OE Webex 15Jul08

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07/15/2008    09:27:39 AM    from Amina:	Hi Midori
07/15/2008    09:27:40 AM    from midori:	hello!
07/15/2008    09:28:23 AM    from Amina:	Hi Jen
07/15/2008    09:28:32 AM    from Jen Deegan:	Hi!
07/15/2008    09:28:35 AM    from Jen Deegan:	How's it going?
07/15/2008    09:29:04 AM    from Jen Deegan:	Amina, could I tell you a quick thing before the meeting starts?
07/15/2008    09:29:07 AM    from Amina:	good..hows it going with you
07/15/2008    09:29:11 AM    from Amina:	yea sure
07/15/2008    09:29:13 AM    from Jen Deegan:	great thanks.
07/15/2008    09:29:24 AM    from Jen Deegan:	I was looking at the obomerge interface in oboedit
07/15/2008    09:29:52 AM    from Jen Deegan:	and I realised that all the feedback that is meant to show on the screen for the users had been converted from sys.out commands to logger commands.
07/15/2008    09:30:06 AM    from Amina:	yes thats right
07/15/2008    09:30:08 AM    from Jen Deegan:	I have converted it back but would you like me to duplicate them all so they also show as logger commands?
07/15/2008    09:30:25 AM    from Jen Deegan:	they needs to be there as sys.out commands for the application to work.
07/15/2008    09:30:30 AM    from Nomi Harris:	The logger calls should print on the terminal as well as in the logfile
07/15/2008    09:30:38 AM    from Jen Deegan:	oh I see.
07/15/2008    09:30:45 AM    from Nomi Harris:	Do they not?
07/15/2008    09:30:55 AM    from Jen Deegan:	so how would I capture them and put them on the gui?
07/15/2008    09:30:59 AM    from Amina:	ok so this is how we can achieve both objectives - use logger.debug("your sys.out statement")
07/15/2008    09:31:12 AM    from Jen Deegan:	currently I am diverting system.setOut and setErr to the gui.
07/15/2008    09:31:18 AM    from Amina:	you can use debug or info
07/15/2008    09:31:21 AM    from Jen Deegan:	Ah!
07/15/2008    09:31:24 AM    from Jen Deegan:	Fab!
07/15/2008    09:31:30 AM    from Jen Deegan:	I thought you might have a cunning plan
07/15/2008    09:31:37 AM    from Nomi Harris:	(By the way, I wanted to say: welcome back, Jen!)
07/15/2008    09:31:47 AM    from Jen Deegan:	Thanks Nomi :-)
07/15/2008    09:31:55 AM    from Amina:	once you type logger. (if developing with eclipse) it will show you all the options available
07/15/2008    09:31:58 AM    from Jen Deegan:	so I just do a straight conversion then.
07/15/2008    09:32:04 AM    from Jen Deegan:	brilliant.
07/15/2008    09:32:08 AM    from Jen Deegan:	thanks for that.
07/15/2008    09:32:17 AM    from Amina:	how was your vacation Jen?
07/15/2008    09:32:27 AM    from Jen Deegan:	It was really great actually, thanks for asking.
07/15/2008    09:32:44 AM    from Amina:	I was looking at the filtered save bug report you updated this morning
07/15/2008    09:32:45 AM    from Jen Deegan:	I pottered around Dublin for ten days and now I feel properly exercised.
07/15/2008    09:32:58 AM    from Jen Deegan:	Did it make any sense?
07/15/2008    09:33:02 AM    from Amina:	oh wow.. sounds like an exciting trip
07/15/2008    09:33:04 AM    from Nomi Harris:	Sounds nice.  I've never been to Ireland but I'd like to someday.
07/15/2008    09:33:14 AM    from Jen Deegan:	It's really quite a fun place.
07/15/2008    09:33:56 AM    from Amina:	the latest gene_ontology_edit seems gives a fatal error while trying to do a save as..
07/15/2008    09:34:10 AM    from Jen Deegan:	oh dear
07/15/2008    09:34:24 AM    from Jen Deegan:	I will have a look
07/15/2008    09:34:33 AM    from Amina:	Definition of GO:0008467 cannot contain extended characters
07/15/2008    09:34:48 AM    from Nomi Harris:	I'm trying the July 1 version now.
