June 16th, 2008

gene_association.reactome.gz -- Contains GO annotations extracted from Reactome annotations.

Reactome - a curated knowledgebase of biological pathways
http://www.reactome.org/ 

The gene_association.reactome.gz file uses the standard file format for
gene_association files of the Gene Ontology (GO) Consortium.  A more
complete description of the file format is found here:

 http://www.geneontology.org/doc/GO.annotation.html#file

This file is updated when a new Reactome release is published, roughly every three months.

Columns are:

 1: DB, database contributing the file (always "UniProt" for this file).
 2: DB_Object_ID, UniProt accession.
 3: DB_Object_Symbol, UniProt identifier
 4: Qualifier (optional), one or more of 'NOT', 'contributes_to',
    'colocalizes_with' as qualifier(s) for a GO annotation, when needed,
    multiples separated by pipe (|)
 5: GO ID, unique numeric identifier for the GO term
 6: DB:Reference(|DB:Reference), the reference associated with the GO
    annotation (see below)
 7: Evidence, the evidence code for the GO annotation (see below)
 8: With (or) From (optional), any With or From qualifier for the GO
    annotation
 9: Aspect, which ontology the GO term belongs (Function, Process or
    Component)
10: DB_Object_Name(|Name) (optional), a name for the gene product in
    words, e.g. 'acid phosphatase'
11: DB_Object_Synonym(|Synonym) (optional), see below
12: DB_Object_Type, type of object annotated, e.g. gene, protein, etc.
13: taxon(|taxon), taxonomic identifier of species encoding gene
    product
14: Date, date GO annotation was defined in the format YYYYMMDD
15: Assigned_by, source of the annotation (always "Reactome" for this file)

Notes:

Column 6: When more than one literature references are assigned to a Reactome reaction (the source of the GO annotation), the Reactome stable id is given here, rather than a Pubmed id (e.g. REACTOME:REACT_1848.1).

Column 7: When the Reference column (6) contains a Reactome stable id, the evidence code used here is TAS.



Questions about this file should be sent to: help@reactome.org