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Fwd: Re: Fwd: Database abbreviations

Suzanna Lewis suzi at bdgp.lbl.gov
Fri Nov 2 08:48:35 PST 2001


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: 
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> > > >Subscribing   send   "subscribe"   to   
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> > > >Unsubscribing send   "unsubscribe"  to  
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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/
> 
> 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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