TAIR Progress Report for October 2008: Difference between revisions
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Tanya Berardini, Donghui Li | Tanya Berardini, Donghui Li | ||
The total number of FTE working on GOC tasks is 1.5 | The total number of FTE working on GOC tasks is 1.5. | ||
=== 2. Annotation progress === | === 2. Annotation progress === | ||
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(please note % effort on literature curation vs. computational annotation methods) | (please note % effort on literature curation vs. computational annotation methods) | ||
a. Literature curation: | a. Literature curation: We continue to put most of our effort (95%) into annotation of gene products from the literature. | ||
b. Computational annotation strategies: | b. Computational annotation strategies: With every genome release, we rerun two computational GO annotation pipelines, one based on INTERPROtoGO mapping and the other based on a TargetP analysis. These results are intergrated into our GO annotation file. | ||
c. Priorities for annotation | c. Priorities for annotation: (1) literature of any age pertaining to Reference Genome genes, (2) literature describing the characterization of previously undescribed ('novel') genes, (3) recent literature from high impact factor journals | ||
=== 4. Presentations and publications === | === 4. Presentations and publications === | ||
a. Papers with substantial GO content | a. Papers with substantial GO content | ||
* | * Rhee SY, Wood V, Dolinski K, Draghici S. Nature Reviews Genetics 2008(7):509-15. Use and misuse of the gene ontology annotations. | ||
b. Presentations including Talks and Tutorials and Teaching | b. Presentations including Talks and Tutorials and Teaching | ||
* Donghui Li, Functional annotation at TAIR, ASPB (American Society of Plant Biologists) Plant Biology Meeting, June 29 2008, Merida Mexico | * Donghui Li, Functional annotation at TAIR, ASPB (American Society of Plant Biologists) Plant Biology Meeting, June 29 2008, Merida Mexico | ||
* | * Debbie Alexander, Functional Annotation at TAIR, 19th International Conference on Arabidopsis Research, July 23 2008, Montreal Canada | ||
c. Poster presentations - none | c. Poster presentations - none | ||
| Line 38: | Line 38: | ||
* '''GO terms contributed by TAIR''' | * '''GO terms contributed by TAIR''' | ||
We have submitted 48 SourceForge term requests from May to October 2008 (each request may contain multiple terms). Of these 48 requests, 44 have been closed. 43 new GO terms have been created. | We have submitted 48 SourceForge term requests from May to October 2008 (each request may contain multiple terms). Of these 48 requests, 44 have been closed. 43 new GO terms have been created. | ||
Tanya Berardini, working with David Hill of MGI, addressed regulation related Sourceforge items. | |||
* Worked with David Hill to address quality control reports that can now be generated due to the use of the reasoner and sparked by the implementation of the regulates relationship. This is an ongoing effort that we address as issues arise. http://wiki.geneontology.org/index.php/Ontology_Quality_Control#External_reasoner-based_checks | |||
* '''Contribution to PAMGO''' | * '''Contribution to PAMGO''' | ||
Donghui Li contributed to the development of PAMGO, specifically the discussion involving programmed cell death. Manuscript: Manipulation of programmed cell death during host-symbiont associations (2008), Marcus C Chibucos, Candace W Collmer, Trudy Torto-Alalibo, Michelle Gwinn-Giglio, Magdalen Lindeberg, Donghui Li, Brett M Tyler. | Donghui Li contributed to the development of PAMGO, specifically the discussion involving programmed cell death. Manuscript: Manipulation of programmed cell death during host-symbiont associations (2008), Marcus C Chibucos, Candace W Collmer, Trudy Torto-Alalibo, Michelle Gwinn-Giglio, Magdalen Lindeberg, Donghui Li, Brett M Tyler. | ||
Revision as of 17:06, 3 November 2008
TAIR, The Arabidopsis Information Resource, October 2008
1. Staff working on GOC tasks
Tanya Berardini, Donghui Li
The total number of FTE working on GOC tasks is 1.5.
