package org.biointerchange.vocabulary; import java.util.Arrays; import java.util.Map; import java.util.HashMap; import java.util.HashSet; import java.util.Set; import com.hp.hpl.jena.rdf.model.Property; import com.hp.hpl.jena.rdf.model.Resource; import com.hp.hpl.jena.rdf.model.ResourceFactory; import org.apache.commons.collections.CollectionUtils; import org.apache.commons.collections.Predicate; public class GOXRef { /** * Returns the link-out URI for objects of "Arabidopsis Genome Initiative". */ public static Resource AGI_LocusCode() { return ResourceFactory.createResource("http://arabidopsis.org/servlets/TairObject?type=locus&name="); } /** * Returns the link-out URI for objects of "PlasmoDB Plasmodium Genome Resource". */ public static Resource ApiDB_PlasmoDB() { return ResourceFactory.createResource("http://www.plasmodb.org/gene/"); } /** * Returns the link-out URI for objects of "AraCyc metabolic pathway database for Arabidopsis thaliana". */ public static Resource AraCyc() { return ResourceFactory.createResource("http://www.arabidopsis.org:1555/ARA/NEW-IMAGE?type=NIL&object="); } /** * Returns the link-out URI for objects of "A Systematic Annotation Package for Community Analysis of Genomes". */ public static Resource ASAP() { return ResourceFactory.createResource("https://asap.ahabs.wisc.edu/annotation/php/feature_info.php?FeatureID="); } /** * Returns the link-out URI for objects of "Aspergillus Genome Database". */ public static Resource AspGD() { return ResourceFactory.createResource("http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid="); } /** * Returns the link-out URI for objects of "Aspergillus Genome Database". */ public static Resource AspGD_LOCUS() { return ResourceFactory.createResource("http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus="); } /** * Returns the link-out URI for objects of "Aspergillus Genome Database". */ public static Resource AspGD_REF() { return ResourceFactory.createResource("http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid="); } /** * Returns the link-out URI for objects of "Basic Formal Ontology". */ public static Resource BFO() { return ResourceFactory.createResource("http://purl.obolibrary.org/obo/BFO_"); } /** * Returns the link-out URI for objects of "BioCyc collection of metabolic pathway databases". */ public static Resource BioCyc() { return ResourceFactory.createResource("http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object="); } /** * Returns the link-out URI for objects of "BioModels Database". */ public static Resource BIOMD() { return ResourceFactory.createResource("http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid="); } /** * Returns the link-out URI for objects of "BRENDA, The Comprehensive Enzyme Information System". */ public static Resource BRENDA() { return ResourceFactory.createResource("http://www.brenda-enzymes.info/php/result_flat.php4?ecno="); } /** * Returns the link-out URI for objects of "Magnaporthe grisea Database". */ public static Resource Broad_MGG() { return ResourceFactory.createResource("http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/GeneLocus.html?sp=S"); } /** * Returns the link-out URI for objects of "Catalog of Fishes genus database". */ public static Resource CASGEN() { return ResourceFactory.createResource("http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Genus&id="); } /** * Returns the link-out URI for objects of "Catalog of Fishes publications database". */ public static Resource CASREF() { return ResourceFactory.createResource("http://research.calacademy.org/research/ichthyology/catalog/getref.asp?id="); } /** * Returns the link-out URI for objects of "Catalog of Fishes species database". */ public static Resource CASSPC() { return ResourceFactory.createResource("http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Species&id=1979"); } /** * Returns the link-out URI for objects of "Conserved Domain Database at NCBI". */ public static Resource CDD() { return ResourceFactory.createResource("http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid="); } /** * Returns the link-out URI for objects of "Candida Genome Database". */ public static Resource CGD() { return ResourceFactory.createResource("http://www.candidagenome.org/cgi-bin/locus.pl?dbid="); } /** * Returns the link-out URI for objects of "Candida Genome Database". */ public static Resource CGD_LOCUS() { return ResourceFactory.createResource("http://www.candidagenome.org/cgi-bin/locus.pl?locus="); } /** * Returns the link-out URI for objects of "Candida Genome Database". */ public static Resource CGD_REF() { return ResourceFactory.createResource("http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid="); } /** * Returns the link-out URI for objects of "Chemical Entities of Biological Interest". */ public static Resource CHEBI() { return ResourceFactory.createResource("http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:"); } /** * Returns the link-out URI for objects of "Cell Type Ontology". */ public static Resource CL() { return ResourceFactory.createResource("http://purl.obolibrary.org/obo/CL_"); } /** * Returns the link-out URI for objects of "NCBI COG cluster". */ public static Resource COG_Cluster() { return ResourceFactory.createResource("http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog="); } /** * Returns the link-out URI for objects of "NCBI COG function". */ public static Resource COG_Function() { return ResourceFactory.createResource("http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun="); } /** * Returns the link-out URI for objects of "NCBI COG pathway". */ public static Resource COG_Pathway() { return ResourceFactory.createResource("http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw="); } /** * Returns the link-out URI for objects of "CORUM - the Comprehensive Resource of Mammalian protein complexes". */ public static Resource CORUM() { return ResourceFactory.createResource("http://mips.gsf.de/genre/proj/corum/complexdetails.html?id="); } /** * Returns the link-out URI for objects of "NCBI dbSNP". */ public static Resource dbSNP() { return ResourceFactory.createResource("http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs="); } /** * Returns the link-out URI for objects of "DNA Databank of Japan". */ public static Resource DDBJ() { return ResourceFactory.createResource("http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch?KeyWord="); } /** * Returns the link-out URI for objects of "dictyBase". */ public static Resource dictyBase() { return ResourceFactory.createResource("http://dictybase.org/gene/"); } /** * Returns the link-out URI for objects of "dictyBase". */ public static Resource dictyBase_gene_name() { return ResourceFactory.createResource("http://dictybase.org/gene/"); } /** * Returns the link-out URI for objects of "dictyBase literature references". */ public static Resource dictyBase_REF() { return ResourceFactory.createResource("http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo="); } /** * Returns the link-out URI for objects of "Digital Object Identifier". */ public static Resource DOI() { return ResourceFactory.createResource("http://dx.doi.org/DOI:"); } /** * Returns the link-out URI for objects of "Enzyme Commission". */ public static Resource EC() { return ResourceFactory.createResource("http://www.expasy.org/enzyme/"); } /** * Returns the link-out URI for objects of "EchoBASE post-genomic database for Escherichia coli". */ public static Resource EchoBASE() { return ResourceFactory.createResource("http://www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID="); } /** * Returns the link-out URI for objects of "EcoGene Database of Escherichia coli Sequence and Function". */ public static Resource ECK() { return ResourceFactory.createResource("http://www.ecogene.org/geneInfo.php?eck_id="); } /** * Returns the link-out URI for objects of "Encyclopedia of E. coli metabolism". */ public static Resource EcoCyc() { return ResourceFactory.createResource("http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object="); } /** * Returns the link-out URI for objects of "Encyclopedia of E. coli metabolism". */ public static Resource EcoCyc_REF() { return ResourceFactory.createResource("http://biocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object="); } /** * Returns the link-out URI for objects of "EcoGene Database of Escherichia coli Sequence and Function". */ public static Resource ECOGENE() { return ResourceFactory.createResource("http://www.ecogene.org/geneInfo.php?eg_id="); } /** * Returns the link-out URI for objects of "EMBL Nucleotide Sequence Database". */ public static Resource EMBL() { return ResourceFactory.createResource("http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id="); } /** * Returns the link-out URI for objects of "European Nucleotide Archive". */ public static Resource ENA() { return ResourceFactory.createResource("http://www.ebi.ac.uk/ena/data/view/"); } /** * Returns the link-out URI for objects of "Ensembl database of automatically annotated genomic data". */ public static Resource ENSEMBL() { return ResourceFactory.createResource("http://www.ensembl.org/id/"); } /** * Returns the link-out URI for objects of "Ensembl database of automatically annotated genomic data". */ public static Resource ENSEMBL_GeneID() { return ResourceFactory.createResource("http://www.ensembl.org/id/"); } /** * Returns the link-out URI for objects of "Ensembl database of automatically annotated genomic data". */ public