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Fwd: Database abbreviations

Marie-Paule Lefranc lefranc at ligm.igh.cnrs.fr
Thu Nov 1 04:09:42 PST 2001


Dear Mike,

Since your message from the 27 september, IMGT/LIGM-DB and 
IMGT/HLA-DB  have been added to the list of databases which can be 
referenced in /db_xref qualifiers. I should be grateful if they could be 
added to the GO list. Please find below  the information as it appears in 
the NCBI page for the /db_xref qualifier:

>abbreviation: IMGT/LIGM
>definition: Immunogenetics database, immunoglobulins and T-cell receptors
>example: IMGT/LIGM:U03895
>generic_url: http://imgt.cines.fr
>url_syntax:
>
>abbreviation: IMGT/HLA
>definition: Immunogenetics database, human MHC
>example: IMGT/HLA:HLA00031
>generic_url: http://www.ebi.ac.uk/imgt/hla
>url_syntax:



With many thanks
Best regards
Marie-Paule




>X-POP3-Rcpt: lefranc at ligm.igh.cnrs.fr
>X-Authentication-Warning: alberich.Stanford.EDU: majordom set sender to 
>owner-gofriends at genome-mail.stanford.edu using -f
>To: go-friends at geneontology.org
>Subject: Database abbreviations
>X-Sun-Charset: US-ASCII
>From: Michael Ashburner (Genetics) <ma11 at gen.cam.ac.uk>
>Date: Thu, 27 Sep 2001 17:23:08 +0100
>Sender: owner-gofriends at genome.Stanford.EDU
>
>I propose that the syntax for database cross-references either within 
>nodes in an
>ontology or within other GO documents, eg GO.defs be standardised 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>:<databaseidentifier>
>
>What follows is a draft of a document defining the abbreviations
>and including urls.
>
>Before I go any further I want some input !
>
>Michael
>===================
>
>abbreviation: CGEN
>definition:
>example:
>generic_url:
>url_syntax:
>
>abbreviation: dbEST
>definition: EST database maintained at the NCBI.
>example: dbEST:123456
>generic_url:
>url_syntax:
>
>abbreviation: EC
>definition:
>example:
>generic_url:
>url_syntax:
>
>abbreviation: EcoCyc
>definition:
>example:
>generic_url:
>url_syntax:
>
>abbreviation: EMBL
>definition: EMBL-EBI International Nucleotide Sequence Data Library
>example:
>generic_url: http://www.ebi.ac.uk/embl/
>url_syntax:
>
>abbreviation: ENSEMBL
>definition: Database of automatically annotated genomic data.
>example: ENSEMBL:HUMAN-Clone-AC005612
>generic_url: http://www.ensembl.org/
>url_syntax:
>
>abbreviation: ENZYME
>definition:
>example:
>generic_url:
>url_syntax:
>
>abbreviation: FB
>definition: FlyBase; FlyBase accession number.
>note: [NCBI use FLYBASE]
>example: FB:FBgn0000024
>generic_url: http://fly.ebi.ac.uk:7081/
>generic_url: http://flybase.bio.indiana.edu/
>url_syntax:
>
>abbreviation: FLYBASE
>definition: FlyBase gene symbol.
>example: FLYBASE:Adh
>generic_url: http://fly.ebi.ac.uk:7081/
>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: GDB
>definition: Human Genome Database accession number.
>example: GDB:G00-128-600
>generic_url:
>url_syntax:
>
>abbreviation: GO
>definition: Gene Ontology Database identifier.
>example:GO:1234567
>generic_url: http://www.geneontology.org/
>url_syntax:
>
>abbreviation: INTERPRO
>definition:
>example:
>generic_url: http://www.ebi.ac.uk/interpro/
>url_syntax:
>
>abbreviation: LocusID
>definition: NCBI LocusLink ID.
>example: LocusID:51199
>generic_url:
>url_syntax:
>
>abbreviation: ISBN
>definition:
>example:
>generic_url:
>url_syntax:
>
>abbreviation: MaizeDB
>definition: Maize Genome Database unique identifier.
>example:
>generic_url:
>url_syntax:
>
>abbreviation: MEDLINE
>definition:
>example:
>generic_url:
>url_syntax:
>
>abbreviation: MGD
>definition:Mouse Genome Database; Mouse Genome Database gene symbol.
>example:
>generic_url:
>url_syntax:
>
