TAIR Progress Report for October 2008

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TAIR, The Arabidopsis Information Resource, October 2008

1. Staff working on GOC tasks

Tanya Berardini, Donghui Li

The total number of FTE working on GOC tasks is 1.5???.

2. Annotation progress

Tanya

3. Methods and strategies for annotation

Tanya

(please note % effort on literature curation vs. computational annotation methods) a. Literature curation:

b. Computational annotation strategies:

c. Priorities for annotation

4. Presentations and publications

a. Papers with substantial GO content

  • ?? Rhee SY, Wood V, Dolinski K, Draghici S. Nature Reviews Genetics 2008(7):509-15. Use and misuse of the gene ontology annotations.

b. Presentations including Talks and Tutorials and Teaching

  • Donghui Li, Functional annotation at TAIR, ASPB (American Society of Plant Biologists) Plant Biology Meeting, June 29 2008, Merida Mexico
  • xxxxxx, title, 19th International Conference on Arabidopsis Research, July 23 2008, Montreal Canada

c. Poster presentations - none

5. Other Highlights

A. Ontology Development Contributions

  • GO terms contributed by TAIR
  • Tanya please describe your contribution to 'regulates' etc
  • Contribution to PAMGO

Donghui Li contributed to the development of PAMGO, specifically the discussion involving programmed cell death. Manuscript: Manipulation of programmed cell death during host-symbiont associations (2008), Marcus C Chibucos, Candace W Collmer, Trudy Torto-Alalibo, Michelle Gwinn-Giglio, Magdalen Lindeberg, Donghui Li, Brett M Tyler.

B. Annotation outreach and user advocacy efforts

  • TAIR/Plant Physiology collaboration

A unique partnership has been formed between Plant Physiology and TAIR to create an efficient mechanism that will ensure that genetic and molecular data on Arabidopsis published in the Journal are reliably captured in TAIR’s public database. This collaboration - the first of its kind - provides authors with the ability to submit manuscripts to the Journal for publication and gene information to the TAIR database at the same time. Our annotation of Arabidopsis papers published in Plant Physiology has increased from 25% (2006 to 2007) to nearly 100% since May 2008. We hope this model can be extended to other journals, organisms, and databases. [Reference: Ort D, Grennan AK, Plant Physiology 2008 (146):1022-1023. Editorial: Plant Physiology and TAIR Partnership]

The following table summarizes the results of this collaboration so far:

Month Submitters Genes Submitted annotations Final GO annotations Final PO annotations Other data (alleles)
May-08 7 12 31 20 12
Jun-08 4 4 14 10 1
Jul-08 4 8 15 12 0
Aug-08 1 4 8 7 1
Sep-08 14 30 75 54 1 3
  • Talks

We presented talks on GO annotations at the following conferences:

1) ASPB (American Society of Plant Biologists) Plant Biology Meeting, June 29 2008, Merida Mexico

2) 19th International Conference on Arabidopsis Research, July 23 2008, Montreal Canada

C. Other highlights - none