static Resource ENSEMBL_ProteinID() { return ResourceFactory.createResource("http://www.ensembl.org/id/"); } /** * Returns the link-out URI for objects of "Ensembl database of automatically annotated genomic data". */ public static Resource ENSEMBL_TranscriptID() { return ResourceFactory.createResource("http://www.ensembl.org/id/"); } /** * Returns the link-out URI for objects of "Swiss Institute of Bioinformatics enzyme database". */ public static Resource ENZYME() { return ResourceFactory.createResource("http://www.expasy.ch/cgi-bin/nicezyme.pl?"); } /** * Returns the link-out URI for objects of "Drosophila gross anatomy". */ public static Resource FBbt() { return ResourceFactory.createResource("http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:"); } /** * Returns the link-out URI for objects of "Human Genome Database". */ public static Resource GDB() { return ResourceFactory.createResource("http://www.gdb.org/gdb-bin/genera/accno?accessionNum=GDB:"); } /** * Returns the link-out URI for objects of "GenBank". */ public static Resource GenBank() { return ResourceFactory.createResource("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val="); } /** * Returns the link-out URI for objects of "Domain Architecture Classification". */ public static Resource Gene3D() { return ResourceFactory.createResource("http://gene3d.biochem.ucl.ac.uk/superfamily/?accession="); } /** * Returns the link-out URI for objects of "Glossina morsitans GeneDB". */ public static Resource GeneDB_Gmorsitans() { return ResourceFactory.createResource("http://www.genedb.org/genedb/Search?organism=glossina&name="); } /** * Returns the link-out URI for objects of "Leishmania major GeneDB". */ public static Resource GeneDB_Lmajor() { return ResourceFactory.createResource("http://www.genedb.org/genedb/Search?organism=leish&name="); } /** * Returns the link-out URI for objects of "Plasmodium falciparum GeneDB". */ public static Resource GeneDB_Pfalciparum() { return ResourceFactory.createResource("http://www.genedb.org/genedb/Search?organism=malaria&name="); } /** * Returns the link-out URI for objects of "Schizosaccharomyces pombe GeneDB". */ public static Resource GeneDB_Spombe() { return ResourceFactory.createResource("http://old.genedb.org/genedb/Search?organism=pombe&name="); } /** * Returns the link-out URI for objects of "Trypanosoma brucei GeneDB". */ public static Resource GeneDB_Tbrucei() { return ResourceFactory.createResource("http://www.genedb.org/genedb/Search?organism=tryp&name="); } /** * Returns the link-out URI for objects of "NCBI Gene Expression Omnibus". */ public static Resource GEO() { return ResourceFactory.createResource("http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc="); } /** * Returns the link-out URI for objects of "Gene Ontology Database". */ public static Resource GO() { return ResourceFactory.createResource("http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:"); } /** * Returns the link-out URI for objects of "Gene Ontology Database references". */ public static Resource GO_REF() { return ResourceFactory.createResource("http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:"); } /** * Returns the link-out URI for objects of "Gene Ontology Normal Usage Tracking System (GONUTS)". */ public static Resource GONUTS() { return ResourceFactory.createResource("http://gowiki.tamu.edu/wiki/index.php/"); } /** * Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains". */ public static Resource GR() { return ResourceFactory.createResource("http://www.gramene.org/db/searches/browser?search_type=All&RGN=on&query="); } /** * Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains". */ public static Resource GR_GENE() { return ResourceFactory.createResource("http://www.gramene.org/db/genes/search_gene?acc="); } /** * Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains". */ public static Resource GR_PROTEIN() { return ResourceFactory.createResource("http://www.gramene.org/db/protein/protein_search?acc="); } /** * Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains". */ public static Resource GR_QTL() { return ResourceFactory.createResource("http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id="); } /** * Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains". */ public static Resource GR_REF() { return ResourceFactory.createResource("http://www.gramene.org/db/literature/pub_search?ref_id="); } /** * Returns the link-out URI for objects of "H-invitational Database". */ public static Resource H_invDB_cDNA() { return ResourceFactory.createResource("http://www.h-invitational.jp/hinv/spsoup/transcript_view?acc_id="); } /** * Returns the link-out URI for objects of "H-invitational Database". */ public static Resource H_invDB_locus() { return