759
|
def PubChem_BioAssay(cls):
|
760
760
|
"""Returns the link-out URI for objects of "NCBI PubChem database of bioassay records".
|
761
761
|
"""
|
762
|
-
|
762
|
+
cls.Namespace("http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=")
|
763
763
|
|
764
764
|
@classmethod
|
765
765
|
def PubChem_Compound(cls):
|
766
766
|
"""Returns the link-out URI for objects of "NCBI PubChem database of chemical structures".
|
767
767
|
"""
|
768
|
-
|
768
|
+
cls.Namespace("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term=")
|
769
769
|
|
770
770
|
@classmethod
|
771
771
|
def PubChem_Substance(cls):
|
772
772
|
"""Returns the link-out URI for objects of "NCBI PubChem database of chemical substances".
|
773
773
|
"""
|
774
|
-
|
774
|
+
cls.Namespace("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcsubstance&term=")
|
775
775
|
|
776
776
|
@classmethod
|
777
777
|
def Reactome(cls):
|
778
778
|
"""Returns the link-out URI for objects of "Reactome - a curated knowledgebase of biological pathways".
|
779
779
|
"""
|
780
|
-
|
780
|
+
cls.Namespace("http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=")
|
781
781
|
|
782
782
|
@classmethod
|
783
783
|
def RefSeq(cls):
|
784
784
|
"""Returns the link-out URI for objects of "RefSeq".
|
785
785
|
"""
|
786
|
-
|
786
|
+
cls.Namespace("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=")
|
787
787
|
|
788
788
|
@classmethod
|
789
789
|
def RefSeq_NA(cls):
|
790
790
|
"""Returns the link-out URI for objects of "RefSeq (cls, Nucleic Acid)".
|
791
791
|
"""
|
792
|
-
|
792
|
+
cls.Namespace("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=")
|
793
793
|
|
794
794
|
@classmethod
|
795
795
|
def RefSeq_Prot(cls):
|
796
796
|
"""Returns the link-out URI for objects of "RefSeq (cls, Protein)".
|
797
797
|
"""
|
798
|
-
|
798
|
+
cls.Namespace("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=")
|
799
799
|
|
800
800
|
@classmethod
|
801
801
|
def Rfam(cls):
|
802
802
|
"""Returns the link-out URI for objects of "Rfam database of RNA families".
|
803
803
|
"""
|
804
|
-
|
804
|
+
cls.Namespace("http://rfam.sanger.ac.uk/family/")
|
805
805
|
|
806
806
|
@classmethod
|
807
807
|
def RGD(cls):
|
808
808
|
"""Returns the link-out URI for objects of "Rat Genome Database".
|
809
809
|
"""
|
810
|
-
|
810
|
+
cls.Namespace("http://rgd.mcw.edu/generalSearch/RgdSearch.jsp?quickSearch=1&searchKeyword=")
|
811
811
|
|
812
812
|
@classmethod
|
813
813
|
def RHEA(cls):
|
814
814
|
"""Returns the link-out URI for objects of "Rhea, the Annotated Reactions Database".
|
815
815
|
"""
|
816
|
-
|
816
|
+
cls.Namespace("http://www.ebi.ac.uk/rhea/reaction.xhtml?id=")
|
817
817
|
|
818
818
|
@classmethod
|
819
819
|
def RNAmods(cls):
|
820
820
|
"""Returns the link-out URI for objects of "RNA Modification Database".
|
821
821
|
"""
|
822
|
-
|
822
|
+
cls.Namespace("http://s59.cas.albany.edu/RNAmods/cgi-bin/rnashow.cgi?")
|
823
823
|
|
824
824
|
@classmethod
|
825
825
|
def RO(cls):
|
826
826
|
"""Returns the link-out URI for objects of "OBO Relation Ontology Ontology".
|
827
827
|
"""
|
828
|
-
|
828
|
+
cls.Namespace("http://purl.obolibrary.org/obo/RO_")
|
829
829
|
|
830
830
|
@classmethod
|
831
831
|
def SABIO_RK(cls):
|
832
832
|
"""Returns the link-out URI for objects of "SABIO Reaction Kinetics".
