TAIR December 2010

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TAIR, The Arabidopsis Information Resource, December 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 (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 (12/10) BP (12/09) change MF (12/10) MF (12/09) change CC (12/10) CC (12/09) change
non-IEA/non-ND 7981 7385 + 533 7189 6988 + 201 7619 7378 + 241
IEA 6973 6807 + 166 7924 8135 - 211 7538 7783 - 245
ND 9875 14284 - 4409 5059 8812 - 3753 10233 14497 - 4264
  • Numbers of ND annotations/genes annotated decreased as annotations to pseudogenes and transposable element genes were removed after a QC check revealed that these existed.

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


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. Submitters must be registered at TAIR.

  • 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