ResourceFactory.createResource("http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id="); } /** * Returns the link-out URI for objects of "High-quality Automated and Manual Annotation of microbial Proteomes". */ public static Resource HAMAP() { return ResourceFactory.createResource("http://us.expasy.org/unirules/"); } /** * Returns the link-out URI for objects of "HUGO Gene Nomenclature Committee". */ public static Resource HGNC() { return ResourceFactory.createResource("http://www.genenames.org/data/hgnc_data.php?hgnc_id=HGNC:"); } /** * Returns the link-out URI for objects of "HUGO Gene Nomenclature Committee". */ public static Resource HGNC_gene() { return ResourceFactory.createResource("http://www.genenames.org/data/hgnc_data.php?app_sym="); } /** * Returns the link-out URI for objects of "Human Protein Atlas tissue profile information". */ public static Resource HPA() { return ResourceFactory.createResource("http://www.proteinatlas.org/tissue_profile.php?antibody_id="); } /** * Returns the link-out URI for objects of "Human Protein Atlas antibody information". */ public static Resource HPA_antibody() { return ResourceFactory.createResource("http://www.proteinatlas.org/antibody_info.php?antibody_id="); } /** * Returns the link-out URI for objects of "Integrated Microbial Genomes; JGI web site for genome annotation". */ public static Resource IMG() { return ResourceFactory.createResource("http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid="); } /** * Returns the link-out URI for objects of "IntAct protein interaction database". */ public static Resource IntAct() { return ResourceFactory.createResource("http://www.ebi.ac.uk/intact/search/do/search?searchString="); } /** * Returns the link-out URI for objects of "InterPro database of protein domains and motifs". */ public static Resource InterPro() { return ResourceFactory.createResource("http://www.ebi.ac.uk/interpro/IEntry?ac="); } /** * Returns the link-out URI for objects of "International Standard Book Number". */ public static Resource ISBN() { return ResourceFactory.createResource("http://my.linkbaton.com/get?lbCC=q&nC=q&genre=book&item="); } /** * Returns the link-out URI for objects of "International Union of Pharmacology". */ public static Resource IUPHAR_GPCR() { return ResourceFactory.createResource("http://www.iuphar-db.org/DATABASE/FamilyMenuForward?familyId="); } /** * Returns the link-out URI for objects of "International Union of Pharmacology". */ public static Resource IUPHAR_RECEPTOR() { return ResourceFactory.createResource("http://www.iuphar-db.org/DATABASE/ObjectDisplayForward?objectId="); } /** * Returns the link-out URI for objects of "Comprehensive Microbial Resource at the J. Craig Venter Institute". */ public static Resource JCVI_CMR() { return ResourceFactory.createResource("http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus="); } /** * Returns the link-out URI for objects of "Comprehensive Microbial Resource at the J. Craig Venter Institute". */ public static Resource JCVI_EGAD() { return ResourceFactory.createResource("http://cmr.jcvi.org/cgi-bin/CMR/EgadSearch.cgi?search_string="); } /** * Returns the link-out URI for objects of "Genome Properties database at the J. Craig Venter Institute". */ public static Resource JCVI_GenProp() { return ResourceFactory.createResource("http://cmr.jcvi.org/cgi-bin/CMR/shared/GenomePropDefinition.cgi?prop_acc="); } /** * Returns the link-out URI for objects of "Medicago truncatula genome database at the J. Craig Venter Institute ". */ public static Resource JCVI_Medtr() { return ResourceFactory.createResource("http://medicago.jcvi.org/cgi-bin/medicago/search/shared/ORF_infopage.cgi?orf="); } /** * Returns the link-out URI for objects of "TIGRFAMs HMM collection at the J. Craig Venter Institute". */ public static Resource JCVI_TIGRFAMS() { return ResourceFactory.createResource("http://search.jcvi.org/search?p&q="); } /** * Returns the link-out URI for objects of "Digital archive of scholarly articles". */ public static Resource JSTOR() { return ResourceFactory.createResource("http://www.jstor.org/stable/"); } /** * Returns the link-out URI for objects of "KEGG Enzyme Database". */ public static Resource KEGG_ENZYME() { return ResourceFactory.createResource("http://www.genome.jp/dbget-bin/www_bget?ec:"); } /** * Returns the link-out URI for objects of "KEGG LIGAND Database". */ public static Resource KEGG_LIGAND() { return ResourceFactory.createResource("http://www.genome.jp/dbget-bin/www_bget?cpd:"); } /** * Returns the link-out URI for objects of "KEGG Pathways Database". */ public static Resource KEGG_PATHWAY() { return ResourceFactory.createResource("http://www.genome.jp/dbget-bin/www_bget?path:"); } /** * Returns the link-out URI for