Difference between revisions of "TAIR December 2013"

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== TAIR, The Arabidopsis Information Resource, December 2013 ==
 
== TAIR, The Arabidopsis Information Resource, December 2013 ==
 
<pre style="color: red">IN PROGRESS, NOT READY FOR PUBLIC CONSUMPTION</pre>
 
  
 
=== 1. Staff working on GOC tasks ===
 
=== 1. Staff working on GOC tasks ===
Line 7: Line 5:
 
Tanya Berardini, Donghui Li
 
Tanya Berardini, Donghui Li
  
The total number of FTE working on GOC tasks is 1.4.
+
The total number of FTE working on GOC tasks is 1.2.
  
 
=== 2. Annotation progress ===
 
=== 2. Annotation progress ===
  
  
Dates are 11/11 = 11/03/2011 and 12/12 = 12/07/2012.
+
Dates are 12/12 = 12/07/2012 and 12/13 = 12/02/13.
  
 
'''Table 1: Number of Annotations to Various GO Aspects'''
 
'''Table 1: Number of Annotations to Various GO Aspects'''
Line 19: Line 17:
 
|-
 
|-
 
! Annotations
 
! Annotations
! BP (11/11)
+
! BP (12/13)
 
! BP (12/12)
 
! BP (12/12)
 
! change
 
! change
! MF (11/11)
+
! MF (12/13)
 
! MF (12/12)
 
! MF (12/12)
 
! change
 
! change
! CC (11/11)
+
! CC (12/13)
 
! CC (12/12)
 
! CC (12/12)
 
! change
 
! change
 
|-
 
|-
| non-IEA/non-ND|| 19401 || 57626 ||+ 38225* ||12293 || 13268 ||+ 975 || 24348 || 55265  ||  + 30917** ||
+
| non-IEA/non-ND|| 57816 || 57626 ||+ 190 ||13649 || 13268 ||+ 381 || 55665 || 55265  ||  + 400 ||
 
|-
 
|-
| IEA || 11276 || 18361 || + 7085 || 18479 || 34881 || + 16402 || 8335 ||  7331 || - 1004 ||
+
| IEA || 17665 || 18361 || - 696  || 34239 || 34881 || - 642  || 7200 ||  7331 || - 131 ||
 
|-
 
|-
| ND || 9904 || 9268 || - 636 || 5271 || 5217 || - 54 || 9120 || 4480 || - 4640||
+
| ND || 9206 || 9268 || - 62 || 5199 || 5217 || - 18 || 4471 || 4480 || - 9||
  
 
|}
 
|}
 
<nowiki>*</nowiki>including 36884 new RCA from Klaas Vandepoele - combined analysis [http://www.ncbi.nlm.nih.gov/pubmed/22589469 PMID:22589469]
 
 
<nowiki>**</nowiki>including 27917 new ISM from Rakesh Kaundal - AtSubP method applied to TAIR10 [http://www.ncbi.nlm.nih.gov/pubmed/20647376 PMID:20647376]
 
  
  
Line 47: Line 41:
 
|-
 
|-
 
! Genes
 
! Genes
! BP (11/11)
+
! BP (12/13)
 
! BP (12/12)
 
! BP (12/12)
 
! change
 
! change
! MF (11/11)
+
! MF (12/13)
 
! MF (12/12)
 
! MF (12/12)
 
! change
 
! change
! CC (11/11)
+
! CC (12/13)
 
! CC (12/12)
 
! CC (12/12)
 
! change
 
! change
 
|-
 
|-
| non-IEA/non-ND|| 8463 || 13256|| + 4793 || 7410 || 7707 || + 297 || 8661 ||  23690 || + 15029 ||
+
| non-IEA/non-ND|| 13335 || 13256|| + 79 || 7805 || 7707 || + 98 || 23723 ||  23690 || +  33 ||
 
|-
 
|-
| IEA || 6620 || 10337 || + 3717 || 7672 || 12795 || + 5123 || 6148 ||  4475 || - 1673 ||
+
| IEA || 10038 || 10337 || - 299  || 12602 || 12795 || - 193  || 4404 ||  4475 || - 71  ||
 
|-
 
|-
| ND || 9904 || 9268 || - 636 || 5270 || 5217 || - 53 || 9116 || 4480 || - 4636||
+
| ND || 9206 || 9268 || - 62 || 5199 || 5217 || - 18 || 4471 || 4480 || - 9 ||
  
 
|}
 
|}
Line 69: Line 63:
 
a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.
 
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: With every genome release, we run two computational GO annotation pipelines, one based on INTERPROtoGO mapping and the other based on a TargetP analysisThese results are integrated into our GO annotation file. This represents roughly 5% of our annotation effort.  
+
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 [http://bioinfo3.noble.org/AtSubP/ AtSubP] with an ISM evidence code.  The analysis was run for TAIR by the author on the last Arabidopsis genome release, TAIR10We 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:  We integrate GOA Arabidopsis GO annotations into our gene association file so that all Arabidopsis annotations, regardless of original source, are now relayed to GO via TAIR with the appropriate source attribution. The following types of annotations are included in our Arabidopsis gene association file:
+
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
 
   1. Literature-based annotations made by TAIR curators
Line 87: Line 81:
  
 
e.      Review of user-submitted annotations (see TOAST section below)
 
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  
+
   Donghui and Tanya review the annotations submitted via TOAST,  
   proper evidence_with information is entered, if necessary.  Sometimes, follow-up with the submitter via email is necessary.
+
  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 ===
 
=== 4. Presentations and publications ===
[http://gocwiki.geneontology.org/index.php/Publications,_Talks,_Posters_2013- GO 2013 Publications, Talks, Posters]
+
[http://wiki.geneontology.org/index.php/Publications,_Talks,_Posters_2013 GO 2013 Publications, Talks, Posters]
  
 
'''Publications - GO-related but not primarily about GO'''
 
'''Publications - GO-related but not primarily about GO'''
  
<pre style="color: red">ANYTHING NEW?</pre>
+
None.
  
