Manager 20Feb2013

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Review what we want for the GOC/SAB meeting in April

See agenda page:

Agenda items for GOC

1. Website

Won't be able to push website out for SAB

Can show a beta site

Standard datasets for enrichment - status?

Have started looking at sets in SGD, would like to have a standard set for yeast before requesting sets for other organisms, to iron out any problems. Is working with Ben Good.

Will be used to give users more direction in enrichment, will put together parameters guidelines for users so you can say these terms are enriched with confidence. Investigate effect of diluting background set, removing sets of gene products from background sets and poisoning the background set with gene products that enrich for other terms.

Want to discover what are the consistent set of variables for various tools.

Chris can automate the enrichment in various tools in Galaxy.

Rama will report on this in GOC meeting.

2. PAINT progress

Only for human we will go through protein2go to add missing annotations - for other MODs we will send to individual curators to do, hopefully this will only happen rarely.


Formal spec is well underway, working issues are being ironed out, should have a robust format and conversion tools by GOC meeting.

Groups should have a choice of what format to submit and consume in since a lot of MODs won't be able to create a GPAD format or enter data for explicit relations.

Can't add explicit relations yet in P2GO, waiting for final decision on relations

4. Ontology

Cell cycle meeting is next week

Will have submitted the ChEBI paper by the GOC meeting

Chris will give an update on transition to OWL

Also will give an apoptosis update, curation manual is almost ready

5. LEGO/Annotation Expressivity

Will give a report on worked examples

Call tomorrow about LEGO consistency with annotation extensions - AE should be transferable to LEGO

Also include report on annotation extension paper

Nothing to report on phenotype plans

6. Ontology changes

Would like feedback from curators about how term requests are going. Will show new termgenie freeform

Also sourceforge and JIRA facilities for term/ontology requests

7. Submissions from outside groups

There is a group wanting to submit algae annotations (see gohelp), who will evaluate? Should send to JGI via Suzi, Suzi will respond to them.

Transcription annotations from NTNU - workflow: providing annotation help via email and conference calls, had a workshop at EBI, will evaluate the annotations and give feedback, they will submit annotations to GOA.