Managers 21Oct09

Participants: Judy, Suzi, Jane, Pascale, Jen, Midori, Chris, David

Agenda: Jane

Minutes: Pascale

Action items from previous calls

• David, Chris: organize the xp webex. (There has been a great tutorial by David OS at the Buffalo Ontology meeting)
• Jane: email Amelia to put xp documentation (for GO users): ongoing
• Midori awaiting webex on XPs before sending announcement mail.

Action items from 09-09 Cambridge GO meeting

1. ACTION: [Judy, Chris, Darren, Suzi] Primary stake holders in GO and PRO need to agree on how GO components and PRO will relate to each other. Next PRO meeting end of April
2. ACTION: [Pascale, Kara, Paul] Ref genome annotation groups need to get ISS annotations from PAINT into their databases this year. This includes having a repository to put the annotations.
3. ACTION: [Pascale, Kara, Paul] Ref genome participating groups need to provide a file of their comprehensively annotated genes. To be discussed - how to do this
4. ACTION: [Pascale, Kara, Paul, Dan] Keep working on getting the gene indices from the MODs
5. Species to consider outreach to:
   1. daphnia (Indiana)has GO annotations (Judy: Michael Lynch)
   2. Xenopus : ask Erik Segerdell
   3. Sea Urchin (Judy will investigate: Andy Cameron)
   4. plasmodium (in progress - Suzi, Pascale)
6. ACTION: [Judy, Pascale] MODs-make an effort to highlight Ref Genome annotation; eventually we need to see high-quality ISS annotations in the MODs
7. ACTION ITEM: [Pascale, ref genome] Community interaction and outreach: Val presented the form where users annotated their papers : http://www.sanger.ac.uk/Projects/S_pombe/community_curation.shtml . Should we try extending the experiment to other groups? We can try using it when we work with experts on 'annotation projects' such as lung development.
8. ACTION: [Jane] Build a survey for grant update (Val, Jane, Jen), determine where to send it. (Mike has subscription to SurveyMonkey). Jane will send an email she wrote about that
9. ACTION: provide two survey urls and compare responses from a targeted list like the submitters to GO help list with responses from a random list of biologists

Infrastructure

1. ACTION: OBO format 1.3 tags (creation date, etc.) is already in gene ontology ext. Chris wants to add it to the main GO file.
2. ACTION: OBO version number added to all OBO files

GAF publishing pipelines

1. ACTION: GAF files from PAINT will need to be GAF 2.0 format
2. ACTION: Switch to GAF 2.0 in publishing pipeline with substantially long (3 Months) public notice to this change.
3. ACTION: add notices like this change to GAF 2.0 to GO News Feeds

Unannotated genes and GAFs

1. ACTION: post a clear spec of the desired format for gp2protein files for all MODs-include 1 row for every gene? 1 protein ID per row? No protein ID is OK if no protein is available?
2. ACTION: keep GAF file as is. Provide a new file (gpfile?) to describe gene products. Provide a detailed spec of the contents of this new file. This file may subsume gp2protein

Function->Process inferred annotations by IC

1. ACTION: MODS please look at the F->P IC annotations proposed for your species in http://geneontology.org/scratch/gaf-inference. If you have issues get back to Chris in the next 2 weeks.
2. ACTION: MODS will load these F->P IC annotations to their database
3. ACTION: Taxon constraint checks, report should be sent back to group but not filtered out..still load.
4. ACTION: chris check that interontology inferred annotations limited to inference from experimental annotations only.

Changes to GO Database management practices

1. ACTION: use a more relaxed schedule for building GO Full (quarterly perhaps?)
2. ACTION: reduce load of go lite from 3 to 1 time per week.

XP term request template

1. ACTION: implement a version like shown for curators to try before next GO meeting
2. Annotation Relationships (Chris/Jane): There is an implicit relation between an annotation and the gene to which it applies; an explicit relation between annotation and gene would be better. The relations may be like ‘extrinic to’ or ‘acted on during’ to relate annotation to gene
3. UniPath:
   1. ACTION:Pascale, Anne, Harold, Chris, Peter D’Eustachio, and Mary Dolan will work together to provide cross products b/t MFunction and Chebi to provide and report back to the group in the Spring meeting

Binding terms:

1. ACTION:more work needed to iron out HOW to transfer binding term annotations properly to retain all information
   • Paul NEEDS us to be able to do this for PAINT tree annotation
2. ACTION: Current working group will edit the binding term annotation gielines in line with the comments from discussion and distribute to PI’s for approval and then include in guidelines.
3. ACTION: Paul and Emily interested in joining new working group discussion on ISS/IC topic

(Rex) ACTION:actin-dependent ATPase activity and tubulin-dependent GTPase activity terms are incorrect

1. ChEBI(Marcus Ennis): Increase effort to get GO and ChEBI aligned
2. ACTION:Have another annotation camp, perhaps just for current GO curators

Discussion items

• Function-process proposal [David and Jane]
• GOC meeting - dates fixed? will be last week of March at Stanford, SAB on April 2.
• After going to the Cardiovascular meeting, Yasmin and David Hill were very interested in carrying out a similar meeting for renal development. However the Kidney research charity's grant could not support travel costs etc. associated with such a meeting. I had a vague recollection that Judy might have some funds to support content meetings (although I may have just dreamt this up!), if so would there be any possibility of financial support coming from GOC for a renal development content meeting? [Emily]
  • Judy - yes there are funds for content meetings.
  • I suspect the cast of people coming from the states would be the same as for the heart meeting: Doug, David, Tanya.

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