!version: $Revision: 1.1.1.1 $
!date: $Date: 04/4/2013 $
!Title:PO_DBxref.txt
!Plant Ontology Consortium
!www.plantontology.org
!created by: Pankaj Jaiswal
!modified by: Justin Elser
!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, 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 adopted by GO). 
!This file has been updated to reflect the perl file that includes the current abbreviations being used on AmiGO by the Plant Ontology. Stanzas for abbreviations that are no longer in use are still included, but are followed by a comment to that effect and moved to the end of the file.
!unknown fields have been left blank.
!additional comments are included for clarity

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=$acc_no
url_example: http://www.agbase.msstate.edu/cgi-bin/getEntry.pl?db_pick=all&database=UniProtKB/TrEMBL&uid=Q8VWP8_GOSHI&gb_acc=Q8VWP8 

abbreviation: APweb
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
!Looks like there are only references to the generic_url: http://www.mobot.org/mobot/research/apweb/

abbreviation: APSNET
database: APSNET Common Names of Plant Diseases
object: Reference identifier
example_id: APSNET:AfricanDaisy
generic url: http://www.apsnet.org/publications/commonnames/Pages
url_syntax: http://www.apsnet.org/publications/commonnames/Pages/$acc_no.aspx
url_example: http://www.apsnet.org/publications/commonnames/Pages/AfricanDaisy.aspx

abbreviation: CO_125
database: Crop Ontology CGIAR Musa Anatomy
object: 
example_id:  CO_125:0000002
generic_url:  http://www.cropontology.org/ontology/CO_125/Musa Anatomy
url_syntax:"http://www.cropontology.org/terms/CO_125:$acc_no"
url_syntax: 
url_example: 
!about 29 of these, mostly narrow synonyms, so the dbxrefs do not show up in browser, but are in the OBO file.

"cosmoss"=>"https://www.cosmoss.org/annotation/genonaut?accession=$acc_no&version=V1.2"
!from namemunger file

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 

"plantco.de|cosmoss.org"=>"https://www.cosmoss.org/annotation/genonaut?accession=$acc_no&version=V1.2"
!from namemunger file

abbreviation: cribi_vitis
database: 
example_id:  
generic_url: http://genomes.cribi.unipd.it
url_syntax: http://genomes.cribi.unipd.it/cgi-bin/pqs2/report.pl?gene_name=$acc_no&release=v1
url_example: 
!in association file

abbreviation: GenBank
database: NCBI GenBank
object: 
example_id: 
generic_url: http://www.ncbi.nlm.nih.gov
url_syntax: http://www.ncbi.nlm.nih.gov/nucest/$acc_no",
url_example: 
!in association file?

abbreviation: GO
database: Gene Ontology Database
object: Gene Ontology term identifier
example: GO:0097218
generic_url: http://www.geneontology.org/
url_syntax: http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?action=query&view=query&search_constraint=terms&query=$acc_no
url_syntax: http://amigo.geneontology.org/cgi-bin/amigo/gp-details.cgi?gp=$acc_no
url_example: http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?action=query&view=query&search_constraint=terms&query=0097218

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_search?acc=$acc_no
url_syntax: http://www.gramene.org/db/pub_search?ref_id=$acc_no
url_syntax: http://www.gramene.org/perl/protein_search?acc=$acc_no
url_example: http://www.gramene.org/db/protein/protein_search?acc=P93436
!in association file

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=$acc_no
url_example: http://www.gramene.org/db/genes/search_gene?acc=GR:0060198
!in association file?


abbreviation: GR_PROTEIN
database: Gramene: A Comparative Mapping Resource for Grains
object: Proteins
example:
generic_url: http://www.gramene.org/
url_syntax: http://www.gramene.org/db/protein/protein_search?acc=$acc_no
url_example:
!in association file


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/db/qtl/qtl_display?qtl_accession_id=$acc_no
url_example: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=CQA11
!in association file


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/db/literature/pub_search?ref_id=$acc_no
url_example: http://www.gramene.org/perl/pub_search?ref_id=659
!in association file?



