ZFIN December 2017

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Zebrafish Model Organism Database Summary, December 12, 2017

Overview

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 made available to the central GO Consortium repository on a weekly basis.

Staff:

Name Position Type FTE for GO
Doug Howe Data Curation Manager
Principle GO contact at ZFIN
0.2
Sabrina Toro Curatorial
GO lead
0.2
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

GOC AnnualReport Stats 20171212.jpg


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 uncurated 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 and gp2protein files were generated and manually checked into the GO SVN repository on a weekly basis until March 2017. After that date, GAF files were made available for direct pull by GOC.

GPI files were generated and made available for direct pull by GOC.

Danio rerio annotations were reviewed and updated in the context of the Signaling project and in the context of ontology work.

Sabrina Toro took part in the Signaling project and attended the Signaling workshop in Cambridge in October, 2017.

Sabrina Toro attends the bimonthly annotation advocacy conference calls, as well as the bimonthly meetings on the development of the Noctua tool. Doug Howe and Sabrina Toro attended the GO meeting in Corvallis in June, 2017. ZFIN curators joined them for the subsequent Noctua workshop. Sabrina Toro attended the GO meeting in Cambridge in October, 2017.