!version: $Revision: 1.1.1.1 $
!date: $Date: 2003/12/10 21:06:53 $
!Title: poc-dbxref 
!Plant Ontology Consortium
!www.plantontology.org
!created by : Pankaj Jaiswal
!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: 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: bib
database: AGRICOLA
object: call number
example: MARC TAG 016 or bib=0000-05160
generic_url: http://www.nal.usda.gov/ag98/

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: GR:P93436
generic_url: http://www.gramene.org/
url_syntax:  http://www.gramene.org/perl/protein_search?acc=Accession number 
example: http://www.gramene.org/perl/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
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: GR_MUT:GR:0060198
generic_url: http://www.gramene.org/
url_syntax: http://www.gramene.org/perl/mutant/search_mutant?id=ID number
example: http://www.gramene.org/perl/mutant/search_mutant?id=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
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: 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 Genome Database.
object: Canonical name of gene.
example: MaizeGDB:apb1
generic_url: http://www.maizegdb.org/
url_syntax: http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=
object: Phenotype of gene variant
example: MaizeGDB:liguleless
url_syntax: http://www.maizegdb.org/cgi-bin/displayphenoresults.cgi?term=
 
abbreviation: MaizeGDBID
database: Maize Genome Database.
object: locus Identifier.
example: MaizeGDBID:12008
generic_url: http://www.maizegdb.org/
url_syntax: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=
object: phenotype identifier
example:MaizeGDBID:61504
url_syntax:http://www.maizegdb.org/cgi-bin/displayphenorecord.cgi?id=

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: 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: 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: 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.