TAIR, March 2010

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TAIR, The Arabidopsis Information Resource, March 2010 (NOT FINAL, STILL IN PROGRESS)

covers the period from September 2009 to March 2010

1. Staff working on GOC tasks

Tanya Berardini, Donghui Li

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 (10/08) BP (09/09) change MF (10/08) MF (09/09) change CC (10/08) CC (09/09) change
non-IEA/non-ND 13757 15584 + 1827 9648 10392 + 744 18281 19175 + 894
IEA 6584 10776 + 4192 5575 20147 + 14572 8767 10490 + 1723
ND 8027 14327 + 6300 2267 8820 + 6553 7302 14519 + 7217

Table 2: Number of Genes Annotated to Various GO Aspects

Genes BP (10/08) BP (09/09) change MF (10/08) MF (09/09) change CC (10/08) CC (09/09) change
non-IEA/non-ND 6761 7263 + 502 6575 6904 + 329 6953 7333 + 380
IEA 4309 6857 + 2548 2676 8205 + 5529 6904 7806 + 902
ND 7973 14327 + 6354 2219 8819 + 6600 7268 14515 + 7247

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 integrated into our GO annotation file. This represents roughly 5% of our annotation effort. We integrate 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

Hill DP, Berardini TZ, Howe DG, Van Auken KM. (2009). Representing Ontogeny Through Ontology: A Developmental Biologist’s Guide to The Gene Ontology. Mol Reprod. Dev. 77(4):314-29.

Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. (2010). Cross-Product Extensions of the Gene Ontology. J. Biomed. Inform. doi:10.1016/j.jbi.2010.02.002

The Gene Ontology Consortium. (2010). The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 38:D331-5. (TB, corresponding author)

b. Presentations including Talks and Tutorials and Teaching

c. Poster presentations - none

5. Other Highlights

A. Ontology Development Contributions

  • GO terms contributed by TAIR

Donghui Li has submitted 101 SourceForge term requests on behalf of TAIR curators from October 2008 to September 2009 (each request may contain multiple terms). Of these 101 requests, 99 have been closed. 122 new GO terms have been created.

Tanya Berardini coordinated the writing of the 2010 Nucleic Acids Research Database Issue paper for the consortium.

Tanya Berardini, working with David Hill of MGI, continues to work on:

(1) quality control reports that are generated by OBOL and reasoner, both within OBO-Edit and in external scripts. This is an ongoing effort that we address as issues arise. [[1]]

(2) regulation related SF items submitted by the GO community.

(3) development specific ontology development. Both curators attended the Annual meeting of the American Society for Cell Biology. Ontology improvements from this meeting are detailed here [[2]]

B. Annotation outreach and user advocacy efforts

The TAIR-Plant Physiology collaboration continues to gather Arabidopsis gene function data directly from authors whose articles have just been accepted for publication. This partnership has resulted in direct author submission of function or expression information for 422 genes drawn from 104 articles published in Plant Physiology over the last 12 months (March 09 - February 10) (574 GO annotations and 35 PO annotations). We reevaluated the submission rate after last year's changes in the wording of the data request. Sampling one month's worth of papers, we found that the base submission rate had increased from 21% to about 50%.

We expanded our journal collaboration to include The Plant Journal in Fall 2009 and have received 2 submissions from Plant Journal containing function information for 3 genes (8 GO annotations and 3 PO annotations) since then.

We are currently in talks with editors and publishers from 6 additional journals: Journal of Integrative Plant Biology, Journal of Experimental Botany, Plant Science, Environmental Botany, Plant Physiology and Biochemistry, and Plant, Cell and Environment, to establish similar collaborations. At the same time, we are developing a web-based data submission tool that will be hosted by TAIR that can be used by authors from any journal and will accelerate the incorporation of this type of data into the TAIR database.

C. Other highlights - none