abbreviation: ISBN
database: International Standard Book Number
object: book identifier
example: ISBN:0471738433
generic_url: http://openisbn.com
url_syntax: http://openisbn.com/search.php?q=$acc_no&isbn=1/
url_example: http://openisbn.com/search.php?q=0471738433&isbn=1/

abbreviation: ISRR
database: International Society for Root Research
object: reference identifier
example: ISRR:Richard Zobel
generic_url: http://www.rootresearch.org/
url_syntax: http://wiki.plantontology.org/index.php/ISRR_references
url_example: http://wiki.plantontology.org/index.php/ISRR_references

abbreviation: Jaiswal_Lab
database: Jaiswal_Lab
object: mRNA
example_id: Jaiswal_Lab:gene00002
generic_url: http://wiki.plantontology.org/index.php/PO_REF:00008
url_syntax: http://wiki.plantontology.org/index.php/PO_REF:00008
url_example: http://wiki.plantontology.org/index.php/PO_REF:00008

abbreviation: JSTOR
database: Digital archive of scholarly articles
object: journal article
example_id: JSTOR:3093870
generic_url: http://www.jstor.org/
url_syntax: http://www.jstor.org/stable/$acc_no
url_example: http://www.jstor.org/stable/3093870 


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=$acc_no
url_example: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=881225 

abbreviation: MaizeGDB_QTL
database: Maize Genetics and Genomics Database
object: MaizeGDB trait records
example_id: MaizeGDB_QTL:78112
generic_url: http://www.maizegdb.org/
url_syntax: http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=$acc_no
url_example: http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=78112


abbreviation: MGCSC_GENETIC_STOCKS
database: Maize Genetics and Genomics Database
object: 
example:
generic_url: http://www.maizegdb.org/cgi-bin/displaystockrecord.cgi?id=$acc_no
url_syntax:http:

abbreviation: MACSC_REF
database: Maize Genetics and Genomics Database
object: 
example:
generic_url: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=$acc_no
url_syntax: 

abbreviation: NASC
database: Nottingham Arabidopsis Stock Centre Seeds Database
object: 
example:
generic_url: http://arabidopsis.info
url_syntax: http://arabidopsis.info/StockInfo?NASC_id=$acc_no
example_url:


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=$acc_no&group_id=76834&atid=835555
url_example: https://sourceforge.net/tracker/index.php?func=detail&aid=3184921&group_id=76834&atid=835555

abbreviation: OBO_SF2_PO
database: Source Forge OBO Plant Ontology (PO) term request tracker
object: Plant Ontology term request
example_id: OBO_SF2_PO:500
generic_url: 
url_syntax: http://sourceforge.net/p/obo/plant-ontology-po-term-requests/$acc_no
url_example: 

abbreviation: PlantSystematics_image_archive
database: PlantSystematics.org
object: image id
example: PlantSystematics_image_archivee:37658
generic_url: http://plantsystematics.org
url_syntax: http://www.plantsystematics.org/imagebyid_$acc_no.html
url_example: http://www.plantsystematics.org/imagebyid_37658.html

abbreviation: PMID
database: PubMed
object: Identifier
example: PMID:4208797
generic_url: http://www.ncbi.nlm.nih.gov/PubMed/
url_syntax: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=$acc_no
url_example: 

abbreviation: PO
database:Plant Ontology Consortium AmiGO browser
object: Plant Ontology term
example_id: PO:0025034
generic_url:http://www.plantontology.org
url_syntax:
url_example:

abbreviation: POC
database: Plant Ontology Consortium
object: curator
example_id: POC:curators
generic url: http://wiki.plantontology.org/index.php/Main_Page
url_syntax: http://wiki.plantontology.org/index.php/Plant_Ontology_curators
url_example: http://wiki.plantontology.org/index.php/Plant_Ontology_curators

abbreviation: PO_REF
database: Plant Ontology custom references
object: Reference identifier
example_id: PO_REF:00001
generic url: http://wiki.plantontology.org/index.php/PO_references
url_syntax: http://wiki.plantontology.org/index.php/PO_REF:$acc_no
url_example: http://wiki.plantontology.org/index.php/PO_REF:00001


abbreviation: PUBMED
database: PubMed
object: Identifier
synonym: PMID
example: PUBMED:4208797
generic_url: http://www.ncbi.nlm.nih.gov/PubMed/
url_syntax: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=$acc_no
url_example: 
!In use?