|
833
833
|
"""
|
834
|
-
|
834
|
+
cls.Namespace("http://sabio.villa-bosch.de/reacdetails.jsp?reactid=")
|
835
835
|
|
836
836
|
@classmethod
|
837
837
|
def SEED(cls):
|
838
838
|
"""Returns the link-out URI for objects of "The SEED;".
|
839
839
|
"""
|
840
|
-
|
840
|
+
cls.Namespace("http://www.theseed.org/linkin.cgi?id=")
|
841
841
|
|
842
842
|
@classmethod
|
843
843
|
def SGD(cls):
|
844
844
|
"""Returns the link-out URI for objects of "Saccharomyces Genome Database".
|
845
845
|
"""
|
846
|
-
|
846
|
+
cls.Namespace("http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=")
|
847
847
|
|
848
848
|
@classmethod
|
849
849
|
def SGD_LOCUS(cls):
|
850
850
|
"""Returns the link-out URI for objects of "Saccharomyces Genome Database".
|
851
851
|
"""
|
852
|
-
|
852
|
+
cls.Namespace("http://db.yeastgenome.org/cgi-bin/locus.pl?locus=")
|
853
853
|
|
854
854
|
@classmethod
|
855
855
|
def SGD_REF(cls):
|
856
856
|
"""Returns the link-out URI for objects of "Saccharomyces Genome Database".
|
857
857
|
"""
|
858
|
-
|
858
|
+
cls.Namespace("http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=")
|
859
859
|
|
860
860
|
@classmethod
|
861
861
|
def SGN(cls):
|
862
862
|
"""Returns the link-out URI for objects of "Sol Genomics Network".
|
863
863
|
"""
|
864
|
-
|
864
|
+
cls.Namespace("http://www.sgn.cornell.edu/phenome/locus_display.pl?locus_id=")
|
865
865
|
|
866
866
|
@classmethod
|
867
867
|
def SGN_ref(cls):
|
868
868
|
"""Returns the link-out URI for objects of "Sol Genomics Network".
|
869
869
|
"""
|
870
|
-
|
870
|
+
cls.Namespace("http://www.sgn.cornell.edu/chado/publication.pl?pub_id=")
|
871
871
|
|
872
872
|
@classmethod
|
873
873
|
def SMART(cls):
|
874
874
|
"""Returns the link-out URI for objects of "Simple Modular Architecture Research Tool".
|
875
875
|
"""
|
876
|
-
|
876
|
+
cls.Namespace("http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=")
|
877
877
|
|
878
878
|
@classmethod
|
879
879
|
def SO(cls):
|
880
880
|
"""Returns the link-out URI for objects of "Sequence Ontology".
|
881
881
|
"""
|
882
|
-
|
882
|
+
cls.Namespace("http://song.sourceforge.net/SOterm_tables.html#SO:")
|
883
883
|
|
884
884
|
@classmethod
|
885
885
|
def SUPERFAMILY(cls):
|
886
886
|
"""Returns the link-out URI for objects of "SUPERFAMILY protein annotation database".
|
887
887
|
"""
|
888
|
-
|
888
|
+
cls.Namespace("http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/scop.cgi?ipid=SSF")
|
889
889
|
|
890
890
|
@classmethod
|
891
891
|
def Swiss_Prot(cls):
|
892
892
|
"""Returns the link-out URI for objects of "UniProtKB/Swiss-Prot".
|
893
893
|
"""
|
894
|
-
|
894
|
+
cls.Namespace("http://www.uniprot.org/uniprot/")
|
895
895
|
|
896
896
|
@classmethod
|
897
897
|
def TAIR(cls):
|
898
898
|
"""Returns the link-out URI for objects of "The Arabidopsis Information Resource".
|
899
899
|
"""
|
900
|
-
|
900
|
+
cls.Namespace("http://arabidopsis.org/servlets/TairObject?accession=")
|
901
901
|
|
902
902
|
@classmethod
|
903
903
|
def taxon(cls):
|
904
904
|
"""Returns the link-out URI for objects of "NCBI Taxonomy".
