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Fwd: Database abbreviations

Pankaj Jaiswal pj37 at cornell.edu
Fri Nov 2 09:06:35 PST 2001


Hi,

After going through your mails, I can make out a suggestion.

IMGT is the project and that should be the primary identifier and that's all.
Where as 
HLA is for histocompatibility complex (HLA) so do not confuse with this.
Secondly LIGM is the Laboratory name. It should be avoided. As long as the
project identifier IMGT is there that should be fine. 

Best regards

Pankaj

Marie-Paule Lefranc wrote:
> 
> Thank you Evelyn for your comment.
> I agree that IMGT_LIGM and IMGT_HLA should be acceptable if the slashes are
> a problem for GO (I prefer "_" rather than a dash (-)
> Best regards
> Marie-Paule
> 
> >Date: Fri, 02 Nov 2001 09:34:04 +0000
> >From: Evelyn Camon <camon at ebi.ac.uk
> >
> >To: Suzanna Lewis <suzi at bdgp.lbl.gov>, lefranc at ligm.igh.cnrs.fr,
> >         ma11 at gen.cam.ac.uk, go-friends at geneontology.org
> >Subject: Re: Fwd: Database abbreviations
> >
> >
> >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
> > > > >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/
> > >
> > > --
> > > 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/

-- 

**************************************************************
Pankaj Jaiswal, Ph.D.                                   
Postdoctoral Associate
Dept. of plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   http://ars-genome.cornell.edu/rice
**************************************************************


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