Manager 2Jun10

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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.
    • All groups other than software have provided this
    • ACTION: Chris
    • ACTION: Suzi provide categories
  • (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).

we will up at Geneva and ISMB.

Suzi: wants wider discussion of PRO issues with go-managers.

Judy: anyone free to call PC calls. No decisions made until.

Chris: circulate proposals in advance of the meeting?

We discuss the nature of the PC call. It's about how to annotated F/P or gene products, not about PRO per se.

David: Harold is the person who deals with PRO/GO intersection. Keep him updated.

Suzi: Harold also has a role to report back to GO

  • 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?

ACTION: ongoing

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]

ACTION: Amelia

Rama: both running and generating scripts.

Chris: centralization at stanford, but harder to run scripts e.g. Moose.

ACTION: Chris to report on this next time. in 3 weeks.

Chris: F->P inferences.

Set a date for when F->P goes into basic GO file.

  1. 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]

David: Higher level Synaptic processes not well represented in GO. Ditto higher level neural processes like cognition. D&T have met with Toronto person on higher level processes. Need to coordinate.

Pascale: coordinate with annotation

Jane: they are interested in annotation

But we are resource limited

We don't have time to put proposal into writing.

Judy: write a proposal in conjunction with these people.

Suzi: first thing is for ontology group to write a proposal

  1. 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]

Suzi: this is essential

Request Mike to add check to GAF pipeline

  1. 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]

Rama: email OEWG

David: lots of people have edit priveleges.

Chris: OE should not be barrier of entry.

ACTION: Chris - compositional term interface

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.
  1. Next annotation targets: wnt signaling (Varsha)? is everyone okay with that?

Emily: Varsha revamped proposal based on feedback from BH. Shouldn't keep changing targets. Need targets soon.

Paul: get a quick turnaround