>abbreviation: MGI
>definition: Mouse Genome Informatics accession number
>example: MGI
>generic_url:
>url_syntax:
>
>abbreviation: NCBI
>definition: National Center for Biotechnology Information, Bethesda.
>example:
>generic_url:
>url_syntax:
>
>abbreviation: NCBI_gi
>definition:
>example:
>generic_url:
>url_syntax:
>
>abbreviation: NCBI_NM
>definition:
>example:
>generic_url:
>url_syntax:
>
>abbreviation: NCBI_NP
>definition:
>example:
>generic_url:
>url_syntax:
>
>abbreviation: OMIM
>definition: Mendelian Inheritance in Man number.
>synonym: MIM [used by NCBI]
>example: OMIM:123456
>generic_url:
>url_syntax:
>
>abbreviation: PDB
>definition:
>example:
>generic_url: http://msd.ebi.ac.uk/
>generic_url: http://www.rcsb.org/pdb/
>url_syntax:
>
>abbreviation: PIR
>definition: Protein Information Resource accession number.
>example:
>generic_url:
>url_syntax:
>
>abbreviation: Pompep
>definition:
>example:
>generic_url:
>url_syntax:
>
>abbreviation: protein_id
>definition:
>example:
>generic_url:
>url_syntax:
>
>abbreviation: PUBMED
>definition:
>synonym: PMID
>example:
>generic_url:
>url_syntax:
>
>abbreviation: RATMAP
>definition: Rat Genome Database.
>example:
>generic_url:
>url_syntax:
>
>abbreviation: REMTREMBL
>definition: Computer-annotated protein sequence database containing the 
>translations of those codings sequences (CDS) present
>in the EMBL Nucleotide Sequence Database that will not be included in 
>SWISS-PROT. These include: immunoglobulins and T-cell receptors, synthetic 
>sequences, patent application sequences, small fragments, CDS not coding 
>for real proteins and truncated proteins.
>example: REMTREMBL:CAC01666
>generic_url:
>url_syntax:
>
>abbreviation: RESID
>definition:
>example:
>generic_url:
>url_syntax:
>
>abbreviation: RiceGenes
>definition: Rice database accession number.
>example:
>generic_url:
>url_syntax:
>
>abbreviation: SGD
>definition: Saccharomyces Genome Database; Saccharomyces Genome Database 
>gene names/symbol.
>example:
>generic_url:
>url_syntax:
>
>abbreviation: SGDID
>definition: Saccharomyces Genome Database accession number.
>example:
>generic_url:
>url_syntax:
>
>abbreviation: SPTREMBL
>definition: 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.
>example: SPTREMBL:Q00177
>generic_url:
>url_syntax:
>
>abbreviation: SWISS-PROT
>definition: Swiss-Prot protein database accession number.
>synonym: SWP
>example:
>generic_url: http://www.ebi.ac.uk/swissprot/
>url_syntax:
>
>abbreviation: SWALL
>definition:
>example:
>generic_url:
>url_syntax:
>
>abbreviation: SUBTILIST
>definition:
>example:
>generic_url:
>url_syntax:
>
>abbreviation: TAIR
>definition:
>example:
>generic_url:
>url_syntax:
>
>abbreviation: taxon
>definition: NCBI Taxman taxonomic identifier.
>example: taxon:493
>generic_url:
>url_syntax:
>
>abbreviation: TC
>definition:
>example:
>generic_url:
>url_syntax:
>
>abbreviation: UM-BBD
>definition:
>example:
>generic_url:
>url_syntax:
>
>abbreviation: UM-BBD_enzymeID
>definition:
>example:
>generic_url:
>url_syntax:
>
>abbreviation: UM-BBD_pathwayID
>definition:
>example:
>generic_url:
>url_syntax:
>
>abbreviation: WB
>definition:
>example:
>generic_url:
>url_syntax:
>
>abbreviation: WP
>definition:
>example:
>generic_url:
>url_syntax:
>
>
>
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IMGT, the international ImMunoGeneTics database
http://imgt.cines.fr
LIGM, IGH, UPR CNRS 1142
141 rue de la Cardonille
34396 Montpellier Cedex 5
FRANCE
Tel: +33 (0)4 99 61 99 65
Fax: +33 (0)4 99 61 99 01


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This message is from the GOFriends moderated mailing list.  A list of public
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