WormBase Progress Report
Gene Ontology Consortium Meeting, September 26th-27th, 2003



1. Current GO Annotations in WormBase

           As of September 23, 2003:


                Total gene products annotated:                                      6909


                Total number of biological process terms:                           5096

                Total number of molecular function terms:                           5739

                Total number of cellular component terms:                           3040

                Total number of non-IEA annotations:                                2446
                Total number of IEA annotations:                                    4463



2. GO Curation at WormBase

           Manual, literature-based annotations are continuously added to WormBase
           to provide experimentally derived evidence for our GO term assignments.  


           Interpro-to-GO mappings (IEA) are updated bi-weekly. 


           GO term definitions are updated on our website bi-weekly.

           We are updating and automating RNAi-to-GO mappings that assign
           biological process terms based on RNAi mutant phenotypes. 
           Currently, there are 4,201 genes with RNAi phenotypes that could 
           be given an RNAi-to-GO mapping.  Our previous mapping provided
           GO terms for 1,306 genes; the update will now give us IMP-based 
           terms for an additional 2,895 genes.  This will expand RNAi-based 
           coverage to 22% of the genome.


           Reannotation of obsolete GO terms: 11 genes that had one or more
           obsoleted terms associated with them; these have been manually
           reannotated.  
           We have also replaced obsoleted terms from our first RNAi-to-GO                  
           mappings (i.e. embryogenesis and morphogenesis, histogenesis and 
           morphogenesis, cytokinesis); this replaced 1,093 lines of annotation. 



3. Other Areas of Interest      


            14th International C. elegans Meeting, UCLA, June 29-July 3, 2003
                 GO curation highlighted in:
                      Opening Plenary Session Talk (Keith Bradnam, Sanger Center)
                               and
                      Daily WormBase workshops. 


             Textpresso, An information retrieval and extraction system for C. elegans        
                 literature-Eimear Kenny



4. Future Plans

          WormBase has been awarded another five years of funding and with
          that, we are moving towards a more integrated curation process.  
          As a result, more curators will be entering GO annotations as part 
          of our ongoing gene function and cell and anatomy curation. 


          Within the next 1-2 months, we will be caught up on entering data
          from microarray experiments.  We plan to incorporate microarray-
          to-GO term mappings as part of this curation.


          One of our immediate goals is to incorporate a controlled vocabulary
          for describing mutant phenotypes.  This may lead to developing some
          new phenotype and/or behavioral terms.