ZFIN December 2012: Difference between revisions
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'''''Literature curation:''''' | '''''Literature curation:''''' | ||
We curate many data types from current publications, including GO. As such, our curators routinely curate GO from the new publications they are curating. The only real exception to that is when we participate in a focused annotation effort spearheaded by members of the GO consortium. During those efforts, Doug curates GO from any papers associated with genes in the set of genes being focused on for the project. | We curate many data types from current publications, including GO. As such, our curators routinely curate GO from the new publications they are curating. The only real exception to that is when we participate in a focused annotation effort spearheaded by members of the GO consortium. During those efforts, Doug curates GO from any papers associated with genes in the set of genes being focused on for the project. | ||
'''''Computational annotation strategies:''''' | '''''Computational annotation strategies:''''' | ||
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example) and the inferred annotations. | We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example) and the inferred annotations. | ||
'''''Priorities for annotation''''' | '''''Priorities for annotation:''''' | ||
Our curation priority remains on keeping up with the current zebrafish literature generally, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focussed annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation. | Our curation priority remains on keeping up with the current zebrafish literature generally, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focussed annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation. | ||
Revision as of 20:18, 11 December 2012
Zebrafish Model Organism Database Summary, December 2012
Overview
Staff:
Name | Position Type | FTE for GO |
---|---|---|
Doug Howe | Data Curation Manager Principle GO contact at ZFIN |
0.3 |
7 Curators | Curatorial | ~0.1 each; 0.7 in aggregate |
4 Technical | 3 Developers, 1 DBA | Variable; ~0.1 in aggregate |
Annotation Progress
ZFIN GO STATS as of December 2012
Methods and strategies for annotation
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.
Literature curation:
We curate many data types from current publications, including GO. As such, our curators routinely curate GO from the new publications they are curating. The only real exception to that is when we participate in a focused annotation effort spearheaded by members of the GO consortium. During those efforts, Doug curates GO from any papers associated with genes in the set of genes being focused on for the project.
Computational annotation strategies:
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example) and the inferred annotations.
Priorities for annotation:
Our curation priority remains on keeping up with the current zebrafish literature generally, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focussed annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.