OE Webex 24Jun08

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June 24, 2008	    5:30:51 PM	    from Jen Deegan to All Participants:	Hi
June 24, 2008	    5:30:52 PM	    from Karen to All Participants:	No, I'm on a Mac. As for my name, I'll try to remember to put my last initial when I join the meetings in future 
June 24, 2008	    5:31:17 PM	    from midori to All Participants:	hi all 
June 24, 2008	    5:31:20 PM	    from Nomi Harris to All Attendees:	Hi, midori. 
June 24, 2008	    5:31:25 PM	    from Jen Deegan to All Participants:	Hi
June 24, 2008	    5:31:27 PM	    from Nomi Harris to All Attendees:	Hi, Jen.  You got on successfully. 
June 24, 2008	    5:31:32 PM	    from Jen Deegan to All Participants:	Yes all fixed now.
June 24, 2008	    5:31:41 PM	    from Nomi Harris to All Attendees:	Great. 
June 24, 2008	    5:31:42 PM	    from Jen Deegan to All Participants:	firefox stopped working for webex for some reason.
June 24, 2008	    5:31:49 PM	    from Amina to All Participants:	Hi Modori and Jen 
June 24, 2008	    5:31:53 PM	    from Nomi Harris to All Attendees:	Did you upgrade firefox?  Or maybe they changed WebEx. 
June 24, 2008	    5:31:55 PM	    from Jen Deegan to All Participants:	Hi Amina
June 24, 2008	    5:32:04 PM	    from midori to All Participants:	really? I'm usinf firefox 3 ... 
June 24, 2008	    5:32:05 PM	    from Jen Deegan to All Participants:	yes I'm not sure what it was. 
June 24, 2008	    5:32:08 PM	    from Nomi Harris to All Attendees:	I use Safari on Mac.  WebEx has actually worked well for me the last few times--I haven't gotten booted off. 
June 24, 2008	    5:32:12 PM	    from Amina to All Participants:	The new firefox is not compatible with webex 
June 24, 2008	    5:32:14 PM	    from midori to All Participants:	(using ...) 
June 24, 2008	    5:32:19 PM	    from Amina to All Participants:	the workarounds dont work too 
June 24, 2008	    5:32:27 PM	    from Jen Deegan to All Participants:	oddly I was using old firefox.
June 24, 2008	    5:32:37 PM	    from Amina to All Participants:	firefox2? 
June 24, 2008	    5:32:42 PM	    from Jen Deegan to All Participants:	yes
June 24, 2008	    5:33:02 PM	    from Jen Deegan to All Participants:	it used to realod continuously anyway, but then eventually just fell over.
June 24, 2008	    5:33:08 PM	    from Nomi Harris to All Attendees:	Oh well.  You're here.  I think we can start now. 
June 24, 2008	    5:33:12 PM	    from Jen Deegan to All Participants:	great
June 24, 2008	    5:33:20 PM	    from Amina to All Participants:	could be a webex problem too 
June 24, 2008	    5:33:24 PM	    from midori to All Participants:	GO did have its Webex upgraded a few weeks back, and I haven't been booted since then. 
June 24, 2008	    5:33:24 PM	    from Jen Deegan to All Participants:	yes
June 24, 2008	    5:33:26 PM	    from Nomi Harris to All Attendees:	I just started looking into a Java profiling tool that looks promising.  It's called YourKit. 
June 24, 2008	    5:33:33 PM	    from Nomi Harris to All Attendees:	Apparently it is the one used by Google and other big companies. 
June 24, 2008	    5:33:35 PM	    from Jen Deegan to All Participants:	sounds good.
June 24, 2008	    5:33:41 PM	    from Jen Deegan to All Participants:	is it expensive?
June 24, 2008	    5:33:42 PM	    from Nomi Harris to All Attendees:	It seems pretty good, and can be hooked into Eclipse (which I didn't try yet). 
June 24, 2008	    5:33:57 PM	    from Nomi Harris to All Attendees:	For academics, it's only like $130 or something. 
June 24, 2008	    5:33:57 PM	    from Nomi Harris to All Attendees:	So, not bad at all. 
June 24, 2008	    5:34:06 PM	    from Jen Deegan to All Participants:	oh that's not so bad.
June 24, 2008	    5:34:24 PM	    from Nomi Harris to All Attendees:	Amina's going to finish her current work with filtered save and the reasoner, and then try YourKit. 
June 24, 2008	    5:34:49 PM	    from Jen Deegan to All Participants:	sounds excellent.
June 24, 2008	    5:34:50 PM	    from Nomi Harris to All Attendees:	Also, Ed has spent a few days debugging some stuff in the reasoner and is going to commit his changes and then go back to working on Apollo. 
June 24, 2008	    5:35:00 PM	    from Nomi Harris to All Attendees:	I think he got pretty fed up with OBO-Edit just in the few days he spent on it. 
June 24, 2008	    5:35:06 PM	    from Jen Deegan to All Participants:	oh dear
June 24, 2008	    5:35:15 PM	    from Nomi Harris to All Attendees:	It is pretty hairy code. 
June 24, 2008	    5:35:57 PM	    from David OS to All Attendees:	Cool. What aspects of the reasoner has he been working on?
June 24, 2008	    5:35:58 PM	    from Nomi Harris to All Attendees:	midori and Jen, I will try to find the gray used for local selection mode in OE1 and use that. 
June 24, 2008	    5:36:07 PM	    from midori to All Participants:	excellent 
June 24, 2008	    5:36:08 PM	    from Jen Deegan to All Participants:	thanks :-)
June 24, 2008	    5:36:10 PM	    from Nomi Harris to All Attendees:	I don't think it's worth making it user-customisable. 
June 24, 2008	    5:36:19 PM	    from Amina to All Participants:	David, Ed was working on incremental reasoning 
June 24, 2008	    5:36:25 PM	    from midori to All Participants:	fair enough; no one else has commented 
June 24, 2008	    5:36:36 PM	    from Jen Deegan to All Participants:	did you know that the source code respository is on the wiki?
