Conference call developers 20090805 notes

2009-08-05

1. Set the chair’s for the next set of devel calls, assuming people are happy with the current twice weekly call frequency, which should also probably be reviewed.

We'd like to have dev call twice a week since it is very productive. 2nd Wednesday of every month is kept for coord call. (I updated the relative information in obi homepage: http://obi-ontology.org/page/Main_Page)

Alan is excluded from chair list for next round since he is hard to join all the dev calls. Besides, Jennifer Fostel and Ryan Brinkman offered to cover his spot. Helen Parkinson and Jennifer Fostel would like to be added in the chair list.

We will recycle current list. Here it is:

August 10 2009 Dev Call - chair RB August 12 2009 Coord Call - chair BP August 17 2009 Dev Call - chair JM August 19 2009 Dev Call - chair LS August 24 2009 Dev Call - chair CS August 26 2009 Dev Call - chair JF August 31 2009 Dev Call - chair YH (Oliver) September 2 2009 Dev Call - chair MC September 7 2009 Dev Call - chair JZ September 9 2009 Coord Call - September 14 2009 Dev Call - chair HP September 16 2009 Dev Call - chair RB

Please check the time assigned for you as a chair of call, if you cannot make it, please find a replacement. Since I do not who will be coord call chair, I leave it empty.

I also updated the corresponding webpage: http://obi-ontology.org/page/Conference_call_developers_agenda#Conference_Call_Agenda_Items

2. Possible OBI workshop in Sep/Oct - Alan made some comments about aligning with OWLED. Can we agree on date place perhaps?

It will be a 3-day workshop.

Date: Most people in the call would like to have this meeting late October, around Oct 18 - Oct 20. Place: Washington DC, if cannot make it, should be in east coast of US

Helen modified doodle poll including Saturday and Sunday.

Please vote if you'd like to attend the workshop: http://www.doodle.com/wmf7frhqp98c9pxr

Please contact Helen if you want to attend the workshop and need support for traveling and/or accommodation.

3. Manuscript progress - Melanie currently has doc, wondering where it is going next and actually wondering how close it is to being finished.

AI for MC: finish review and commit under SVN - then send email on dev for next reviewer

Action items about manuscript has been added or edited by BJ and JM in the review queue google doc.

http://docs.google.com/Doc?docid=0AXCcXy8doOC3ZGd4cmhiYjRfMGczZjU0czlk&hl=en

Bjoern is in charge of manuscript right now and the work needs to be assigned out to people. Some action items has been added in tracker.

4. status of release

New id files have been generated and commited. MC: We stoped producing reports as it is an extra step. Remove use of obsolete classes before release 0.9

Agreement on moving separate branch files to one file durng editing process. will include ONTIE for this release

AI: Alan will find and fix all the obsolete classes in use AI: Alan to add disjoint obsolete

5. solution of restrictions of obsolete_classes, please check the link for detailed: https://sourceforge.net/mailarchive/forum.php?thread_name=29af5e2d0907292300g633ab3eco17f0761cc3d20395%40mail.gmail.com&forum_name=obi-devel

Agree to make obsolete disjoint from rest of obi

6. OBI documentation Is it better to create other types of tracker other than OBI terms, such as, Action items (assigned in Dev call) or some other issues discussed in mail list? If agree, I volunteer to add those in after Dev call and from mail list.

AI for MC: add Jie as SVN admin AI for JZ: will add some tracker items from mail list and oganize other issues from mail list in doc files.

7. Tracker items - there are quite a few high priority tracker items to go through (with more added) so we should continue to address these (this will probably absorb most of call time) https://sourceforge.net/tracker/?group_id=177891&atid=886178 Any blocker items for the manuscript?

No time to address it. Will leave for next dev call.

RB will be chair for next Monday's (Aug 10) call.

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Recorded chat during Dev call:

jie zheng: Agenda:

1.set the chair’s for the next set of devel calls, assuming people are happy with the current twice weekly call frequency, which should also probably be reviewed.

2. Possible OBI workshop in Sep/Oct - Alan made some comments about aligning with OWLED. Can we agree on date place perhaps?

