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[GO] Re: [MOBY] Re: GO Xref Abbs now served by MOBY

Mark Wilkinson markw at illuminae.com
Thu Feb 26 08:18:38 PST 2004


http://mobycentral.cbr.nrc.ca/cgi-bin/XrefAbbs

just click the link above to instantiate the cat... whether it is
smiling or not will depend on the parse-test :-)

Attached is a saved version of the output from the script above as of
this AM.

M


On Thu, 2004-02-26 at 07:57, Michael Ashburner (Genetics) wrote:
> Then can you instantiate the cat & send it (|her|him) to me.
> Keep the smile on its (|hers|his) face please.
> M
> 
> 
> --
> This message is from the GOFriends moderated mailing list.  A list of public
> announcements and discussion of the Gene Ontology (GO) project.
> Problems with the list?           E-mail: owner-gofriends at geneontology.org
> Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
> Unsubscribing send   "unsubscribe"  to  gofriends-request at geneontology.org
> Web:          http://www.geneontology.org/
-- 
Mark Wilkinson (mwilkinson at mrl.ubc.ca)
University of British Columbia iCAPTURE Centre
-------------- next part --------------
!version:  Auto-generated by MOBY
!date: 2004-02-26 12:16:02
!
!Gene Ontology/BioMOBY
!Abbreviations for cross-referenced databases.
!
!Note that url's are not necessarily stable entities and that some
!databases may have many other access routes or mirror sites.
!

abbreviation: NCBI_AccVer
database:  An identifier representing an NCBI (GenBank) Accession number, including the version suffix (e.g. J00522.1)

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_example: http://umbbd.ahc.umn.edu/acr/acr_map.html

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
database:  The University of Minnesota Biocatalysis/Biodegradation Database.
object: Prefix.
generic_url: http://umbbd.ahc.umn.edu/index.html

abbreviation: ATH_DonorNumber
database:  ID given by donor for Arabidopsis stock donated (e.g. BFM2)

abbreviation: WB
database:  WormBase, database of nematode biology.
object: Gene symbol.
example: WB:lin-12
generic_url: http://www.wormbase.org/
url_syntax: http://www.wormbase.org/db/get?class=Locus;name=
url_example: http://www.wormbase.org/db/get?class=Locus;name=lin-12

abbreviation: NCBI_Acc
database:  An identifier representing an NCBI (GenBank) Accession number, without a version (e.g. J00522)

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=?

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=

abbreviation: TIGR_Tba1
database:  The Institute for Genomic Research, Trypanosoma brucei database.
object: Accession.
example: TIGR_Tba1:25N14.10
generic_url: http://www.tigr.org/tdb/e2k1/tba1/
url_syntax: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=tba1&orf=
url_example: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=tba1&orf=25N14.10

abbreviation: TIGR_EGAD
database:  The Institute for Genomic Research, EGAD database
object: Accession.
example: TIGR_EGAD:74462
generic_url: http://www.tigr.org/
url_syntax: http://www.tigr.org/tigr-scripts/CMR2/ht_report.spl?prot_id=

abbreviation: TIGR_CMR
database:  The Institute for Genomic Research, Comprehensive Microbial Resource.
object: Locus.
example: TIGR_CMR:VCA0557
generic_url: http://www.tigr.org/
url_syntax: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=ath1&orf=
url_syntax: http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=
url_example: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=ath1&orf=At3g01440

abbreviation: TIGR_Ath1
database:  Accession from The Institute for Genomic Research, Arabidopsis thaliana database. (e.g. TIGR_Ath1:At3g01440)

abbreviation: TIGR
database:  The Institute for Genomic Research.
generic_url: http://www.tigr.org/

