Difference between revisions of "ZFIN December 2010"

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[[Category:ZFIN]] [[Category:Reports]]
1. Staff:
1. Staff:

Revision as of 18:29, 16 July 2014

1. Staff:

   Doug Howe (Principle GO Curator)
   Ceri Van Slyke
   Sridhar Ramachandran
   Ken Frazer
   Amy Singer
   Yvonne Bradford
   Leyla Bayraktaroglu
   Barbara Ruef
   Dave Fashena
   Sierra Moxon
   Brock Sprunger
   Xiang Shao
   Prita Ramachandran
   Kevin Schaper
   Nathan Dunn
   Christian Pich
   Tom Conlin
   As lead GO curator, Doug spends ~0.75FTE on GOC tasks including literature curation, Ref Genome curation and related work, ontology development, meetings, community support, etc. 
   Other curators are primarily involved through GO curation and commit ~0.05-0.10FTE of their time to GO as a routine part of literature curation.
   Technical staff and DBAs are invoked on an ad hoc basis as needed to support GO activities.  This probably averages out to about 0.1FTE total over the course of the year.
   Total FTE committed by ZFIN to GOC related activities : ~1.5FTE 
   (0FTE funded by GOC grant)

2. Annotation Progress

ZFIN GO STATS as of November 14, 2010
Annotation Type Dec. 6, 2009 Nov. 14, 2010 Change % Change
Number of genes with at least one GO annotation of any kind
Number of Genes with manual annotation
Number of genes with IEA annotation

3. Methods and strategies for annotation (please note % effort on literature curation vs. computational annotation methods)

a. Literature curation:

       We generally use ~10% of our curation time making GO annotations from the literature.  Close to 0% is spent on computational methods currently.

b. Computational annotation strategies:

       We populate our database with ec2go, interpro2go, and spkw2go translations once per month during our UniProt load process.  We use no other computational annotation approaches. 

c. Priorities for annotation:

       Priority is placed on manual curation of the current literature.  Doug also curates older papers as required for the Reference Genomes project.

4. Presentations and Publications with substantial GO content

       LePendu P, Dou D, Howe, D 2009 Detecting Inconsistencies in the Gene Ontology Using Ontology Databases with Not-gadgets.  
       Lecture Notes in Computer Science 5871:948-965
          DOI: 10.1007/978-3-642-05151-7_15
       Su, AI and Howe, DG (2010) Mining the Gene Wiki to Prioritize Literature Curation Efforts. FWCS 2010

5, Other Highlights:

A. Ontology Development Contributions:

  Participated in the heart and renal development ontology development meetings.  
  Made regular contributions of SourceForge requesting new terms or ontology corrections.

B. Other Highlights:

-The ZFIN GAF file is now in GAF2.0 format

-ZFIN now has a generic structure in place in our schema and we have begun using it primarily in our curation interface. This will allow us to provide more sophisticated and ontologically aware query results in the future.

-The ability to import externally supplied GAF files into the ZFIN database is in our project que. Completion in the first quarter of 2011 is realistic. This will allow the import of any externally supplied GAF2.0 file, including those from PAINT, UniProt curators, Chris's Function->Process links file and any other external GAF2.0 source.