see also http://ff.im/qGQbN - Ruchira S. Datta

how to select targets? ideally: large families that are assayable. other criteria: practical => fundable, impact, biomedical, biodefense, fuels, environment. Need to find intersection between experimentally assayable and computationally predictable. Universal proteins? - Ruchira S. Datta

what is a good prediction? granularity: the more specific the better. tweakable specificity/sensitivity tradeoff. a prediction should have: provenance (traceable to origin), confidence score - Ruchira S. Datta

i object: people will think confidence scores are comparable - Ruchira S. Datta

martin steffen: apply methods across a common gold standard set, and use that to generate confidence - Ruchira S. Datta

gary gippert: idea of uber-confidence score from ComBrEx itself - Ruchira S. Datta

what is a good method? keep history of method's performance - somewhat controversial, would this keep people to entering? it doesn't in CASP - Ruchira S. Datta

controlled vocabulary: Gene Ontology is the only game in town, but need to be able to quickly update the gaps in GO. many parts of the ontology are not descriptive enough, terms are missing. some of the relationships are misannotated. - Ruchira S. Datta

maybe enzyme commision numbers also for enzymes - Ruchira S. Datta

martin steffen: 2.7 million genes have no GO annotation - Ruchira S. Datta

what to do about that? - Ruchira S. Datta

martin steffen: they may be assigned to clusters - Ruchira S. Datta

then start annotating it - Ruchira S. Datta

michael galperin: we expect to find new functions that are not represented in GO - Ruchira S. Datta

peter karp: not every function prediction can have GO terms attached to it, as not all have an assigned GO term, but when possible it's very useful to attach GO terms so people can query for their interests - Ruchira S. Datta

barry wanner: GO is geared at eukaryotes, not very well aimed for infectious disease - Ruchira S. Datta

if GO does not have the terms, we should update it. the other alternatives: use your own standard vocabulary, or annotate in english, will not be helpful - Ruchira S. Datta

john hunt: ComBrEx should be a leader in making better controlled vocabulary. - Ruchira S. Datta

expand GO - Ruchira S. Datta

GOlets: provisional submission to GO, while GO is considering them ComBrEx can use them - Ruchira S. Datta

hard or easy targets? manage a portfolio, combination of "hard" and "easy" targets. Friedberg enjoys the challenge of hard targets, using e.g. micromotifs, genome location, etc. But not everyone may be interested in these. Sjölander had suggested the "portfolio" idea. - Ruchira S. Datta

Gary Gippert: question of outreach - how to share the findings so users of public databases can also benefit. - Ruchira S. Datta

also question of how to pair the appropriate computationalists and experimentalists. - Ruchira S. Datta