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: 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/

abbreviation: SUBTILISTG
database:  Bacillus subtilis Genome Sequence Project.
object: Gene symbol.
example: SUBTILISTG:accC
generic_url: http://genolist.pasteur.fr/SubtiList/

abbreviation: SUBTILIST
database:  Bacillus subtilis Genome Sequence Project.
object: Accession number.
example: SUBTILISTG:BG11384
generic_url: http://genolist.pasteur.fr/SubtiList/

abbreviation: GO
database:  Gene Ontology Database.
object: Identifier.
example: GO:0046703
generic_url: http://godatabase.org/cgi-bin/go.cgi?query=
url_syntax: http://godatabase.org/cgi-bin/go.cgi?query=GO:0046703

abbreviation: SPTR
database:  The combination of SWISS-PROT and TrEMBL; includes TrEMBLnew.
object: Accession number.
synonym: SWALL
example: SPTR:P45867
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: Swiss-Prot
database:  Swiss-Prot protein database.
object: Accession number.
synonym: SP
synonym: SWP
synonym: SWISS-PROT
example: Swiss-Prot:P45867
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: SMD
database:  Stanford Microarray Database
generic_url: http://genome-www.stanford.edu/microarray

abbreviation: TrEMBL
database:  Computer-annotated protein sequence database supplementing
object: Accession number.
synonym: SPTREMBL
synonym: TREMBL
synonym: TR
example: TrEMBL:Q00177
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: SGD_REF
database:  Saccharomyces Genome Database.
object: Literature Reference Identifier.
example: SGD_REF:19239
generic_url: http://genome-www.stanford.edu/Saccharomyces/
url_syntax: http://genome-www4.stanford.edu/cgi-bin/SGD/reference/reference.pl?refNo=
url_example: http://genome-www4.stanford.edu/cgi-bin/SGD/reference/reference.pl?refNo=19239

abbreviation: SGD_LOCUS
database:  Saccharomyces Genome Database.
object: Gene name (gene symbol in mammalian nomenclature).
example: SGD_LOCUS:GAL4 or SGD_LOCUS:YEL001C
generic_url: http://genome-www.stanford.edu/Saccharomyces/
note: This object also includes the systematic S. cerevisiae ORF names, eg. YEL001C.
url_syntax: http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=
url_example: http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=GAL4

abbreviation: SGD
database:  Saccharomyces Genome Database.
object: Identifier for SGD Loci
synonym: SGDID
example: SGD:S0006169
generic_url: http://genome-www.stanford.edu/Saccharomyces/
note: The SGD is a synonym for the SGDID
url_syntax: http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?sgdid=
url_example: http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?sgdid=S0006169

abbreviation: REMTREMBL
database:  Computer-annotated protein sequence database containing the
object: Identifier.
example: REMTREMBL:CAC01666

abbreviation: RESID
database:  RESID Database of Protein Modifications.
object: Identifier.
example: RESID:AA0062
generic_url: ftp://ftp.ncifcrf.gov/pub/users/residues/

abbreviation: RGD
database:  Rat Genome Database.
object: Accession Number
example: RGD:2340
generic_url: http://rgd.mcw.edu/
url_syntax: http://rgd.mcw.edu/query/query.cgi?id=

abbreviation: PROW
database:  Protein Reviews on the Web.
generic_url: http://www.ncbi.nlm.nih.gov/prow/

abbreviation: protein_id
database:  The protein identifier shared by DDBJ/EMBL-bank/GenBank nucleotide
object: Identifier.
example: protein_id:CAA71991

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: PompepG
database:  Gene from Schizzosaccharomyces pompbe genes. (e.g. PompepG:YTM1)

abbreviation: Pompep
database:  Schizosaccharomyces pombe protein data.
object: Gene/protein identifier.
example: Pompep:SPAC890.04C
generic_url: ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Protein_data/

abbreviation: PMID
database:  PubMed.
object: Identifier.
synonym: PUBMED
example: PMID:4208797
generic_url: http://www.ncbi.nlm.nih.gov/PubMed/
url_example: http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=4208797&dopt=Abstract

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: 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: PDB
database:  Protein Data Bank.
object: Identifier.
example: PDB:1A4U
generic_url: http://www.rcsb.org/pdb/
url_example: http://www.rcsb.org/pdb/cgi/explore.cgi?pid=223051005992697&pdbId=1A4U

abbreviation: OMIM
database:  Mendelian Inheritance in Man.
object: Identifier.
synonym: MIM [used by NCBI]
example: OMIM:190198
generic_url: http://www3.ncbi.nlm.nih.gov/Omim/searchomim.html
url_syntax: http://www3.ncbi.nlm.nih.gov/htbin-post/Omim/dispmim?
url_example: http://www3.ncbi.nlm.nih.gov/htbin-post/Omim/dispmim?190198

abbreviation: NCBI_NP
database:  NCBI RefSeq.
object: Protein identifier.
example: NCBI_NP:123456
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_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/

abbreviation: NCBI
database:  National Center for Biotechnology Information, Bethesda.
object: Prefix.
example: NCBI_gi
generic_url: http://www.ncbi.nlm.nih.gov/