 
'''Talks - GO-related but not primarily about GO'''
 
'''Talks - GO-related but not primarily about GO'''
  
<pre style="color: red">ANYTHING NEW?</pre>
+
Donghui Li, GO task at BioCreative IV. April, 2013. Biocuration 2013. Cambridge, UK.
  
 
=== 5. Other Highlights ===
 
=== 5. Other Highlights ===
Line 105: Line 101:
 
'''A. Ontology Development Contributions'''
 
'''A. Ontology Development Contributions'''
 
* '''GO terms contributed by TAIR'''  
 
* '''GO terms contributed by TAIR'''  
 
+
Tanya Berardini and Donghui Li have created 145 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: 12/7/12 - 12/4/13).
<pre style="color: red">EDIT PLEASE</pre>
 
 
 
Donghui Li has submitted term requests involving 46 GO terms via SourceForge and TermGenie on behalf of TAIR curators from November 2011 to November 2012.
 
  
 
* '''Other ontology development work'''
 
* '''Other ontology development work'''
Line 123: Line 116:
 
Donghui Li:
 
Donghui Li:
 
*attends regular GO annotation conference calls as the TAIR representative
 
*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'''
 
'''B. Annotation outreach and user advocacy efforts'''
Line 128: Line 122:
 
* '''PAINT annotation'''
 
* '''PAINT annotation'''
 
Donghui Li does PAINT-based annotation.  
 
Donghui Li does PAINT-based annotation.  
 +
*attends regular PAINT annotation conference calls
 +
*participated in the PAINT workshop at Stanford (December 2012)
 +
*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 eight PANTHER families
  
 
* '''TOAST (TAIR Online Annotation Submission Tool)'''
 
* '''TOAST (TAIR Online Annotation Submission Tool)'''
Line 138: Line 137:
 
* '''GO help'''
 
* '''GO help'''
  
Tanya Berardini continues to participate in manning the GO helpdesk.  This involves answering the questions that come in through gohelp@geneontology.org or forwarding them to the appropriate parties for response.  There are 8 GOC curators that rotate this task, one week at a time.   
+
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.  There have been several large spam batches that have come through but the google spam filter has now caught up to them (uggs).
  
  
 
'''C. Other highlights'''
 
'''C. Other highlights'''
  
Donghui Li continues to serve as a member of the BioCreative User Advisory Group. 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.
+
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.
  
[[Category:Reports]]
+
[[Category:Reports - TAIR]]
[[Category:TAIR]]
 

Latest revision as of 15:19, 6 March 2020

TAIR, The Arabidopsis Information Resource, December 2013

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 12/12 = 12/07/2012 and 12/13 = 12/02/13.

Table 1: Number of Annotations to Various GO Aspects

Annotations BP (12/13) BP (12/12) change MF (12/13) MF (12/12) change CC (12/13) CC (12/12) change
non-IEA/non-ND 57816 57626 + 190 13649 13268 + 381 55665 55265 + 400
IEA 17665 18361 - 696 34239 34881 - 642 7200 7331 - 131
ND 9206 9268 - 62 5199 5217 - 18 4471 4480 - 9


Table 2: Number of Genes Annotated to Various GO Aspects

Genes BP (12/13) BP (12/12) change MF (12/13) MF (12/12) change CC (12/13) CC (12/12) change
non-IEA/non-ND 13335 13256 + 79 7805 7707 + 98 23723 23690 + 33
IEA 10038 10337 - 299 12602 12795 - 193 4404 4475 - 71
ND 9206 9268 - 62 5199 5217 - 18 4471 4480 - 9

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 2013 Publications, Talks, Posters

Publications - GO-related but not primarily about GO

None.

Talks - GO-related but not primarily about GO

Donghui Li, GO task at BioCreative IV. April, 2013. Biocuration 2013. Cambridge, UK.

5. Other Highlights

A. Ontology Development Contributions

  • GO terms contributed by TAIR

Tanya Berardini and Donghui Li have created 145 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: 12/7/12 - 12/4/13).

  • 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
  • working on aligning the Plant Ontology (PO) with GO with respect to anatomical structures used in the development branch of the biological process ontology
  • participates in the rota for Sourceforge requests (6 total people in rota, one week at a time, weekly conference call)
  • participates in the rota for the gatekeeper for the TermGenie requests (6 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
  • participated in the PAINT workshop at Stanford (December 2012)
  • 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 eight 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. There have been several large spam batches that have come through but the google spam filter has now caught up to them (uggs).


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.