07/15/2008    09:34:53 AM    from Amina:	sorry I'm so slow - OE is running on the linux machine
07/15/2008    09:35:06 AM    from Nomi Harris:	I'll be right back, I'm getting a cup of tea
07/15/2008    09:35:27 AM    from Amina:	did you work with the latest ontology for the example you posted today Jen
07/15/2008    09:35:39 AM    from Amina:	Hi David
07/15/2008    09:35:45 AM    from David OS:	Hiya
07/15/2008    09:35:49 AM    from midori:	Huh. I though Colin spotted that, and I fixed it, weeks ago. (the def characters)
07/15/2008    09:36:01 AM    from David OS:	Did you just mention something about filtered save?
07/15/2008    09:36:04 AM    from Jen Deegan:	No I would have been using a branch file.
07/15/2008    09:36:40 AM    from Amina:	Yes Jen had another example for when its not workin g
07/15/2008    09:37:04 AM    from David OS:	Any progress in fixing this one?
07/15/2008    09:37:29 AM    from Jen Deegan:	I think it may be that it's not meant to do what I want it to do, or that maybe I just don't know how to work it.
07/15/2008    09:37:55 AM    from Amina:	Just to hive everyone a quick update on the filtered save - I have throughly investigated the filter for write ontology - I'm not convinced I've fixed it
07/15/2008    09:38:34 AM    from Jen Deegan:	I don't really understand the link filter.
07/15/2008    09:38:41 AM    from Amina:	Jen did you try the same filter in the search panel?
07/15/2008    09:38:58 AM    from Jen Deegan:	I don't think it would really make sense in that panel.
07/15/2008    09:39:02 AM    from Jen Deegan:	I'm not sure.
07/15/2008    09:39:25 AM    from Jen Deegan:	I just want to be able to get a flat list of terms that have a given relationship type.
07/15/2008    09:39:32 AM    from Jen Deegan:	I could try it and see what happens.
07/15/2008    09:39:37 AM    from Nomi Harris:	Yes, try it.
07/15/2008    09:39:38 AM    from Amina:	I just tried it
07/15/2008    09:39:44 AM    from Jen Deegan:	Did it work?
07/15/2008    09:39:48 AM    from Amina:	Use the wildcard search
07/15/2008    09:39:52 AM    from Nomi Harris:	A filter that works for search should work for save, and vice versa
07/15/2008    09:39:54 AM    from midori:	I think Harold was after something similar ...
07/15/2008    09:39:55 AM    from Jen Deegan:	ok
07/15/2008    09:40:01 AM    from Nomi Harris:	although some filters might be more useful in one context or the other.
07/15/2008    09:40:09 AM    from Amina:	with "*" in the value field
07/15/2008    09:40:22 AM    from Jen Deegan:	ok I'll try that.
07/15/2008    09:40:27 AM    from Amina:	Midori - I managed to help Harold solve his problem
07/15/2008    09:40:42 AM    from midori:	oh good
07/15/2008    09:41:01 AM    from Amina:	or rather - show him how to do the search he needed in OE2
07/15/2008    09:41:39 AM    from Nomi Harris:	gene_ontology_edit.obo from July 1 doesn't have any fatal errors.  I'm trying the latest version now.
07/15/2008    09:41:54 AM    from Jen Deegan:	what did you do in the search with the *?
07/15/2008    09:42:06 AM    from Jen Deegan:	Is it the link search?
07/15/2008    09:42:16 AM    from Amina:	Jen - Select terms that "have" a ""Any text field" that "contains" the value "*" in "Self" that can be reached via "part_of"
07/15/2008    09:42:16 AM    from Jen Deegan:	[type][name] something?
07/15/2008    09:42:29 AM    from Jen Deegan:	wow
07/15/2008    09:42:37 AM    from Amina:	does that help?
07/15/2008    09:42:41 AM    from Jen Deegan:	yes
07/15/2008    09:42:46 AM    from Jen Deegan:	I'll try it
07/15/2008    09:42:49 AM    from Nomi Harris:	Thanks, Amina
07/15/2008    09:42:58 AM    from Nomi Harris:	Maybe we should add this to the help page about searching.
07/15/2008    09:43:01 AM    from Nomi Harris:	Examples are always good.
07/15/2008    09:43:31 AM    from Jen Deegan:	where do I put the part_of bit?