3. Manuscript progress - Melanie currently has doc, wondering where it is going next and actually wondering how close it is to being finished.

4. status of release

Helen Parkinson: Hi everyone. Looks like a better turnout today, no

canadian holidays ;-)

jie zheng: 5. solution of restrictions of obsolete_classes, please check the link for detailed:

https://sourceforge.net/mailarchive/forum.php?thread_name=29af5e2d0907292300g633ab3eco17f0761cc3d20395%40mail.gmail.com&forum_name=obi-devel

jie zheng: +1
Helen :)
Ryan Brinkman: yes
Alan Ruttenberg: yes
Helen Parkinson: yes
Ryan Brinkman: yes
Alan Ruttenberg: I think we need 2
Alan Ruttenberg: +1
jennifer fostel: agree we need two meetings; easier to meet if they are same time. is it possible to move this meeting one hour later?
Ryan Brinkman: +2
jie zheng: twice a week.
James Malone: and we keep 2nd wed for coord every month of course
Helen Parkinson: I can be added to the chair list
Alan Ruttenberg: moving wed call later is sometimes difficult for me
Alan Ruttenberg: I would like to be removed from the chair list
James Malone: lol
James Malone: so would I
jennifer fostel: i can volunteer to join the chairing list
James Malone: :P
Alan Ruttenberg: seriously :)
jie zheng: I want to :)
Helen Parkinson: Alan, there are no free lunches.
Melanie Courtot: - keep calls twice a week
James Malone: i think we can give alan hall pass :)
Melanie Courtot: - chairs : we will recycle current list
Helen Parkinson: Ok with me.
Ryan Brinkman: I'll cover Alan's spot's
Alan Ruttenberg: Helen, I will text you each time I start working on OBI, ok ;-)
jie zheng: I think take alan off the list until OBI o.9 released.
jie zheng: great!
jennifer fostel: i was skipped -- can i volunteer to chair in alan's place?
Ryan Brinkman: I second Jen's offer
Alan Ruttenberg: thanks Jie
Helen Parkinson: thanks Jen.
Helen Parkinson: what's next?
jie zheng: OK. I will make a list to ad Jen and Ryan.
jennifer fostel: i am on a simultaneous call for the next 30 minutes so will use text
jennifer fostel: re manuscript - cani have another go at editing?
Helen Parkinson: I'll take another go at it if needed as well
Ryan Brinkman: Can yuo add them to th review queue on Google then?
Ryan Brinkman: sweet
jennifer fostel: first in, next up
Helen Parkinson: larissa is on holiday too
James Malone: i am wondering at one point we stop the review process?
Melanie Courtot: AI: MC: finish review and commit under SVN - then send email on dev for next reviewer
Helen Parkinson: Add me after you Bjoern please
Helen Parkinson: sure
jennifer fostel: re james -- stop when we run out of people who want to edit
Alan Ruttenberg: ouch
jennifer fostel: or when we are cycling through issues
Melanie Courtot: sounds real bad Ryan
Bjoern Peters: could not undesrtand Ryan
jie zheng: better now.
Helen Parkinson: Ryan asked if everyone gets another go at review
Ryan Brinkman: sorry plan to have an open editing at the end?
Helen Parkinson: not if we want to complete this in realtime
jie zheng: AI: Bjoern update the queue of review list
Ryan Brinkman: all authors should have a go at the very end I guess
jennifer fostel: i suspect i should update my section
Helen Parkinson: Bjoern is in charge right and the work needs to be assigned out to people.
James Malone: so review is useful but adding new parts is more important, I agree
Helen Parkinson: Ok which use case is missing, and which needs work>?
Alan Ruttenberg: yes, but I can't e.g. pop in and rewrite a section when I have time.
jennifer fostel: i am delinquent on my use case
jennifer fostel: yes, i can do that
jie zheng: work on use case. Jen will work on figures.
Helen Parkinson: That sounded loike a short list to me.
Helen Parkinson: OK, you can assign something to me if you like
