ZFIN December 2016: Difference between revisions

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Revision as of 19:23, 14 December 2016

Zebrafish Model Organism Database Summary, December 14, 2016



ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use. These data are checked in to the central GO Consortium repository on a weekly basis.


Name Position Type FTE for GO
Doug Howe Data Curation Manager
Principle GO contact at ZFIN
Sabrina Toro Curatorial
GO lead
6 Curators Curatorial Variable; ~0.1 each; 0.6 in aggregate
6 Technical 5 Developers, 1 DBA Variable; ~0.1 in aggregate

No direct funding from GOC NHGRI grant.

Annotation Progress

[[File:|ZFIN curation stats from X, 2015 to Y, 2016]]


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, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in focused annotation efforts such as those spearheaded by members of the GO consortium, or when we do "back curation" to find important uncharted data when we release new curation capabilities.

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 from function to process or component terms 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).

Priorities for annotation:

Our curation priority remains focused on keeping up with the current zebrafish literature, 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 focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.

Presentations and Publications

Ontology Development Contributions

Annotation Outreach and User Advocacy Efforts

Other Highlights

GAF files are currently checked into the GO SVN repository on a weekly basis. We rely largely on QC reports that come from the GO GAF validation steps after file check-in. We also have internal processes that monitor annotations for use of obsolete or secondary GO term usage in annotations. Sabrina Toro, a ZFIN curator, continues with the primary responsibility for weekly submission of our GAF and gp2protein files in consultation with Doug