June 24, 2008	    5:36:48 PM	    from Nomi Harris to All Attendees:	You mean for OE1? 
June 24, 2008	    5:36:51 PM	    from Jen Deegan to All Participants:	yes
June 24, 2008	    5:36:56 PM	    from Nomi Harris to All Attendees:	Yes, I have the source. 
June 24, 2008	    5:36:58 PM	    from Jen Deegan to All Participants:	great
June 24, 2008	    5:37:26 PM	    from Nomi Harris to All Attendees:	Hey, Tanya! 
June 24, 2008	    5:37:36 PM	    from David OS to All Attendees:	Hi Tanya
June 24, 2008	    5:37:40 PM	    from Karen to All Participants:	Hi Tanya 
June 24, 2008	    5:37:43 PM	    from Nomi Harris to All Attendees:	I wanted to remind everyone that next week is the Week of Testing and Documenting. 
June 24, 2008	    5:37:43 PM	    from Tanya Berardini to All Participants:	Hi !
June 24, 2008	    5:37:58 PM	    from Jen Deegan to All Participants:	I have a question, whenever there's a good moment.
June 24, 2008	    5:38:00 PM	    from Amina to All Participants:	Editors I have a resoner Q: how often do you prefer the forward chanining to the linkpile reasoner 
June 24, 2008	    5:38:02 PM	    from Nomi Harris to All Attendees:	The OBO-Editors have agreed to devote much of the week to testing OE2 and writing user help pages. 
June 24, 2008	    5:38:08 PM	    from Amina to All Participants:	hi Tanya 
June 24, 2008	    5:38:17 PM	    from Jen Deegan to All Participants:	I have no preference
June 24, 2008	    5:38:25 PM	    from Jen Deegan to All Participants:	I don't understand the difference.
June 24, 2008	    5:38:39 PM	    from midori to All Participants:	Same as Jen here ... 
June 24, 2008	    5:38:40 PM	    from Nomi Harris to All Attendees:	According to John, the forward chaining reasoner in OE2 doesn't always get the right answers--have you noticed that? 
June 24, 2008	    5:38:48 PM	    from Jen Deegan to All Participants:	I think that if Chris explained the difference I would come to appreciate that the slower one is the better one.
June 24, 2008	    5:38:48 PM	    from Amina to All Participants:	ok.. I'm testing both  
June 24, 2008	    5:38:56 PM	    from David OS to All Attendees:	I shall be editing the ontology next week so should be able to fit some testing in to that.
June 24, 2008	    5:39:03 PM	    from midori to All Participants:	I haven't worked with it enough ... 
June 24, 2008	    5:39:04 PM	    from Jen Deegan to All Participants:	I hadn't noticed.
June 24, 2008	    5:39:05 PM	    from Nomi Harris to All Attendees:	The slower (LinkPile) is better because the Forward Chaining doesn't work in all situations. 
June 24, 2008	    5:39:18 PM	    from Nomi Harris to All Attendees:	But I'm not clear on exactly what those situations are.  It would be nice to have a test case. 
June 24, 2008	    5:39:21 PM	    from Amina to All Participants:	yes we would have to stop using it in the near future 
June 24, 2008	    5:39:26 PM	    from Jen Deegan to All Participants:	I hardly used it before oboedit 2's graphviewer
June 24, 2008	    5:39:34 PM	    from Tanya Berardini to All Participants:	stop using which one?
June 24, 2008	    5:39:35 PM	    from Nomi Harris to All Attendees:	Also, apparently the Forward Chaining reasoner is not fixable or maintainable (according to Chris). 
June 24, 2008	    5:39:41 PM	    from Amina to All Participants:	the old reasoner 
June 24, 2008	    5:39:52 PM	    from Tanya Berardini to All Participants:	old = LinkPile or
June 24, 2008	    5:39:58 PM	    from Tanya Berardini to All Participants:	old = Forward Chaining?
June 24, 2008	    5:39:58 PM	    from Amina to All Participants:	or atleast put up the cases when it should not be used 
June 24, 2008	    5:40:04 PM	    from Jen Deegan to All Participants:	once the other is faster that won't matter though wil it?
June 24, 2008	    5:40:05 PM	    from Nomi Harris to All Attendees:	old = Forward Chaining 
June 24, 2008	    5:40:07 PM	    from Amina to All Participants:	old = forward chaining 
June 24, 2008	    5:40:14 PM	    from Tanya Berardini to All Participants:	thanks
June 24, 2008	    5:40:25 PM	    from midori to All Participants:	So it sounds like there are good reasons to lay the forward chaining reasoner to rest. I'm happy to take your word for it, and concentrate development and testing on LinkPile. 
June 24, 2008	    5:40:28 PM	    from Nomi Harris to All Attendees:	Right, if we can make the new LinkPile reasoner faster, no one will miss the old Forward Chaining one. 
June 24, 2008	    5:40:36 PM	    from David OS to All Attendees:	The new/slow/linkpile reasoner doesn't work on my ontology.  I got the impression from CHris that the old one doesn't work with non-transitives.
June 24, 2008	    5:40:39 PM	    from Jen Deegan to All Participants:	yes that seems right.
June 24, 2008	    5:40:50 PM	    from midori to All Participants:	But that brings us back to the OE-with-reasoner-on performance issue ... 
June 24, 2008	    5:40:54 PM	    from Nomi Harris to All Attendees:	Right. 
June 24, 2008	    5:41:06 PM	    from Nomi Harris to All Attendees:	midori, I'm trying to figure out why you were getting CPU spikes when you weren't really doing anything. 
June 24, 2008	    5:41:14 PM	    from Nomi Harris to All Attendees:	You didn't have the reasoner on, and did you say you didn't have the Graph Editor open either? 
