Difference between revisions of "WormBase December 2012"

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'''''Computational annotation strategies:'''''  
'''''Computational annotation strategies:'''''  


As always, current strategies involve use of translation table to mine SwissProt keywords, InterPro domains, and EC numbers for IEA annotation. These are performed automatically on a nightly basis and require little human intervention.
Our computational annotation strategies include mapping gene product to GO terms using InterPro domains, and  


'''''Priorities for annotation'''''
'''''Priorities for annotation'''''
Selection of genes for annotation was guided by several criteria, including the publication of newly characterized genes as well as pilot curation of genes involved in several different processes for LEGO-style annotation.





Revision as of 16:15, 13 December 2012

WormBase Summary, December 2012

Overview

WormBase has two main tasks. One is to work on Aim 4 (Common Annotation Framework), which is described under Software Group. The second is annotation. Most of our efforts over the past year were directed towards software development; remaining efforts were focused on annotation.

Staff:

WormBase

  • Paul Sternberg, PI
  • Juancarlos Chan, software developer
  • Ranjana Kishore, curator
  • Kimberly Van Auken, curator

Textpresso

  • Hans Michael Mueller, PI
  • James Done, software developer
  • Yuling Li, software developer


Annotation Progress

WormBase GO Annotation Statistics as of December 2012

Table 1: Number of Genes Annotated

Type of Annotation Genes Annotated, Dec 2012 % Change from Dec 2011 Number of Unique GO Terms % Change from 2011 Total Number of GO Terms % Change from Dec 2011
Manual Annotation 2,601 +9.93 2,310 +17.8 13392 +16.9
Phenotype2GO Mappings 6,423 +3.1 116 +0.87 44,256 +2.9
IEA/Electronic 13,739 +1.0 1,548 +3.4 55,091 -6.1
Total 16,493 +1.4 3,420 +4.8 106,604 +2.6


Methods and strategies for annotation

Literature curation:

Curation of the primary literature continues to be the major focus of our manual annotation efforts.

Computational annotation strategies:

Our computational annotation strategies include mapping gene product to GO terms using InterPro domains, and

Priorities for annotation

Selection of genes for annotation was guided by several criteria, including the publication of newly characterized genes as well as pilot curation of genes involved in several different processes for LEGO-style annotation.




Kimberely Van Auken is developing GO-CAT.

Ranjana Kishore particpated in the PAINT training workshop in December 2012.

Ranjana Kishore is working on evaluation of website usability.

Caltech hosted the GOC meeting in October 2012.

Back to Project Reports 2012