OE Webex 8Jul08

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07/08/2008    09:25:59 AM    from midori:	Hi Nomi 
07/08/2008    09:26:29 AM    from Nomi Harris:	Hello 
07/08/2008    09:30:29 AM    from midori:	Wonder who else is coming ... 
07/08/2008    09:30:44 AM    from Nomi Harris:	I guess Jen is away, isn't she? 
07/08/2008    09:30:55 AM    from midori:	yup 
07/08/2008    09:30:59 AM    from Nomi Harris:	Karen Eilbeck said she's in class until 9:30 but will try to show up later 
07/08/2008    09:31:02 AM    from Nomi Harris:	Amina just came in. 
07/08/2008    09:31:34 AM    from midori:	Hi Amina 
07/08/2008    09:31:41 AM    from Amina:	Hi Midori 
07/08/2008    09:32:13 AM    from Nomi Harris:	Hi, Melissa! 
07/08/2008    09:32:30 AM    from melissaH:	hi!
07/08/2008    09:32:34 AM    from midori:	hi 
07/08/2008    09:33:06 AM    from melissaH:	I am happy to report that I have saved my first production ontology in OE2! hooray!
07/08/2008    09:33:08 AM    from midori:	ok 
07/08/2008    09:33:10 AM    from midori:	yay!! 
07/08/2008    09:33:46 AM    from Nomi Harris:	Yay!  So it all worked ok? 
07/08/2008    09:33:54 AM    from melissaH:	yep, worked just fine.
07/08/2008    09:34:13 AM    from melissaH:	I wasn't doing any filtered saves, though.
07/08/2008    09:34:21 AM    from Amina:	thats great news 
07/08/2008    09:34:30 AM    from melissaH:	I do have a question though about the tree editor.
07/08/2008    09:34:35 AM    from Nomi Harris:	You reloaded it and it all looked right? 
07/08/2008    09:34:47 AM    from Nomi Harris:	Yes, question about the tree editor? 
07/08/2008    09:34:47 AM    from melissaH:	yes, perfect as far as I can tell.
07/08/2008    09:34:49 AM    from Amina:	filtered save should be fixed in the next release 
07/08/2008    09:34:56 AM    from melissaH:	nice!
07/08/2008    09:35:23 AM    from melissaH:	question, so I often have two tree editors open at once, and drag and drop to move or merge terms.
07/08/2008    09:35:32 AM    from midori:	yes, so do I 
07/08/2008    09:36:01 AM    from Nomi Harris:	I have not done much testing with two tree editors open--I should do more. 
07/08/2008    09:36:03 AM    from melissaH:	the problem for me is that as soon as I click on a term in one panel, the other panel moves to that term too. this is fixed by changing that panel to local selection mode.
07/08/2008    09:36:11 AM    from Nomi Harris:	Right. 
07/08/2008    09:36:48 AM    from melissaH:	but then, my searches don't work on that panel. is there an easier way? it ends up being a lot of clicking back and forth from local/global. what do you do midori?
07/08/2008    09:37:05 AM    from Nomi Harris:	OE1 has a "lock" button to keep the panel from scrolling. 
07/08/2008    09:37:21 AM    from Nomi Harris:	I don't really understand why that stopped working in OE2; the relevant code looks the same, but it doesn't work. 
07/08/2008    09:37:31 AM    from melissaH:	gotcha.
07/08/2008    09:37:46 AM    from Nomi Harris:	It's still on the bug list. 
07/08/2008    09:37:52 AM    from midori:	Actually, it's good that you brought this up. I'm still working out what's thebest approach, and Jen has put in a feature request (I think; lemme see if I can find it). 
07/08/2008    09:38:04 AM    from melissaH:	(sorry figured this needn't be an official question -probably should  have waited for more people)
07/08/2008    09:38:14 AM    from Nomi Harris:	No, it's fine. 
07/08/2008    09:38:24 AM    from midori:	I don't mind; it affects lots of us. 
07/08/2008    09:39:11 AM    from Nomi Harris:	If this is really a major annoyance, we can bump up the priority of the locking bug and try to look into it soon. 
