Manager 20Mar2013

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  • LEGO. Can we have a discussion about how might best proceed with this work. We need to decide what things need to happen, by who and in what order. At the moment it's slipping between the cracks.
  • Apoptosis. Paola has sent a list of gps recommended for reannotation to the PIs. Any questions about that, does it look reasonable?
  • Some curators have asked if there will be breakout sessions on the Friday PM of the GOC meeting. There are probably several that could be arranged (annotation issues, ontology, annotation extension...), shall we formalise this by scheduling breakout sessions throughout the afternoon and advertising this to the attendees?



1. LEGO Jane: Organizational issue - What are the next steps, who should be doing what?

Chris: Some examples in SVN; we need more.

We need more experiments where we 'blindly' annotate the same pathway.

All the ontology group should do an example using the Protege plug-in.

David: Examples in Protege are modeling examples, not annotation.

Next step - take a set of annotations and map onto LEGO model to see what they look like. That's how we'll see if we can be fully expressive with our current annotation paradigm.

Kimberly: Have some examples, need to use those for LEGO modeling.

Chris: Use illustrative diagrams for annotations and relationships we're using.

Paul: Compare LEGO and annotation relations - need more, fewer relations or modifications to LEGO model?

Jane: Does LEGO use a subset of relations?

Chris: Yes, but some are 'short-cut' relations.

Paul: Need to have clear semantics so use of relations is clear.

Chris: Need a proper tool for this - would be nice to have a web-based tool for this.

David: How would this tool fit in with the Common Annotation Tool?

Chris: CAT for now is Protein2GO; LEGO tool would eventually be a component of that tool.

David: No single paper tells a whole story - want to see the LEGO diagram view and update/change the view as needed.

Jane: Add examples, check out okay, then what?

Chris/Jane: Next step would be a tool. Heiko (?)

Chris: Also have use-case queries, e.g. show me everything that's downstream of this activity?

ACTION ITEM: Add more annotation examples.

ACTION ITEM: Third Tuesday will be the LEGO call time slot.

2. APOPTOSIS Jane: Paola sent a list to PIs of gene names to be re-annotated under the apoptosis efforts.

Pablo finished comparison of enrichment results with human gene products (same set) for before and after ontology development.

Power Point slides (see Jane's email and Dropbox link) illustrate the changes in annotation - see slide 20.

David: Same issue will come up with the cell cycle. If work of ontology group is going to be fulfilled, then re-annotation will have to be part of the ontology projects. How to sell this to curators?

Kimberly: Combine re-annotation with LEGO modeling.

Suzi, Paul: Would like to try that approach.

3. BREAK-OUT SESSIONS FOR GO MEETING For Friday, during the SAB day afternoon.

David: Small group to talk about annotation extensions. Pombe, Rachael, Tony, anyone else capturing that kind of data.

SAB afternoon will be just the PIs.

Jane: Put potential discussion areas on wiki, let people sign up or vote.

4. UPDATE ON GO WEBSITE Rama and Rachael took pages on SVN and put into google spreadsheet to mark which pages should go to website, which to wiki, etc.

Jane: looking at ontology pages, should this be done in parallel?

Rama: can share list/spreadsheet with everyone to get additional input

Chris: is there a broad plan for organization, i.e. which are Drupal pages and which might be books with chapters, e.g. Annotation Guide?

Amelia - has done a great job with the documentation!