TAIR December 2017

From GO Wiki
Jump to navigation Jump to search

TAIR, The Arabidopsis Information Resource, December 2017

1. Staff working on GOC tasks

Tanya Berardini, Leonore Reiser (Donghui Li left the project in July 2017)

TAIR no longer receives GO funding (ended Feb. 28, 2017).

2. Annotation progress

Dates of query are 12/16 = 12/31/2016 and 12/17 = 12/22/2017.

Table 1: Number of Annotations to Various GO Aspects

Annotations BP (12/17) BP (12/16) change MF (12/17) MF (12/16) change CC (12/17) CC (12/16) change
non-IEA/non-ND 24546 23902 + 644 16197 15707 + 490 57194 56832 + 362
IEA 5591 5441 + 150 7848 8603 - 755 1045 966 + 79
ND 7708 7921 - 213 4645 4753 - 108 4036 4053 - 17

Table 2: Number of Genes Annotated to Various GO Aspects

Genes BP (12/17) BP (12/16) change MF (12/17) MF (12/16) change CC (12/17) CC (12/16) change
non-IEA/non-ND 9862 9646 + 216 8604 8417 + 187 23557 23529 + 28
IEA 4876 4785 + 91 5897 66112 - 639 972 899 + 73
ND 7708 7921 - 231 4645 4753 - 108 4036 4053 - 17

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 GOC
 5. Function-Process link-based annotations from GOC 
 6. IEA annotations based on various methods from the GOA group
 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)

 TAIR curators 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

Publications - GO-related but not primarily about GO

Reiser L, Subramaniam S, Li D, Huala E. Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes. Curr Protoc Bioinformatics. 2017 Dec 8;60:1.11.1-1.11.45. doi: 10.1002/cpbi.36.

Talks - GO-related but not primarily about GO

Eva Huala and Shabari Subramaniam, New Tools and Data at TAIR, 2017 International Conference on Arabidopsis Research (ICAR), St. Louis, MO

Leonore Reiser, The Arabidopsis Information Resource: A curated reference resource for translational plant biology. 2017 Annual Meeting of the American Society for Plant Biology (ASPB), Honolulu, HI

Tanya Berardini and Leonore Reiser, Introduction to TAIR Resources, Workshop sponsored by Stanford University Science library, November 2017. Stanford, CA

5. Other Highlights

A. Ontology Development Contributions

  • GO terms contributed by TAIR

Tanya Berardini created 12 new GO terms using Protege (id: GO:0090730 through id: GO:0090741) and 8 new GO terms through TermGenie before that service was discontinued.

  • Other ontology development work

Tanya Berardini:

  • participated in the rota for GitHub requests until the end of Feb. 2017
  • participated in the rota for the gatekeeper for the TermGenie requests until the end of Feb. 2017
  • attends weekly GO editors conference call
  • attends biweekly GO annotation conference calls
  • participates in the Protein Complexes Working Group conference calls
  • attended the GO Ontology Editing workshop in Berkeley in August 2017

B. Annotation outreach and user advocacy efforts

Tanya Berardini performs QC review of TAIR annotations as issues with particular terms or evidence codes are brought up by the consortium.

  • 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 participated in manning the GO helpdesk for one week each in January 2017. 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