Managers 21Oct09

Participants:

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: Primary stake holders in GO and PRO need to agree on how GO components and PRO will relate to each other
2. ACTION: Ref genome annotation groups need to get ISS annotations from PAINT into their databases this year.
3. ACTION: Ref genome participating groups need to provide a file of their comprehensively annotated genes
4. Species to consider outreach to
   1. daphnia (Indiana)has GO annotations (Michael Lynch)
   2. Xenopus
   3. Sea Urchin
   4. plasmodium (in progress - Suzi, Pascale)
5. ACTION: MODs-make an effort to highlight Ref Genome annotation
6. 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?

1. ACTION: Build a survey for grant update (Val, Jane, Jen), determine where to send it. (Mike has subscription to SurveyMonkey)
2. 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.) will be added to gene ontology ext
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?

1. 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

[edit] 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.

1. ACTION: MODS will load these F->P IC annotations to their database

1. ACTION: Taxon constraint checks, report should be sent back to group but not filtered out..still load.

1. 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?)

1. 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

1. 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

1. UniPath:

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

1. Binding terms:

1. 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

1. 1. 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.

1. 1. 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

1. 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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