June 24, 2008	    5:41:25 PM	    from Nomi Harris to All Attendees:	Your latest logfile didn't give us much info. 
June 24, 2008	    5:41:29 PM	    from Jen Deegan to All Participants:	I get that too I think.
June 24, 2008	    5:41:40 PM	    from midori to All Participants:	And lately I've been getting piss-poor (that would be the technical term) performance even with the reasoner off. 
June 24, 2008	    5:41:48 PM	    from Jen Deegan to All Participants:	yes me too
June 24, 2008	    5:41:48 PM	    from Nomi Harris to All Attendees:	I'm adding some more logging statements to parts of the code to help us figure out what you were doing when it started thrashing. 
June 24, 2008	    5:42:01 PM	    from Nomi Harris to All Attendees:	That is discouraging!  I don't know what would have happened to make the performance worse. 
June 24, 2008	    5:42:07 PM	    from midori to All Participants:	Correct: reasoners off, graph editor off. Plain vanilla searches and edits. 
June 24, 2008	    5:42:16 PM	    from Nomi Harris to All Attendees:	Is it possible that the latest version of GO has something tricky in it (loops or something)? 
June 24, 2008	    5:42:18 PM	    from Jen Deegan to All Participants:	I'm not completely sure it's worse recently for me. 
June 24, 2008	    5:42:43 PM	    from Nomi Harris to All Attendees:	Chris has been making some changes in the underlying layer that possibly could be affecting speed (but presumably are helping in other ways). 
June 24, 2008	    5:42:43 PM	    from Jen Deegan to All Participants:	I think we'd have noticed that.
June 24, 2008	    5:42:57 PM	    from David OS to All Attendees:	I haven't noticed newer version being slower. So guess it could be ontology specific.
June 24, 2008	    5:43:10 PM	    from midori to All Participants:	I don't think GO has cycles, 'cos we use OE1 with the don't-allow-cycles setting, and it doesn't complain. Nor does it CPU spike, or go unresponsive. 
June 24, 2008	    5:43:22 PM	    from Nomi Harris to All Attendees:	I haven't noticed worse performance (with the reasoner off).  I've been doing more testing with the reasoner on, and that of course slows it down. 
June 24, 2008	    5:43:47 PM	    from Nomi Harris to All Attendees:	Hi Chris! 
June 24, 2008	    5:44:01 PM	    from Nomi Harris to All Attendees:	midori was just saying that she has been finding OE2 slower lately even with the reasoner off. 
June 24, 2008	    5:44:07 PM	    from Jen Deegan to All Participants:	could we discuss cross products for a sec while chris is here?
June 24, 2008	    5:44:19 PM	    from midori to All Participants:	I could try OE2 with an older GO -- without the regulates relationships (just because I can't think of any other major recent changes). 
June 24, 2008	    5:44:20 PM	    from Amina to All Participants:	Hi Chris 
June 24, 2008	    5:44:21 PM	    from Nomi Harris to All Attendees:	Ok, but first, 
June 24, 2008	    5:44:33 PM	    from Nomi Harris to All Attendees:	Chris, do you think any of your recent changes could be affecting performance? 
June 24, 2008	    5:44:41 PM	    from Chris Mungall to All Participants:	hi 
June 24, 2008	    5:45:05 PM	    from midori to All Participants:	I've been pestering Nomi and Amina about some godawful CPU spikes with OE2 & GO. 
June 24, 2008	    5:45:21 PM	    from Chris Mungall to All Participants:	no 
June 24, 2008	    5:46:07 PM	    from Nomi Harris to All Attendees:	Ok. 
June 24, 2008	    5:46:09 PM	    from Amina to All Participants:	the profiler will definately shed some more light on these issues 
June 24, 2008	    5:46:19 PM	    from Nomi Harris to All Attendees:	Jen, what did you want to discuss about cross products? 
June 24, 2008	    5:46:23 PM	    from Jen Deegan to All Participants:	thanks.
June 24, 2008	    5:46:25 PM	    from Amina to All Participants:	I'll look into it  
June 24, 2008	    5:46:54 PM	    from Jen Deegan to All Participants:	Chris I wondered if it might be good to discuss the idea of retrofitting the cross-products round tripping to 1.101 to take the pressure of OBO-Edit 2
June 24, 2008	    5:46:58 PM	    from Jen Deegan to All Participants:	what do you think?
June 24, 2008	    5:47:20 PM	    from Jen Deegan to All Participants:	off OBO-Edit2 I mean.
June 24, 2008	    5:48:33 PM	    from Jen Deegan to All Participants:	I think I lost him.
June 24, 2008	    5:48:38 PM	    from Chris Mungall to All Participants:	no i'm here 
June 24, 2008	    5:48:44 PM	    from Jen Deegan to All Participants:	oh good.
June 24, 2008	    5:49:12 PM	    from Chris Mungall to All Participants:	i dont think it's a good idea to retrofit anything onto 1.101 
June 24, 2008	    5:49:17 PM	    from Jen Deegan to All Participants:	oh okay then.
June 24, 2008	    5:49:34 PM	    from Nomi Harris to All Attendees:	Would it be a big pain to do that, though, just so the curators could use that 
June 24, 2008	    5:49:39 PM	    from Nomi Harris to All Attendees:	while we try to get OE2 more usable? 
June 24, 2008	    5:49:54 PM	    from Tanya Berardini to All Participants:	Have you looked into the possibility at all?
June 24, 2008	    5:49:58 PM	    from Nomi Harris to All Attendees:	I mean, it's kind of a depressing prospect, 
June 24, 2008	    5:49:59 PM	    from Jen Deegan to All Participants:	it seems to be the only thing that's actually urgent.
June 24, 2008	    5:50:01 PM	    from Tanya Berardini to All Participants:	I mean, it could be easy
June 24, 2008	    5:50:01 PM	    from Nomi Harris to All Attendees:	but it might make sense. 
