TAIR December 2009

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TAIR, The Arabidopsis Information Resource, December 2009

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 (12/08) BP (12/09) change MF (12/08) MF (12/09) change CC (12/08) CC (12/09) change
non-IEA/non-ND 14038 15868 +1830 9723 10603 +880 18360 19209 +849
IEA 6561 10688 + 4127 5572 19934 + 14362 8760 10452 + 1692
ND 8013 14284 + 6271 2264 8813 + 6549 7285 14501 + 7216

Table 2: Number of Genes Annotated to Various GO Aspects

Genes BP (12/08) BP (12/09) change MF (12/08) MF (12/09) change CC (12/08) CC (12/09) change
non-IEA/non-ND 6831 7385 + 554 6610 6988 + 378 6996 7378 + 382
IEA 4296 6807 + 2311 2674 8135 + 5461 6898 7783 + 885
ND 7960 14284 + 6324 2217 8812 + 6595 7252 14497 + 7245

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

GO 2009 Publications, Tutorials & Workshops, Presentations, Posters, and Resources

5. Other Highlights

A. Ontology Development Contributions

  • GO terms contributed by TAIR

Donghui Li has submitted 95 SourceForge term requests on behalf of TAIR curators from December 2008 to December 2009 (each request may contain multiple terms). Of these 95 requests, 92 have been closed. 117 new GO terms have been created.

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 Society for Developmental Biology in San Francisco in July 2009. Ontology improvements from this meeting are detailed here [[2]]

(4) cell biology specific ontology development. Both curators attended the Annual meeting of the American Society for Cell Biology in San Diego in December 2009. As of 12/15/2009, over 100 terms have been added to the ontology and another 30 or so existing terms have been updated as a result of this meeting. There are still more terms to be added and areas of the ontology to be revisited. So far, areas touched have include COPII vesicle formation, sphingolipid metabolism, planar cell polarity establishment, cell migration, mitochondrial fission and intracellular cholesterol transport.

B. Annotation outreach and user advocacy efforts

  • TAIR/Plant Physiology collaboration

The collaboration to collect functional information about Arabidopsis genes from authors at the time of submission to Plant Phys continues. We have implemented an AJAX auto-complete feature in the webform [[3]] that suggests GO and PO terms pulled from the TAIR database.

  • TAIR/Plant Journal collaboration

We have also begun a new collaboration (live in September 2009) with The Plant Journal that is similar to that with Plant Physiology. In the case of TPJ, the authors are asked to fill in and submit a spreadsheet with the functional annotation. This file is considered supplemental data for TPJ and will be published with the article. The spreadsheets will be forwarded to TAIR from TPJ after the manuscripts have been accepted for publication. We received our first data submission in October 2009.

  • GO help

Tanya Berardini continues to participate in manning the GO helpdesk. This involves answering the questions that come in through gohelp@geneontology.org or forwarding them to the appropriate parties for response. There are 10 GOC curators that rotate this task, one week at a time.

C. Other highlights - none