Reference "Gene Ontology Annotation By The Gramene Database"

Reference ID

8030

Title

Gene Ontology Annotation By The Gramene Database

Source

Gramene database, 2003, vol. 1, pp. 1-1

Authors (7)

Jaiswal-P	Ren-L
Zhao-W	Schmidt-S-C
Ratnapu-K-K	Lincoln-S
McCouch-S

Abstract

The large-scale assignment of Gene Ontology (GO) terms to protein accessions
involves electronic techniques. This strategy involves the initial step of
mapping the Interpro (a database of protein motifs) qualifiers, Swissprot
keywords and Enzyme Commission (EC) numbers to the protein sequences. These
mappings are then converted into GO mappings by converting the respective
mappings to GO accessions by using the interpro2go, ec2go and spkw2go mappings
files available from the Gene Ontology website (www.geneontology.org).
Electronically combining these mappings with a table of matching protein entries
generates a table of associations. For each GO annotation, an associated
evidence code summarizes how the association is drawn. Associations drawn from
computational methods are labeled as 'inferred from electronic annotation�
(IEA). As a part of the quality checks and manual annotation process, the
Gramene curators go through these associations and validate the respective Gene
Ontology assignments by converting them into 'inferred from Sequence or
structural similarity' (ISS) or any other evidence code of a higher order. Often
the electronic GO associations to the protein entries in Gramene are imported
from EBI's SWALL database, however, the associations based on manual curation
always supercede the electronic annotation.