June 24, 2008	    5:50:07 PM	    from Tanya Berardini to All Participants:	or it could be a huge pain in the #$%.
June 24, 2008	    5:50:14 PM	    from Nomi Harris to All Attendees:	Right, I have no idea. 
June 24, 2008	    5:50:15 PM	    from Tanya Berardini to All Participants:	If the former...
June 24, 2008	    5:50:22 PM	    from Tanya Berardini to All Participants:	it might be worth it.
June 24, 2008	    5:50:46 PM	    from midori to All Participants:	For everyone else: GO wants to deploy cross-products roughly yesterday, but we need one of OE2's cross-product-related features.
June 24, 2008	    5:50:46 PM	    from Chris Mungall to All Participants:	We can make an oe1.102 for bug fixes that are really indering 1.101 users right now 
June 24, 2008	    5:51:12 PM	    from Jen Deegan to All Participants:	I think that is really just cross prodcuts.
June 24, 2008	    5:51:18 PM	    from Nomi Harris to All Attendees:	How hard do you think it would be to add the cross-product support to 1.102, Chris? 
June 24, 2008	    5:51:25 PM	    from Chris Mungall to All Participants:	but we can't do major retrofits since that would entail turning it into oe2, so we may as well work on oe2 anyway 
June 24, 2008	    5:51:43 PM	    from Jen Deegan to All Participants:	perhaps it would be good to see how major this would be?
June 24, 2008	    5:51:48 PM	    from Jen Deegan to All Participants:	just a quick look?
June 24, 2008	    5:52:03 PM	    from Chris Mungall to All Participants:	It's an object model change that could have highly unpredictable side effects and oe1.101 has no test suite. 
June 24, 2008	    5:52:06 PM	    from David OS to All Attendees:	What about XPs doesn't work in 1.101?
June 24, 2008	    5:52:09 PM	    from Nomi Harris to All Attendees:	Hmm. 
June 24, 2008	    5:52:12 PM	    from Nomi Harris to All Attendees:	That doesn't sound good. 
June 24, 2008	    5:52:23 PM	    from Jen Deegan to All Participants:	I think that for 1.101 we are the test suite.
June 24, 2008	    5:52:43 PM	    from Tanya Berardini to All Participants:	We tried but cannot make new 'regulates' cross products.
June 24, 2008	    5:53:06 PM	    from Jen Deegan to All Participants:	how do you mean 'make'?
June 24, 2008	    5:53:07 PM	    from Tanya Berardini to All Participants:	I don't remember the exact error or sequence of events but I'm pretty sure I have it documented in an email somewhere.
June 24, 2008	    5:53:08 PM	    from David OS to All Attendees:	Ahhhh - 'cos non-transitive relation?
June 24, 2008	    5:53:13 PM	    from midori to All Participants:	oooh. ungood. 
June 24, 2008	    5:53:21 PM	    from Jen Deegan to All Participants:	eh?
June 24, 2008	    5:53:27 PM	    from Nomi Harris to All Attendees:	this is in 1.101 or in 2? 
June 24, 2008	    5:53:31 PM	    from Jen Deegan to All Participants:	oh the reasoner?
June 24, 2008	    5:53:31 PM	    from Tanya Berardini to All Participants:	so, create 'regulation of x'
June 24, 2008	    5:53:34 PM	    from Tanya Berardini to All Participants:	in 1.101
June 24, 2008	    5:53:42 PM	    from Tanya Berardini to All Participants:	then try to make it a cross product of
June 24, 2008	    5:53:47 PM	    from Tanya Berardini to All Participants:	'biological regulation'
June 24, 2008	    5:53:47 PM	    from Tanya Berardini to All Participants:	and
June 24, 2008	    5:53:50 PM	    from Tanya Berardini to All Participants:	'x'
June 24, 2008	    5:53:55 PM	    from Tanya Berardini to All Participants:	doesn't happen
June 24, 2008	    5:54:08 PM	    from Tanya Berardini to All Participants:	(using the cross products tab)
June 24, 2008	    5:54:12 PM	    from David OS to All Attendees:	What's the XP relation?
June 24, 2008	    5:54:23 PM	    from Jen Deegan to All Participants:	is this to do with the old reasoner?
June 24, 2008	    5:55:15 PM	    from Tanya Berardini to All Participants:	hang on, I'll pull out an example
June 24, 2008	    5:56:21 PM	    from Tanya Berardini to All Participants:	[Term]
id: GO:0000018
name: regulation of DNA recombination
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of DNA recombination, a process by which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents." [GOC:go_curators, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"]
subset: gosubset_prok
is_a: GO:0051052 ! regulation of DNA metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0006310 ! DNA recombination
relationship: regulates GO:0006310 ! DNA recombination
June 24, 2008	    5:56:40 PM	    from Tanya Berardini to All Participants:	So it's this bit:
June 24, 2008	    5:56:41 PM	    from Tanya Berardini to All Participants:	intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0006310 ! DNA recombination
June 24, 2008	    5:57:05 PM	    from David OS to All Attendees:	The old reasoner doesn't cope with regulates realtions right?
June 24, 2008	    5:57:17 PM	    from David OS to All Attendees:	Have been assuming this is becasue non-trans
June 24, 2008	    5:57:27 PM	    from Tanya Berardini to All Participants:	Not sure.  Chris?
June 24, 2008	    5:57:31 PM	    from midori to All Participants:	I just made one in OE 1.101 ... 
June 24, 2008	    5:57:39 PM	    from midori to All Participants:	[Term] id: GO:0070001 name: regulation of ultradian rhythm namespace: biological_process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007624 ! ultradian rhythm  
June 24, 2008	    5:57:48 PM	    from midori to All Participants:	(oops, lost the newlines) 
June 24, 2008	    5:58:10 PM	    from midori to All Participants:	that's with the reasoner off 
June 24, 2008	    5:58:21 PM	    from midori to All Participants:	name: regulation of ultradian rhythm 
June 24, 2008	    5:58:28 PM	    from midori to All Participants:	namespace: biological_process 
June 24, 2008	    5:58:41 PM	    from Jen Deegan to All Participants:	what was the problem exactly Tanya?
