27 May 2014 PAINT Conference Call

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May 27 2014 PAINT conference call

Participants: Rama, Donghui, Moni, Kimberley, Suzi, Huaiyu, Pascale, Li, Paul T

PINT Jamboree

  • The kickoff meeting will be held during the week of July 28 (28-31). It is likely to be at SGD office at Porter Drive. Rama is going to confirm with Mike. Once the venue is confirmed, Huaiyu will send the announcement to the go-discuss mailing list, and create a meeting wiki page.
  • Rama raised the question about how much effort will be on training new curators. Huaiyu said that the main goal was to produce more paint curation. It has been agreed that we will put 30 people week effort to the jamboree. We need to make sure to deliver results correspond to that level of effort. If there are committed new curators, that will be a bonus. We can train them by pairing them with one of the curator paint curators.

Follow up on adding or removing experimental annotations real-time in PAINT

  • The conclusion from the last meeting was that it is a nice feature to have, but not a show-stopper and we should look into how much time will be required to add the feature, and decide. So far no more information availalbe to reach a decision.
  • Li: Adding experimental annotation is more useful than removing one, because it is more often that we can't make proper paint annotation because of the incomplete annotation.
  • Pascale agreed with Li.

Family demo

  • Rama showed PTHR11352, a proliferating cell nuclear antigen (PCNA) family, a DNA repair and processivity factor. In general, it is a quite straightforward family with few duplications. All the propagation was to the Eukaryota node. There were some discussion about the ontology relationship between DNA repair and DNA duplication.
  • Huaiyu showed PTHR11559, which is a carboxylesterase family. Within a clade of acetylcholinesterase, there is a clade genes that lost the specificity, and became a more generic cholinesterase. It is named as butyrylcholinesterase. It would be helpful to annotate this clade as a loss of specificity, but one gene (mouse) has an annotation of acetylcholinesterase, therefore, it is not possible to do so without removing the mouse annotation. The argument is that if the cholinesterase can catalyze the degradation of acetylcholinesterase, GO annotation would consider that it has the acetylcholinesterase activity. The counter argument (by Kimberley and Huaiyu) is that a gene with non-specific enzyme function can basically be annotated to all its specific MF terms. It is suggested that the topic should also be discussed in the annotation calls.
    • Paul suggested that maybe we should have weekly calls since we have more issues recently.
    • Suzi suggested that there should be more communications between the paint working group and the annotation group. It would be helpful to pass the issues raised at the paint call in the annotation calls.