!version: $Revision: 1.1.1.1 $ !date: $Date: 12/15/2011 13:15:00 $ !Title:PO_DBxref.txt !Plant Ontology Consortium !www.plantontology.org !created by: Pankaj Jaiswal !modified by: Laurel Cooper !Note that url's are not necessarily stable entities and that some databases may have many other access routes or mirror sites. ! Syntax for database cross-references either within nodes in an ontology or within other PO documents, e.g. PO.defs, will be standardized and that, as far as possible, we use the abbreviations used by the NCBI. See: http://www.ncbi.nlm.nih.gov/collab/db_xref.html. The syntax would then be: Database_Abbreviation:identifier (as recently proposed/adopted by GO). abbreviation: PO definition:Plant Ontology Consortium example:PO generic_url:http://www.plantontology.org url_syntax: abbreviation: AgBase database: AgBase object: Anything with a Uniprot Gene Name or GenBank ID or GO ID example_id: AgBase:Q8VWP8 generic_url: http://agbase.msstate.edu/index.html url_syntax: http://www.agbase.msstate.edu/cgi-bin/getEntry.pl?db_pick=all&database=UniProtKB/TrEMBL&gb_acc=[example_id] url_example: http://www.agbase.msstate.edu/cgi-bin/getEntry.pl?db_pick=all&database=UniProtKB/TrEMBL&uid=Q8VWP8_GOSHI&gb_acc=Q8VWP8 abbreviation: AGI_LocusCode database: Arabidopsis Genome Initiative (TAIR, TIGR, MIPS) object: Locus identifier example: AGI_LocusCode:At2g17950 generic_url: http://www.arabidopsis.org url_syntax: http://mips.gsf.de/cgi-bin/proj/thal/search_gene?code= url_syntax: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=ath1&orf= url_syntax: http://arabidopsis.org/servlets/TairObject?type=locus&name= example_url: http://mips.gsf.de/cgi-bin/proj/thal/search_gene?code=At2g17950 example_url: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=ath1&orf=At2g17950 example_url: http://arabidopsis.org/servlets/TairObject?type=locus&name=At2g17950 abbreviation: AP database: Angiosperm Phylogeny Website object: definitions for anatomy terms example_id: APweb:Glossary generic_url: http://www.mobot.org/mobot/research/apweb/ url_syntax: http://www.mobot.org/mobot/research/apweb/top/glossarya_h.html url_example: http://www.mobot.org/mobot/research/apweb/top/glossarya_h.html abbreviation: bib database: AGRICOLA object: call number example: MARC TAG 016 or bib=0000-05160 generic_url: http://www.nal.usda.gov/ag98/ abbreviation: cosmoss_PpV1.2 database: plantco.de|cosmoss.org object: Anything with a Cosmoss accession number example_id: cosmoss_PpV1.2:Pp1s47_77V2.1 generic_url: https://www.cosmoss.org/annotation/genonaut url_syntax: https://www.cosmoss.org/annotation/genonaut?accession=ACCESSION&version=V1.2 url_example: https://www.cosmoss.org/annotation/genonaut?accession=Pp1s53_22V2.1&version=V1.2 abbreviation: EC database: The Enzyme Commission. example: EC:1.1.1.1 generic_url: http://www.chem.qmw.ac.uk/iubmb/enzyme/ url_syntax: url_example: http://www.chem.qmw.ac.uk/iubmb/enzyme/EC1/1/1/1.html abbreviation: EMBL database: EMBL-EBI International Nucleotide Sequence Data Library/DDBJ/GenBank. object: Sequence accession number. synonym: GB synonym: DDBJ example: EMBL:AA816246 generic_url: http://www.ebi.ac.uk/embl/ url_syntax: http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=10727410&dopt=GenBank abbreviation: ENZYME database: The Swiss Institute of Bioinformatics database of Enzymes. object: Identifier. example: ENZYME:EC 1.1.1.1 generic_url: http://www.expasy.ch/ url_syntax: http://www.expasy.ch/cgi-bin/nicezyme.pl? url_example: http://www.expasy.ch/cgi-bin/nicezyme.pl?1.1.1.1 abbreviation: GO database: Gene Ontology