|
905
905
|
"""
|
906
|
-
|
906
|
+
cls.Namespace("http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=")
|
907
907
|
|
908
908
|
@classmethod
|
909
909
|
def TC(cls):
|
910
910
|
"""Returns the link-out URI for objects of "Transport Protein Database".
|
911
911
|
"""
|
912
|
-
|
912
|
+
cls.Namespace("http://www.tcdb.org/tcdb/index.php?tc=")
|
913
913
|
|
914
914
|
@classmethod
|
915
915
|
def TGD_LOCUS(cls):
|
916
916
|
"""Returns the link-out URI for objects of "Tetrahymena Genome Database".
|
917
917
|
"""
|
918
|
-
|
918
|
+
cls.Namespace("http://db.ciliate.org/cgi-bin/locus.pl?locus=")
|
919
919
|
|
920
920
|
@classmethod
|
921
921
|
def TGD_REF(cls):
|
922
922
|
"""Returns the link-out URI for objects of "Tetrahymena Genome Database".
|
923
923
|
"""
|
924
|
-
|
924
|
+
cls.Namespace("http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=")
|
925
925
|
|
926
926
|
@classmethod
|
927
927
|
def TrEMBL(cls):
|
928
928
|
"""Returns the link-out URI for objects of "UniProtKB-TrEMBL protein sequence database".
|
929
929
|
"""
|
930
|
-
|
930
|
+
cls.Namespace("http://www.uniprot.org/uniprot/")
|
931
931
|
|
932
932
|
@classmethod
|
933
933
|
def UBERON(cls):
|
934
934
|
"""Returns the link-out URI for objects of "Uber-anatomy ontology".
|
935
935
|
"""
|
936
|
-
|
936
|
+
cls.Namespace("http://purl.obolibrary.org/obo/UBERON_")
|
937
937
|
|
938
938
|
@classmethod
|
939
939
|
def UM_BBD_enzymeID(cls):
|
940
940
|
"""Returns the link-out URI for objects of "University of Minnesota Biocatalysis/Biodegradation Database".
|
941
941
|
"""
|
942
|
-
|
942
|
+
cls.Namespace("http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=ep&enzymeID=")
|
943
943
|
|
944
944
|
@classmethod
|
945
945
|
def UM_BBD_reactionID(cls):
|
946
946
|
"""Returns the link-out URI for objects of "University of Minnesota Biocatalysis/Biodegradation Database".
|
947
947
|
"""
|
948
|
-
|
948
|
+
cls.Namespace("http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=r&reacID=")
|
949
949
|
|
950
950
|
@classmethod
|
951
951
|
def UM_BBD_ruleID(cls):
|
952
952
|
"""Returns the link-out URI for objects of "University of Minnesota Biocatalysis/Biodegradation Database".
|
953
953
|
"""
|
954
|
-
|
954
|
+
cls.Namespace("http://umbbd.msi.umn.edu/servlets/rule.jsp?rule=")
|
955
955
|
|
956
956
|
@classmethod
|
957
957
|
def UniMod(cls):
|
958
958
|
"""Returns the link-out URI for objects of "UniMod".
|
959
959
|
"""
|
960
|
-
|
960
|
+
cls.Namespace("http://www.unimod.org/modifications_view.php?editid1=")
|
961
961
|
|
962
962
|
@classmethod
|
963
963
|
def UniParc(cls):
|
964
964
|
"""Returns the link-out URI for objects of "UniProt Archive".
|
965
965
|
"""
|
966
|
-
|
966
|
+
cls.Namespace("http://www.uniprot.org/uniparc/")
|
967
967
|
|
968
968
|
@classmethod
|
969
969
|
def UniPathway(cls):
|
970
970
|
"""Returns the link-out URI for objects of "UniPathway".
|
971
971
|
"""
|
972
|
-
|
972
|
+
cls.Namespace("http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=")
|
973
973
|
|
974
974
|
@classmethod
|
975
975
|
def UniProtKB(cls):
|
976
976
|
"""Returns the link-out URI for objects of "Universal Protein Knowledgebase".