James Malone: ok as long as review is helping paper be compelted i'm happy, i just wanted to make sure it wasn't generating more work rather than finishing it
jie zheng: If I can, I would like to help.
Helen Parkinson: Alan will you do the addition to the task list doc please?
Alan Ruttenberg: yes
jie zheng: I can work on item 4)
James Malone: we should put these in tracker with priority 9 i think
James Malone: they are essentialy blockers
Alan Ruttenberg: james, agreed
Melanie Courtot: +1 add to tracker
James Malone: i will add my item to the tracker and will get to it asap
Helen Parkinson: Ok with me. Philippe's away and so can the other people commit to their tasks now?
jie zheng: Sorry, what did you say, bjoern?
jie zheng: Thanks.
Helen Parkinson: Add an AI for alan to add commenst to the review queue doc.
Alan Ruttenberg: cool
Alan Ruttenberg: :)
Alan Ruttenberg: easy
James Malone: i trust your judgment bjoern, you have my proxy vote:)
jie zheng: obi release, commit newids, there are some problems of these files.
Helen Parkinson: Is the status up to date in general?
Helen Parkinson: prev conversations indicate not
jie zheng: obirelease: need clean up some terms.
Alan Ruttenberg: helen: which status?
Helen Parkinson: I added a tracker item for one of the obsolete terms in use. Protege 4 allows used by queries that means we can check all the obsolete classes
Alan Ruttenberg: no
Alan Ruttenberg: spellcheck on definitions would be good too
Melanie Courtot: we stoped producing reports as it is an extra step, and they were not really used I think
Helen Parkinson: if they are not up to date, then this shouldn't delay release for these
Alan Ruttenberg: I would really like the use of obsolete classes cleaned up
Helen Parkinson: I agree with Bjoern, there's so much wrong that these things are minor
Helen Parkinson: that sounded very negative - sorrt
Alan Ruttenberg: use of obsolete classes can effect performance too
Alan Ruttenberg: to be clear - remove use of obsolete classes before .9 is my vote
jie zheng: so what should we do?
James Malone: alan - did we agree to make obsolete disjoint from rest of obi?
Melanie Courtot: ok for release - not ok for report
Helen Parkinson: OK, how long will it take to remove the obs classes and can you find these?
Alan Ruttenberg: I will write a query to get a report
Helen Parkinson: yes, I think we agreed on the disjoint. Agree on the meta data issues with Bjoern
Helen Parkinson: AI: Alan will find and fix all the obsolete classes in use
jie zheng: ok
Melanie Courtot: +1 on disjoint
Alan Ruttenberg: alan will find and someone else will fix
Melanie Courtot: "someone"? :)
Helen Parkinson: Alan can you text me whenyou do your AI as well?
Alan Ruttenberg: :)
jie zheng: so try to release then clean up items later.
Melanie Courtot: main issue in my opinion is that we keep running into clean up issues that may be hard to debug
Helen Parkinson: Ok we should defer some of the clean up unless it's critical
Melanie Courtot: some of the clean up is critical, eg, ID issues
jie zheng: accumulate too many terms now, if this round release works, not hard for later regularly release.
Helen Parkinson: I have to agree on the branch set, up, I'd move to a single file
Melanie Courtot: they are soemtimes difficult to find
Ryan Brinkman: Branches concept seems obsolete
Helen Parkinson: Ok, but now this is a causing more probs than it solves
James Malone: i agree, looking at commit log it is very rare people edit concurrently now
Ryan Brinkman: flatten obi
Helen Parkinson: Can we vote to move to a single file?
Alan Ruttenberg: ok by me
Ryan Brinkman: Anyone not want to flatten OBI?
Helen Parkinson: no obsolete will be disjoint as you propsed.
Melanie Courtot: AI: alan to add disjoint obsolete
Melanie Courtot: Agreement on moving to one file durng editing process
Helen Parkinson: sounds sensible
