TAIR December 2016

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TAIR, The Arabidopsis Information Resource, December 2016

1. Staff working on GOC tasks

Tanya Berardini (0.35 FTE), Donghui Li (0.3 FTE), Leonore Reiser (0.5 FTE)

The total number of FTE working on GOC tasks is 1.15.

2. Annotation progress

Dates of query are 12/15 = 12/31/2015 and 12/16 = 12/31/2016.

Table 1: Number of Annotations to Various GO Aspects

Annotations BP (12/15) BP (12/16) change MF (12/15) MF (12/16) change CC (12/15) CC (12/16) change
non-IEA/non-ND 22786 23902 + 1116 14584 15707 + 1123 56339 56832 + 493
IEA 5689 5441 - 248 9236 8603 - 633 1354 966 - 388
ND 8106 7921 - 185 4861 4753 - 108 4065 4053 - 12

Table 2: Number of Genes Annotated to Various GO Aspects

Genes BP (12/15) BP (12/16) change MF (12/15) MF (12/16) change CC (12/15) CC (12/16) change
non-IEA/non-ND 9730 9646 - 84 8020 8417 + 397 23782 23810 + 28
IEA 4593 4785 - 192 6574 66112 - 38 1224 899 - 325
ND 8106 7921 - 185 4861 4753 - 108 4065 4053 - 12

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. 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. INTERPRO2GO-based IEA annotations from UniProtKB
 7. TIGR's annotations from Arabidopsis functional annotation project

c. 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
 4. user requested annotation requests

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

 Donghui, Leonore, 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 2016 Publications, Talks, Posters

Publications - GO-related but not primarily about GO

Reiser L, Berardini TZ, Li D, Muller R, Strait EM, Li Q, Mezheritsky Y, Vetushko A, Huala E. Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model. Database (Oxford). 2016 Mar 17;2016. pii: baw018. doi: 10.1093/database/baw018.

Talks - GO-related but not primarily about GO

Donghui Li, TAIR: A Sustainable Community Resource for Arabidopsis Research, International Conference on Arabidopsis Research (ICAR 2016), GyeongJu, Korea

Tanya Berardini, Using biological ontologies to accelerate progress in plant biology research, ASPB Plant Biology Annual Meeting, 2016, Minneapolis, MN

5. Other Highlights

A. Ontology Development Contributions

  • GO terms contributed by TAIR

Tanya Berardini created 102 new GO terms using TermGenie and Obo-Edit (search GO flat file by 'created_by: tanyaberardini', 'created_by: tb', date range: 1/1/16 - 12/31/16).

  • Other ontology development work

Tanya Berardini:

  • participates in the rota for GitHub (formerly 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 (4 total people in rota, one week at a time)
  • attends weekly GO editors conference call
  • attends biweekly GO annotation conference calls

B. Annotation outreach and user advocacy efforts

  • PAINT annotation

Donghui Li does PAINT-based annotation.

  • attends PAINT annotation conference calls
  • curated 40 families.
  • 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 and Donghui Li 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 several GOC curators that rotate this task, one week at a time.

C. Other highlights