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: MGI
database:  Mouse Genome Informatics.
object: Accession number.
example: MGI:80863
generic_url: http://www.informatics.jax.org/

abbreviation: MGD
database:  Mouse Genome Database.
object: Gene symbol.
example: MGD:Adcy9
generic_url: http://www.informatics.jax.org/
url_syntax: http://www.informatics.jax.org/searches/marker.cgi?

abbreviation: MetaCyc
database:  The Metabolic Encyclopedia of metabolic and other pathways.
object: Pathway identifier.
example: MetaCyc:GLUTDEG-PWY
generic_url: http://ecocyc.org/ecocyc/metacyc.html?
url_syntax: http://malibu.ai.sri.com:1555//META/NEW-IMAGE?type=PATHWAY&object=?
url_example: http://malibu.ai.sri.com:1555//META/NEW-IMAGE?type=PATHWAY&object=GLUTDEG-PWY

abbreviation: MEDLINE
database:  The Medline literature database.
object: Identifier.
example: MEDLINE:20572430

abbreviation: MaizeDBID
database:  Identifier from Maize Genome Database. (e.g. MaizeDBID:12008)

abbreviation: MaizeDB
database:  Canonical from Maize Genome Database. (e.g. MaizeDB:apb1)

abbreviation: LocusID
database:  NCBI LocusLink ID.
object: Identifier.
example: LocusID:3195
generic_url: http://www.ncbi.nlm.nih.gov/
url_example: http://www.ncbi.nlm.nih.gov:80/LocusLink/LocRpt.cgi?l=3195

abbreviation: LIGAND
database:  KEGG LIGAND Database.
object: Enzyme or Compound.
example: LIGAND:EC 1.1.1.1
generic_url: http://www.genome.ad.jp/kegg/docs/upd_ligand.html#COMPOUND
url_syntax: http://www.genome.ad.jp/dbget-bin/www_bget?ec:
url_syntax: http://www.genome.ad.jp/dbget-bin/www_bget?cpd:
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: 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: KEGG
database:  Kyoto Encyclopedia of Genes and Genomes.
generic_url: http://www.genome.ad.jp/kegg/

abbreviation: IUPHAR
database:  The IUPHAR Compendium of Receptor Characterization and Classification.
object: Receptor code.
example: IUPHAR:2.1.CBD

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: IPI
database:  International Protein Index.
object: Identifier.Version
example: IPI:IPI00000005.1
generic_url: http://www.ebi.ac.uk/IPI/IPIhelp.html

abbreviation: INTERPRO
database:  The InterPro database of protein domains and motifs.
synonym: INTERPRO
generic_url: http://www.ebi.ac.uk/interpro/

abbreviation: IMGT_LIGM
example: IMGT_LIGM:U03895
generic_url: http://imgt.cines.fr

abbreviation: IMGT_HLA
example: IMGT_HLA:HLA00031
generic_url: http://www.ebi.ac.uk/imgt/hla

abbreviation: HGNC
database:  HUGO Gene Nomenclature Committee.
object: Gene symbol.
example: HGNC:HNRPK
generic_url: http://www.gene.ucl.ac.uk/nomenclature/
url_example: http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl?field=symbol&anchor=begins&match=HNRPK&symbol_search=Search&page_size=25&limit=1000&.cgifields=limit&.cgifields=page_size

abbreviation: HUGO
database:  Human Genome Organisation
generic_url: http://www.gene.ucl.ac.uk/hugo/

abbreviation: GOA:spkw
database:  Gene Ontology Annotation at EBI annotations from keyword mapping.
object: Reference (points to web page).
url_example: http://www.ebi.ac.uk/proteome/goa/goaHelp.html

abbreviation: GOA:spec
database:  Gene Ontology Annotation at EBI annotations from EC mapping.
object: Reference (points to web page).
url_example: http://www.ebi.ac.uk/proteome/goa/goaHelp.html

