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Fwd: Database abbreviations

Evelyn Camon camon at ebi.ac.uk
Fri Nov 2 01:32:28 PST 2001


Hi,

Suzanna, is it possible to have IMGT-LIGM or IMGT_LIGM?
I think it would be nice to keep the IMGT name which is part
of the database name. Marie Paule?

Evelyn

Suzanna Lewis wrote:

> the slash character in the abbreviation is a bit of a nuisance
> for the software. treatable, but i'd like to make a request
> that the abbreviations be drawn from the plain alpha character
> set so life is keep simple and fewer bugs creep in.
>
> that is a-z, A-Z, 0-9 (the dashes are not included) and no numbers
> as the first character.
>
> In this case the abbreviations would be LIGM and HLA
>
> -S
>
> >
> > 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:
> > >
> > >
> > >
> > >--
> > >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
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> > >Web:          http://www.geneontology.org/
> >
> > 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
> >
> >
> > --
> > 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/
>
> --
> 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/


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