TAIR, March 2009
TAIR, The Arabidopsis Information Resource, March 2009 / WORKING VERSION, NOT FINAL VERSION
1. Staff working on GOC tasks
Tanya Berardini, Donghui Li
The total number of FTE working on GOC tasks is 1.4.
2. Annotation progress
Table 1: Number of Annotations to Various GO Aspects ========TO BE UPDATED=====
|Annotations||BP (12/07)||BP (10/08)||change||MF (12/07)||MF (10/08)||change||CC (12/07)||CC (10/08)||change|
|non-IEA/non-ND||11038||13757||+ 2719||9048||9648||+ 600||5976||18281||+ 12305|
|IEA||6627||6584||- 43||5062||5575||+ 513||10334||8767||- 1567|
|ND||9062||8027||- 1035||2453||2267||- 186||8693||7302||- 1391|
Table 2: Number of Genes Annotated to Various GO Aspects
|Genes||BP (12/07)||BP (10/08)||change||MF (12/07)||MF (10/08)||change||CC (12/07)||CC (10/08)||change|
|non-IEA/non-ND||5897||6761||+ 864||6247||6575||+ 328||3787||6953||+ 3166|
|IEA||4516||4309||- 207||2833||2676||-157||8085||6904||- 1181|
|ND||8368||7973||- 395||2286||2219||- 67||8080||7268||- 812|
3. Methods and strategies for annotation
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. This represents roughly 5% of our annotation effort. We have also finally automated the processing and integration of 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.
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 - none
b. Presentations including Talks and Tutorials and Teaching - ???
c. Poster presentations - none
5. Other Highlights
A. Ontology Development Contributions
- GO terms contributed by TAIR TO BE UPDATED BY DONGHUI
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:
(1) 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
(2) regulation related SF items submitted by the GO community. Between April and September 2008, 63 such Sourceforge items closed.
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. 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)|
C. Other highlights - none