RefGenProgress 2009-07 (Archived)

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Reference genome paper is now published

The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. Reference Genome Group of the Gene Ontology Consortium. PLoS Comput Biol. 2009 Jul;5(7):e1000431. Epub 2009 Jul 3. PMID: 19578431 You should have a look at PLoS Computational Biology put authors as 'collaborators', so that although the author is 'Reference Genome Group of the Gene Ontology Consortium', it's indexed by author name in PubMed and you can click on collaborators to view all authors. :)

PAINT update

New software release (Aug 1, 2009), but work in progress allows curators to annotate to parents of terms with annotations. Also - paint now has flexible docking, proper gaf files, proper go hierarchy, some degree of speedup thanks to threading, annotation by dragging terms from the term tree onto the gene info, and highlighting of nodes that share annotations to terms (thanks for the suggestion pascale it really looks great doing this), negation, qualifiers, and more--including some known bugs.

Visualising PAINT annotations with GO nuts wiki

  • Pascale asked Jim to upload a GAF file from PAINT so that annotators from

MODs can see what annotations are being made and decide to upload them or not. (in progress)

Quest for Orthologs meeting

(Hinxton, UK, July 3-5). Pascale, Paul, Suzi, Mike, Judy attended. Included people form all the major orthology resources: In paranoid, OrthoMCL, Treefam, etc. We discussed to use the same protein sets, which will be a major step in comparing all the resources.

PPOD update

From Kara, July 24, 2009: We have just released new PPOD families based on the new protein sets assembled by Paul Thomas' group. Note that we also have run InParanoid/MultiParanoid this time around, in addition to OrthoMCL. We are in contact with Mary about re-generating her GO graphs for the new families, and we will add back those links when the graphs are available. One interface change note: the Functional Conservation info is now on a different page, rather than on the bottom of the family page as it was previously.

Electronic annotation jamboree: ETFDH and SLC11A1, SLC11A2


Lots of issues brought up:

ACTION ITEM: Improve definition of GO:0033539 fatty acid beta-oxidation using acyl-CoA dehydrogenase

ACTION ITEM: Improve ISS documentation: EcoWiki were using P-POD reference, which is not right

ACTION ITEM: Add to SOP's: Agreement that experiments from other organisms should be annotated when annotations in the 12 ref genome organisms are scarce. However - who should add those? Anyone? GOA?

ACTION ITEM: Debby could send a link to where E. coli group was looking in the documentation regarding IDA vs IMP for subcellular localization of fusion proteins.

ACTION ITEM: Add to SOPs: Does a functional assay inform localization?

ACTION ITEM: (from ruth) next jamboree, decide on proteins, try to encourage ontology experts for relevant branches of the ontology to participate

ACTION ITEM: add equivalent metal ion terms to the ontology for different metal ions

ACTION ITEM: there's a link to the binding term documentation on the talk page - please give feedback to work out a range of opinions before the consortium meeting

ACTION ITEM create a wiki page where people can start suggesting/annotating genes for future jamborees to encourage broader participation

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