TAIR Mar 3 to June 5

IN PROGRESS

TAIR, The Arabidopsis Information Resource, June 2014

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

Table 1: Number of Annotations to Various GO Aspects

Annotations	BP (12/13)	BP (6/14)	change	MF (12/13)	MF (6/14)	change	CC (12/13)	CC (6/14)	change
non-IEA/non-ND	57816	58041	+ 225	13649	13991	+ 342	55665	55738	+ 73
IEA	17665	17373	- 292	34239	33997	- 242	7200	7191	- 9
ND	9206	9191	- 15	5199	5197	- 2	4471	4467	- 4

Table 2: Number of Genes Annotated to Various GO Aspects

Genes	BP (12/13)	BP (6/14)	change	MF (12/13)	MF (6/14)	change	CC (12/13)	CC (6/14)	change
non-IEA/non-ND	13335	13363	+ 28	7805	7825	+ 20	23723	23728	+ 5
IEA	10038	9929	- 109	12602	12495	- 107	4404	4399	- 5
ND	9206	9191	- 15	5199	5197	- 2	4471	4467	- 4

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 continue to work 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
 4. user requested annotations

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

None.

Talks - GO-related but not primarily about GO

None.

5. Other Highlights

A. Ontology Development Contributions

• GO terms contributed by TAIR

Tanya Berardini and Donghui Li have created 40 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: 03/03/14 - 06/05/14).

• 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 Noctua prototyping and modeling
• participates in the rota for GO Sourceforge requests (5 total people in rota, one week at a time, weekly conference call)
• participates in the rota for the gatekeeper for the TermGenie requests (5 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
• 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
• contributed to the development of PAINT SOP and user guide http://gocwiki.geneontology.org/index.php/PAINT_SOP
• testing and improvement (debugging, feature request) of PAINT tool
• curated six PANTHER 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 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.

TAIR took on management of the JIRA system for the GO helpdesk on June 25, 2013. All gohelp questions are now handled through jira.geneontology.org.

C. Other highlights

Donghui Li continues to serve as a member of the BioCreative User Advisory Group and an organizer for the GO task for BioCreative IV (2013). 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. Currently a paper is being written to present the results for this task.