abbreviation: RiceSES
database: Rice Knowledge Bank
object: Reference identifier
example_id: RiceSES:bakanae-diseases-bak
generic url: http://www.knowledgebank.irri.org/extension/crop-damage-diseases/
url_syntax: http://www.knowledgebank.irri.org/extension/crop-damage-diseases/$acc_no.html
url_example: http://www.knowledgebank.irri.org/extension/crop-damage-diseases/bakanae-diseases-bak.html

"rap-db"=>"http://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$acc_no",

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=$acc_no
url_syntax: http://www.sgn.cornell.edu/phenome/locus_display.pl?locus_id=$acc_no
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/$acc_no/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=$acc_no
url_example: http://www.sgn.cornell.edu/chado/publication.pl?pub_id=800

abbreviation: SOY_QTL
database: SoyBase
object: QTL Name
example: Abn+sdlg+1-1
generic_url: http://soybase.org/
url_syntax: http://soybase.org/sbt/search/search_results.php?category=QTLName&search_term=$acc_no
url_example: http://www.soybase.org/sbt/search/search_results.php?category=QTLName&search_term=Abn+sdlg+1-1


"soybase_qtl"=>"http://soybase.org/sbt/search/search_results.php?category=QTLName&search_term=$acc_no",
!new

abbreviation: TAIR
database: The Arabidopsis Information Resource.
object: Accession number.
example: TAIR:gene:2062713
generic_url: http://www.arabidopsis.org/
url_syntax: http://arabidopsis.org/servlets/TairObject?accession=$acc_no
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:
!not in use

abbreviation: TreeGenes
database: Forest Tree Genome Database
object: Anything with a TreeGenes ID Number
example_id: TreeGenes:254
generic_url: http://dendrome.ucdavis.edu/treegenes/
url_syntax:http://dendrome.ucdavis.edu/treegenes/protein/view_protein.php?id=$acc_no
url_example:http://dendrome.ucdavis.edu/treegenes/protein/view_protein.php?id=254


#not in use:

abbreviation: REACTOME
database: Reactome pathway database
object: 
example: 
generic_url: http://www.reactome.org
url_syntax: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=$acc_no


abbreviation: RAD
database: RGD database
object: 
example: 
generic_url: http://rgd.mcw.edu
url_syntax: http://rgd.mcw.edu/tools/references/references_view.cgi?id=$acc_no

abbreviation: SGD
database: Saccharomyces Genome Database
object: 
example: 
generic_url: http://db.yeastgenome.org
url_syntax: http://db.yeastgenome.org/cgi-bin/locus.pl?sgdid=$acc_no
url_syntax: http://db.yeastgenome.org/cgi-bin/SGD/reference/reference.pl?refNo=$acc_no

abbreviation: SGD_REF
database: Saccharomyces Genome Database
object: reference
example: 
generic_url: http://db.yeastgenome.org
url_syntax: http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=$acc_no


abbreviation: SMD
database: Stanford Microarray Database
object:
example:
generic_url: http://genome-www.stanford.edu/microarray
url_syntax:
!not in use

abbreviation: SP
database: SRS database at EBI
object: 
example: 
generic_url: 
url_syntax: http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[SWALL-acc:$acc_no]

abbreviation: SPTR
database: SRS database at EBI
object: 
example: 
generic_url: http://srs.ebi.ac.uk
url_syntax: http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[SWALL-acc:$acc_no]

abbreviation: SWALL
database: ExPASY Bioinformatics Resource Portal
object: 
example: 
generic_url: http://ca.expasy.org
url_syntax: http://ca.expasy.org/cgi-bin/sprot-search-de?S=1&T=1&SEARCH=$acc_no

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.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinac=$acc_no
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
!not in use


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://www.tcdb.org/tcdb/index.php?tc=$acc_no
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=$acc_no
url_example: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=ath1&orf=At3g01440

abbreviation: TIGR
database: The Institute for Genomic Research.
object: 
example: 
generic_url: http://www.tigr.org/
url_syntax:
"tigr_cmr"=>"http://cmr.tigr.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=$acc_no",

abbreviation: TIGR
database: The Institute for Genomic Research.
object: 
example: 
generic_url: http://www.tigr.org/
url_syntax:        
"tigr_egad"=>"http://www.tigr.org/tigr-scripts/CMR2/ht_report.spl?prot_id=$acc_no",
 