objects of "KEGG Reaction Database". */ public static Resource KEGG_REACTION() { return ResourceFactory.createResource("http://www.genome.jp/dbget-bin/www_bget?rn:"); } /** * Returns the link-out URI for objects of "LifeDB". */ public static Resource LIFEdb() { return ResourceFactory.createResource("http://www.dkfz.de/LIFEdb/LIFEdb.aspx?ID="); } /** * Returns the link-out URI for objects of "Adult Mouse Anatomical Dictionary". */ public static Resource MA() { return ResourceFactory.createResource("http://www.informatics.jax.org/searches/AMA.cgi?id=MA:"); } /** * Returns the link-out URI for objects of "MaizeGDB". */ public static Resource MaizeGDB() { return ResourceFactory.createResource("http://www.maizegdb.org/cgi-bin/id_search.cgi?id="); } /** * Returns the link-out URI for objects of "MaizeGDB". */ public static Resource MaizeGDB_Locus() { return ResourceFactory.createResource("http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term="); } /** * Returns the link-out URI for objects of "MEROPS peptidase database". */ public static Resource MEROPS() { return ResourceFactory.createResource("http://merops.sanger.ac.uk/cgi-bin/pepsum?mid="); } /** * Returns the link-out URI for objects of "MEROPS peptidase database". */ public static Resource MEROPS_fam() { return ResourceFactory.createResource("http://merops.sanger.ac.uk/cgi-bin/famsum?family="); } /** * Returns the link-out URI for objects of "Medical Subject Headings". */ public static Resource MeSH() { return ResourceFactory.createResource("http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term="); } /** * Returns the link-out URI for objects of "Metabolic Encyclopedia of metabolic and other pathways". */ public static Resource MetaCyc() { return ResourceFactory.createResource("http://biocyc.org/META/NEW-IMAGE?type=NIL&object="); } /** * Returns the link-out URI for objects of "Mouse Genome Informatics". */ public static Resource MGI() { return ResourceFactory.createResource("http://www.informatics.jax.org/accession/"); } /** * Returns the link-out URI for objects of "MIPS Functional Catalogue". */ public static Resource MIPS_funcat() { return ResourceFactory.createResource("http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert="); } /** * Returns the link-out URI for objects of "MGED Ontology". */ public static Resource MO() { return ResourceFactory.createResource("http://mged.sourceforge.net/ontologies/MGEDontology.php#"); } /** * Returns the link-out URI for objects of "ModBase comprehensive Database of Comparative Protein Structure Models". */ public static Resource ModBase() { return ResourceFactory.createResource("http://salilab.org/modbase/searchbyid?databaseID="); } /** * Returns the link-out URI for objects of "Nottingham Arabidopsis Stock Centre Seeds Database". */ public static Resource NASC_code() { return ResourceFactory.createResource("http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code="); } /** * Returns the link-out URI for objects of "NCBI Gene". */ public static Resource NCBI_Gene() { return ResourceFactory.createResource("http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=gene&list_uids="); } /** * Returns the link-out URI for objects of "NCBI databases". */ public static Resource NCBI_gi() { return ResourceFactory.createResource("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val="); } /** * Returns the link-out URI for objects of "NCBI GenPept". */ public static Resource NCBI_GP() { return ResourceFactory.createResource("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val="); } /** * Returns the link-out URI for objects of "Neuroscience Information Framework standard ontology, subcellular hierarchy". */ public static Resource NIF_Subcellular() { return ResourceFactory.createResource("http://www.neurolex.org/wiki/"); } /** * Returns the link-out URI for objects of "National Microbial Pathogen Data Resource". */ public static Resource NMPDR() { return ResourceFactory.createResource("http://www.nmpdr.org/linkin.cgi?id="); } /** * Returns the link-out URI for objects of "Mendelian Inheritance in Man". */ public static Resource OMIM() { return ResourceFactory.createResource("http://omim.org/entry/"); } /** * Returns the link-out URI for objects of "Genome Annotation Tool (Agrobacterium tumefaciens C58); PAMGO Interest Group". */ public static Resource PAMGO_GAT() { return ResourceFactory.createResource("http://agro.vbi.vt.edu/public/servlet/GeneEdit?