TAIR December 2014

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TAIR, The Arabidopsis Information Resource, December 2014

IN PROGRESS NOT YET COMPLETED

1. Staff working on GOC tasks

Tanya Berardini, Donghui Li

The total number of FTE working on GOC tasks is 1.2.

2. Annotation progress

Dates are 12/13 = 12/02/2013 and 12/14 = 12/9/14.

Table 1: Number of Annotations to Various GO Aspects

Annotations BP (12/13) BP (12/14) change MF (12/13) MF (12/14) change CC (12/13) CC (12/14) change
non-IEA/non-ND 57816 58326 + 510 13649 14098 + 449 55665 55941 + 276
IEA 17665 17211 - 454 34239 33757 - 482 7200 7158 - 42
ND 9206 9176 - 30 5199 5193 - 6 4471 4452 - 19


Table 2: Number of Genes Annotated to Various GO Aspects

Genes BP (12/13) BP (12/14) change MF (12/13) MF (12/14) change CC (12/13) CC (12/14) change
non-IEA/non-ND 13335 + 7805 + 23723 +
IEA 10038 - 12602 - 4404 -
ND 9206 - 5199 - 4471 -

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: Last year, we switched to using a new program for our cellular component IEA annotations. Instead of TargetP, we now use AtSubP with an ISM evidence code. 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: The following types of external 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 2014 Publications, Talks, Posters

Publications - GO-related but not primarily about GO

Li D, Dreher K, Knee E, Brkljacic J, Grotewold E, Berardini TZ, Lamesch P, Garcia-Hernandez M, Reiser L, Huala E (2014) Arabidopsis database and stock resources. Methods Mol Biol. 2014;1062:65-96. doi: 10.1007/978-1-62703-580-4_4. PMID: 24057361

Talks - GO-related but not primarily about GO

Donghui Li, TAIR: A Sustainable Community Database for International Arabidopsis Research. July 28, 2014. International Conference on Arabidopsis Research (ICAR), Vancouver, Canada.

5. Other Highlights

A. Ontology Development Contributions

  • GO terms contributed by TAIR

UPDATE Tanya Berardini and Donghui Li have created 108 new GO terms using TermGenie and Obo-Edit (search GO flat file by 'created_by: tanyaberardini', 'created_by: tb', 'created_by: dhl', 'created_by: donghui', date range: 12/5/13 - 12/9/14).

  • 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
  • participates in the rota for Sourceforge requests (4 total people in rota, one week at a time, biweekly conference call)
  • participates in the rota for the gatekeeper for the TermGenie requests (8 total people in rota, one week at a time)
  • attends weekly GO editors conference call
  • periodically attends biweekly GO annotation conference calls

Donghui Li:

  • attends regular GO annotation conference calls as the TAIR representative
  • continues to request and create GO terms related to Arabiodopsis and plants

B. Annotation outreach and user advocacy efforts

  • PAINT annotation

Donghui Li does PAINT-based annotation.

  • attends regular PAINT annotation conference calls
  • participated in the PAINT jamboree between July 1st and September 30th. Curated 38 families with a total of 2896 sequences.
  • 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 the gohelp email address or forwarding them to the appropriate parties for response. There are 8 GOC curators that rotate this task, one week at a time. Beginning in 2015, Donghui Li will participate in the GO helpdesk rota as well.

C. Other highlights