Difference between revisions of "ZFIN Dec 5-March 11 - in progress"

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= Zebrafish Model Organism Database Summary, December  5, 2013 -March 10, 2014 =
= Zebrafish Model Organism Database Summary, December  5, 2013 -March 10, 2014 =
= Overview =
= Staff: =
= Staff: =
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Revision as of 12:43, 11 March 2014


Zebrafish Model Organism Database Summary, December 5, 2013 -March 10, 2014

Staff:

Name Position Type FTE for GO
Doug Howe Data Curation Manager
Principle GO contact at ZFIN
0.2
7 Curators Curatorial ~0.1 each; 0.7 in aggregate
4 Technical 3 Developers, 1 DBA Variable; ~0.1 in aggregate


No direct funding from GO.

Annotation Progress

--DATA COMING SOON--

Methods and strategies for annotation

ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of literature focusing first on new mutants, phenotypes, expression, and Human disease models from the current literature. We also generate literature sets for seminal papers from heavily published genes. 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. 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, we curate 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).


Priorities for annotation:

Our curation priority remains focused on keeping up with the current zebrafish literature generally, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We also curate papers from a list of the seminal publications associated with heavily published genes. 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

From zebrafish heart jogging genes to mouse and human orthologs: using Gene Ontology to investigate mammalian heart development. Varsha K Khodiyar, Doug Howe, Philippa J Talmud, Ross Breckenridge, Ruth C Lovering F1000

Ontology Development Contributions

Annotation Outreach and User Advocacy Efforts

Other Highlights