07/15/2008    09:43:47 AM    from Amina:	sorry I cant paste or share screen - I'll get my linux workstation hooked on so I can do that
07/15/2008    09:44:08 AM    from Jen Deegan:	is it all in the plain search or shoudl I use the link search?
07/15/2008    09:44:27 AM    from midori:	hmmm. when I select 'self' I don't get the 'can be reached via' pulldown
07/15/2008    09:44:36 AM    from Amina:	your right
07/15/2008    09:44:40 AM    from midori:	it only appears when I select 'ancestor' or 'descendant'
07/15/2008    09:45:03 AM    from Jen Deegan:	Ah! Got it. Thanks.
07/15/2008    09:45:17 AM    from Amina:	I was working with ancestor
07/15/2008    09:45:25 AM    from midori:	ok
07/15/2008    09:45:31 AM    from Amina:	and went back to self - but OE didnt refresh
07/15/2008    09:46:07 AM    from Amina:	So I did this in plain search but I'm sure the Link filter panel should be able to do this
07/15/2008    09:46:21 AM    from Jen Deegan:	It is thinking hard now.
07/15/2008    09:47:47 AM    from David OS:	"from Amina to All Participants:
Just to hive everyone a quick update on the filtered save - I have throughly investigated the filter for write ontology - I'm not convinced I've fixed it"  Could you expand on this a bit?  Are there bigger issues than getting the reasoner to work on query filters as it does with regular filters/searches?
07/15/2008    09:48:12 AM    from Amina:	for link filter - Select links where "Type" that "have" and all terms from the search panel
07/15/2008    09:49:14 AM    from Amina:	David the existing code for both those filters works differently - I'm trying to diagnose which would be there correct way to go
07/15/2008    09:49:39 AM    from Jen Deegan:	I got a really funny result from that save.
07/15/2008    09:49:43 AM    from Nomi Harris:	BTW, Tanya just emailed me, "Sorry I'm not in but every time I try to enter the meeting, my browser crashes. This hasn't happened before!"
07/15/2008    09:49:44 AM    from David OS:	Which both?
07/15/2008    09:49:53 AM    from Amina:	I can get filtered save to save the correcy terms in write ontology
07/15/2008    09:50:19 AM    from Amina:	the search panel and save as filters i mean
07/15/2008    09:50:24 AM    from Jen Deegan:	I searched the criteria you said but with the disjoint relationship and only got three terms
07/15/2008    09:50:35 AM    from Jen Deegan:	but it was not the three I expected.
07/15/2008    09:51:19 AM    from David OS:	Is the reasoner on?
07/15/2008    09:51:28 AM    from Jen Deegan:	me?
07/15/2008    09:51:35 AM    from Amina:	I'll try to post the filtered save fix by tomorrow - I'm not convinced it will work in all siuations though
07/15/2008    09:52:02 AM    from Jen Deegan:	thanks.
07/15/2008    09:52:42 AM    from Nomi Harris:	midori, about % being accepted as a legal character, since that change was made on purpose (by someone), if you are ok with it, let's leave it as is and document it.  Ok?
07/15/2008    09:52:51 AM    from David OS:	Jen: The search panel often gives nonsense results for complex searches if the reasoner is not on. May be worth comparing results for on vs off.
07/15/2008    09:53:10 AM    from Jen Deegan:	oh right. Good to know.
07/15/2008    09:53:23 AM    from midori:	Nomi - % is fine; just wanted to make sure it WAS on purpose.
07/15/2008    09:53:28 AM    from Nomi Harris:	David, we were talking about that issue yesterday, but couldn't come up with a simple automated way to decide whether a given search requires the reasoner
07/15/2008    09:53:42 AM    from Amina:	I got 3 terms for Jens search with the reasoner off too
07/15/2008    09:53:43 AM    from Nomi Harris:	Chris may have some ideas.
07/15/2008    09:54:06 AM    from Jen Deegan:	I am trying with the reasoner on.
07/15/2008    09:54:17 AM    from Nomi Harris:	Did you all hear that Chris managed to get the (new) reasoner to run much much faster on SO and Fly Anatomy?
07/15/2008    09:54:25 AM    from midori:	yes :)
07/15/2008    09:54:31 AM    from Nomi Harris:	That is good news.
07/15/2008    09:54:39 AM    from David OS:	Amina: It'd be great if I could test the save fix you've made. Even if it's not perfect.  As it's totally broken right now for filters requireing the reaonser, a partial fix could be an improvement.