June 24, 2008	    5:58:45 PM	    from midori to All Participants:	intersection_of: GO:0065007 ! biological regulation 
June 24, 2008	    5:58:53 PM	    from midori to All Participants:	intersection_of: regulates GO:0007624 ! ultradian rhythm 
June 24, 2008	    5:59:04 PM	    from midori to All Participants:	it wrote out the intersection_of tags, no problem 
June 24, 2008	    5:59:08 PM	    from Tanya Berardini to All Participants:	Sorry, but I need to run to another meeting.
June 24, 2008	    5:59:11 PM	    from Tanya Berardini to All Participants:	Really sorry!
June 24, 2008	    5:59:15 PM	    from Jen Deegan to All Participants:	see ya
June 24, 2008	    5:59:16 PM	    from Tanya Berardini to All Participants:	I will dig through my email archives.
June 24, 2008	    5:59:17 PM	    from David OS to All Attendees:	BYe
June 24, 2008	    5:59:18 PM	    from midori to All Participants:	how tantalizing! 
June 24, 2008	    5:59:18 PM	    from Nomi Harris to All Attendees:	Bye Tanya 
June 24, 2008	    5:59:26 PM	    from Jen Deegan to All Participants:	a real cliff hanger
June 24, 2008	    5:59:28 PM	    from Tanya Berardini to All Participants:	and send the series of events that triggers the problem.
June 24, 2008	    5:59:30 PM	    from Amina to All Participants:	bye Tanya 
June 24, 2008	    5:59:32 PM	    from Tanya Berardini to All Participants:	Sorry again.
June 24, 2008	    5:59:34 PM	    from Tanya Berardini to All Participants:	Bye.
June 24, 2008	    5:59:40 PM	    from midori to All Participants:	bye, tanya! 
June 24, 2008	    6:00:06 PM	    from Chris Mungall to All Participants:	I am writing up 
June 24, 2008	    6:00:27 PM	    from Jen Deegan to All Participants:	we need one of those little writing pencil icons like in skype.
June 24, 2008	    6:00:31 PM	    from Jen Deegan to All Participants:	so we know when to wait.
June 24, 2008	    6:00:53 PM	    from Jen Deegan to All Participants:	I will submit a feature request.
June 24, 2008	    6:01:17 PM	    from Nomi Harris to All Attendees:	You will submit it to WebEx, you mean? 
June 24, 2008	    6:01:20 PM	    from Jen Deegan to All Participants:	yes
June 24, 2008	    6:01:25 PM	    from Nomi Harris to All Attendees:	Ok. 
June 24, 2008	    6:01:26 PM	    from midori to All Participants:	I'm gonna have to run here too ... 
June 24, 2008	    6:01:33 PM	    from Nomi Harris to All Attendees:	Bye! 
June 24, 2008	    6:01:34 PM	    from Jen Deegan to All Participants:	bye then
June 24, 2008	    6:01:42 PM	    from Nomi Harris to All Attendees:	Jen, we should ask them to color-code the from lines by person. 
June 24, 2008	    6:01:43 PM	    from David OS to All Attendees:	Bye MIdori
June 24, 2008	    6:01:48 PM	    from Amina to All Participants:	Chris, did the fly_anatomyXP file work with obo2linkfile 
June 24, 2008	    6:01:51 PM	    from Nomi Harris to All Attendees:	It's so silly that they're all blue, whereas everyone has a color in the Participants window. 
June 24, 2008	    6:02:05 PM	    from David OS to All Attendees:	Haven't had chance to try it yet.
June 24, 2008	    6:02:11 PM	    from David OS to All Attendees:	Sorry
June 24, 2008	    6:02:50 PM	    from David OS to All Attendees:	Oh erm - what am I sorry for... I don't even know what obo2link is....
June 24, 2008	    6:02:58 PM	    from midori to All Participants:	bye  all!
June 24, 2008	    6:03:04 PM	    from Jen Deegan to All Participants:	bye!
June 24, 2008	    6:03:10 PM	    from David OS to All Attendees:	Was assuming I'd missed something in a mail from Chris
June 24, 2008	    6:03:20 PM	    from Nomi Harris to All Attendees:	David, I haven't seen anything you've said. 
June 24, 2008	    6:03:31 PM	    from Nomi Harris to All Attendees:	Are you sending to All Attendees rather than All Participants? 
June 24, 2008	    6:03:32 PM	    from Jen Deegan to All Participants:	he's on all atttendees
June 24, 2008	    6:03:39 PM	    from Amina to All Participants:	Oh no that was directed to chris 
June 24, 2008	    6:03:51 PM	    from Nomi Harris to All Attendees:	What a dumb way they've set that up.  There's another gripe for the WebEx bug list. 
June 24, 2008	    6:04:01 PM	    from Jen Deegan to All Participants:	3 and counting.
June 24, 2008	    6:04:06 PM	    from Jen Deegan to All Participants:	I'll submit.
June 24, 2008	    6:04:09 PM	    from Nomi Harris to All Participants:	Thanks! 
June 24, 2008	    6:04:18 PM	    from David OS to All Attendees:	Sending to 'All Attendees'. May not be making much sense though :)
June 24, 2008	    6:04:19 PM	    from Amina to All Participants:	david did you have filters on while working with the problematic ontology that doesn't save/commit 
June 24, 2008	    6:05:01 PM	    from Amina to All Participants:	sorry that was daniels bug 
June 24, 2008	    6:05:03 PM	    from Amina to All Participants:	not yours 
June 24, 2008	    6:05:06 PM	    from David OS to All Attendees:	Not sure. But think the commit bug now fixed. Worked after I deleted perspectives are recommended by NOmi
June 24, 2008	    6:05:27 PM	    from David OS to All Attendees:	as recommended...
