OE Webex 2Dec08

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12/02/2008 09:28:49 AM from Amina Abdulla: Hi everyone
12/02/2008 09:29:29 AM from Jen Deegan: Harold, you need to change to all participants.
12/02/2008 09:29:40 AM from Karen: Hi all
12/02/2008 09:29:40 AM from Harold: yup
12/02/2008 09:30:15 AM from Amina Abdulla: I can read Harold too now
12/02/2008 09:30:34 AM from Amina Abdulla: No more secret OE2 talks
12/02/2008 09:30:43 AM from Nomi Harris: ?
12/02/2008 09:30:44 AM from Amina Abdulla: Hi Nomi
12/02/2008 09:30:54 AM from Nomi Harris: Hi, were you having secret OE2 talks? Should I leave?
12/02/2008 09:31:28 AM from midori: We hadn't said much yet (but then, that's what we'd say if we were having secret talks ...)
12/02/2008 09:31:29 AM from Amina Abdulla: last week harold was set to send messages to "all participants" which does not include the host
12/02/2008 09:31:48 AM from Nomi Harris: Ah.
12/02/2008 09:31:49 AM from Harold: yet it does today?
12/02/2008 09:31:53 AM from Nomi Harris: I hate that feature of webex. So annoying.
12/02/2008 09:31:59 AM from Jen Deegan: Amina meant all attendees.
12/02/2008 09:32:22 AM from Harold: what is dif between an attendee and a participant?
12/02/2008 09:32:35 AM from Karen: attendee is everyone but the host
12/02/2008 09:32:59 AM from Harold: I'm sure this is some "feature'
12/02/2008 09:33:20 AM from Nomi Harris: It's the "chat behind the boss's back" feature.
12/02/2008 09:34:06 AM from Amina Abdulla: ok should we start..
12/02/2008 09:34:21 AM from Jen Deegan: yes
12/02/2008 09:34:36 AM from Amina Abdulla: So the verification manager is buggy in b51
12/02/2008 09:34:52 AM from Jen Deegan: yes
12/02/2008 09:35:20 AM from Amina Abdulla: I think the suggestion to have seperate user built and standard dictionaries is the best option
12/02/2008 09:35:31 AM from midori: I agree.
12/02/2008 09:35:43 AM from Jen Deegan: great
12/02/2008 09:36:11 AM from Harold: but both used for the spell check right?
12/02/2008 09:36:14 AM from Amina Abdulla: Its not on the tracker yet since I haven't looked into it - I'll do this today
12/02/2008 09:36:30 AM from David OS: Seems sensible to me. I'm happy as long as the user one doesn't get stomped on without warning.
12/02/2008 09:36:58 AM from Amina Abdulla: yes - overwriting the users dictionary was a serious misfeature
12/02/2008 09:37:47 AM from Amina Abdulla: The agenda page for today is mostly about testing - does anyone have any topics to discuss
12/02/2008 09:38:16 AM from David OS: Harold has a good point - will the user dictionary be built on top some version of the one provided - or will it be a set of additional terms that will be used in addition to the default dictionary?
12/02/2008 09:38:17 AM from Jen Deegan: nope
12/02/2008 09:39:19 AM from Jen Deegan: I originally assumed that there would be a GO dictionary and that there could be other ones too. Also a separate default one.
12/02/2008 09:39:20 AM from Amina Abdulla: I would think the best way to implement this is additional terms
12/02/2008 09:39:23 AM from Harold: what I wanted to make sure was that during a session, both would be automatically consulted for spelling, not one or the other.
12/02/2008 09:40:27 AM from David OS: "from Amina Abdulla to All Attendees:
I would think the best way to implement this is additional terms" I agree
12/02/2008 09:41:42 AM from Jen Deegan: Would it also make sense to add David's dictionary to svn? That way we have the benefit of his spell checking, and if he accidentlly deletes all of his config folder without saving his spelling list, he won't lose it all.