07/15/2008    09:54:40 AM    from Jen Deegan:	weird! Much faster with the reasoner on, and no results this time.
07/15/2008    09:54:54 AM    from Amina:	Jen - maybe we need to work more on the search terms
07/15/2008    09:54:56 AM    from Nomi Harris:	He had to turn off the symmetry rule.  Not sure whether that has any negative effects.
07/15/2008    09:55:08 AM    from Jen Deegan:	good idea.
07/15/2008    09:55:20 AM    from Jen Deegan:	maybe another time? I seem to be talking over people.
07/15/2008    09:55:38 AM    from Nomi Harris:	Amina will be away this Thursday through next Wednesday, just so you know.
07/15/2008    09:55:46 AM    from Jen Deegan:	thanks.
07/15/2008    09:55:51 AM    from midori:	Is the new improved reasoner available to test on GO?
07/15/2008    09:55:52 AM    from Amina:	yes I'm on skype - I'll try your search again after the meeting
07/15/2008    09:56:11 AM    from Jen Deegan:	I have to go after the meeting but I'll try tomorrow.
07/15/2008    09:56:26 AM    from Amina:	ok
07/15/2008    09:56:30 AM    from Nomi Harris:	midori, I will do a release later this week and you can try it.  I don't think performance on GO is affected.  It's not really new & improved; he just fixed an issue that was making it run forever on SO and fly anatomy.
07/15/2008    09:56:50 AM    from Nomi Harris:	Removing that disjoint_from filter helped a lot, though, didn't it?
07/15/2008    09:56:59 AM    from midori:	oh well ... will be good for me to get back into OE2 testin g anyway.
07/15/2008    09:57:01 AM    from Jen Deegan:	yes it did.
07/15/2008    09:57:37 AM    from midori:	As for removing that filter, I think it helped me too, but I've done very little testing using GO lately. I'll keep you posted.
07/15/2008    09:57:43 AM    from Nomi Harris:	Jen, I'm not sure why your text commits are taking longer than mine.  Could just be a matter of different computers and different stuff running on them.
07/15/2008    09:57:47 AM    from David OS:	Yep - the problem was bogus 'symmetric' relations in the two ontologies (not likely to ever be valid at the type level - so wonder why OBOedit gives use the option)
07/15/2008    09:57:55 AM    from Nomi Harris:	You can send me your oboedit-beta config directory and I can take a look.
07/15/2008    09:57:56 AM    from David OS:	us
07/15/2008    09:58:33 AM    from Nomi Harris:	David, Chris made it so the reasoner ignores those symmetric relations for now, though it sounds like they should be removed from the ontologies anyway.
07/15/2008    09:58:36 AM    from Jen Deegan:	yes I'll do that. My computer is very fast and gives me no other speed problems so it would be good to have a look.
07/15/2008    09:58:58 AM    from Nomi Harris:	Has anyone other than midori and Jen had a look at the proposed reorganization of the help guide, http://wiki.geneontology.org/index.php/New_O E_user_guide_TOC? I'd like to make those changes this week.
07/15/2008    09:59:19 AM    from Nomi Harris:	Oops, URL got a space in it:  http://wiki.geneontology.org/index.php/New_O  E_user_guide_TOC
07/15/2008    09:59:20 AM    from midori:	Melissa made a couple of suggestions, which sounded good to me.
07/15/2008    09:59:31 AM    from Nomi Harris:	Whoa, weird, it stuck a space in it again.
07/15/2008    09:59:54 AM    from midori:	lemme try ...
07/15/2008    09:59:55 AM    from midori:	http://wiki.geneontology.org/index.php/New_OE_user_guide_TOC
07/15/2008    09:59:57 AM    from Nomi Harris:	Ok, sounds like I can go ahead with the reorg.  I don't expect it to be massively controversial.  It just affects the Table of Contents.
07/15/2008    10:00:22 AM    from Nomi Harris:	On another topic, I've been working on getting Verification checks to happen "On text commit".  Strangely, that capability doesn't appear to have been implement ed, even though it's offered as an option.
07/15/2008    10:00:41 AM    from Nomi Harris:	It seems to me this is a more useful option than "During text edit", which can be annoying, as it tends to whine about misspelled words while  you're still in the middle of typing them.
