Wikiomics:Afp06 panel

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The Automated Function Prediction 2006 meeting will have a discussion panel, with our keynote speakers answering audience questions.

We have decided to solicit questions from participants prior to the meeting, out of which a few will be picked for the panel session.

Any questions relevant to the computational prediction of the function of biological molecules are welcome.

OK, I'll go first:

  1. What are the main challenges to creating a Critical Assessment of Function Annotation (CAFA) contest, in the spirit of CASP and CAPRI? (Iddo Friedberg)
  2. How would metagenomics impact the field? (Iddo)
  3. How is structural genomics already impacting the field? (Iddo)
  4. description of function: are ontologies the only way to go about it? (Iddo)
  5. How can we have an expected level of function assignment for a genome depending on literature coverage? Example: PMID 15864286 [1] (Christos)
  6. Derive a more sophisticated scale of function assignment/annotation consistency? What is a 'good' function prediction? Example: PMID 11864365 [2] (Christos)
  7. Function prediction for non-coding or non-translated elements. Example of the first would be genomic regulatory elements, of the second would be RNA. (Iddo, Adam)
  8. What is the proportion of proteins that have multiple functions at the molecular level? no function at all? (troll warning) - the point being: what evolutionary path does a protein follow in terms of function? (a) Gain of function first and eventually duplication (2 functions at the same time) or (b) duplication, loss of function, gain of a new function (Martin)
  9. Do we need to include structural information into prediction models or does the primary structure already contain all the information we need to know to infer function? (Dani)


  1. Janssen P, Goldovsky L, Kunin V, Darzentas N, and Ouzounis CA. Genome coverage, literally speaking. The challenge of annotating 200 genomes with 4 million publications. EMBO Rep. 2005 May;6(5):397-9. DOI:10.1038/sj.embor.7400412 | PubMed ID:15864286 | HubMed [janssen05]
  2. Ouzounis CA and Karp PD. The past, present and future of genome-wide re-annotation. Genome Biol. 2002;3(2):COMMENT2001. DOI:10.1186/gb-2002-3-2-comment2001 | PubMed ID:11864365 | HubMed [ouzounis02]

All Medline abstracts: PubMed | HubMed