June 24, 2008	    6:05:36 PM	    from Nomi Harris to All Participants:	David, change the "Send to" pulldown to "All Participants". 
June 24, 2008	    6:06:01 PM	    from David OS to All Participants:	Done
June 24, 2008	    6:06:16 PM	    from Amina to All Participants:	ok thats good 
June 24, 2008	    6:06:19 PM	    from David OS to All Participants:	Don't know how that got changed.
June 24, 2008	    6:06:48 PM	    from David OS to All Participants:	Who
June 24, 2008	    6:07:02 PM	    from Nomi Harris to All Participants:	Who what? 
June 24, 2008	    6:07:03 PM	    from David OS to All Participants:	Who's not been seeing my posts then?
June 24, 2008	    6:07:04 PM	    from Karen to All Participants:	You joined before Nomi did. For some reason, if you join before the host does, then the default setting is only to all attendees 
June 24, 2008	    6:07:08 PM	    from Nomi Harris to All Participants:	Only me. 
June 24, 2008	    6:07:12 PM	    from Amina to All Participants:	Nomi couldnt see it 
June 24, 2008	    6:07:17 PM	    from Amina to All Participants:	since shes the host 
June 24, 2008	    6:07:27 PM	    from Nomi Harris to All Participants:	Ah.  Thanks, Karen.  So whenever I join and people are already in the meeting, I should remind everyone to change their Send to. 
June 24, 2008	    6:07:31 PM	    from David OS to All Participants:	Ahh - OK. Sorry NOmi
June 24, 2008	    6:07:37 PM	    from Amina to All Participants:	and you were only sending it out to all attendees 
June 24, 2008	    6:07:39 PM	    from Nomi Harris to All Participants:	Otherwise, it just looks like people are being quiet. 
June 24, 2008	    6:07:46 PM	    from Nomi Harris to All Participants:	It's ok, David, not your fault. 
June 24, 2008	    6:07:52 PM	    from Nomi Harris to All Participants:	Anyway, please continue... 
June 24, 2008	    6:07:53 PM	    from Chris Mungall to All Participants:	http://wiki.geneontology.org/index.php/OBO-Edit:Why_xps_wont_work_for_GO_in_OE1 
June 24, 2008	    6:08:05 PM	    from David OS to All Participants:	"Otherwise, it just looks like people are being quiet." And that wouldn't be like me at all...
June 24, 2008	    6:08:23 PM	    from Jen Deegan to All Participants:	reading...
June 24, 2008	    6:08:55 PM	    from Jen Deegan to All Participants:	xp links (ie. necessary and sufficient conditions) alongside normal links (ie. necessary conditions): Eh?
June 24, 2008	    6:09:16 PM	    from Jen Deegan to All Participants:	is that just intersection ones then?
June 24, 2008	    6:09:31 PM	    from Jen Deegan to All Participants:	yes I see
June 24, 2008	    6:10:37 PM	    from Jen Deegan to All Participants:	Thanks, that makes it very clear.
June 24, 2008	    6:11:12 PM	    from Chris Mungall to All Participants:	good. As you can see there may be some awful hack to get round this but we must avoid hacks 
June 24, 2008	    6:11:24 PM	    from Jen Deegan to All Participants:	even in the short term?
June 24, 2008	    6:12:02 PM	    from Jen Deegan to All Participants:	that taxon project is one big hack right now.
June 24, 2008	    6:13:08 PM	    from David OS to All Participants:	Interesting. I've been avoiding duplicating is_a and genus like this.  Get regular is_a back when I use the reasoner to write infered links before a release. You can't do this for GO?
June 24, 2008	    6:14:06 PM	    from David OS to All Participants:	Is this because you use repair mode rather than making all infered links?
June 24, 2008	    6:15:23 PM	    from Chris Mungall to All Participants:	exactly. I would state it as "it is because we use the reasoner in repair mode rather than depending on the reasoner to infer all inferrable links during an editing session" 
June 24, 2008	    6:15:49 PM	    from Chris Mungall to All Participants:	One option is to abandon repair mode for gene_ontology_write 
June 24, 2008	    6:15:54 PM	    from David OS to All Participants:	Because you want to check and validate all infered links?
June 24, 2008	    6:16:19 PM	    from Jen Deegan to All Participants:	and go to continuous reasoner or to hard wired links?
June 24, 2008	    6:16:54 PM	    from Chris Mungall to All Participants:	Everyone editing this uses OE1 with the reasoner on constantly, with the regulation xps loaded, and never asserts an is_a links between regulation terms if it can be implied 
June 24, 2008	    6:17:19 PM	    from Chris Mungall to All Participants:	OE1 may be up to this. This is exactly how SO works. 
June 24, 2008	    6:17:23 PM	    from Jen Deegan to All Participants:	there would be computer speed problems with that. 
June 24, 2008	    6:17:28 PM	    from Chris Mungall to All Participants:	Testing required. 
June 24, 2008	    6:17:53 PM	    from Jen Deegan to All Participants:	I used to use the reasoner on 1.101 but I have to turn it off when I can as I can't run webex and skype at the same time. 
June 24, 2008	    6:18:05 PM	    from Chris Mungall to All Participants:	David: the reason we plan to use repair mode with GO is to avoid making ediotrs utterly dependent on the reasoner 
June 24, 2008	    6:18:28 PM	    from Chris Mungall to All Participants:	for SO Karen is utterly dependent on the reasoner but it's a smaller ontology 
June 24, 2008	    6:18:43 PM	    from Jen Deegan to All Participants:	Do you think it's CPU rather than ram that is needed for this?
June 24, 2008	    6:18:51 PM	    from Nomi Harris to All Participants:	But right now, the LinkPile reasoner can't even finish on SO. 
June 24, 2008	    6:18:53 PM	    from Jen Deegan to All Participants:	we could get more ram, but more cpu is harder.
