TAIR Progress Report December 2008

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TAIR, The Arabidopsis Information Resource, December 2008

1. Staff working on GOC tasks

Tanya Berardini, Donghui Li, Eva Huala

The total number of FTE working on GOC tasks is 1.4.

2. Annotation progress

Table 1: Number of Annotations to Various GO Aspects

Annotations BP (12/07) BP (12/08) change MF (12/07) MF (12/08) change CC (12/07) CC (12/08) change
non-IEA/non-ND 11038 14038 + 3000 9048 9723 + 675 5976 18360 + 12384
IEA 6627 6561 - 66 5062 5572 + 510 10334 8760 - 1574
ND 9062 8013 - 1049 2453 2264 - 189 8693 7285 - 1408

Table 2: Number of Genes Annotated to Various GO Aspects

Genes BP (12/07) BP (12/08) change MF (12/07) MF (12/08) change CC (12/07) CC (12/08) change
non-IEA/non-ND 5897 6831 + 934 6247 6610 + 363 3787 6996 + 3209
IEA 4516 4296 - 220 2833 2674 -159 8085 6898 - 1187
ND 8368 7960 - 408 2286 2217 - 69 8080 7252 - 828

3. Methods and strategies for annotation

a. Literature curation: We continue to put most of our effort (95%) into annotation of gene products from the literature.

b. Computational annotation strategies: With every genome release, we rerun two computational GO annotation pipelines, one based on INTERPROtoGO mapping and the other based on a TargetP analysis. These results are intergrated into our GO annotation file. This represents roughly 5% of our annotation effort. We have also finally automated the processing and integration of GOA Arabidopsis GO annotations into our gene association file so that all Arabidopsis annotations, regardless of original source, are now relayed to GO via TAIR with the appropriate source attribution.

c. Priorities for annotation:

(1) literature of any age pertaining to Reference Genome genes,

(2) literature describing the characterization of previously undescribed ('novel') genes,

(3) recent literature from high impact factor journals

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
  • Debbie Alexander, Functional Annotation at TAIR, 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

We have submitted 75 SourceForge term requests from December 1, 2007 to November 30, 2008 (each request may contain multiple terms). Of these 75 requests, 70 have been closed. 74 new GO terms have been created.

Tanya Berardini, working with David Hill of MGI, addressed:

(1) quality control reports that can now be generated due to the use of the reasoner and sparked by the implementation of the regulates relationship. This is an ongoing effort that we address as issues arise. http://wiki.geneontology.org/index.php/Ontology_Quality_Control#External_reasoner-based_checks

(2) regulation related SF items submitted by the GO community. Between Dec. 2007 and November 2008, 124 such Sourceforge items were closed.

  • 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. 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
Oct-08 4 7 23 17 0
Nov-08 3 9 16 20 1


C. Other highlights - none