biointerchange 0.2.2 → 1.0.0
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- data/Gemfile +1 -0
- data/README.md +269 -19
- data/VERSION +1 -1
- data/examples/bininda_emonds_mammals.new +1 -0
- data/examples/rdfization.rb +17 -0
- data/examples/tree1.new +1 -0
- data/examples/tree2.new +1 -0
- data/examples/vocabulary.rb +26 -5
- data/generators/javaify.rb +12 -18
- data/generators/make_supplement_releases.rb +2 -0
- data/generators/pythonify.rb +21 -8
- data/generators/rdfxml.rb +15 -1
- data/lib/biointerchange/cdao.rb +2014 -0
- data/lib/biointerchange/core.rb +70 -77
- data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +16 -0
- data/lib/biointerchange/genomics/gff3_reader.rb +18 -4
- data/lib/biointerchange/genomics/gvf_reader.rb +14 -0
- data/lib/biointerchange/phylogenetics/cdao_rdf_ntriples.rb +108 -0
- data/lib/biointerchange/phylogenetics/newick_reader.rb +81 -0
- data/lib/biointerchange/phylogenetics/tree_set.rb +50 -0
- data/lib/biointerchange/registry.rb +50 -8
- data/lib/biointerchange/so.rb +150 -0
- data/lib/biointerchange/textmining/pdfx_xml_reader.rb +21 -2
- data/lib/biointerchange/textmining/pubannos_json_reader.rb +24 -1
- data/lib/biointerchange/textmining/text_mining_rdf_ntriples.rb +9 -0
- data/lib/biointerchange/textmining/text_mining_reader.rb +5 -5
- data/spec/phylogenetics_spec.rb +79 -0
- data/supplemental/java/biointerchange/pom.xml +1 -1
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/CDAO.java +2602 -0
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/FALDO.java +30 -28
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GFF3O.java +136 -104
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GVF1O.java +367 -278
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SIO.java +4388 -3127
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SO.java +5970 -4351
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SOFA.java +733 -544
- data/supplemental/java/biointerchange/src/test/java/org/biointerchange/AppTest.java +3 -1
- data/supplemental/python/biointerchange/cdao.py +2021 -0
- data/supplemental/python/biointerchange/faldo.py +37 -38
- data/supplemental/python/biointerchange/gff3o.py +156 -157
- data/supplemental/python/biointerchange/goxref.py +172 -172
- data/supplemental/python/biointerchange/gvf1o.py +428 -429
- data/supplemental/python/biointerchange/sio.py +3133 -3134
- data/supplemental/python/biointerchange/so.py +6626 -6527
- data/supplemental/python/biointerchange/sofa.py +790 -791
- data/supplemental/python/example.py +23 -5
- data/supplemental/python/setup.py +2 -2
- data/web/about.html +1 -0
- data/web/api.html +223 -15
- data/web/biointerchange.js +27 -6
- data/web/cli.html +8 -3
- data/web/index.html +6 -2
- data/web/ontologies.html +3 -0
- data/web/service/rdfizer.fcgi +7 -15
- data/web/webservices.html +6 -2
- metadata +30 -3
@@ -9,1032 +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
|
|