Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

Fwd: Database abbreviations

Suzanna Lewis suzi at bdgp.lbl.gov
Thu Nov 1 15:02:32 PST 2001


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/



More information about the go-friends mailing list