07/15/2008    10:01:06 AM    from midori:	Bizarre, given that "on text commit" was when the OE1 checks marked "on text edit"  actually happened.
07/15/2008    10:01:19 AM    from Nomi Harris:	I think it was something that never made it into OE2.
07/15/2008    10:01:34 AM    from Nomi Harris:	It's not just buggy; there's simply no code that would actually do the checks on text commit.
07/15/2008    10:01:36 AM    from Jen Deegan:	I quite like the spell check as I type.
07/15/2008    10:01:49 AM    from Nomi Harris:	Ok, I'll leave that as an option.
07/15/2008    10:01:55 AM    from Jen Deegan:	thanks :-)
07/15/2008    10:02:03 AM    from midori:	An yone who doesn't like it can turn it off.
07/15/2008    10:02:12 AM    from Nomi Harris:	One tricky aspect of fixing the "on text commit" behavior is to make it work properly for autocommit and manual commit.
07/15/2008    10:02:42 AM    from midori:	Not having "on text commit" work would amount to losing a bit of functionality compared to OE1.
07/15/2008    10:02:42 AM    from Nomi Harris:	Once I get it fixed, we might want to change the default configuration of some of the verification checks--turn some off "during text edit" and make them "on text commit" instead.
07/15/2008    10:02:49 AM    from midori:	makes sense
07/15/2008    10:03:00 AM    from Nomi Harris:	Oh, I agree, that's why I think it's a bug worth fixing, and I'm surprised you guys haven't complained more about it.
07/15/2008    10:03:20 AM    from midori:	There's at least one bug report ...
07/15/2008    10:03:22 AM    from Nomi Harris:	(I was agreeing with "Not having "on text commit" work would amount to losing a bit of functionality compared to OE1. ")
07/15/2008    10:03:43 AM    from Jen Deegan:	is there a speed problem on having the checks run as we type rather than when we commit?
07/15/2008    10:03:49 AM    from midori:	... oh, the bug report is yours (Nomi) ... never mind
07/15/2008    10:04:04 AM    from Amina:	Jen there should'nt be any
07/15/2008    10:04:06 AM    from Nomi Harris:	Jen, it does affect the speed some.
07/15/2008    10:04:14 AM    from midori:	I noticed but there have been other problems bothering me more, I guess
07/15/2008    10:04:21 AM    from Jen Deegan:	I really like the checks happening while I type.
07/15/2008    10:04:48 AM    from Jen Deegan:	I sometimes edit in front of an audience and the checks that make things red as I type save people shouting stuff out.
07/15/2008    10:04:51 AM    from Amina:	Nomi just told me there are so more checks while typing which migh affect speed
07/15/2008    10:04:56 AM    from Nomi Harris:	The slowdown shouldn't be major, but you might want to experiment with turning some of the checks on and off.
07/15/2008    10:04:57 AM    from Jen Deegan:	or at least discourage them from doing it.
07/15/2008    10:05:16 AM    from Jen Deegan:	ok
07/15/2008    10:05:39 AM    from Jen Deegan:	it's just spelling and full stops and capital letters that are useful, also double spaces.
07/15/2008    10:05:39 AM    from Nomi Harris:	When you send me your config files I can take a look at that.
07/15/2008    10:05:44 AM    from Jen Deegan:	thanks.
07/15/2008    10:05:52 AM    from Jen Deegan:	I have it all turned off for speed just now.
07/15/2008    10:05:56 AM    from Nomi Harris:	Getting midori's config files was key to figuring out why she had such slow text edit commits.
07/15/2008    10:06:03 AM    from Jen Deegan:	oh great.
07/15/2008    10:06:04 AM    from Nomi Harris:	It was pretty baffling at first!
07/15/2008    10:06:08 AM    from Jen Deegan:	That's good to know.
07/15/2008    10:06:12 AM    from midori:	airing the dirty laundry ... ;)
07/15/2008    10:06:17 AM    from Jen Deegan:	:-)
07/15/2008    10:06:32 AM    from Jen Deegan:	It's kind of freaky that you can tell so much about us from our config files.
07/15/2008    10:06:38 AM    from Nomi Harris:	I now mention that disjoint filter on two different help pages.
07/15/2008    10:06:40 AM    from Nomi Harris:	:-)
07/15/2008    10:06:46 AM    from midori:	:D
07/15/2008    10:06:48 AM    from Jen Deegan:	good idea
07/15/2008    10:07:13 AM    from Nomi Harris:	Thanks to everyone who helped update the help pages.