12/02/2008 09:42:27 AM from midori: Hmm, sounds ok for this once, but it's not gonna scale.
12/02/2008 09:43:18 AM from Amina Abdulla: David it would be helpful if you could provide details of the reasoner tests you work on so others could carry out the same on a different platform
12/02/2008 09:43:49 AM from David OS: Don't worry - I can keep backups on my own svn. Perhaps worth warning users to take backups in the doc?
12/02/2008 09:44:04 AM from midori: We can't give svn access to every OE user who might want to save a custom dictionary.
12/02/2008 09:44:13 AM from midori: Re reasoner tests: excellent idea.
12/02/2008 09:44:40 AM from Amina Abdulla: Infact I think we should all put up details on the wiki so others can check off/ add to it
12/02/2008 09:45:00 AM from David OS: I agree with Midori.
12/02/2008 09:45:46 AM from Nomi Harris: Maybe OE could save a backup copy of the dictionary every session (overwriting the previous backup copy, so there would be only one backup at a time)
12/02/2008 09:45:52 AM from Amina Abdulla: Yeah the user guide should mention the backups
12/02/2008 09:47:18 AM from David OS: Nomi: Agreed - Auto backup of the dictionary would be worth having.
12/02/2008 09:47:36 AM from Nomi Harris: That should be easy to implement.
12/02/2008 09:47:39 AM from midori: I like that idea too.
12/02/2008 09:47:59 AM from midori: We're all just agreeing with each other all over the place today
12/02/2008 09:48:24 AM from David OS: Amina: I'm mainly characterising reasoner bugs that cause the reasoner manager to stop working - rather than much technical stuff to do with output.
12/02/2008 09:49:10 AM from David OS: The major bug besides that is over-flagging of redundant links by the LPR
12/02/2008 09:49:50 AM from David OS: I'll link to the tickets that document this. Chris tells me it should be fixed in latest - rule based reasoner
12/02/2008 09:50:41 AM from Amina Abdulla: Thanks David
12/02/2008 09:52:17 AM from Amina Abdulla: What do you all think about discussing testing tasks we worked on next wg meeting onwards
12/02/2008 09:52:39 AM from Jen Deegan: to find out how many we have left?

12/02/2008 09:52:58 AM from midori: I'll be happy to ... must set aside some time for the said testing!
12/02/2008 09:52:59 AM from Amina Abdulla: I plan on looking into filtering and could cetainly use some help with examples
12/02/2008 09:53:52 AM from midori: There are still some unclaimed tasks -- I put a list on today's agenda page.
12/02/2008 09:54:08 AM from midori: http://wiki.geneontology.org/index.php/Oewg_20081202
12/02/2008 09:54:22 AM from Amina Abdulla: Last week was slow here since we were off most of the week..
12/02/2008 09:54:34 AM from midori: (reminder: full list here: http://wiki.geneontology.org/index.php/OBO-Edit_2.000_Testing_Tasks
12/02/2008 09:55:44 AM from midori: I hadn't thought about it until now (sorry!)
12/02/2008 09:55:57 AM from melissaH: yeah me too. just claimed a few...
12/02/2008 09:56:33 AM from midori: thanks!
12/02/2008 09:56:45 AM from Amina Abdulla: Any demo ideas for today?
12/02/2008 09:56:45 AM from Jen Deegan: One of my volunteerings had been deleted. I have added it again.
12/02/2008 09:57:32 AM from Amina Abdulla: oh ok Jen
12/02/2008 09:58:51 AM from Amina Abdulla: We could end early today since there aren't many discussion topics
12/02/2008 09:58:54 AM from Jen Deegan: I can't think of any things to demo or discuss.
12/02/2008 09:59:21 AM from Jen Deegan: perhaps good idea to end early.
12/02/2008 09:59:22 AM from Amina Abdulla: I promise it will be more interesting next week
12/02/2008 09:59:24 AM from midori: neither can I; I've been swimming in cross-product statements lately instead of testing.