07/08/2008    09:39:14 AM    from midori:	aha ... https://sourceforge.net/tracker/index.php?func=detail&aid=1944849&group_id=36855&atid=418260 
07/08/2008    09:39:21 AM    from Nomi Harris:	I was hoping it would be a quick fix, and when it wasn't, I put it aside. 
07/08/2008    09:39:54 AM    from Nomi Harris:	I can look into implementing that feature (only one OTE in global mode at a time). 
07/08/2008    09:40:11 AM    from Amina:	I like Jen's suggestion about having the checkbox  
07/08/2008    09:40:13 AM    from midori:	I haven't properly thought through Jen's feature request to decide whether I'd ask for exactly the same thing, but cleraly she's also had the inconvenience. 
07/08/2008    09:40:33 AM    from Nomi Harris:	Well, before I work on it, do you want to think about it a bit and tell me what you think? 
07/08/2008    09:40:56 AM    from Nomi Harris:	I'm still finishing up some documentation. 
07/08/2008    09:41:26 AM    from Nomi Harris:	I want to do some more documenting today and then I will go back to debugging. 
07/08/2008    09:41:46 AM    from midori:	ok ... just thinking a bit now, and I'm not coming up with situations where I'd need more than one global OTE at a time .... 
07/08/2008    09:42:13 AM    from Nomi Harris:	In Jen's proposal, you could use the Configuration Manager to turn that restriction off if you wanted to allow 2+ global OTEs. 
07/08/2008    09:42:16 AM    from melissaH:	so for furthering my example. here is what I do, all the time.
07/08/2008    09:42:33 AM    from midori:	Configurability lowers the barrier :) 
07/08/2008    09:42:59 AM    from melissaH:	I want one global OTE, and one local. but I want to search on the local one.
07/08/2008    09:43:22 AM    from melissaH:	I think I like jen's suggestion too.
07/08/2008    09:44:03 AM    from Amina:	So I'm thinking this checkbox for search criteria should only come up when there are 2 OTE's in session 
07/08/2008    09:44:15 AM    from melissaH:	yes, this sounds good. 
07/08/2008    09:44:22 AM    from melissaH:	midori, do you need this too?
07/08/2008    09:44:26 AM    from melissaH:	the searching I mean.
07/08/2008    09:44:29 AM    from Karen:	I didn't think you could search on the local in OE1 either. You had to find your term in one panel, and then switch which panel was active and find the other term in it, same as in OE2, except that OE2 requires 2 clicks instead of 1 to switch both panels 
07/08/2008    09:44:41 AM    from Nomi Harris:	No, the checkbox would just be a configuration option.  It would be irrelevant if you happen to only have one OTE open, but that's ok. 
07/08/2008    09:45:19 AM    from midori:	Melissa - I think so, if I understand correctly 
07/08/2008    09:45:35 AM    from midori:	Karen - th at sounds right
07/08/2008    09:45:41 AM    from melissaH:	yes, so right now, if I leave one panel on local, searches don't take me to a term there.
07/08/2008    09:46:37 AM    from midori:	So what we miss is the convenient focus switching in OE1. 
07/08/2008    09:46:40 AM    from melissaH:	so I have to switch back to global, then back again. but maybe keeping them both on global, but having a lock button would solve the problem easier. am I making any sense?
07/08/2008    09:46:48 AM    from melissaH:	yes.
07/08/2008    09:47:01 AM    from midori:	maybe ... what would the lock button do? (sorry if I'm being dense) 
07/08/2008    09:47:16 AM    from Nomi Harris:	The lock button keeps the OTE from scrolling in response to an external selection. 
07/08/2008    09:47:47 AM    from midori:	OK, so you'd keep looking at the same bit of ontology even if the selection in that OTE changed? 
07/08/2008    09:48:07 AM    from Nomi Harris:	If the selection changed from a click outside that OTE, yes. 
07/08/2008    09:48:21 AM    from Nomi Harris:	I guess to change the selection inside that OTE you'd have to scroll it anyway. 
07/08/2008    09:48:25 AM    from midori:	ok, sounds useful 
07/08/2008    09:48:38 AM    from Nomi Harris:	So would that be more useful than the only-one-OTE-global feature? 
