Difference between revisions of "ZFIN December 2015"

From GO Wiki
Jump to navigation Jump to search
Line 52: Line 52:
= Ontology Development Contributions =
= Ontology Development Contributions =


Several term requests from Ceri:
response to sodium azide
cellular response to sodium azide
Researched and submitted request for terms related to "alarm substance" in teleost both via TermGenie and GO tracker. Requested template for development of structure.
GO TermGenie request for templates and new terms.  These are all pending.
https://github.com/geneontology/termgenie/issues/71#issuecomment-112330898
response to chondroitin 4'-sulfate
response to chondroitin 6'-sulfate
response to schreckstoff
GO term request:
https://github.com/geneontology/go-ontology/issues/12077


= Annotation Outreach and User Advocacy Efforts =
= Annotation Outreach and User Advocacy Efforts =

Revision as of 14:39, 6 October 2015

Zebrafish Model Organism Database Summary, September 30, 2015

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.

Staff:

Name Position Type FTE for GO
Doug Howe Data Curation Manager
Principle GO contact at ZFIN
0.2
9 Curators Curatorial ~0.1 each; 0.9 in aggregate
6 Technical 5 Developers, 1 DBA Variable; ~0.1 in aggregate


No direct funding from GOC NHGRI grant.

Annotation Progress

ZFIN curation stats from Dec 10, 2014 to Sept. 30, 2015

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 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 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

Several term requests from Ceri: response to sodium azide cellular response to sodium azide

Researched and submitted request for terms related to "alarm substance" in teleost both via TermGenie and GO tracker. Requested template for development of structure. GO TermGenie request for templates and new terms. These are all pending. https://github.com/geneontology/termgenie/issues/71#issuecomment-112330898 response to chondroitin 4'-sulfate response to chondroitin 6'-sulfate response to schreckstoff

GO term request: https://github.com/geneontology/go-ontology/issues/12077

Annotation Outreach and User Advocacy Efforts

Other Highlights

GAF file quality control is now routinely done via the OWL Tools scripts run as a job on the GO Jenkins. Sabrina Toro, a ZFIN curator, has now taken on primary responsibility for weekly submission of our GAF and gp2protein files in consultation with Doug.