abbreviation: TIGRFAMS
database: The Institute for Genomic Research.
object: 
example: 
generic_url: http://www.tigr.org/
url_syntax: http://cmr.tigr.org/tigr-scripts/CMR/HmmReport.cgi?hmm_acc=$acc_no

abbreviation: TIGR_PFG1
database: The Institute for Genomic Research.
object: 
example: 
generic_url: http://www.tigr.org/
url_syntax: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=pfa1&orf=$acc_no

abbreviation: TIGR_REF
database: The Institute for Genomic Research.
object: 
example: 
generic_url: http://www.tigr.org/
url_syntax: http://www.tigr.org/tdb/GO_REF/GO_REF.shtml

abbreviation: TIGR_TBA1
database: The Institute for Genomic Research.
object: 
example: 
generic_url: http://www.tigr.org/
url_syntax: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=tba1&orf=$acc_no       

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
!not in use

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://cmr.tigr.org/tigr-scripts/CMR/HmmReport.cgi?hmm_acc=$acc_no
url_example:
http://www.tigr.org/tigr-scripts/CMR2/hmm_report.spl?acc=TIGR00254

abbreviation: TR
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: TrEMBL
generic_url: http://www.ebi.ac.uk/swissprot/
generic_url: http://ca.expasy.org/sprot/
url_syntax: http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[SWALL-acc:$acc_no]
url_example: http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[SWALL-acc: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:
!not in use

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
!not in use

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
!not in use

abbreviation: UNIPROT
database: Uniprot protein sequence database
object: 
example: 
generic_url: http://www.ebi.uniprot.org
url_syntax: http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinac=$acc_no
url_example:

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:
!not in use

abbreviation: WB
database: WormBase
object: 
example: 
generic_url: http://www.wormbase.org
url_syntax: http://www.wormbase.org/db/searches/basic?class=Any&query=$acc_no
url_example:

abbreviation: ZFIN
database: The Zebrafish Model Organism Database
object: 
example: 
generic_url: http://zfin.org
url_syntax: 
url_example: http://zfin.org/cgi-bin/ZFIN_jump?record=$acc_no


Not in Use:
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
!not in use


abbreviation: bib
database: AGRICOLA
object: call number
example: MARC TAG 016 or bib=0000-05160
generic_url: http://www.nal.usda.gov/ag98/
!not in use

abbreviation: CDG
database: Candida Genomome Database
object: 
example_id: 
generic_url: http://www.candidagenome.org
url_syntax: http://www.candidagenome.org/cgi-bin/locus.pl?locus=$acc_no
url_example: 
!not in use

abbreviation: DDB
database: Dictybase
object: 
example_id: 
generic_url: http://dictybase.org
url_syntax: http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo=$acc_no
url_syntax: http://dictybase.org/db/cgi-bin/gene_page.pl?dictybaseid=$acc_no
url_example: 
!not in use

abbreviation: dros_cdna
database: 
object: 
example_id: 
generic_url: http://weasel.lbl.gov
url_syntax: http://weasel.lbl.gov/cgi-bin/EST/community_query/ctgReport.pl?db=estlabtrack&id_type=0&id_value=$acc_no
url_example: 
!generic link not working
!not in use

abbreviation: EC
database: The Enzyme Commission.
example: EC:1.1.1.1
generic_url: http://ca.expasy.org/
url_syntax: http://ca.expasy.org/cgi-bin/nicezyme.pl?$acc_no
url_example: 
!not in use

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.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=$acc_no
url_example: http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=AA816246
!not in use

abbreviation: ENSEMBL
database: Ensembl genome database
object: 
example_id: 
generic_url: http://www.ensembl.org
url_syntax: http://www.ensembl.org/perl/protview?peptide=$acc_no
url_example: 
!not in use


abbreviation: FB
database: Flybase
object: 
example_id: 
generic_url: http://flybase.bio.indiana.edu
url_syntax: http://flybase.bio.indiana.edu/reports/$acc_no.html
url_example: 
!not in use

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
!not in use

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
!not in use

! 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
!not in use

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
!not in use

abbreviation: GOC:unpublished
database: Temporary reference for unpublished papers.
object: Doesn't link anywhere yet.
!not in use

