TAIR, September 2009

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TAIR, The Arabidopsis Information Resource, September 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 (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 - none

b. Presentations including Talks and Tutorials and Teaching

Kate Dreher, Extracting Information from Scientific Papers: Challenges and Opportunities for Researchers and Curators. June 2009. Carnegie Institution, Stanford CA

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, 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]]

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 (going 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.

C. Other highlights - none