2. Annotation progress
Tanya
3. Methods and strategies for annotation
Tanya
(please note % effort on literature curation vs. computational annotation methods) a. Literature curation: We continue to put most of our effort (95%) into annotation of gene products from the literature.
b. Computational annotation strategies: With every genome release, we rerun two computational GO annotation pipelines, one based on INTERPROtoGO mapping and the other based on a TargetP analysis. These results are intergrated into our GO annotation file.
c. Priorities for annotation: (1) literature of any age pertaining to Reference Genome genes, (2) literature describing the characterization of previously undescribed ('novel') genes, (3) recent literature from high impact factor journals
4. Presentations and publications
a. Papers with substantial GO content
- Rhee SY, Wood V, Dolinski K, Draghici S. Nature Reviews Genetics 2008(7):509-15. Use and misuse of the gene ontology annotations.
b. Presentations including Talks and Tutorials and Teaching
- Donghui Li, Functional annotation at TAIR, ASPB (American Society of Plant Biologists) Plant Biology Meeting, June 29 2008, Merida Mexico
- Debbie Alexander, Functional Annotation at TAIR, 19th International Conference on Arabidopsis Research, July 23 2008, Montreal Canada
c. Poster presentations - none
5. Other Highlights
A. Ontology Development Contributions
- GO terms contributed by TAIR
We have submitted 48 SourceForge term requests from May to October 2008 (each request may contain multiple terms). Of these 48 requests, 44 have been closed. 43 new GO terms have been created.
Tanya Berardini, working with David Hill of MGI, addressed regulation related Sourceforge items.
- Worked with David Hill to address quality control reports that can now be generated due to the use of the reasoner and sparked by the implementation of the regulates relationship. This is an ongoing effort that we address as issues arise. http://wiki.geneontology.org/index.php/Ontology_Quality_Control#External_reasoner-based_checks
- Contribution to PAMGO
Donghui Li contributed to the development of PAMGO, specifically the discussion involving programmed cell death. Manuscript: Manipulation of programmed cell death during host-symbiont associations (2008), Marcus C Chibucos, Candace W Collmer, Trudy Torto-Alalibo, Michelle Gwinn-Giglio, Magdalen Lindeberg, Donghui Li, Brett M Tyler.
B. Annotation outreach and user advocacy efforts
- TAIR/Plant Physiology collaboration
A unique partnership has been formed between Plant Physiology and TAIR to create an efficient mechanism that will ensure that genetic and molecular data on Arabidopsis published in the Journal are reliably captured in TAIR’s public database. This collaboration - the first of its kind - provides authors with the ability to submit manuscripts to the Journal for publication and gene information to the TAIR database at the same time. Our annotation of Arabidopsis papers published in Plant Physiology has increased from 25% (2006 to 2007) to nearly 100% since May 2008 (?????appropriate or not). We hope this model can be extended to other journals, organisms, and databases. [Reference: Ort D, Grennan AK, Plant Physiology 2008 (146):1022-1023. Editorial: Plant Physiology and TAIR Partnership]
The following table summarizes the results of this collaboration so far:
| Month | Submitters | Genes | Submitted annotations | Final GO annotations | Final PO annotations | Other data (alleles) |
|---|---|---|---|---|---|---|
| May-08 | 7 | 12 | 31 | 20 | 12 | |
| Jun-08 | 4 | 4 | 14 | 10 | 1 | |
| Jul-08 | 4 | 8 | 15 | 12 | 0 | |
| Aug-08 | 1 | 4 | 8 | 7 | 1 | |
| Sep-08 | 14 | 30 | 75 | 54 | 1 | 3 |
- Talks
We presented talks on GO annotations at the following conferences:
1) ASPB (American Society of Plant Biologists) Plant Biology Meeting, June 29 2008, Merida Mexico
2) 19th International Conference on Arabidopsis Research, July 23 2008, Montreal Canada
C. Other highlights - none