Database. object: Identifier. example: GO:1234567 generic_url: http://www.geneontology.org/ url_syntax: abbreviation: GO_REF database: Gene Ontology Database references. object: Reference (points to web page). example: GO_REF:nd generic_url: http://www.geneontology.org/#ref url_example: http://www.geneontology.org/doc/GO.ndref.html ! note: the following three entries, GOA:interpro, GOA:spec, and ! GOA:spkw, will be moved to the GO_REF dataset at some point; in the ! meantime, they are here so they'll be documented somewhere abbreviation: GOA:interpro database: Gene Ontology Annotation at EBI annotations from InterPro to GO mapping. object: Reference (points to web page). url_example: http://www.geneontology.org/goa.interpro.html abbreviation: GOA:spec database: Gene Ontology Annotation at EBI annotations from EC mapping. object: Reference (points to web page). url_example: http://www.geneontology.org/goa.spec.html abbreviation: GOA:spkw database: Gene Ontology Annotation at EBI annotations from keyword mapping. object: Reference (points to web page). url_example: http://www.geneontology.org/goa.spkw.html abbreviation: GOC:unpublished database: Temporary reference for unpublished papers. object: Doesn't link anywhere yet. abbreviation: GR database: Gramene: A Comparative Mapping Resource for Grains. object: Protein example_id: GR:P93436 generic_url: http://www.gramene.org/ url_syntax: http://www.gramene.org/db/protein/protein_search?acc=[example_id] url_example: http://www.gramene.org/db/protein/protein_search?acc=P93436 abbreviation: GR_REF database: Gramene: A Comparative Mapping Resource for Grains. object: Reference example: GR_REF:659 generic_url: http://www.gramene.org/ url_syntax: http://www.gramene.org/perl/pub_search?ref_id=ID number url_example: http://www.gramene.org/perl/pub_search?ref_id=659 abbreviation: GR_MUT database: Gramene: A Comparative Mapping Resource for Grains. object: Mutants example_id: GR_MUT:GR:0060198 generic_url: http://www.gramene.org/ url_syntax: http://www.gramene.org/db/genes/search_gene?acc=[example_id] url_example: http://www.gramene.org/db/genes/search_gene?acc=GR:0060198 abbreviation: GR_QTL database: Gramene: A Comparative Mapping Resource for Grains. object: Mutants example: GR_QTL:CQA11 generic_url: http://www.gramene.org/ url_syntax: http://www.gramene.org/perl/mutant/search_mutant?id=ID number url_example: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=CQA11 abbreviation: IND database: AGRICOLA object: call number example: IND84014403 generic_url: http://agricola.cos.com/ abbreviation: InterPro database: The InterPro database of protein domains and motifs. object: synonym: INTERPRO example: generic_url: http://www.ebi.ac.uk/interpro/ url_syntax: abbreviation: IPI database: International Protein Index. object: Identifier.Version example: IPI:IPI00000005.1 generic_url: http://www.ebi.ac.uk/IPI/IPIhelp.html abbreviation: ISBN database: International Standard Book Number. object: Identifier. example: ISBN:0781702534 generic_url: http://isbntools.com/ url_syntax: http://my.linkbaton.com/get?lbCC=q&nC=q&genre=book&item= url_example: http://my.linkbaton.com/get?lbCC=q&nC=q&genre=book&item=0781702534 abbreviation: Jaiswal_Lab database: Jaiswal_Lab object: mRNA example_id: Jaiswal_Lab:gene00002 generic_url: http://wiki.plantontology.org:8080/index.php/PO_REF:00008 url_syntax: http://wiki.plantontology.org:8080/index.php/PO_REF:00008 url_example: http://wiki.plantontology.org:8080/index.php/PO_REF:00008 abbreviation: KEGG database: Kyoto Encyclopedia of Genes and Genomes. generic_url: http://www.genome.ad.jp/kegg/ abbreviation: KEGG_PATHWAY database: KEGG Pathways Database. object: Pathway. example: KEGG_PATHWAY:ot00020 generic_url: http://www.genome.ad.jp/kegg/docs/upd_pathway.html url_syntax: http://www.genome.ad.jp/dbget-bin/www_bget?path: url_example: http://www.genome.ad.jp/dbget-bin/www_bget?path:ot00020 abbreviation: LIGAND database: KEGG LIGAND Database. object: Enzyme or Compound. example: LIGAND:C00577 example: LIGAND:EC 1.1.1.1 url_syntax: http://www.genome.ad.jp/dbget-bin/www_bget?ec: url_syntax: http://www.genome.ad.jp/dbget-bin/www_bget?cpd: generic_url: http://www.genome.ad.jp/kegg/docs/upd_ligand.html#ENZYME generic_url: http://www.genome.ad.jp/kegg/docs/upd_ligand.html#COMPOUND url_example: http://www.genome.ad.jp/dbget-bin/www_bget?ligand+1.1.1.1 url_example: http://www.genome.ad.jp/dbget-bin/www_bget?cpd:C00577 abbreviation: LocusID database: NCBI LocusLink ID. object: Identifier. example: LocusID:3195 generic_url: http://www.ncbi.nlm.nih.gov/ url_syntax: url_example: http://www.ncbi.nlm.nih.gov:80/LocusLink/LocRpt.cgi?l=3195 abbreviation: MaizeGDB database: Maize Genetics and Genomics Database object: Anything with a MaizeGDB Object ID Number or Gene Model Name example_id: MaizeGDB:881225 generic_url: http://www.maizegdb.org/ url_syntax: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=[example_id] url_example: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=881225 abbreviation: MEDLINE database: The Medline literature database. object: Identifier. example: MEDLINE:20572430 generic_url: url_syntax: abbreviation: NAL database: AGRICOLA object: call number example: NAL:TP248.2 P76 v.14 generic_url: http://www.nal.usda.gov/ag98/ag98.html abbreviation: NASC_code database: Nottingham Arabidopsis Stock Centre Seeds Database object: NASC code Identifier example: NASC_code:N3371 generic_url: http://arabidopsis.info url_syntax: http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code= example_url: http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=N3371 abbreviation: NCBI database: National Center for Biotechnology Information, Bethesda. object: Prefix. example: NCBI_gi generic_url: http://www.ncbi.nlm.nih.gov/ abbreviation: NCBI_gi database: NCBI databases. object: Identifier. example: NCBI_gi:10727410 generic_url: http://www.ncbi.nlm.nih.gov/ url_syntax: url_example: http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=10727410&dopt=GenBank abbreviation: NCBI_NM database: NCBI RefSeq. object: mRNA identifier. example: NCBI_NM:123456 generic_url: http://www.ncbi.nlm.nih.gov/ url_syntax: abbreviation: NCBI_NP database: NCBI RefSeq. object: Protein identifier. example: NCBI_NP:123456 generic_url: http://www.ncbi.nlm.nih.gov/ url_syntax: abbreviation: OBO_SF_PO database: Source Forge OBO Plant Ontology (PO) term request tracker object: Plant Ontology term request example_id: OBO_SF_PO:3184921 generic_url: http://sourceforge.net/tracker/?func=browse&group_id=76834&atid=835555 url_syntax: https://sourceforge.net/tracker/index.php?func=detail&aid=[example_id]&group_id=76834&atid=835555 url_example: https://sourceforge.net/tracker/index.php?func=detail&aid=3184921&group_id=76834&atid=835555 abbreviation: PDB database: Protein Data Bank. object: Identifier. example: PDB:1A4U generic_url: http://msd.ebi.ac.uk/ generic_url: http://www.rcsb.org/pdb/ url_syntax: url_example: http://www.rcsb.org/pdb/cgi/explore.cgi?pid=223051005992697&pdbId=1A4U abbreviation: Pfam database: Pfam: Protein families database of alignments and HMMs. object: Accession number. example: Pfam:PF00046 generic_url: http://www.sanger.ac.uk/Software/Pfam/ url_syntax: http://www.sanger.ac.uk/cgi-bin/Pfam/getacc? url_example: http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00046 abbreviation: PIR database: Protein Information Resource. object: Accession number. example: PIR:I49499 generic_url: http://www-nbrf.georgetown.edu/pir/ url_syntax: http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?uid= url_example: http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?uid=I49499 abbreviation: PMID database: PubMed. object: Identifier. synonym: PUBMED example: PMID:4208797 generic_url: http://www.ncbi.nlm.nih.gov/PubMed/ url_syntax: url_example: http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=4208797&dopt=Abstract abbreviation: PO_REF database: Plant Ontology custom references object: Reference identifier example_id: PO_REF:00001 generic url: http://wiki.plantontology.org:8080/index.php/PO_references url_syntax: http://wiki.plantontology.org:8080/index.php/PO_REF:[example_id] url_example: http://wiki.plantontology.org:8080/index.php/PO_REF:00001 abbreviation: Prosite database: Prosite. Database of protein families and domains. object: Accession number. example: Prosite:PS00365 generic_url: http://www.expasy.ch/prosite/ url_syntax: http://www.expasy.ch/cgi-bin/prosite-search-ac? url_example: http://www.expasy.ch/cgi-bin/prosite-search-ac?PS00365 abbreviation: protein_id database: The protein identifier shared by DDBJ/EMBL-bank/GenBank nucleotide sequence databases. object: Identifier. example: protein_id:CAA71991 generic_url: url_syntax: abbreviation: PROW database: Protein Reviews on the Web. generic_url: http://www.ncbi.nlm.nih.gov/prow/ abbreviation: RESID database: RESID Database of Protein Modifications. object: Identifier. example: RESID:AA0062 generic_url: ftp://ftp.ncifcrf.gov/pub/users/residues/ url_syntax: abbreviation: SGN_gene database: Sol Genomics Network object: locus identifier example_id: SGN_gene:7740 generic url: http://solgenomics.net/ url_syntax: http://solgenomics.net/phenome/locus_display.pl?locus_id=[example_id] url_example: http://solgenomics.net/phenome/locus_display.pl?locus_id=7740 abbreviation: SGN_germplasm database: Sol Genomics Network object: stock/accession/germplasm identifier example_id: SGN_germplasm:6583 generic url: http://solgenomics.net/ url_syntax: http://solgenomics.net/stock/[example_id]/view/ url_example: http://solgenomics.net/stock/6583/view/ abbreviation: SGN_ref database: Sol Genomics Network object: reference identifier example_id: SGN_ref:800 generic url: http://solgenomics.net/ url_syntax: http://www.sgn.cornell.edu/chado/publication.pl?pub_id=[example_id] url_example: http://www.sgn.cornell.edu/chado/publication.pl?pub_id=800 abbreviation: SMD database: Stanford Microarray Database object: example: generic_url: http://genome-www.stanford.edu/microarray url_syntax: abbreviation: Swiss-Prot database: Swiss-Prot protein database. object: Accession number. synonym: SP synonym: SWP synonym: SWISS-PROT example: Swiss-Prot:P45867 generic_url: http://www.ebi.ac.uk/swissprot/ generic_url: http://ca.expasy.org/sprot/ url_syntax: http://www.expasy.ch/cgi-bin/sprot-search-ac? url_example: http://www.expasy.ch/cgi-bin/sprot-search-ac?P45867 abbreviation: SPTR database: The combination of SWISS-PROT and TrEMBL; includes TrEMBLnew. object: Accession number. synonym: SWALL example: SPTR:P45867 generic_url: http://www.ebi.ac.uk/swissprot/ generic_url: http://ca.expasy.org/sprot/ url_syntax: http://www.expasy.ch/cgi-bin/sprot-search-ac? url_example: http://www.expasy.ch/cgi-bin/sprot-search-ac?P45867 