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Fwd: Re: Fwd: Re: Fwd: Database abbreviations

Marie-Paule Lefranc lefranc at ligm.igh.cnrs.fr
Fri Nov 2 09:19:25 PST 2001


That is fine.
Thanks
Marie-Paule

>X-POP3-Rcpt: lefranc at ligm.igh.cnrs.fr
>Date: Fri, 2 Nov 2001 08:48:35 -0800 (PST)
>From: Suzanna Lewis <suzi at bdgp.lbl.gov>
>Reply-To: Suzanna Lewis <suzi at bdgp.lbl.gov>
>Subject: Re: Fwd: Re: Fwd: Database abbreviations
>To: suzi at bdgp.lbl.gov, ma11 at gen.cam.ac.uk, lefranc at ligm.igh.cnrs.fr
>Cc: go-friends at geneontology.org
>X-Mailer: dtmail 1.3.0 @(#)CDE Version 1.4 SunOS 5.8 sun4u sparc
>
>
>Okay, lets use the underscore and make them
>IMGT_LIGM and
>IMGT_HLA
>
>thanks, S
>
> > Mime-Version: 1.0
> >
> > Thank you for your comment.
> > If possible, I would prefer to keep with the original abbreviation
> > IMGT/LIGM and IMGT/HLA as they are at NCBI.
> > If the slash is a problem for GO, there is the possibility of 
> putting  a "_
> > " instead of the slash, or at worst to write IMGTLIGM and IMGTHLA. The
> > abbreviations LIGM and HLA  cannot be used by themselves, they need to be
> > joined, in some way, to IMGT.
> > Best wishes
> > Marie-Paule Lefranc
> >
> >
> > >X-POP3-Rcpt: lefranc at ligm.igh.cnrs.fr
> > >Date: Thu, 1 Nov 2001 15:02:32 -0800 (PST)
> > >From: Suzanna Lewis <suzi at bdgp.lbl.gov>
> > >Reply-To: Suzanna Lewis <suzi at bdgp.lbl.gov>
> > >Subject: Re: Fwd: Database abbreviations
> > >To: ma11 at gen.cam.ac.uk, lefranc at ligm.igh.cnrs.fr
> > >Cc: go-friends at geneontology.org
> > >X-Mailer: dtmail 1.3.0 @(#)CDE Version 1.4 SunOS 5.8 sun4u sparc
> > >
> > >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
> > > > >Subscribing   send   "subscribe"   to
>gofriends-request at geneontology.org
> > > > >Unsubscribing send   "unsubscribe"  to
>gofriends-request at geneontology.org
> > > > >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/
> >
> > 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
> >

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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