&Search=Search&level=2&genename="); } /** * Returns the link-out URI for objects of "Magnaporthe grisea database". */ public static Resource PAMGO_MGG() { return ResourceFactory.createResource("http://scotland.fgl.ncsu.edu/cgi-bin/adHocQuery.cgi?adHocQuery_dbName=smeng_goannotation&Action=Data&QueryName=Functional+Categorization+of+MGG+GO+Annotation&P_KeyWord="); } /** * Returns the link-out URI for objects of "Virginia Bioinformatics Institute Microbial Database". */ public static Resource PAMGO_VMD() { return ResourceFactory.createResource("http://vmd.vbi.vt.edu/cgi-bin/browse/go_detail.cgi?gene_id="); } /** * Returns the link-out URI for objects of "Protein ANalysis THrough Evolutionary Relationships". */ public static Resource PANTHER() { return ResourceFactory.createResource("http://pantree.org/node/annotationNode.jsp?id="); } /** * Returns the link-out URI for objects of "PathoSystems Resource Integration Center". */ public static Resource PATRIC() { return ResourceFactory.createResource("http://patric.vbi.vt.edu/gene/overview.php?fid="); } /** * Returns the link-out URI for objects of "Protein Data Bank". */ public static Resource PDB() { return ResourceFactory.createResource("http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId="); } /** * Returns the link-out URI for objects of "Pfam database of protein families". */ public static Resource Pfam() { return ResourceFactory.createResource("http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?"); } /** * Returns the link-out URI for objects of "Pharmacogenetics and Pharmacogenomics Knowledge Base". */ public static Resource PharmGKB() { return ResourceFactory.createResource("http://www.pharmgkb.org/do/serve?objId="); } /** * Returns the link-out URI for objects of "Protein Information Resource". */ public static Resource PIR() { return ResourceFactory.createResource("http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?uid="); } /** * Returns the link-out URI for objects of "PIR Superfamily Classification System". */ public static Resource PIRSF() { return ResourceFactory.createResource("http://pir.georgetown.edu/cgi-bin/ipcSF?id="); } /** * Returns the link-out URI for objects of "Pubmed Central". */ public static Resource PMCID() { return ResourceFactory.createResource("http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term="); } /** * Returns the link-out URI for objects of "PubMed". */ public static Resource PMID() { return ResourceFactory.createResource("http://www.ncbi.nlm.nih.gov/pubmed/"); } /** * Returns the link-out URI for objects of "Plant Ontology Consortium Database". */ public static Resource PO() { return ResourceFactory.createResource("http://www.plantontology.org/amigo/go.cgi?action=query&view=query&search_constraint=terms&query=PO:"); } /** * Returns the link-out URI for objects of "Plant Ontology custom references". */ public static Resource PO_REF() { return ResourceFactory.createResource("http://wiki.plantontology.org:8080/index.php/PO_REF:"); } /** * Returns the link-out URI for objects of "PomBase". */ public static Resource PomBase() { return ResourceFactory.createResource("http://www.pombase.org/spombe/result/"); } /** * Returns the link-out URI for objects of "Protein Ontology". */ public static Resource PR() { return ResourceFactory.createResource("http://www.proconsortium.org/cgi-bin/pro/entry_pro?id=PR:"); } /** * Returns the link-out URI for objects of "PRINTS compendium of protein fingerprints". */ public static Resource PRINTS() { return ResourceFactory.createResource("http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn="); } /** * Returns the link-out URI for objects of "ProDom protein domain families". */ public static Resource ProDom() { return ResourceFactory.createResource("http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query="); } /** * Returns the link-out URI for objects of "Prosite database of protein families and domains". */ public static Resource Prosite() { return ResourceFactory.createResource("http://www.expasy.ch/cgi-bin/prosite-search-ac?"); } /** * Returns the link-out URI for objects of "Pseudomonas Genome Project". */ public static Resource PseudoCAP() { return ResourceFactory.createResource("http://v2.pseudomonas.com/getAnnotation.do?locusID="); } /** * Returns the link-out URI for objects of "Proteomics Standards Initiative protein modification ontology". */ public static Resource PSI_MOD() { return ResourceFactory.createResource("http://www.ebi.ac.uk/ontology-lookup/?termId=MOD:"); } /** * Returns the link-out URI for objects of "NCBI PubChem database of bioassay records". */ public static Resource PubChem_BioAssay() { return ResourceFactory.createResource("http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid="); } /** * Returns the link-out URI for objects of "NCBI PubChem database of chemical structures". */ public static Resource PubChem_Compound() { return ResourceFactory.createResource("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term="); } /** * Returns the link-out URI for objects of "NCBI PubChem database