June 24, 2008	    6:19:09 PM	    from Nomi Harris to All Participants:	I would like to find the smallest subset of SO for which the reasoner can't finish, 
June 24, 2008	    6:19:16 PM	    from Chris Mungall to All Participants:	Nomi: that's solvable 
June 24, 2008	    6:19:17 PM	    from Nomi Harris to All Participants:	in order to help us track down where it's getting stuck. 
June 24, 2008	    6:20:49 PM	    from Jen Deegan to All Participants:	LinkPile is the new one is it?
June 24, 2008	    6:21:01 PM	    from Amina to All Participants:	yes jen 
June 24, 2008	    6:21:06 PM	    from Nomi Harris to All Participants:	Yes 
June 24, 2008	    6:21:23 PM	    from Jen Deegan to All Participants:	I think all the problems in OBO-Edit2 are solvable but it will take a lot of time.
June 24, 2008	    6:21:24 PM	    from Chris Mungall to All Participants:	Anyway, that's the situation for OE1, the reasoner, and regulation xps. If we want to get the regulation xps in the core ontology before OE2 then the solution is to abandon repair mode, go full hog, and buy Jen a decent machine (which is far less expensiv
June 24, 2008	    6:21:47 PM	    from Jen Deegan to All Participants:	:-)
June 24, 2008	    6:21:51 PM	    from Jen Deegan to All Participants:	I could get behind that.
June 24, 2008	    6:21:57 PM	    from Chris Mungall to All Participants:	e than retrofitting oe1) 
June 24, 2008	    6:22:59 PM	    from Jen Deegan to All Participants:	Shoudl we be seriously considering that?
June 24, 2008	    6:23:13 PM	    from Jen Deegan to All Participants:	it seems likeit would take a lot of pressure off oboedit2 development
June 24, 2008	    6:23:52 PM	    from Jen Deegan to All Participants:	The last thing we want is to force OBO-Edit 2 out before it is ready just because we need cross prodcuts.
June 24, 2008	    6:24:00 PM	    from Chris Mungall to All Participants:	I think there will be no less pressure on OE2 development, but that ishouldnt factor into the equation anyway 
June 24, 2008	    6:24:14 PM	    from Jen Deegan to All Participants:	why do you think that?
June 24, 2008	    6:24:16 PM	    from Nomi Harris to All Participants:	I agree with Jen 
June 24, 2008	    6:24:19 PM	    from Jen Deegan to All Participants:	nothing else is nearly so pressing
June 24, 2008	    6:24:42 PM	    from Jen Deegan to All Participants:	there is a real risk just now that oboedit gets rushed and ends up being like DAG-Edit.
June 24, 2008	    6:24:46 PM	    from Jen Deegan to All Participants:	(buggy)
June 24, 2008	    6:25:00 PM	    from Chris Mungall to All Participants:	OE2 will not be released before it is ready 
June 24, 2008	    6:25:17 PM	    from Jen Deegan to All Participants:	but surely you would like to have the cross products sooner?
June 24, 2008	    6:25:26 PM	    from Jen Deegan to All Participants:	and if it just means we need to run the reasoner on 1.101
June 24, 2008	    6:25:36 PM	    from Jen Deegan to All Participants:	am I missing something?
June 24, 2008	    6:25:58 PM	    from Jen Deegan to All Participants:	maybe we should test to see what the actual speed implications are?
June 24, 2008	    6:26:56 PM	    from Chris Mungall to All Participants:	Yes, you should go ahead and do that anyway. It was my hope that everyone would be regularly loading the xps such as the regulation xps into OE1 and OE2 anyway 
June 24, 2008	    6:26:57 PM	    from David OS to All Participants:	1.101 reasoner and old-reasoner in beta2 are both working for me to correctly infer links from XP before a release.  I haven't missed being able to see these implied links while editing.
June 24, 2008	    6:27:40 PM	    from David OS to All Participants:	Although I still don't have many XP terms.
June 24, 2008	    6:27:56 PM	    from Jen Deegan to All Participants:	what file should I be using for this Chris?
June 24, 2008	    6:28:07 PM	    from Chris Mungall to All Participants:	It is as more a function of ontology size as # of xp terms; though there are many factors 
June 24, 2008	    6:28:38 PM	    from Chris Mungall to All Participants:	http://wiki.geneontology.org/index.php/XP:biological_process_xp_regulation 
June 24, 2008	    6:28:59 PM	    from Chris Mungall to All Participants:	I will write some additional notes on this page hold on 
June 24, 2008	    6:29:07 PM	    from Jen Deegan to All Participants:	thanks.
June 24, 2008	    6:29:16 PM	    from Nomi Harris to All Participants:	Thanks, Chris. 
June 24, 2008	    6:31:26 PM	    from Nomi Harris to All Participants:	Are we done for today? 
June 24, 2008	    6:31:39 PM	    from Jen Deegan to All Participants:	I think Chris is writing maybe
June 24, 2008	    6:31:51 PM	    from Jen Deegan to All Participants:	this was a good discussion though
June 24, 2008	    6:31:54 PM	    from Jen Deegan to All Participants:	useful
June 24, 2008	    6:33:06 PM	    from Jen Deegan to All Participants:	I am starting the reasoner on 1.101.
June 24, 2008	    6:33:43 PM	    from Chris Mungall to All Participants:	http://wiki.geneontology.org/index.php/XP:biological_process_xp_regulation#Alternate_plan 
June 24, 2008	    6:34:01 PM	    from Chris Mungall to All Participants:	I have also added a note to http://wiki.geneontology.org/index.php/OBO-Edit:Why_xps_wont_work_for_GO_in_OE1 
June 24, 2008	    6:34:13 PM	    from Jen Deegan to All Participants:	title is informative. :-)
June 24, 2008	    6:34:26 PM	    from Chris Mungall to All Participants:	to the effect that it wont work only if we stick to repair mode 
June 24, 2008	    6:34:38 PM	    from Jen Deegan to All Participants:	oh right.