|
977
977
|
"""
|
978
|
-
|
978
|
+
cls.Namespace("http://www.uniprot.org/uniprot/")
|
979
979
|
|
980
980
|
@classmethod
|
981
981
|
def UniProtKB_KW(cls):
|
982
982
|
"""Returns the link-out URI for objects of "UniProt Knowledgebase keywords".
|
983
983
|
"""
|
984
|
-
|
984
|
+
cls.Namespace("http://www.uniprot.org/keywords/")
|
985
985
|
|
986
986
|
@classmethod
|
987
987
|
def UniProtKB_SubCell(cls):
|
988
988
|
"""Returns the link-out URI for objects of "UniProt Knowledgebase Subcellular Location vocabulary".
|
989
989
|
"""
|
990
|
-
|
990
|
+
cls.Namespace("http://www.uniprot.org/locations/")
|
991
991
|
|
992
992
|
@classmethod
|
993
993
|
def VBRC(cls):
|
994
994
|
"""Returns the link-out URI for objects of "Viral Bioinformatics Resource Center".
|
995
995
|
"""
|
996
|
-
|
996
|
+
cls.Namespace("http://vbrc.org/query.asp?web_id=VBRC:")
|
997
997
|
|
998
998
|
@classmethod
|
999
999
|
def VEGA(cls):
|
1000
1000
|
"""Returns the link-out URI for objects of "Vertebrate Genome Annotation database".
|
1001
1001
|
"""
|
1002
|
-
|
1002
|
+
cls.Namespace("http://vega.sanger.ac.uk/perl/searchview?species=all&idx=All&q=")
|
1003
1003
|
|
1004
1004
|
@classmethod
|
1005
1005
|
def VMD(cls):
|
1006
1006
|
"""Returns the link-out URI for objects of "Virginia Bioinformatics Institute Microbial Database".
|
1007
1007
|
"""
|
1008
|
-
|
1008
|
+
cls.Namespace("http://vmd.vbi.vt.edu/cgi-bin/browse/browserDetail_new.cgi?gene_id=")
|
1009
1009
|
|
1010
1010
|
@classmethod
|
1011
1011
|
def WB(cls):
|
1012
1012
|
"""Returns the link-out URI for objects of "WormBase database of nematode biology".
|
1013
1013
|
"""
|
1014
|
-
|
1014
|
+
cls.Namespace("http://www.wormbase.org/db/gene/gene?name=")
|
1015
1015
|
|
1016
1016
|
@classmethod
|
1017
1017
|
def WB_REF(cls):
|
1018
1018
|
"""Returns the link-out URI for objects of "WormBase database of nematode biology".
|
1019
1019
|
"""
|
1020
|
-
|
1020
|
+
cls.Namespace("http://www.wormbase.org/db/misc/paper?name=")
|
1021
1021
|
|
1022
1022
|
@classmethod
|
1023
1023
|
def Wikipedia(cls):
|
1024
1024
|
"""Returns the link-out URI for objects of "Wikipedia".
|
1025
1025
|
"""
|
1026
|
-
|
1026
|
+
cls.Namespace("http://en.wikipedia.org/wiki/")
|
1027
1027
|
|
1028
1028
|
@classmethod
|
1029
1029
|
def WP(cls):
|
1030
1030
|
"""Returns the link-out URI for objects of "Wormpep database of proteins of C. elegans".
|
1031
1031
|
"""
|
1032
|
-
|
1032
|
+
cls.Namespace("http://www.wormbase.org/db/get?class=Protein;name=WP:")
|
1033
1033
|
|
1034
1034
|
@classmethod
|
1035
1035
|
def ZFIN(cls):
|
1036
1036
|
"""Returns the link-out URI for objects of "Zebrafish Information Network".
|
1037
1037
|
"""
|
1038
|
-
|
1038
|
+
cls.Namespace("http://zfin.org/cgi-bin/ZFIN_jump?record=")
|
1039
1039
|
|
1040
1040
|
|