07/08/2008    09:49:18 AM    from Nomi Harris:	I can look into the lock again.  Apparently something changed between OE1 and OE2 that made that feature not work, but it was puzzling, because the actual OTE code didn't change in any relevant-seeming way. 
07/08/2008    09:49:25 AM    from Karen:	I remember the lock feature in OE1. To be honest, I never used it much, it didn't really seem that useful to me. 
07/08/2008    09:49:46 AM    from Nomi Harris:	But this is a clear case where it would be useful, right? 
07/08/2008    09:50:07 AM    from melissaH:	sorry to be wishy washy, but I'm trying to think through what would be less clicks  
07/08/2008    09:50:25 AM    from midori:	I use it occasionally -- not often, but when I do, I really appreciate it. I find it most useful when I have to do more than one move or copy on "nearby" terms. 
07/08/2008    09:51:17 AM    from Karen:	Jen's suggestion to have only one panel be active at a time would make OE2 comparable to OE1 in that 1 click would change both panels, instead of needing 2 
07/08/2008    09:51:39 AM    from Nomi Harris:	I will look into that and see if it's easy to implement. 
07/08/2008    09:51:45 AM    from Nomi Harris:	Harold just emailed me, "I cannot get webex to acknowledge I have java enabled on any browser of my new machine (intel mac), so I won't be able to join" 
07/08/2008    09:51:47 AM    from midori:	I'd even go so far as to say I'm a fan of the lock feature, but I'm not sure it's directly a solution to the global/local sw itching problem (at least the way I use it in OE1).
07/08/2008    09:52:21 AM    from midori:	I'll try emailing Harold ... 
07/08/2008    09:52:31 AM    from Nomi Harris:	Do you have advice for him? 
07/08/2008    09:52:39 AM    from melissaH:	yes I think you are right- both may be needed for slightly different purposes.
07/08/2008    09:53:12 AM    from melissaH:	I suppose we should prioritize then...
07/08/2008    09:53:15 AM    from Nomi Harris:	So, midori put up a proposal for a reorganization of the user guide table of contents: 
07/08/2008    09:53:16 AM    from Nomi Harris:	http://wiki.geneontology.org/index.php/New_OE_user_guide_TOC 
07/08/2008    09:53:26 AM    from Nomi Harris:	Did anyone get a chance to look at that? 
07/08/2008    09:53:38 AM    from midori:	(re Harold: maaaaybe I can help ...) no guarantees! 
07/08/2008    09:53:39 AM    from Nomi Harris:	Maybe I should wait for Jen to get back before I do the reorganization. 
07/08/2008    09:54:54 AM    from melissaH:	yes, I looked at it. and loved it.
07/08/2008    09:55:02 AM    from Nomi Harris:	I liked it too. 
07/08/2008    09:55:12 AM    from midori:	ooh thanks! 
07/08/2008    09:55:22 AM    from Nomi Harris:	Maybe I'll go ahead and do the reorg while I'm in documentation mode. 
07/08/2008    09:55:37 AM    from midori:	 I also want to look over a couple more doc pages later this week. 
07/08/2008    09:55:43 AM    from Nomi Harris:	If Jen has issues with it, and makes a good case for changing it, it's not a big deal to change it again later. 
07/08/2008    09:55:50 AM    from midori:	(But I don't think that would change my organization proposal.) 
07/08/2008    09:55:58 AM    from melissaH:	I can do some more documentation too.
07/08/2008    09:56:00 AM    from Nomi Harris:	Ok. 
07/08/2008    09:56:03 AM    from Nomi Harris:	Thanks, that would be great. 
07/08/2008    09:56:11 AM    from Nomi Harris:	Be sure to do an svn update before you make any changes. 
07/08/2008    09:56:24 AM    from Nomi Harris:	I have committed a lot of changes (and so have others such as midori). 
07/08/2008    09:57:06 AM    from melissaH:	so, I promised to look at the filtering doc. can someone make sure that what is on the wiki for that is up to date? since I am not saavy to edit the html
07/08/2008    09:57:08 AM    from Nomi Harris:	melissa, if you have always wanted to learn a bit about html, this might be a good time to give it a go.  It was kind of a pain merging your changes from Word into the html pages. 
