TAIR December 2010: Difference between revisions

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[[Publications,_Talks,_Posters_2010-]]
[[Publications,_Talks,_Posters_2010-]]
Donghui Li, Accessing GO annotations from TAIR, 21st International Conference on Arabidopsis Research, June 06-10, 2010. Yokohama, Japan


=== 5. Other Highlights ===
=== 5. Other Highlights ===

Revision as of 18:43, 30 November 2010

TAIR, The Arabidopsis Information Resource, December 2010

IN PROGRESS, NUMBERS ARE NOT VALID

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 (12/10) BP (12/09) change MF (12/10) MF (12/09) change CC (12/10) CC (12/09) change
non-IEA/non-ND 17690 15868 + 1822 11219 10603 + 616 19841 19209 + 632
IEA 12095 10688 + 1407 19293 19934 - 641 10505 10452 + 53
ND 9875 14284 - 4409 5060 8813 - 3753 10237 14501 - 4264

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 run 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

Publications,_Talks,_Posters_2010-

5. Other Highlights

A. Ontology Development Contributions

  • GO terms contributed by TAIR

Donghui Li has submitted 58 SourceForge term requests on behalf of TAIR curators from December 2009 to December 2010 (each request may contain multiple terms). Of these 58 requests, 52 have been closed. 56 new GO terms have been created.

  • Other ontology development work

Tanya Berardini:

  • worked on a team with David Hill, Chris Mungall, Midori Harris and Jane Lomax to develop cross-products within and among the three GO namespaces
  • worked on a team with David Hill, Harold Drabkin, Chris Mungall, Midori Harris, Jane Lomax and ChEBI curators to align GO with ChEBI. This will result in the first set of cross-products with GO and an external ontology.
  • continues to work with Chris Mungall and David Hill on inter-ontology links within GO.
  • acts as the gatekeeper for the TermGenie requests, merging and committing these into the main ontology using the scripts written by Chris Mungall,

B. Annotation outreach and user advocacy efforts

  • TAIR/Journal collaboration

The collaboration to collect functional information about Arabidopsis genes from authors at the time of submission has expanded from Plant Physiology to include nine other journals (Plant Cell, The Plant Journal, Molecular Plant, Journal of Experimental Botany, Plant Science, Plant, Cell and Environment, Environmental Botany, Plant Physiology and Biochemistry, and the Journal of Integrative Plant Biology). We have also developed and released an online data submission tool for collecting structured annotations to GO and PO terms. The URL for this tool is:

TAIR Online Submission Tool

TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID.


  • 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 9 GOC curators that rotate this task, one week at a time.


C. Other highlights - none