TAIR December 2013

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Revision as of 13:53, 2 December 2013 by TanyaB (talk | contribs) (3. Methods and strategies for annotation)

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TAIR, The Arabidopsis Information Resource, December 2013

IN PROGRESS, NOT READY FOR PUBLIC CONSUMPTION

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

Dates are 11/11 = 11/03/2011 and 12/12 = 12/07/2012.

Table 1: Number of Annotations to Various GO Aspects

Annotations BP (11/11) BP (12/12) change MF (11/11) MF (12/12) change CC (11/11) CC (12/12) change
non-IEA/non-ND 19401 57626 + 38225* 12293 13268 + 975 24348 55265 + 30917**
IEA 11276 18361 + 7085 18479 34881 + 16402 8335 7331 - 1004
ND 9904 9268 - 636 5271 5217 - 54 9120 4480 - 4640

*including 36884 new RCA from Klaas Vandepoele - combined analysis PMID:22589469

**including 27917 new ISM from Rakesh Kaundal - AtSubP method applied to TAIR10 PMID:20647376


Table 2: Number of Genes Annotated to Various GO Aspects

Genes BP (11/11) BP (12/12) change MF (11/11) MF (12/12) change CC (11/11) CC (12/12) change
non-IEA/non-ND 8463 13256 + 4793 7410 7707 + 297 8661 23690 + 15029
IEA 6620 10337 + 3717 7672 12795 + 5123 6148 4475 - 1673
ND 9904 9268 - 636 5270 5217 - 53 9116 4480 - 4636

3. Methods and strategies for annotation

a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.

b. Computational annotation strategies: We have switched to using a new program for our cellular component IEA annotations. Instead of TargetP, we now use AtSubP. The analysis was run for TAIR by the author on the last Arabidopsis genome release, TAIR10. We are working on transitioning to using UniProtKB's IEA results for all other computational predictions to replace our aged Interpro2GO mapped ones.

c. Integration of non-TAIR Arabidopsis annotations: 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. The following types of annotations are included in our Arabidopsis gene association file:

 1. Literature-based annotations made by TAIR curators
 2. Community annotations made via TAIR's TOAST annotation tool (see below)
 3. GOA annotations for Arabidopsis with experimental evidence codes
 4. PAINT-based Arabidopsis annotations from RefGenome group
 5. Function-Process link-based annotations from GOC 
 6. TIGR's annotations from Arabidopsis functional annotation project

d. Priorities for annotation:

 1. literature describing the characterization of previously undescribed ('novel') genes, 
 2. genes that do not have any GO annotations at all (none of the three aspects),
 3. recent literature from high impact factor journals

e. Review of user-submitted annotations (see TOAST section below)

 Donghui and Tanya review the annotations submitted via TOAST, 
 making sure that terms were mapped correctly and that the proper 
 evidence_with information is entered, if necessary.  Sometimes, 
 follow-up with the submitter via email is necessary.

4. Presentations and publications

GO 2013 Publications, Talks, Posters

Publications - GO-related but not primarily about GO

ANYTHING NEW?

Talks - GO-related but not primarily about GO

ANYTHING NEW?

5. Other Highlights

A. Ontology Development Contributions

  • GO terms contributed by TAIR
EDIT PLEASE

Donghui Li has submitted term requests involving 46 GO terms via SourceForge and TermGenie on behalf of TAIR curators from November 2011 to November 2012.

  • Other ontology development work

Tanya Berardini:

  • continues to participate in creating cross-products for terms within and among the three GO namespaces
  • continues to participate in creation, testing, and deployment of new TermGenie templates for use by the broader community
  • participated in Modular Annotation prototyping and modeling
  • working on aligning the Plant Ontology (PO) with GO with respect to anatomical structures used in the development branch of the biological process ontology
  • participates in the rota for Sourceforge requests (6 total people in rota, one week at a time, weekly conference call)
  • participates in the rota for the gatekeeper for the TermGenie requests (6 total people in rota, one week at a time)
  • attends weekly GO editors conference call

Donghui Li:

  • attends regular GO annotation conference calls as the TAIR representative

B. Annotation outreach and user advocacy efforts

  • PAINT annotation

Donghui Li does PAINT-based annotation.

  • TOAST (TAIR Online Annotation Submission Tool)

TAIR continues to collect controlled vocabulary annotations via its online tool. TOAST

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


C. Other highlights

Donghui Li continues to serve as a member of the BioCreative User Advisory Group. This involves developing a GO task for BioCreative V (development of modules to aid GO curators in identifying articles with curatable GO information (triage) and extracting gene function terms and the associated evidence sentences in full-length articles) as well as a strategy to create a gold-standard annotated literature corpus for text mining.