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.ebi.ac.uk/proteome/goa/goaHelp.html

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/GO.ndref.html

abbreviation: GR_REF
database:  Gramene: A Comparative Mapping Resource for Grains.
object: Reference
example: http://www.gramene.org/perl/pub_search?ref_id=659
generic_url: http://www.gramene.org/
url_syntax: http://www.gramene.org/perl/pub_search?ref_id=ID number

abbreviation: GR
database:  Gramene: A Comparative Mapping Resource for Grains.
object: Protein
example: http://www.gramene.org/perl/protein_search?acc=P93436
generic_url: http://www.gramene.org/
url_syntax: http://www.gramene.org/perl/protein_search?acc=Accession number

abbreviation: GenProtEC
database:  GenProtEC E. coli genome and proteome database.
generic_url: http://genprotec.mbl.edu/

abbreviation: GeneDB_Tbrucei
shorthand_name: Tbrucei
database:  GeneDB_Tbrucei.
object: Gene identifier.
example: GeneDB_Tbrucei:Tb927.1.5250
generic_url: http://www.genedb.org/tryp
url_syntax: http://www.genedb.org/genedb/Search?organism=tryp&name=
url_example: http://www.genedb.org/genedb/Search?organism=tryp&name=Tb927.1.5250

abbreviation: GeneDB_Pfalciparum
shorthand_name: Pfalciparum
database:  GeneDB_Pfalciparum.
object: Gene identifier.
example: GeneDB_Pfalciparum:PFD0755c
generic_url: http://www.genedb.org/malaria
url_syntax: http://www.genedb.org/genedb/Search?organism=malaria&name=
url_example: http://www.genedb.org/genedb/Search?organism=malaria&name=PFD0755c

abbreviation: GeneDB_Lmajor
shorthand_name: Lmajor
database:  GeneDB_Lmajor.
object: Gene identifier.
example: GeneDB_Lmajor:LM5.32
generic_url: http://www.genedb.org/leish
url_syntax: http://www.genedb.org/genedb/Search?organism=leish&name=
url_example: http://www.genedb.org/genedb/Search?organism=leish&name=LM5.32

abbreviation: GeneDB_Gmorsitans
shorthand_name: Tsetse
database:  GeneDB_Gmorsitans.
object: Gene identifier.
example: GeneDB_Gmorsitans:Gmm-0142
generic_url: http://www.genedb.org/glossina
url_syntax: http://www.genedb.org/genedb/Search?organism=glossina&name=
url_example: http://www.genedb.org/genedb/Search?organism=glossina&name=Gmm-0142

abbreviation: GeneDB_Spombe
shorthand_name: Spombe
database:  GeneDB_Spombe.
object: Gene identifier.
example: GeneDB_Spombe:SPAC890.04C
generic_url: http://www.genedb.org/pombe
url_syntax: http://www.genedb.org/genedb/Search?organism=pombe&name=
url_example: http://www.genedb.org/genedb/Search?organism=pombe&name=SPAC890.04C

abbreviation: GDB
database:  Human Genome Database.
object: Accession number.
example: GDB:306600
generic_url: http://www.gdb.org/
url_example: http://www.gdb.org/gdb-bin/genera/accno?accessionNum=GDB:306600

abbreviation: FLYBASE
database:  FlyBase.
object: Gene symbol.
example: FLYBASE:Adh
generic_url: http://flybase.bio.indiana.edu/
url_syntax: http://flybase.bio.indiana.edu/.bin/fbidq.html?
url_syntax: http://fly.ebi.ac.uk:7081/.bin/fbidq.html?

abbreviation: FB
database:  FlyBase.
object: Gene identifier.
example: FB:FBgn0000024
generic_url: http://flybase.bio.indiana.edu/
note: [NCBI use FLYBASE]
url_syntax: http://fly.ebi.ac.uk:7081/.bin/fbidq.html?
url_syntax: http://flybase.bio.indiana.edu/.bin/fbidq.html?
url_example: http://fly.ebi.ac.uk:7081/.bin/fbidq.html?FBgn0000055

abbreviation: ENSEMBL
database:  Database of automatically annotated genomic data.
object: Identifier.
example: ENSEMBL:ENSP00000265949
generic_url: http://www.ensembl.org/
url_syntax: http://www.ensembl.org/perl/protview?peptide=
url_example: http://www.ensembl.org/perl/protview?peptide=ENSP00000265949

