Manager 2Jun10

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Participants: Kara Dolinski

Agenda: Pascale

Minutes: Chris

Phone passCode: 801-561

Action items

  • All managers to provide detailed goals and timetable of the work they plan to accomplish (1) in the next 6 month (end of 2010) and (2) in 2011.

  • (In July) The mailing lists for the GO camp will be deleted and further discussions will take place on the Annotation email list.
  • Protein Complexes, resource allocation, PRO/GO synergy (Follow up from last meeting). We need to establish the respective roles of each group. This should probably be an action item (was not assigned to anyone last time).
  • GO_ext file - Jane will re-organize the downloads page to highlight this file. She will bring this up with Chris/Seth to highlight it within AmiGO.
    • DONE.

Discussion items

GO Reference list

  1. At the last meeting we decided to use Connotea to maintain 'GO PUBs' collection on GO web site. A student in Judy's group will be able to help setting that up. After the first 'upload' it should be easy to maintain. Is there an update on this item?

Annotation Group

  1. Annotation QC checks using inter-ontology links. We want to suggest at the annotation camp that whilst annotating, annotators should collect suggestions for new inter-ontology links (e.g. reaction A that is only ever part_of pathway B) and these be collected somewhere centrally. These suggested links could then be used as a QC check over the ontology, in much the same way that the taxon restrictions are used now (e.g are all gps that are annotated to reaction A also annotated to pathway B). Only once we have established that these links are good - i.e. don't generate false positives would we add them to the ontology. These would be just one part of an 'engine' of annotation QC checks - in addition to taxon there will be evidence code rules etc. We need a point person to collect and run all these checks (not Chris!), perhaps someone also who could run the inter-ontology inference script regularly? [Jane & Emily]
  2. We've been approached (via Sandra Orchard) by Mario Albrecht from Max Planck Institute - there are a group of researchers interested in improving the terms and annotations (human) relating to synaptic processes (see email). This would be great but we have no ontology developer time available for the foreseeable future. How best to proceed? [Jane & David]
  3. should we require that all annotation groups who are submitting a GAF file to the GOC site, must equally submit a gp2protein if their identifier type is not from a central sequence database, e.g. UniProtKB, NCBI. There are a number of files without gp2protein - such as aspergillus, PAMGO, GeneDB. [Jane, Emily, Dan]
  4. What to do about SF? We don't have a new ontology developer for the meantime, and the items keep on coming! David & I can do some, but no way we can keep up. Can we get more people editing? [Jane & David]

Reference genome

  1. Work needed for groups to upload PAINT annotations
    • Can files for each taxon ID be dumped out in addition to a file for the entire family? This one has given rise to a lot of discussion on the PAINT list. Should we survey the consumers of those files? It seems less work for us to merge the files once than for all groups to merge the files and the extract the taxon they are interested in.
    • How are the references going to be displayed (they need to be formatted also)? this seems easier to handle than #1, but we need to do it
    • Can IMR and IRD be mapped to ISS for the time being until the ECO accepts these. In principle I don't see why we cant do that. However, is it necessary? We can add those evidence codes ontology.
    • Who will be responsible for implementing this?
    • There is a potential problem with the MODs not integrating the PAINT annotations.
  2. Next annotation targets: wnt signaling (Varsha)? is everyone okay with that?


  1. We're a bit short-staffed! Any ideas how we can keep on top of SF before our new editor starts, probably in the fall?