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Database abbreviations

Michael Ashburner (Genetics) ma11 at gen.cam.ac.uk
Thu Sep 27 09:23:08 PDT 2001


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: 



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