minute taker: Midori
- Present: David, Midori, Eurie, Jane, Michael, Mike, Suzi
- Absent: Rex, Chris, Judy, Jennifer
Review Action Items from previous meeting
Actually, we seem to have re-reviewed the action items from Oct. 11 ... but there are some updates.
Jonathan Liu/MIT GO Engineering collaboration
David gave a summary of the latest documents from Janothan Liu, which include two spreadsheets - terms that are "too specific" and ones that are "too general". David and Midori have had a cursory glance at terms in the spreadsheets.
Next step: send Jonathan the is_a complete BP file. Action: David.
aside on isa complete: David suggests making the last few orphans is_a biological process & send file to Jon Liu. We expect the GO graph should improve according to their metrics during the round-robin work. We must merge the is_a complete file into the current ontology soon! Action: Jane
Anyway, then Jonathan can do computations using only on is_a paths. We hope there will be fewer problem terms this way.
David: There are about 1000 "too specific" -- we should check whether they overlap with is_a orphans. That is, were the orphans more likely to be problematic in Jonathan's analysis?
Also, Midori has responded to some questions from Jonathan
User meeting proposal
Decided to bring up at the January GOC meeting.
Jane to feed [something] back to ChEBI
Jen, Midori and John to look into web conference options more fully and report back
Midori: Jen knows the most about this, so we'll get more from her at the next call.
David: Webex is working well for screen sharing, but not sound; for the is_a complete work we're using Skype + Webex
Jen meant to test one more technology, but not done yet due to confusion over date.
1. GO-tops will assemble the January GOC meeting agenda during the first week of December. Action - everyone add your stuff to the wiki by then!
2. Ontology development meeting on cardiovascular physiology/development. - see below.
Individual Manger reports
1. Nov. newsletter in progress; there will be a reference genome writeup; do we still want to try a "gene of the quarter" feature? yes, if there's room ...
2. AmiGO wg trying for a release before the end of the year.
3. (note: the following was actually at the end of the call)
Mike: the public wiki is up; a few people have done edits so far; Mike has no particular plan
Eurie: AmiGO wg to take care of web site; shall they do the wiki too? AmiGO wg is turning into 'web presence group'. General agreement that that's fine, sensible, etc.
Jane: would like users to be able to submit via wiki - suggestions for terms, annotations, etc.
Action item: Jane & Eurie to go ahead with including public wiki in AmiGO/web presence wg remit.
1. Is_a complete BP as above; the file in go/scratch has few orphans, but those aren't orphans in the live ontology, so the merge result will be is_a complete.
2. Need ways to prioritize SourceForge items
David: At present, the management structure goes only as far down as us ... what about below? Can we say to anyone "do this SF item"? We also need to find out who's doing what GO work in each group. At the moment the managers are doing a lot of the legwork,and we want to distribute more among the rest. General agreement that distribution is good, and that managers should have some say in directing other group members; details remain to be worked out.
Current SF priority criterion: ref genome top priority, because changes are needed for annotation NOW.
Jane: hard to find refgen requests. Midori: there's a tracker "group". Tell refgen annotators to choose "reference genome" group & put "rg" in summary. Action: Midori.
David: an ontology development interest group meeting on heart development and all things cardiological will go ahead. Simon to host at MCW, mid-May 2007 (Request from Suzi: make sure it doesn't conflict with CSHL biology of genomes.)
There will be a web/phone conf with cardiologists in advance. Suzi suggests people at NHLBI; David thinks Judy may be in touch with Carol Bean but will make sure. Action: Suzi & David.
3. David: PNS additions are on the back burner -- not many papers, and haven't identified experts.
4. Processes at higher level, i.e. tissue and organ functions
Suzi: we really need to do this; the WHO is interested.
David: can think of two ways
- (1) add terms directly to GO - uneasy but not sure why; e.g. heart pumping (see the GOC meeting agenda for some thoughts)
- (2) create another way to represent using anatomical structure term plus term from GO
Second seems better because a function is not necessarily done by the same organ in every species.
Remember that GO terms are used to annotate gene products -- but these other terms would be used to annotate organs (eg. heart annotated with heart pumping).
We already have cellular & organismal processes in GO, so in a way we have begun to organize the process ontology with respect to the 'agent' or at what level the process is occuring. However, multicellular organisms and cells are generic and universal, tissues and organs are not. It would be difficult to do the same for tissue & anatomical levels.
Suzi & David both thinking about it; David to add to Jan wiki & make sure considered in content mtg.[done, dph]
Example of kidney - does 2 things: detox & water/blood pressure regulation ...
Conclusion: we have to do this, but we're not yet sure how.
Add this to meeting agendas for Jan. GOC and heart dev. Action: David.[done, dph]
5. Questions about sex determination - many were added for fly, so Michael can take a look at the terms and questions. Action: Michael (David to remind).
6. (actually near end of call) Suzi: Did Chris open a SF item for the "flagellum" definition? Jane: No, but others (e.g. Sanger pathogen folks) have also noticed it's wrong. Suzi & Chris to do the SF item with new def. Action: Suzi & Chris.
Outreach, Software, Reference Genomes
No report; manager absent
Operations and Procedures
See question about management in ontology development report above.
Staffing and Personnel
Jane: The OBO-Edit working group has asked whether we can hire a tech writer to help with documentation. It would free up more of John's time for the actual programming.
Suzi: It's a budget question (unless we have someone already who can do that sort of thing). The PIs will discuss it at their next conf call.
Note: Heather (John's wife) and Monica (David's wife) have both done tech writing.
Collaborations and Interactions, active and new
1. MIT/Jonathan Liu ongoing, as noted above
2. Midori sent meeting report from Ontoverse project to managers; low priority at present, but they might seek collaboration (or just advice) from GO, OBO and/or NCBO.
3. Jane: Working with Melissa Haendel at ZFIN -- they've come up with a way to make GO cellular component consistent with CARO; it's on the Jan. meeting wiki).
November 29 (instead of 22nd), usual time. Agenda: Midori; Minutes: Rex.
- New this time:
- Action item: Jane to merge go/scratch/IsaComplete.obo with live GO.
- Action item: David to send is_a complete GO to Jonathan Liu
- Action item: January meeting agenda suggestions must be on wiki by first week December.
- Action item: GO editors to tell refgen annotators to choose "reference genome" group & put "rg" in summary.
- Action item: David and Suzi to work on list of experts for heart dev content meeting.
- Action item: David to put higher-level function issue on meeting agendas.
- Action item: Michael to look at sex determination terms and questions about them from is_a complete work (David to remind him).
- Action item: Suzi & Chris to send new definition of "flagellum" (SF item).
- Action item: GO-tops to discuss tech writer possibility; budget considerations.
- Action item: Jane & Eurie to go ahead with including public wiki in AmiGO/web presence wg remit.
- Carried over from Oct. 25:
- Action item: Conference call with ChEBI; also including Chris.
- Action item: Chris to look at J. Liu/MIT material.
- Action item: The advocacy group will look into some type of calendar to keep track of which meetings are being attended by GOC members.
- Action item: Judy will send a copy of the instance paper to Chris and Michael.