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: 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: ECOGENE
database:  CGSC: E.coli Genetic Stock Center.
object: EcoGene Accession Number.
example: ECOGENE:EG10818
generic_url: http://cgsc.biology.yale.edu/
url_example: http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/315

abbreviation: ECOGENE_G
database:  CGSC: E.coli Genetic Stock Center.
object: EcoGene Primary Gene Name.
example: ECOGENE_G:deoC
generic_url: http://cgsc.biology.yale.edu/

abbreviation: EcoCyc
database:  The Encylopedia of E. coli metabolism.
object: Pathway identifier.
example: EcoCyc:P2-PWY
generic_url: http://ecocyc.org/
url_syntax: http://malibu.ai.sri.com:1555/ECOLI/new-image?type=PATHWAY&object=?
url_example: http://malibu.ai.sri.com:1555/ECOLI/new-image?type=PATHWAY&object=P2-PWY

abbreviation: EC
database:  The Enzyme Commission.
example: EC:1.1.1.1
generic_url: http://www.chem.qmw.ac.uk/iubmb/enzyme/
url_example: http://www.chem.qmw.ac.uk/iubmb/enzyme/EC1/1/1/1.html

abbreviation: CGEN
database:  Compugen Gene Ontology Gene Association Data.
object: Identifier.
example: CGEN:PrID131022
generic_url: !{see GO/gene-associations/readme/Compugen.README}
url_syntax: !{see GO/gene-associations/readme/Compugen.README}

abbreviation: CGSC
database:  CGSC: E.coli Genetic Stock Center.
object: Gene symbol.
example: CGSC:rbsK
generic_url: http://cgsc.biology.yale.edu/
url_example: http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/315

abbreviation: Global
database:  A somewhat generic prefix for namespaces that are not identifiers for any given database.  This could be a namespace for keywords, for eexample

abbreviation: Global_Keyword
database:  A namespace for keywords; one keyword only

abbreviation: DragonDB_Gene
database:  A namespace for Antirrhinum Gene names

abbreviation: DragonDB_Sequence
database:  A namespace for Antirrhinum Sequence Identifiers according to DragonDB

abbreviation: DragonDB_Allele
database:  A namespace for Antirrhinum Allele names according to DragonDB

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=
url_example: http://mips.gsf.de/cgi-bin/proj/thal/search_gene?code=At2g17950
url_example: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=ath1&orf=At2g17950
url_example: http://arabidopsis.org/servlets/TairObject?type=locus&name=At2g17950

abbreviation: keyword
database:  Any keyword. e.g.'wuschel'

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=
url_example: http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=N3371

abbreviation: ATH_Ecotype
database:  Natural variant of Arabidopsis (e.g. Ler)

abbreviation: MO
database:  The MGED Ontology
object: ontology term
example: MO:Action
generic_url: http://mged.sourceforge.net/ontologies/MGEDontology.php
url_syntax: http://mged.sourceforge.net/ontologies/MGEDontology.php#term
url_example: http://mged.sourceforge.net/ontologies/MGEDontology.php#Action

abbreviation: SDSC_fg
database:  SDSC functional genomics ID as used by PlantsP (http://plantsp.sdsc.edu) and related dbases PlantsT and PlantsUBQ. IDs are unique across these three dbases.