of chemical substances". */ public static Resource PubChem_Substance() { return ResourceFactory.createResource("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcsubstance&term="); } /** * Returns the link-out URI for objects of "Reactome - a curated knowledgebase of biological pathways". */ public static Resource Reactome() { return ResourceFactory.createResource("http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID="); } /** * Returns the link-out URI for objects of "RefSeq". */ public static Resource RefSeq() { return ResourceFactory.createResource("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val="); } /** * Returns the link-out URI for objects of "RefSeq (Nucleic Acid)". */ public static Resource RefSeq_NA() { return ResourceFactory.createResource("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val="); } /** * Returns the link-out URI for objects of "RefSeq (Protein)". */ public static Resource RefSeq_Prot() { return ResourceFactory.createResource("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val="); } /** * Returns the link-out URI for objects of "Rfam database of RNA families". */ public static Resource Rfam() { return ResourceFactory.createResource("http://rfam.sanger.ac.uk/family/"); } /** * Returns the link-out URI for objects of "Rat Genome Database". */ public static Resource RGD() { return ResourceFactory.createResource("http://rgd.mcw.edu/generalSearch/RgdSearch.jsp?quickSearch=1&searchKeyword="); } /** * Returns the link-out URI for objects of "Rhea, the Annotated Reactions Database". */ public static Resource RHEA() { return ResourceFactory.createResource("http://www.ebi.ac.uk/rhea/reaction.xhtml?id="); } /** * Returns the link-out URI for objects of "RNA Modification Database". */ public static Resource RNAmods() { return ResourceFactory.createResource("http://s59.cas.albany.edu/RNAmods/cgi-bin/rnashow.cgi?"); } /** * Returns the link-out URI for objects of "OBO Relation Ontology Ontology". */ public static Resource RO() { return ResourceFactory.createResource("http://purl.obolibrary.org/obo/RO_"); } /** * Returns the link-out URI for objects of "SABIO Reaction Kinetics". */ public static Resource SABIO_RK() { return ResourceFactory.createResource("http://sabio.villa-bosch.de/reacdetails.jsp?reactid="); } /** * Returns the link-out URI for objects of "The SEED;". */ public static Resource SEED() { return ResourceFactory.createResource("http://www.theseed.org/linkin.cgi?id="); } /** * Returns the link-out URI for objects of "Saccharomyces Genome Database". */ public static Resource SGD() { return ResourceFactory.createResource("http://db.yeastgenome.org/cgi-bin/locus.pl?dbid="); } /** * Returns the link-out URI for objects of "Saccharomyces Genome Database". */ public static Resource SGD_LOCUS() { return ResourceFactory.createResource("http://db.yeastgenome.org/cgi-bin/locus.pl?locus="); } /** * Returns the link-out URI for objects of "Saccharomyces Genome Database". */ public static Resource SGD_REF() { return ResourceFactory.createResource("http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid="); } /** * Returns the link-out URI for objects of "Sol Genomics Network". */ public static Resource SGN() { return ResourceFactory.createResource("http://www.sgn.cornell.edu/phenome/locus_display.pl?locus_id="); } /** * Returns the link-out URI for objects of "Sol Genomics Network". */ public static Resource SGN_ref() { return ResourceFactory.createResource("http://www.sgn.cornell.edu/chado/publication.pl?pub_id="); } /** * Returns the link-out URI for objects of "Simple Modular Architecture Research Tool". */ public static Resource SMART() { return ResourceFactory.createResource("http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN="); } /** * Returns the link-out URI for objects of "Sequence Ontology". */ public static Resource SO() { return ResourceFactory.createResource("http://song.sourceforge.net/SOterm_tables.html#SO:"); } /** * Returns the link-out URI for objects of "SUPERFAMILY protein annotation database". */ public static Resource SUPERFAMILY() { return ResourceFactory.createResource("http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/scop.cgi?ipid=SSF"); } /** * Returns the link-out URI for objects of "UniProtKB/Swiss-Prot". */ public static Resource Swiss_Prot() { return ResourceFactory.createResource("http://www.uniprot.org/uniprot/"); } /** * Returns the link-out URI for objects of "The Arabidopsis Information Resource". */ public static Resource TAIR() { return ResourceFactory.createResource("http://arabidopsis.org/servlets/TairObject?accession="); } /** * Returns the link-out URI for objects of "NCBI Taxonomy". */ public static Resource taxon() { return