Reference "Mapping ontology associations between gene and protein entries in the Gramene database."

Reference ID

11089

Title

Mapping ontology associations between gene and protein entries in the Gramene database.

Source

Gramene database, 2006, vol. 1, pp. 1-1

Authors (5)

Jaiswal-P	Ren-L
Ravenscroft-D	Lincoln-S
McCouch-S

Abstract

This reference describes the Gramene curation standards that are adopted for
mapping ontology associations between gene and protein entries. The protocol
is applied to reduce the number of errors from manual curation. The gene
entries import ontology associations from the respective protein entries
(found in the protein database), if the same are mapped to a gene. Since the
protein entries are curated in detail, it is wise to import them into gene
with no further quality check. In the gene pages (found in the gene database),
we only display the ontology terms that are associated, but not their details
such as evidence (cited reference and evidence code). For details one has to
go to the proteins. Further improvements are being made to gene database.
Alternatively, if the gene entry was curated first it is a general practice
that the curator has already scanned the published literature and/or gathered
the useful information associated with it. In such cases the curator enters
the terms associated with the gene, but without further evidence and evidence
code. After the gene entry is curated to have the mapped protein entry in
protein database, the automated mechanism imports all the ontology terms from
gene into respective protein entry. Since these ontology associations need
proper evidence and an evidence code, the curator is prompted to provide these
in the protein database. However by default when for the first time the
automated system of importing ontology associations work, the evidence provide
is this reference and the evidence code IC (Inferred by curator). IC is used
because it is already looked in detail by the curator while adding these
ontology associations in the gene entry. In subsequent steps these IC may be
replaced by a different code and a citation. Sometimes it is required that an
association is deleted in the protein entry. In such case it is automatically
deleted from the gene entry, except in the case(s) where multiple proteins map
to a single gene and one of them still has this association. The curator is
prompted to delete that if applicable in the given protein entry first to
delete it altogether from the gene. Alternatively if the association is first
deleted in the gene entry, then the same term association found in the protein
entry(ies), gets this reference as an evidence and the evidence code NOT
(invalid/not applicable). If there is a NOT code the curator is alerted to
cross check the protein entry for deletion/updating the associations.
Currently the gene entry provides and overview of the genetic/sequenced locus,
where as the proteins are more germplasm/stock/allele centric. Other
significant references on this topic include GR_ref-ID: 8030 and 8210.