07/08/2008    09:57:38 AM    from melissaH:	oh, ok. well I'll have a go then.
07/08/2008    09:57:39 AM    from Nomi Harris:	I still appreciate your input, of course, in whatever form! 
07/08/2008    09:58:05 AM    from melissaH:	I'm a little short on time this week but I have all of tomorrow set aside for OE2
07/08/2008    09:58:09 AM    from Nomi Harris:	I update the wiki copies of the user guide about twice a day (by hand).  I updated them yesterday afternoon and there haven't been any commits since then. 
07/08/2008    09:58:13 AM    from Nomi Harris:	Hi, Karen E!
07/08/2008    09:58:21 AM    from Karen E:	Hello 
07/08/2008    09:58:31 AM    from Nomi Harris:	We were just discussing documentation. 
07/08/2008    09:58:35 AM    from Amina:	Hi Karen 
07/08/2008    09:58:45 AM    from Nomi Harris:	I committed your (Karen E's) changes (with some minor edits of my own). 
07/08/2008    09:58:51 AM    from Karen E:	Sorry I'm late. 
07/08/2008    09:59:06 AM    from Nomi Harris:	I'm as clueless about the mystery components as you are, unfortunately.  Chris M probably knows more, but he's away all week. 
07/08/2008    09:59:19 AM    from Karen E:	Yep, I just had a mail from him. 
07/08/2008    09:59:25 AM    from Karen E:	Hes in england. 
07/08/2008    09:59:27 AM    from Nomi Harris:	Oh, was it informative? 
07/08/2008    09:59:32 AM    from midori:	he's here, in meetings 
07/08/2008    09:59:36 AM    from Nomi Harris:	Right, he and Suzi are both in England. 
07/08/2008    09:59:50 AM    from Nomi Harris:	Oh!  So you can talk to him in person about anything you were wondering about. 
07/08/2008    10:00:00 AM    from Karen E:	Is there a strict deadline for the documentation to be done? 
07/08/2008    10:00:07 AM    from Nomi Harris:	No, it's ongoing. 
07/08/2008    10:00:10 AM    from midori:	When we can drag him out of the OBI meeting, anyway .... 
07/08/2008    10:00:15 AM    from Nomi Harris:	We just chose a week for everyone to focus on it. 
07/08/2008    10:00:39 AM    from Nomi Harris:	I had been neglecting documentation in order to do debugging, so it was good for me to focus on documentation for a week. 
07/08/2008    10:01:04 AM    from midori:	Anyone mind if I bail out early? Might be good to bike to the train station before it starts raining again ... 
07/08/2008    10:01:16 AM    from Nomi Harris:	Sure, midori. 
07/08/2008    10:01:52 AM    from Nomi Harris:	Oh, did you hear the good news from Chris about the new reasoner? 
07/08/2008    10:02:02 AM    from midori:	nope ...  
07/08/2008    10:02:03 AM    from Nomi Harris:	He figured out why it was so slow on SO (unusably slow, in fact). 
07/08/2008    10:02:23 AM    from Karen E:	yep it was my fault. 
07/08/2008    10:02:27 AM    from Nomi Harris:	It was an is_symmetric rule that was being applied and generating gazillions of links 
07/08/2008    10:02:57 AM    from Nomi Harris:	Chris made OE not apply that rule, and now you can reason over SO in a few seconds! 
07/08/2008    10:03:09 AM    from Nomi Harris:	Same issue with fly anatomy. 
07/08/2008    10:03:49 AM    from Nomi Harris:	Anyway, see you next week, midori. 
07/08/2008    10:04:07 AM    from melissaH:	bye midori!
07/08/2008    10:04:18 AM    from midori:	I'll catch up with the transcript. Bye all! 
07/08/2008    10:04:27 AM    from Amina:	bye midori 
07/08/2008    10:04:29 AM    from Nomi Harris:	I think we're pretty much done, aren't we? 
07/08/2008    10:04:40 AM    from Nomi Harris:	Karen E, did you want to chat here about cross product documentation? 
07/08/2008    10:04:45 AM    from Karen E:	does anyone know how to use the xp matrix ed? 