12/02/2008 09:59:28 AM from Harold: I need to go on to another meeting; will look at transcript later
12/02/2008 09:59:43 AM from Amina Abdulla: ok bye Harold
12/02/2008 09:59:45 AM from Jen Deegan: maybe it's a good sign that we have no problems.
12/02/2008 09:59:53 AM from midori: if only ...
12/02/2008 10:00:04 AM from David OS: Swimming in XPs. Know the feeling. Sometimes I dream in them...
12/02/2008 10:00:10 AM from Amina Abdulla: yeah a lot needs to be done though
12/02/2008 10:00:21 AM from Jen Deegan: We'd better get doing it then.
12/02/2008 10:00:26 AM from midori: (it's probably more a sign that more than half of the group had more than half of last week off)
12/02/2008 10:00:31 AM from Jen Deegan: true
12/02/2008 10:00:35 AM from Chris Mungall: I have added a link to the reasoner benchmarks page from the test page.
12/02/2008 10:00:45 AM from Jen Deegan: thanks.
12/02/2008 10:01:08 AM from David OS: Cool. Cheers for doing this Chris. Very useful.
12/02/2008 10:01:14 AM from Amina Abdulla: oh yeah thanks Chris - I forgot about the benchmarks page
12/02/2008 10:01:49 AM from Chris Mungall: Currently there is a lot more information than OEWG participants may find useful. I'm proactively testing OE reasoners plus all others against current and future projections of GO and other ontologies
12/02/2008 10:02:27 AM from midori: there seem to be some big numbers in some of the GO-related table cells ...
12/02/2008 10:04:49 AM from Jen Deegan: what are the units?
12/02/2008 10:05:24 AM from Jen Deegan: minutes I assume.
12/02/2008 10:05:25 AM from midori: it says reasoning time in seconds at the bottom of t he page
12/02/2008 10:05:41 AM from Chris Mungall: units are seconds
12/02/2008 10:06:11 AM from midori: 1384 is kind of a lot of seconds
12/02/2008 10:06:27 AM from Chris Mungall: I need to update the table, some of thenumbers have dropped.
12/02/2008 10:06:38 AM from Chris Mungall: The basic take-home is:
12/02/2008 10:07:06 AM from Chris Mungall: reasoning over ALL xps in GO at once will have to be done in batch rather than whilst-editing
12/02/2008 10:07:19 AM from Chris Mungall: with the current algorithms
12/02/2008 10:07:41 AM from Chris Mungall: Anyway we should have a separate GO xp follow up call.
12/02/2008 10:07:48 AM from Jen Deegan: what are the spec of the machine you used to test?
12/02/2008 10:07:50 AM from midori: yes, good idea
12/02/2008 10:08:13 AM from Chris Mungall: Jen: I'll add to the page
12/02/2008 10:08:16 AM from midori: overlap between this group and GO xp handlers isn't 100%
12/02/2008 10:08:17 AM from Jen Deegan: ta
12/02/2008 10:08:23 AM from Jen Deegan: true
12/02/2008 10:08:47 AM from Jen Deegan: could we discuss on the managers call tomorrow since it's just us?
12/02/2008 10:09:08 AM from David OS: Ouch. I think I'll always need to be able to edit with full reasoning in future - unless I radically change the way I'm working....
12/02/2008 10:09:14 AM from midori: we won't have David tomorrow, and we might want to include Tanya as well.
12/02/2008 10:09:31 AM from Jen Deegan: It'll be easier with your small ontology won't it David?
12/02/2008 10:09:44 AM from midori: (no idea whether Tanya's available at 8 am on weds)
12/02/2008 10:10:05 AM from Chris Mungall: David - the take home message was for GO, you can see the numbers for fly are smaller. Now I know you want to xp out to GO but we can use segmentation strategies here where we extract subsetsof GO
12/02/2008 10:10:59 AM from David OS: I'm already extracting subsets of GO to reason with. I think I can do this with filters.