June 24, 2008	    6:34:39 PM	    from Jen Deegan to All Participants:	yes
June 24, 2008	    6:35:02 PM	    from Chris Mungall to All Participants:	Make sure David and Tanya are aware of this. Can someone start an ontology mai list for GO? 
June 24, 2008	    6:35:15 PM	    from Nomi Harris to All Participants:	Isn't there one already? 
June 24, 2008	    6:35:19 PM	    from Jen Deegan to All Participants:	nope
June 24, 2008	    6:35:25 PM	    from David OS to All Participants:	SUrely several
June 24, 2008	    6:35:26 PM	    from Jen Deegan to All Participants:	we need to get say so from David and Midori.
June 24, 2008	    6:35:38 PM	    from Jen Deegan to All Participants:	we need just an ontology developer general one.
June 24, 2008	    6:35:48 PM	    from Jen Deegan to All Participants:	Chris do you want to mail midori and David and cc me
June 24, 2008	    6:35:56 PM	    from Jen Deegan to All Participants:	I will vigorously second.
June 24, 2008	    6:36:11 PM	    from Karen to All Participants:	Yea, I've asked for a GO ontology developers one several times and been ignored... 
June 24, 2008	    6:36:16 PM	    from Jen Deegan to All Participants:	me too.
June 24, 2008	    6:36:17 PM	    from Nomi Harris to All Participants:	Weird. 
June 24, 2008	    6:36:22 PM	    from Nomi Harris to All Participants:	I would think you'd totally have one already. 
June 24, 2008	    6:36:33 PM	    from Jen Deegan to All Participants:	Maybe cc oboedit list then.
June 24, 2008	    6:36:39 PM	    from Jen Deegan to All Participants:	vigorous seconding needed from all.
June 24, 2008	    6:37:15 PM	    from David OS to All Participants:	"Maybe cc oboedit list then." Yep - keep us posted.
June 24, 2008	    6:37:20 PM	    from Karen to All Participants:	Nope, apparently there was some thought that the OEWG was sufficient, but it isn't entirely overlapping wtih GO developers, nor is it always appropriate to discuss GO specific issues at OEWG 
June 24, 2008	    6:37:31 PM	    from Jen Deegan to All Participants:	when you say batch mode
June 24, 2008	    6:37:42 PM	    from Jen Deegan to All Participants:	do you mean we just run it at the end of an editing session?
June 24, 2008	    6:37:47 PM	    from Jen Deegan to All Participants:	or all the time?
June 24, 2008	    6:38:28 PM	    from Nomi Harris to All Participants:	BRB 
June 24, 2008	    6:38:33 PM	    from Jen Deegan to All Participants:	eh?
June 24, 2008	    6:39:19 PM	    from Chris Mungall to All Participants:	I'm leaving tomorrow for a week but please keep the discussion going on either the wg list or the new ontdev list 
June 24, 2008	    6:39:29 PM	    from Jen Deegan to All Participants:	okay.
June 24, 2008	    6:39:31 PM	    from Jen Deegan to All Participants:	will do
June 24, 2008	    6:39:32 PM	    from Jen Deegan to All Participants:	thanks.
June 24, 2008	    6:39:35 PM	    from Jen Deegan to All Participants:	with testing.
June 24, 2008	    6:39:54 PM	    from Jen Deegan to All Participants:	which files exactly?
June 24, 2008	    6:39:57 PM	    from Jen Deegan to All Participants:	do I load?
June 24, 2008	    6:40:08 PM	    from Chris Mungall to All Participants:	see the README 
June 24, 2008	    6:40:25 PM	    from Jen Deegan to All Participants:	where?
June 24, 2008	    6:40:25 PM	    from Chris Mungall to All Participants:	go is currently withpostneg but lacking B->F links 
June 24, 2008	    6:40:31 PM	    from Chris Mungall to All Participants:	in the directory 
June 24, 2008	    6:40:37 PM	    from Jen Deegan to All Participants:	I don't see it?
June 24, 2008	    6:40:50 PM	    from Chris Mungall to All Participants:	have to go. it should all be thoroughly documented. 
June 24, 2008	    6:41:00 PM	    from Chris Mungall to All Participants:	byee! 
June 24, 2008	    6:41:02 PM	    from Jen Deegan to All Participants:	noooo!
June 24, 2008	    6:41:09 PM	    from Jen Deegan to All Participants:	gosh darn.
June 24, 2008	    6:41:44 PM	    from Jen Deegan to All Participants:	It has been a day of cliff hangers.
June 24, 2008	    6:41:52 PM	    from Jen Deegan to All Participants:	I guess we are done now.
June 24, 2008	    6:42:05 PM	    from Jen Deegan to All Participants:	I will mail Midori and David and ask for a mailing list.
June 24, 2008	    6:42:22 PM	    from Jen Deegan to All Participants:	Thanks Nomi and Amina.
June 24, 2008	    6:42:27 PM	    from Jen Deegan to All Participants:	shall we off now?
June 24, 2008	    6:42:37 PM	    from Amina to All Participants:	yes I think so...  
June 24, 2008	    6:42:49 PM	    from David OS to All Participants:	OK. Bye.
June 24, 2008	    6:42:52 PM	    from Amina to All Participants:	thanks everyone 
June 24, 2008	    6:42:52 PM	    from Jen Deegan to All Participants:	byeeeeeeeeeeeee
June 24, 2008	    6:42:57 PM	    from David OS to All Participants:	cheers
June 24, 2008	    6:42:59 PM	    from Amina to All Participants:	bye 
June 24, 2008	    6:43:03 PM	    from Amina to All Participants:	Cheers 
June 24, 2008	    6:43:09 PM	    from Karen to All Participants:	bye :) 
June 24, 2008	    6:45:15 PM	    from Nomi Harris to All Participants:	Bye!