07/08/2008    10:04:56 AM    from Nomi Harris:	Probably Chris does 
07/08/2008    10:05:18 AM    from Karen E:	Oh,, OK, soI should talk to him. No rush then. 
07/08/2008    10:05:24 AM    from Amina:	Karen I did get a demo from chria a while back 
07/08/2008    10:05:30 AM    from melissaH:	I've tried it a few times
07/08/2008    10:05:38 AM    from Amina:	chris* 
07/08/2008    10:05:46 AM    from Karen E:	whats it supposed to do? 
07/08/2008    10:05:54 AM    from Amina:	I could come up with an example for a demo 
07/08/2008    10:06:02 AM    from Nomi Harris:	That would be great. 
07/08/2008    10:06:51 AM    from Karen E:	The other thing I think would be good for documentation is how to make xp from 2 ontologies. Anyone doing that? 
07/08/2008    10:07:12 AM    from Nomi Harris:	Was that in the document from Chris that I sent you? 
07/08/2008    10:07:37 AM    from Karen E:	No not really - there was theory but no practical 
07/08/2008    10:07:38 AM    from Nomi Harris:	Karen, when you get a chance, please check the updated cross products pages to make sure I got all your changes incorporated correctly. 
07/08/2008    10:07:45 AM    from Karen E:	OK. 
07/08/2008    10:07:46 AM    from Amina:	Karen thats what you use the xp matrix editor for right? 
07/08/2008    10:08:07 AM    from Karen E:	I had a feeling it might be.  
07/08/2008    10:08:22 AM    from Amina:	yes I'm sure about that 
07/08/2008    10:08:23 AM    from Karen E:	That would be why I havent had to use it yet... 
07/08/2008    10:08:50 AM    from Amina:	so I think while working with SO you always have the reasoner ON and are working in repair mode 
07/08/2008    10:09:09 AM    from Karen E:	repair mode? 
07/08/2008    10:09:17 AM    from Amina:	thats what Chris calls it 
07/08/2008    10:09:19 AM    from Karen E:	I call it premptive striking. 
07/08/2008    10:09:28 AM    from Amina:	you must've seen it in the ppt too 
07/08/2008    10:09:30 AM    from Amina:	haha 
07/08/2008    10:10:21 AM    from Karen E:	I will make a list of questions for Chris. I think Nicole may also be able to answer some. I'll get back to Nomi at least with more documentation. 
07/08/2008    10:10:33 AM    from Nomi Harris:	Ok 
07/08/2008    10:10:44 AM    from Karen E:	Or a backbone for chris to fill in the blanks. 
07/08/2008    10:10:52 AM    from Amina:	So my understanding is that the xp matrix editor is used when you need to link two ontologies 
07/08/2008    10:11:21 AM    from Amina:	I think thats a good idea 
07/08/2008    10:12:30 AM    from Nomi Harris:	Who is hurdil? 
07/08/2008    10:12:36 AM    from Karen E:	Harold. 
07/08/2008    10:12:39 AM    from hurdil:	aha! reinstalling webex did it
07/08/2008    10:12:42 AM    from Nomi Harris:	Oh--hi, Harold! 
07/08/2008    10:12:55 AM    from Nomi Harris:	We're pretty much done here, but I'll send out the chat transcript. 
07/08/2008    10:12:57 AM    from Karen E:	I am going to sign off now. 
07/08/2008    10:13:06 AM    from Nomi Harris:	Ok, bye, Karen. 
07/08/2008    10:13:11 AM    from Nomi Harris:	Harold, did you have anything you wanted to bring up? 
07/08/2008    10:13:12 AM    from Karen:	glad that worked hurdil ;) 
07/08/2008    10:13:16 AM    from hurdil:	!!! 
07/08/2008    10:13:29 AM    from hurdil:	There was something 
07/08/2008    10:13:56 AM    from hurdil:	I tried to do a search on terms having a specific relationship 
07/08/2008    10:14:00 AM    from melissaH:	yep, I gotta go now too. so I'll do some more doc looking tomorrow 
07/08/2008    10:14:08 AM    from Nomi Harris:	Ok, thanks, Melissa. 
07/08/2008    10:14:14 AM    from melissaH:	bye!
