26 August 2014 PAINT Conference Call

Discussion points (Pascale)

1. update PAINT to remove HTP annotations: We have noticed a significant increase in HTP annotations in the GO, which are fed into PAINT and make it difficult to annotate (too much noise). Suggestion to deal with the issue: For any paper having more than some threshold of something like 100-200 annotations to the same GO term, that GO term should be excluded form PAINT. Note that it may be that some papers containing HTP data also contains good quality LTP data, so filtering on a term-basis would allow those good quality terms to still be available for propagation.
   •  DECISION: We can make a manual list of papers to exclude. That list would be prepopulated based on a script as described above that looks for papers with very high number of annotations to the same GO term.
   • SGD will provide their list of HTP papers.
2. Should we rely on inter-ontology links for PAINT annotations ? I am concerned that if we rely on inter-ontology links, we may end up missing some annotations if some inter-ontology links get removed for any reason. I propose that we make explicit annotations for all the terms we feel should be propagated.
   • Decided to keep the same process for now, until we have more information on whether we need to make those annotations explicitly. Right now we have no reason to believe the process is not working.