abbreviation: Haplotyping_Study_ns
database:  HapMap related namespace

abbreviation: SGD_ORF
database:  A namespace describing a Sacccharomyces Open Reading Frame Identifier

abbreviation: SGD_CHROMOSOME_ID
database:  A namespace describing a Sacccharomyces Chromosome Identifier (e.g. I, IX, MIT)

abbreviation: Haplotyping_Study
database:  HapMap namespace

abbreviation: ATH_Insert_number
database:  Unique number given to all Arabidopsis inserts (e.g. salk:000001)

abbreviation: PSI-MI
database:  Proteomics Standards Initiative Molecular Interaction methods namespace

abbreviation: IntAct
database:  Proteomics Standards Initiative Molecular Interaction methods namespace

abbreviation: IND
database:  AGRICOLA
object: call number
example: IND84014403
generic_url: http://agricola.cos.com/

abbreviation: SGN_C
database:  EST (clone) from the Solanaceae Genomics Network database (e.g. SGN-C:130510)

abbreviation: REGIA
database:  Regulatory Expression Genes in Arabidopsis

abbreviation: SGN_E
database:  EST from the Solanaceae Genomics Network database (e.g. SGN-E:333157)

abbreviation: SGN_U
database:  Unigene from the Solanaceae Genomics Network database (e.g. SGN-U:147982)

abbreviation: Pathbase_PB
database:  An accession number from Pathbase (European mutant mouse pathology database)

abbreviation: bib
database:  AGRICOLA
object: call number
example: MARC TAG 016 or bib=0000-05160
generic_url: http://www.nal.usda.gov/ag98/

abbreviation: DDB
database:  DictyBase
object: Accession ID
example: DDB0001836
generic_url: http://dictybase.org
url_syntax: http://dictybase.org/db/cgi-bin/dictyBase/locus.pl?locus=
url_example: http://dictybase.org/db/cgi-bin/dictyBase/locus.pl?locus=DDB0001836

abbreviation: DDB_LOCUS
database:  DictyBase
object: Locus
example: mlcE
generic_url: http://dictybase.org
url_syntax: http://dictybase.org/db/cgi-bin/dictyBase/locus.pl?locus=
url_example: http://dictybase.org/db/cgi-bin/dictyBase/locus.pl?locus=mlce

abbreviation: GOA:hamap
database:  Gene Ontology Annotation at EBI annotations from HAMAP to GO mapping.
object: Reference (points to web page).
url_example: http://www.ebi.ac.uk/proteome/goa/goaHelp.html

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

abbreviation: MaizeGDB
shorthand_name: MaizeGDB
database:  MaizeGDB
object: MaizeGDB Object ID Number
example: 881225
generic_url: http://www.maizegdb.org
url_syntax: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=
url_example: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=881225

abbreviation: TIGR_REF
database:  The Institute for Genomic Research, Plasmodium falciparum database.
object: reference locator
example: TIGR_REF:GO_ref
generic_url: http://www.tigr.org/tdb/GO_REF/
url_syntax: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=pfa1&orf=
url_example: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=pfa1&orf=PFB0010w
url_example: http://www.tigr.org/tdb/GO_REF/GO_REF.shtml

abbreviation: UniProt
database:  The Universal Protein Knowledgebase.
object: Accession number.
synonym: SPTR
example: UniProt:P12345
generic_url: http://www.uniprot.org
url_syntax: http://www.expasy.ch/cgi-bin/sprot-search-ac?
url_example: http://www.expasy.ch/cgi-bin/sprot-search-ac?P12345

abbreviation: VIDA
database:  Virus Database at University College London
generic_url: http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html

abbreviation: WB_REF
database:  WormBase, database of nematode biology.
object: Literature Reference Identifier.
example: WB_REF:cgc467
generic_url: http://www.wormbase.org/
url_syntax: http://www.wormbase.org/db/misc/paper?name=
url_example: http://www.wormbase.org/db/misc/paper?name=%5Bcgc467%5D;class=Paper

abbreviation: WP
database:  Wormpep, database of proteins of C. elegans.
object: Identifier.
example: WP:CE25104
generic_url: http://www.wormbase.org/
url_syntax: http://www.wormbase.org/db/get?class=Protein;name=
url_example: http://www.wormbase.org/db/get?class=Protein;name=WP%3ACE15104

abbreviation: ZFIN
database:  The Zebrafish Information Network
object: Accession ID
example: ZDB-GENE-990415-103
generic_url: http://zfin.org
url_syntax: http://zfin.org/cgi-bin/ZFIN_jump?record=
url_example: http://zfin.org/cgi-bin/ZFIN_jump?record=ZDB-GENE-990415-103



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