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
!not in use

abbreviation: GRO
database: Gramene: A Comparative Mapping Resource for Grains
object: growth stage
example: 
generic_url: 
url_syntax: http://www.gramene.org/db/ontology/search_term?id=GRO:$acc_no
url_example: 
!not in use- has been replaced by the PO


abbreviation: IND
database: AGRICOLA
object: call number
example: IND84014403
generic_url: http://agricola.cos.com/
!not in use

abbreviation: IPI
database: International Protein Index.
object: Identifier.Version
example: IPI:IPI00000005.1
generic_url: http://www.ebi.ac.uk/IPI/IPIhelp.html
!not in use

abbreviation: KEGG
database: Kyoto Encyclopedia of Genes and Genomes.
generic_url: http://www.genome.ad.jp/kegg/
!not in use

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
!not in use

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
!not in use

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
!not in use

abbreviation: genedb_lmajor
database: Gene DB, Leishmania
object: 
example_id: 
generic_url: http://www.genedb.org
url_syntax: http://www.genedb.org/genedb/Search?organism=leish&name=$acc_no
url_example: 

abbreviation: genedb_pfalciparum
database: Gene DB, Plasmodium
object: 
example_id: 
generic_url: http://www.genedb.org
url_syntax: http://www.genedb.org/genedb/Search?organism=malaria&name=$acc_no
url_example: 

abbreviation: genedb_spombe
database: Gene DB
object: 
example_id: 
generic_url: http://www.genedb.org
url_syntax: http://www.genedb.org/genedb/Search?organism=pombe&name=$acc_no
url_example: 

abbreviation: genedb_tbrucei
database: Gene DB, Trypaonsoma
object: 
example_id: 
generic_url: http://www.genedb.org
url_syntax: http://www.genedb.org/genedb/Search?organism=tryp&name=$acc_no
url_example: 

abbreviation: METACYC
database: Metacyc Encyclopedia of Metabolic Pathways
object: 
example:
generic_url: http://metacyc.org
url_syntax:http://biocyc.org/META/substring-search?type=NIL&object=$acc_no
        
abbreviation: MGI
database: 
object: 
example:
generic_url: http://www.informatics.jax.org
url_syntax:http://www.informatics.jax.org/searches/accession_report.cgi?id=$acc_no


abbreviation: MaizeGDB_REF
database: Maize Genetics and Genomics Database
object: MaizeGDB references
example_id:
generic_url: http://www.maizegdb.org/
url_syntax: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=$acc_no
url_example:
!has been replaced by universal MaizeGDB

abbreviation: MEDLINE
database: The Medline literature database.
object: Identifier.
example: MEDLINE:20572430
generic_url:
url_syntax:
!not in use

abbreviation: NAL
database: AGRICOLA
object: call number
example: NAL:TP248.2 P76 v.14
generic_url: http://www.nal.usda.gov/ag98/ag98.html
!not in use

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
!not in use

abbreviation: NCBI
database: National Center for Biotechnology Information, Bethesda.
object: Prefix.
example: NCBI_gi
generic_url: http://www.ncbi.nlm.nih.gov/
!not in use


abbreviation: NCBI_NM
database: NCBI RefSeq.
object: mRNA identifier.
example: NCBI_NM:123456
generic_url: http://www.ncbi.nlm.nih.gov/
url_syntax:
!not in use

abbreviation: NCBI_NP
database: NCBI RefSeq.
object: Protein identifier.
example: NCBI_NP:123456
generic_url: http://www.ncbi.nlm.nih.gov/
url_syntax:
!not in use

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
!not in use

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:
!not in use

abbreviation: PROW
database: Protein Reviews on the Web.
generic_url: http://www.ncbi.nlm.nih.gov/prow/
!not in use

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
!not in use

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
!not in use

abbreviation: RESID
database: RESID Database of Protein Modifications.
object: Identifier.
example: RESID:AA0062
generic_url: ftp://ftp.ncifcrf.gov/pub/users/residues/
url_syntax:
!not in use

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:http://www.ebi.ac.uk/interpro/IEntry?ac=$acc_no
!in association file?

abbreviation: NCBI_gi
database: NCBI databases.
object: Identifier.
example: NCBI_gi:10727410
generic_url: http://www.ncbi.nlm.nih.gov/
url_syntax: http://www.ncbi.nlm.nih.gov/nuccore/$acc_no
url_example: http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=10727410&dopt=GenBank
!not in use?

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?$acc_no
url_example: http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00046
!not in use?