TAIR December 2015

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TAIR, The Arabidopsis Information Resource, December 2015

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

In October 2015, we dropped about 37K RCA annotations from a single 2012 paper that we deemed out of date and that many community members had criticized as unreliable. This adversely affects many of the numbers shown below and the increase in experimentally based annotations is masked to some degree. Going forward, it may be more useful to show and compare the number of experimentally based annotations (IDA, IGI, IPI, IMP, IEP) as a better measure of literature based curation.

Dates are 12/15 = 12/31/2015 and 12/14 = 12/09/14.

Table 1: Number of Annotations to Various GO Aspects

Annotations BP (12/15) BP (12/14) change MF (12/15) MF (12/14) change CC (12/15) CC (12/14) change
non-IEA/non-ND 22786 58326 - 35540 14584 14098 + 486 56339 55941 + 398
IEA 5689 17211 - 11522 9236 33757 -24521 1354 7158 -5804
ND 8106 9176 - 1070 4861 5193 - 332 4065 4452 - 387

Table 2: Number of Genes Annotated to Various GO Aspects

Genes BP (12/15) BP (12/14) change MF (12/15) MF (12/14) change CC (12/15) CC (12/14) change
non-IEA/non-ND 9730 13406 -4036 8020 7870 + 150 23782 23756 + 26
IEA 4593 9840 - 5247 6574 12434 - 5860 1224 4379 - 3152
ND 8106 9176 - 1070 4861 5193 - 332 4065 4452 - 387

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. We have transitioned to incorporating UniProtKB's INTERPRO2GO-based IEA annotations on a monthly basis. This replaces our in-house pipeline for generating a similar dataset.

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. INTERPRO2GO-based IEA annotations from UniProtKB
 7. 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
 4. user requested annotation requests

e. 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 2015 Publications, Talks, Posters

Publications - GO-related but not primarily about GO

Berardini TZ, Reiser L, Li D, Mezheritsky Y, Muller R, Strait E, Huala E. The Arabidopsis information resource: Making and mining the "gold standard" annotated reference plant genome. Genesis. 2015 Aug;53(8):474-85. doi: 10.1002/dvg.22877.

Talks - GO-related but not primarily about GO


5. Other Highlights

A. Ontology Development Contributions

  • GO terms contributed by TAIR

Tanya Berardini and Donghui Li have created 90 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: 1/1/2015 to 12/31/2015).

  • 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
  • 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
  • periodically attends biweekly GO annotation conference calls

Donghui Li:

  • attends GO annotation conference calls
  • 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
  • curated 43 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