February 13, 2008

gene_association_PAMGO_oomycetes.gz -- A source for oomycete
(currently, Phytophthora sojae, Phytophthora infestans, Phytophthora
parasitica, Hyaloperonospora parasitica, Pythium aphanidermatum,
Phytophthora capsici, Phytophthora cinnamomi, and Phytophthora
cryptogea) GO annotations. These annotations are based solely on
experimental data from scientific literature. Annotations are made by
the Oomycete Genome Annotation team at the Virginia Bioinformatics
Institute. The annotating database is Identified in column 15.

Questions about this file should be sent to: trudy@vbi.vt.edu

The gene_association.PAMGO_oomycetes.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

Columns are:

 1: DB: database contributing the file (either the VBI microbial
    database (VMD) or NCBI protein database (NCBI_GP)).
 2: DB_Object_ID: (Unique identifier for genes/gene products in
    appropriate database).
 3: DB_Object_Symbol:

 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
 7: Evidence: the evidence code for the GO annotation
 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. ' crinkling and necrosis-inducing protein '
11: DB_Object_Synonym(|Synonym): (optional),  e.g. NLPPs
12: DB_Object_Type: type of object annotated, e.g. gene, protein, etc.
13: taxon: taxonomic identifier of species encoding gene product. The
    dual taxon is used mainly in conjunction with terms that have the
    term "multi-organism process" - GO:0051704 as their ancestor. The
    first taxon id should be that of the organism encoding the gene or
    gene product, and the taxon id after the pipe should be that of
    the other organism in the interaction. (e.g. taxon:1|taxon:1000)
14: Date: date GO annotation was made in the format
15: Assigned_by: source of the annotation (PAMGO_VMD)

Methodology  

An annotator examines each gene product. Terms are then assigned by
examining the literature, and translating the experimental information
contained in experimental results into the appropriate GO terms.