James Malone: though the uninferred view
Alan Ruttenberg: yes, uninferred
James Malone: that would be my wish
James Malone: remove instances and obsolete
Alan Ruttenberg: No, I would say merge all if we are merging
Ryan Brinkman: no instances please
Alan Ruttenberg: why?
James Malone: instances could potentially be huge
jie zheng: merge all .owl files.
James Malone: and irrelevant
Helen Parkinson: I'd agree with merge all and obsolete for now
Alan Ruttenberg: we can split things later
Melanie Courtot: current merge = everything in - other possible, I need to get list of desired
Alan Ruttenberg: I *will* get a split script going at some point
Alan Ruttenberg: Yes
Ryan Brinkman: Instances won't be worked on for now
Alan Ruttenberg: If we have any split, we might as well have everything split
Ryan Brinkman: so can't we jsut leave it out fo rnow
Helen Parkinson: can we fall back to branches if we can't split later,
James Malone: i disagree alan, instances represent something else
Alan Ruttenberg: everything represents something else :)
Helen Parkinson: I'd like all including the instances
Alan Ruttenberg: I don't see the distinction, james
Alan Ruttenberg: all is about investigations
jie zheng: may be exclude some instances files in the future.
Melanie Courtot: we don't have splitting script right now
Ryan Brinkman: easier to work w/o them as we dont' need them for editing atm
Alan Ruttenberg: let's worry about that when there are too many
Helen Parkinson: right but they aren't huge now - so are we solving an
issue we don't have yet
Alan Ruttenberg: helen, agreed
James Malone: ok fine
Melanie Courtot: they don't appear in the class hierarchy though - you need to go to instances tab to see them - so not real issues for editing
Bjoern Peters: helen + alan + 1
jie zheng: +1 alan.
James Malone: let us hit the problem them worry
James Malone: ok
Helen Parkinson: I can see the point, but i'd defer for progress now
Melanie Courtot: :)
Alan Ruttenberg: Let's include ontie too
Melanie Courtot: need work on ID range
James Malone: given the decision we should def include ONTIE
Helen Parkinson: Bjoern, what does ONTIE extend mostly?
Alan Ruttenberg: one big happy class and instance family :)
Melanie Courtot: yes - need to be scripted
Helen Parkinson: I'd be inclined to add ONTIE too,
Bjoern Peters: ONTology of Immune Epitopes
Bjoern Peters: many assays specific for epitops
Helen Parkinson: I meant which parts of OBI - never mind I can look
jie zheng: count on alan + melanie of scripts.
Bjoern Peters: processes
James Malone: chuck it all in
Helen Parkinson: got it. adding to the tracker, or adding to file?
Helen Parkinson: can you add to the tracker and if there are no objections then add them.
Alan Ruttenberg: yes, some are already in tracker
Alan Ruttenberg: yes
Helen Parkinson: ok clear.
Alan Ruttenberg: I'm not a dumper :)
Helen Parkinson: all should be in the tracker, you so are a dumper
Alan Ruttenberg: haven't you seen that already :)
Alan Ruttenberg: (laughing)
Alan Ruttenberg: we're happy to share :)
Alan Ruttenberg: !
Alan Ruttenberg: (hint hint)
James Malone: is it easily repeatable?
Helen Parkinson: Didn't Olivier plan to refactor this
Alan Ruttenberg: yes
James Malone: does it adhere to an ISO standard?
Alan Ruttenberg: there is work to do there too
Helen Parkinson: when will Oliver's guy start?
jie zheng: I will learn how to debug.
jie zheng: I agree with alan.
jie zheng: Unfortunately, scripts did not work in my computer.
Alan Ruttenberg: every little bit helps, of course
Bjoern Peters: ok, done
Helen Parkinson: OK so we agreed, a single file, and instances and ONTIE and Alan's NIF stuff
Ryan Brinkman: documentation tracker?
Helen Parkinson: I'd like one tracker too.
Ryan Brinkman: agreed,categories sound liek better solution
