TAIR Progress Report for October 2008: Difference between revisions

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?? Ort D, Grennan AK, Plant Physiology 2008 (146):1022-1023. Editorial: Plant Physiology and TAIR Partnership
?? Ort D, Grennan AK, Plant Physiology 2008 (146):1022-1023. Editorial: Plant Physiology and TAIR Partnership
?? Rhee SY, Wood V, Dolinski K, Draghici S. Nature Reviews Genetics 2008(7):509-15. Use and misuse of the gene ontology annotations.
?? Rhee SY, Wood V, Dolinski K, Draghici S. Nature Reviews Genetics 2008(7):509-15. Use and misuse of the gene ontology annotations.

Revision as of 11:04, 22 October 2008

TAIR, The Arabidopsis Information Resource, October 2008

Staff working on GOC tasks

Tanya Berardini, Donghui Li

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

Annotation progress since last report

Since April 2008, the following annotations have been added to TAIR

GO aspect Number of annotations added Number of genes update Number of publications used
Biological Process xxxx xxx xxx
Molecular Function xxxx xxx xxx
Cellular Component xxxx xxx xxx


The following table shows our progress in completing the genes selected for the Reference Genome Project

Month Number of Targets Number of Arabidopsis genes Number of genes completed Proportion
May xx xx xx xx%
June xx xx xx xx%
July xx xx xx xx%
August xx xx xx xx%
September xx xx xx xx%
October xx xx xx xx%
Total xx xx xx xx%

Methods and strategies for annotation

Other Highlights

Ontology Development Contributions


New Term Requests submitted by TAIR xx
Ontology changes submitted by TAIR xx

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 [Plant Physiology 146:1022-1023 (2008)]. 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.

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


Contribution to PAMGO

Donghui Li contributed to the development of PAMGO, specifically the discussion involving programmed cell death. He is the co-author of the following 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 Tyler1.

Annotation Outreach and User Advocacy Efforts

  • ASPB (American Society of Plant Biologists) Plant Biology Meeting, June 29 2008, Merida Mexico
  • 19th International Conference on Arabidopsis Research, July 23 2008, Montreal Canada

Publications

?? Ort D, Grennan AK, Plant Physiology 2008 (146):1022-1023. Editorial: Plant Physiology and TAIR Partnership

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