07/08/2008    10:14:48 AM    from Amina:	go ahead Harold.. 
07/08/2008    10:14:55 AM    from hurdil:	However, I noticed that there is no option so search on a relationship 
07/08/2008    10:15:28 AM    from Nomi Harris:	You mean, a link search? 
07/08/2008    10:15:29 AM    from hurdil:	For example: I wanted to get all terms in an ontology that have a relationship  "derives_from" (PRO ontology) 
07/08/2008    10:15:56 AM    from hurdil:	BUt "relationship" is not an option in the dropdown box like id, synonym, name, ec. 
07/08/2008    10:16:02 AM    from hurdil:	I thought it used to be  
07/08/2008    10:16:04 AM    from Amina:	Harold I think you can do that with the link filters 
07/08/2008    10:16:28 AM    from hurdil:	It would seem that it would be easier in the search box 
07/08/2008    10:16:49 AM    from Nomi Harris:	Was there a way to do this in OE1? 
07/08/2008    10:16:55 AM    from Amina:	ic I don't know if there was an option like that in OE1 
07/08/2008    10:18:11 AM    from hurdil:	Especially if it 's to quickly fond terms that have a relationship that contains "derives" and  name contains phosph, for example  
07/08/2008    10:18:49 AM    from hurdil:	i'm calling up oe1 to see if it is there
07/08/2008    10:19:17 AM    from Amina:	Have you tried looking at the little grey gear which lets you do a more specific search 
07/08/2008    10:19:21 AM    from hurdil:	hmm; no it is not there either
07/08/2008    10:19:36 AM    from Amina:	thats where you can specify the exact relationship your interested in 
07/08/2008    10:19:38 AM    from hurdil:	Yes, the gray gives me the same set of things to search no
07/08/2008    10:20:14 AM    from hurdil:	perhaps I'm just remembering wrongly; this was the first time I wanted to do a search like this 
07/08/2008    10:20:42 AM    from Nomi Harris:	It uses the term "link" rather than saying "relationship". 
07/08/2008    10:20:57 AM    from Nomi Harris:	But it should show you the known relationships in the dropdown menu. 
07/08/2008    10:21:37 AM    from hurdil:	it just shows various is_a, but doesn't show any other relattionships 
07/08/2008    10:21:37 AM    from Amina:	So do you see all the relationships present in your ontology? What your looking for is a search only for a particular relationship right? 
07/08/2008    10:21:53 AM    from hurdil:	sorry for the spelling; I am having an odd time with the machine today 
07/08/2008    10:23:14 AM    from hurdil:	the realtinships in the pro are:is_a, part_of, dervices_from, has_part, transitive_over, union_of, disjoint_from 
07/08/2008    10:24:04 AM    from hurdil:	They derives_from displays in the tree and other tools; there appears to be no way to find them in the search 
07/08/2008    10:24:11 AM    from Nomi Harris:	Hmm 
07/08/2008    10:24:15 AM    from Nomi Harris:	Which ontology is this in? 
07/08/2008    10:25:08 AM    from hurdil:	Pro ([protein ontology obo; I can send it. but I think the issue is that the dropdown does not have just "relations" to search on
07/08/2008    10:25:32 AM    from Amina:	I'll take a look at it Harold 
07/08/2008    10:26:05 AM    from Nomi Harris:	Thanks, Amina. 
07/08/2008    10:26:22 AM    from Nomi Harris:	Are we done for today? 
07/08/2008    10:27:04 AM    from Nomi Harris:	See you next week? 
07/08/2008    10:27:14 AM    from Karen:	bye 
07/08/2008    10:27:25 AM    from Nomi Harris:	Hey, wait, Harold: 
07/08/2008    10:27:27 AM    from Amina:	bye Karen 
07/08/2008    10:27:29 AM    from hurdil:	bye 
07/08/2008    10:27:35 AM    from Nomi Harris:	what happened when you brought up OE1 to see if it let you do the search you want to do? 
07/08/2008    10:27:37 AM    from Nomi Harris:	Did it? 
07/08/2008    10:27:51 AM    from Nomi Harris:	Oh well. 
07/08/2008    10:28:13 AM    from Amina:	bye everyone