Helen Parkinson: new categories are Ok with me.
James Malone: you can't
James Malone: no
James Malone: sourceforge rule - once it's added can not remove or rename
James Malone: yes
Helen Parkinson: we can add new tho - e.g. task
Helen Parkinson: OK
James Malone: one of the categories is "no category" as an ontologist I am stuck in a pedantic paradox
Helen Parkinson: do we agree then - Jie will do clean up using doc category
Alan Ruttenberg: James, I am so happy to hear you say that :)
Alan Ruttenberg: we agree, where we = I
Alan Ruttenberg: jie, follow your tracker bliss
Alan Ruttenberg: make it so :)
Helen Parkinson: to change the categories you need admin
jie zheng: I have no idea.
Helen Parkinson: agreed
jie zheng: So far, I won't create category now.
Alan Ruttenberg: ecstatic
Helen Parkinson: Ok one more item - the meeting?
Melanie Courtot: AI for MC: add Jie as SVN admin
jie zheng: I will try to put more information shown in mail list not in tracker items.
jie zheng: yes.
Alan Ruttenberg: damn. no "ecstatic" button to press
jie zheng: clean up meeting: where and when?
Alan Ruttenberg: I think that's right
Melanie Courtot: sounds right to me too
jie zheng: I am OK after MGED 12 and place near Philly.
Alan Ruttenberg: which week in september?
jie zheng: OK for me.
jennifer fostel: +2
jennifer fostel: east coast
Alan Ruttenberg: dc
Helen Parkinson: thanks Bjoern
Melanie Courtot: I would prefer Vancouver in september and dc in october - but I may be biaised :)
jie zheng: so we decided late september?
Alan Ruttenberg: It's possible, but not preferred.
Alan Ruttenberg: who do we lose in october?
jennifer fostel: mged is oct 5 - 8
jennifer fostel: ah! already not on the doodle
Alan Ruttenberg: ok
Alan Ruttenberg: no
Ryan Brinkman: not yet
James Malone: except alan
jie zheng: I see.
James Malone: he's 'fairly' important :)
jie zheng: +1
jie zheng: I am ok late october in DC or east coast
Melanie Courtot: owled is 23 - so we could have 22 too
Alan Ruttenberg: yes
Ryan Brinkman: 2-3
Melanie Courtot: 3 days
Ryan Brinkman: 2 better
jie zheng: how about oct 20, 21?
jie zheng: sorry, 19, 20
James Malone: 19-21
Bjoern Peters: 19 - 21
Melanie Courtot: 19-20-21 or 20-21-22 maybe?
Ryan Brinkman: as long as we dont' gget distracted by "philosophy" questions I'd be happy wtih 3
jie zheng: how about 17,18? (weekend)
Melanie Courtot: 17, 18 is too early in my opinion
James Malone: ok so wait for decision from gilberto and wait to hear from helen?
Alan Ruttenberg: plus some people will continue to be available on the 22, like me
James Malone: 19-21 works for me
Melanie Courtot: 19-21 sounds good
jie zheng: sorry. Sunday
jie zheng: yeah.
Alan Ruttenberg: If sunday makes it much better I will make it
jie zheng: +1 Bjoern.
Bjoern Peters: ahh
Bjoern Peters: good point
Alan Ruttenberg: if necessary I can ask C&P
Alan Ruttenberg: for sunday, anyways
James Malone: we'd have to hold meeting on the Mall
Alan Ruttenberg: :)
Alan Ruttenberg: I like that
James Malone: me too
jie zheng: agree.
Alan Ruttenberg: right
Melanie Courtot: :)
James Malone: I will bring my guitar
Alan Ruttenberg: lol
jie zheng: sounds good!
Alan Ruttenberg: yah - let's rent a suite!
Alan Ruttenberg: jacuzzi breaks sound good
Ryan Brinkman: hot tub ontology party
James Malone: :-o
jie zheng: DC
jie zheng: sounds good for me.
Alan Ruttenberg: Travel/Hotel would be helpful for me
jie zheng: I fine.
Melanie Courtot: who is chairing next call?
Ryan Brinkman: I am
Alan Ruttenberg: I can make it monday, barring brain damage
Alan Ruttenberg: bye
James Malone: thanks all
Melanie Courtot: bye!
jennifer fostel: bye!
Bjoern Peters: bye + thanks!
jie zheng: bye thanks.

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Conference call developers 20090805 notes

2009-08-05

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