abbreviation: TAIR database: The Arabidopsis Information Resource. object: Accession number. example: TAIR:gene:2062713 generic_url: http://www.arabidopsis.org/ url_syntax: http://www.arabidopsis.org/servlets/TairObject?accession= url_example: http://www.arabidopsis.org/servlets/TairObject?accession=gene:2062713 abbreviation: taxon database: NCBI Taxman. object: Identifier. example: taxon:7227 generic_url: http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ url_syntax: abbreviation: TC database: The Transport Protein Database. object: Identifier. example: TC:9.A.4.1.1 generic_url: http://tcdb.ucsd.edu/tcdb/ url_syntax: http://tcdb.ucsd.edu/tcdb/tcprotein.php?substrate= url_example: http://tcdb.ucsd.edu/tcdb/tcprotein.php?substrate=9.A.4.1.1 abbreviation: TIGR database: The Institute for Genomic Research. object: example: generic_url: http://www.tigr.org/ url_syntax: abbreviation: TIGR_Ath1 database: The Institute for Genomic Research, Arabidopsis thaliana database. object: Accession. example: TIGR_Ath1:At3g01440 generic_url: http://www.tigr.org/tdb/e2k1/ath1/ath1.shtml url_syntax: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=ath1&orf= url_example: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=ath1&orf=At3g01440 abbreviation: TIGR_TIGRFAMS database: The Institute for Genomic Research, TIGRFAMs HMM collection. object: Accession. example: TIGR_TIGRFAMS:TIGR00254 generic_url: http://www.tigr.org/ url_syntax: http://www.tigr.org/tigr-scripts/CMR2/hmm_report.spl?acc= url_example: http://www.tigr.org/tigr-scripts/CMR2/hmm_report.spl?acc=TIGR00254 abbreviation: TIGR_TGI database: The Institute for Genomic Research, TIGR Gene Index. object: TC accession. example: TIGR_TGI:Cattle_TC123931 generic_url: http://www.tigr.org/ url_syntax: http://www.tigr.org/tigr-scripts/nhgi_scripts/tc_report.pl?tc=? url_example: http://www.tigr.org/tigr-scripts/nhgi_scripts/tc_report.pl?tc=Cattle_TC123931 abbreviation: TrEMBL database: Computer-annotated protein sequence database supplementing SWISS-PROT and containing the translations of all coding sequences (CDS) present in the EMBL Nucleotide Sequence Database but not yet integrated in SWISS-PROT. Does not include TrEMBLnew. object: Accession number. example: TrEMBL:Q00177 synonym: SPTREMBL synonym: TREMBL synonym: TR generic_url: http://www.ebi.ac.uk/swissprot/ generic_url: http://ca.expasy.org/sprot/ url_syntax: http://www.expasy.ch/cgi-bin/sprot-search-ac? url_example: http://www.expasy.ch/cgi-bin/sprot-search-ac?Q00177 abbreviation: UM-BBD database: The University of Minnesota Biocatalysis/Biodegradation Database. object: Prefix. example: generic_url: http://umbbd.ahc.umn.edu/index.html url_syntax: abbreviation: UM-BBD_enzymeID database: The University of Minnesota Biocatalysis/Biodegradation Database. object: Enzyme identifier. example: UM-BBD_enzymeID:e0413 generic_url: http://umbbd.ahc.umn.edu/index.html url_syntax: http://umbbd.ahc.umn.edu:8007/umbbd/servlet/pageservlet?ptype=ep&enzymeID= url_example: http://umbbd.ahc.umn.edu:8007/umbbd/servlet/pageservlet?ptype=ep&enzymeID=e0413 abbreviation: UM-BBD_pathwayID database: The University of Minnesota Biocatalysis/Biodegradation Database. object: Pathway identifier. example: UM-BBD_pathwayID:acr generic_url: http://umbbd.ahc.umn.edu/index.html url_syntax: url_example: http://umbbd.ahc.umn.edu/acr/acr_map.html abbreviation: VIDA database: Virus Database at University College London object: example: generic_url: http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html url_syntax: url_example: fier.