Outreach October 2008 Report

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From Pascale, on an annotation outreach effort by Pascale, and Michael Ashburner to Swiss-Prot

Here's a summary of the 'outreach' efforts with Swiss-Prot:

  • Following a discussion that took place at the UniProt tripartite collaborative meeting in Washington DC, Amos Bairoch announced to the UniProt SAB, the intention of Swiss-Prot to start using GO in their annotation process. This was enthousiastically approved by the SAB.
  • I spent 3 days from Oct 6-8 where we did a number of things
  • I presented an overview of the GO to the entire group where I described the ontology (term structure, ontology structure), evidence codes, basic relationships (ie the existing ones), manual and electronic annotation process, annotating to the root, gene association file, AmiGO, maintenance of the GO, reference genomes and OBO.
  • We had a number of discussions with the leaders of the annotation groups where we discussed the actual process of annotation, files, who is responsible for which species, tools (I showed them the best I could --which is very limited-- the Protein2GO tool from SwissProt; we also discussed OBO-edit, QuickGO and AmiGO), how consortium meetings take place, creation of new terms and relationships (in the view that they already have a number of controlled vocabularies), making cross links to their vocabularies versus adding terms and relationships in the GO.
  • We also discussed the requirements for this to take place. They of course need information on using the GO and making annotations (Emily and Rachael have already offered to do that); also, they need to modify their software to capture the required information
  • Finally, we talked about their role in the consortium: when this is all in place, they will provide quite a large number of annotations covering many species that we are not covering with the MODs; this can be very useful for the ref genome project. In addition to annotations, as mentioned above, their controlled vocabularies and the expertise of their annotators can be used to improve the GO itself.
  • Time frame for this is from 9 to 12 months before they will start providing annotations.


Rachael Huntley of GO presented a talk "The Gene Ontology Annotation (GOA) Database: central resource for multi-species GO annotation" at the Eurofungbase meeting "Fungal Biology and Biotechnology in the Genomic Era" held in Feliu de Guixols, Spain. 22-24 October 2008. (possible new annotation group).