ResourceFactory.createResource("http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="); } /** * Returns the link-out URI for objects of "Transport Protein Database". */ public static Resource TC() { return ResourceFactory.createResource("http://www.tcdb.org/tcdb/index.php?tc="); } /** * Returns the link-out URI for objects of "Tetrahymena Genome Database". */ public static Resource TGD_LOCUS() { return ResourceFactory.createResource("http://db.ciliate.org/cgi-bin/locus.pl?locus="); } /** * Returns the link-out URI for objects of "Tetrahymena Genome Database". */ public static Resource TGD_REF() { return ResourceFactory.createResource("http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid="); } /** * Returns the link-out URI for objects of "UniProtKB-TrEMBL protein sequence database". */ public static Resource TrEMBL() { return ResourceFactory.createResource("http://www.uniprot.org/uniprot/"); } /** * Returns the link-out URI for objects of "Uber-anatomy ontology". */ public static Resource UBERON() { return ResourceFactory.createResource("http://purl.obolibrary.org/obo/UBERON_"); } /** * Returns the link-out URI for objects of "University of Minnesota Biocatalysis/Biodegradation Database". */ public static Resource UM_BBD_enzymeID() { return ResourceFactory.createResource("http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=ep&enzymeID="); } /** * Returns the link-out URI for objects of "University of Minnesota Biocatalysis/Biodegradation Database". */ public static Resource UM_BBD_reactionID() { return ResourceFactory.createResource("http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=r&reacID="); } /** * Returns the link-out URI for objects of "University of Minnesota Biocatalysis/Biodegradation Database". */ public static Resource UM_BBD_ruleID() { return ResourceFactory.createResource("http://umbbd.msi.umn.edu/servlets/rule.jsp?rule="); } /** * Returns the link-out URI for objects of "UniMod". */ public static Resource UniMod() { return ResourceFactory.createResource("http://www.unimod.org/modifications_view.php?editid1="); } /** * Returns the link-out URI for objects of "UniProt Archive". */ public static Resource UniParc() { return ResourceFactory.createResource("http://www.uniprot.org/uniparc/"); } /** * Returns the link-out URI for objects of "UniPathway". */ public static Resource UniPathway() { return ResourceFactory.createResource("http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid="); } /** * Returns the link-out URI for objects of "Universal Protein Knowledgebase". */ public static Resource UniProtKB() { return ResourceFactory.createResource("http://www.uniprot.org/uniprot/"); } /** * Returns the link-out URI for objects of "UniProt Knowledgebase keywords". */ public static Resource UniProtKB_KW() { return ResourceFactory.createResource("http://www.uniprot.org/keywords/"); } /** * Returns the link-out URI for objects of "UniProt Knowledgebase Subcellular Location vocabulary". */ public static Resource UniProtKB_SubCell() { return ResourceFactory.createResource("http://www.uniprot.org/locations/"); } /** * Returns the link-out URI for objects of "Viral Bioinformatics Resource Center". */ public static Resource VBRC() { return ResourceFactory.createResource("http://vbrc.org/query.asp?web_id=VBRC:"); } /** * Returns the link-out URI for objects of "Vertebrate Genome Annotation database". */ public static Resource VEGA() { return ResourceFactory.createResource("http://vega.sanger.ac.uk/perl/searchview?species=all&idx=All&q="); } /** * Returns the link-out URI for objects of "Virginia Bioinformatics Institute Microbial Database". */ public static Resource VMD() { return ResourceFactory.createResource("http://vmd.vbi.vt.edu/cgi-bin/browse/browserDetail_new.cgi?gene_id="); } /** * Returns the link-out URI for objects of "WormBase database of nematode biology". */ public static Resource WB() { return ResourceFactory.createResource("http://www.wormbase.org/db/gene/gene?name="); } /** * Returns the link-out URI for objects of "WormBase database of nematode biology". */ public static Resource WB_REF() { return ResourceFactory.createResource("http://www.wormbase.org/db/misc/paper?name="); } /** * Returns the link-out URI for objects of "Wikipedia". */ public static Resource Wikipedia() { return ResourceFactory.createResource("http://en.wikipedia.org/wiki/"); } /** * Returns the link-out URI for objects of "Wormpep database of proteins of C. elegans". */ public static Resource WP() { return ResourceFactory.createResource("http://www.wormbase.org/db/get?class=Protein;name=WP:"); } /** * Returns the link-out URI for objects of "Zebrafish Information Network". */ public static Resource ZFIN() { return ResourceFactory.createResource("http://zfin.org/cgi-bin/ZFIN_jump?record="); } }