12/02/2008 10:11:17 AM from David OS: By which I mean filtered saving from GO.
12/02/2008 10:11:56 AM from David OS: What worries me is whether I'll hit a wall with the current strategy - where reasoning in OE is just too slow for me to edit,
12/02/2008 10:12:12 AM from David OS: There are very many XP defs left to add.
12/02/2008 10:12:41 AM from Amina Abdulla: Chris could you please comment on this item after the current discussion : http://sourceforge.net/tracker/index.php?func=detail&aid=2309391&group_id=36855&atid=418257
12/02/2008 10:14:08 AM from Chris Mungall: David: one thing the benchmarks aren't measuring is speed of incremental reasoning. I think this is even more important for you.
12/02/2008 10:15:01 AM from David OS: Incremental reasoning doesn't yet work reliably.
12/02/2008 10:15:42 AM from Chris Mungall: Amina - I've commented on it already, I can clarify late r today at work.
12/02/2008 10:15:52 AM from David OS: So total reasoning time is pretty important as a periodically need to re-reun the reasoner to strip get complete implied links and strip out errors fro incremental reasoning
12/02/2008 10:15:56 AM from Chris Mungall: I think this is an xp panel GUI bug that should be easy to replicate and fix
12/02/2008 10:16:35 AM from David OS: OK - would be great to get incremental reasoning fixed..... but problem looks more fundamental to me.
12/02/2008 10:16:45 AM from David OS: doubt that its just GUI
12/02/2008 10:16:54 AM from Amina Abdulla: It didn't show the comment for me - saw it now
12/02/2008 10:17:55 AM from midori: I should double-check; don't remember now whether the dangling relations showed up in the OTE or not.
12/02/2008 10:21:59 AM from Jen Deegan: should we wrap up? It seems as if the conversation is over.
12/02/2008 10:22:34 AM from David OS: OK. Is there going to be a separate meeting on XPs?
12/02/2008 10:22:57 AM from Chris Mungall: We need to have one for GO. I think it's a good idea if you join in
12/02/2008 10:23:02 AM from midori: I don't have much (one comment on that bug, but I can put it in the tracker)
12/02/2008 10:23:12 AM from midori: agreed re xp mtg
12/02/2008 10:23:22 AM from David OS: OK. Just let me know when.
12/02/2008 10:23:23 AM from Chris Mungall: Thursdays and fridays are good for me for the xp mtg.
12/02/2008 10:23:45 AM from Jen Deegan: Thursday is a bit better for me.
12/02/2008 10:23:56 AM from midori: This Thursday is bad for me, but usually Thursdays are good.
12/02/2008 10:24:16 AM from midori: Netx week? Dec. 11th?
12/02/2008 10:24:54 AM from Jen Deegan: I think that might be the protege meeting.
12/02/2008 10:25:29 AM from midori: ah, I'd totally forgotten the date(s) for that.
12/02/2008 10:25:30 AM from Chris Mungall: continued this over email since we need others
12/02/2008 10:25:33 AM from Jen Deegan: no it's not. That's fine then
12/02/2008 10:25:36 AM from David OS: 11th works for me. But neither Friday does.
12/02/2008 10:25:50 AM from midori: yes, we can do one of those doodle polls
12/02/2008 10:25:56 AM from Jen Deegan: good idea.
12/02/2008 10:26:28 AM from Amina Abdulla: Alright - thanks everyone
12/02/2008 10:26:45 AM from Jen Deegan: thanks, bye.
12/02/2008 10:26:51 AM from Nomi Harris: Bye
12/02/2008 10:26:55 AM from David OS: OK. I'll try to put together those XP notes for the wiki I've been promising for too long before the XP meeting.
12/02/2008 10:26:59 AM from David OS: See ya
12/02/2008 10:27:06 AM from Amina Abdulla: great David
12/02/2008 10:27:09 AM from midori: thanks David; bye all
12/02/2008 10:27:10 AM from Amina Abdulla: bye all