07/15/2008    10:07:19 AM    from Nomi Harris:	They are much more up-to-date now.
07/15/2008    10:07:32 AM    from David OS:	Sorry I didn't have time to contribute
07/15/2008    10:07:34 AM    from midori:	I had a question, but I was kind of hoping Melissa would be here.
07/15/2008    10:07:43 AM    from Nomi Harris:	After I do the reorg, I will redo the wiki page and note what still needs updating.
07/15/2008    10:07:51 AM    from Nomi Harris:	(The TOC reorg, that is.)
07/15/2008    10:08:00 AM    from Nomi Harris:	David, it's not too late to contribute!
07/15/2008    10:08:20 AM    from Nomi Harris:	We'd particularly appreciate if you looked at some of the pages on cross products and the reasoner (though Amina is still working on the reasoner pages, so not yet).
07/15/2008    10:08:50 AM    from Jen Deegan:	Are there any components that don't have an entry at all? I wasn't clear if someone had worked through and made sure everything had at least an empty page with a heading.
07/15/2008    10:08:58 AM    from midori:	I'w wondering how much to do on the search documentation, since on one hand, I thought other people had volunteered for parts of it, but on the other hand I've made all sorts of comments about reorganizing this and dropping  that ...
07/15/2008    10:09:02 AM    from David OS:	'fraid I'm way too snowed under to commit to anything else at the moment. :(
07/15/2008    10:09:04 AM    from Nomi Harris:	I did most of them but I think there are still 2 or 3 that lack a page.
07/15/2008    10:09:18 AM    from midori:	Maybe I should just do it instead of just moaning on the wiki.
07/15/2008    10:09:19 AM    from Nomi Harris:	Which other people, midori?
07/15/2008    10:09:21 AM    from Jen Deegan:	I wondered about the search too.
07/15/2008    10:09:43 AM    from Jen Deegan:	me I think
07/15/2008    10:09:46 AM    from midori:	Well, that's part of the reason I wanted to bring it up - I don't trust my memory to that level of detail
07/15/2008    10:09:52 AM    from Nomi Harris:	I say go for it--maybe send out a message first saying that you're going to work on them, in case anyone else was working on them.
07/15/2008    10:09:58 AM    from Jen Deegan:	good idea
07/15/2008    10:10:17 AM    from midori:	... and it's even possible that what I was thinking of was Amina collecting examples and/or Jen doing the first draft of Advanced Searching.
07/15/2008    10:10:22 AM    from Nomi Harris:	Do you want to add the part_of search that Amina just discussed with Jen?
07/15/2008    10:10:38 AM    from Jen Deegan:	I think it may still need some work.
07/15/2008    10:10:58 AM    from Nomi Harris:	Ok
07/15/2008    10:11:16 AM    from midori:	Happy to take over much of the reorg; then I'll probably have a better idea where examples would fit in.
07/15/2008    10:11:43 AM    from Amina:	I actually need to come up with some real examples for the reasoner pages too
07/15/2008    10:11:57 AM    from Nomi Harris:	midori, the reorg involves editing OBO-EditTOC.xml--are you comfortable doing that?
07/15/2008    10:12:07 AM    from midori:	Maybe a new page, which we could extend in the future ... a subcategory of the How-To department?
07/15/2008    10:12:08 AM    from Amina:	using real ontologies that is - currently the screenshots have John's toy ontology
07/15/2008    10:12:15 AM    from Nomi Harris:	You can then use "ant docindex" to update toc.xml
07/15/2008    10:12:55 AM    from midori:	I'll try editing a copy of that xml file ... I can edit xml a bit, but I don't do it a lot. I'll holler if I get stuck!
07/15/2008    10:13:33 AM    from midori:	Amina - SO is a good one to use for reasoner examples.
07/15/2008    10:14:04 AM    from Amina:	oh thanks midori - I've been working with fly_anatomy and GO
07/15/2008    10:14:24 AM    from Nomi Harris:	midori, just be sure to run "ant docindex" and check the resulting toc.html (which lives in docs/, not in docs/html).
07/15/2008    10:14:32 AM    from David OS:	Amina - are the examples I've posted for the filtered save bug any good? They work fine in regular searching.  Could also save other interesting examples for you if/when I come across them.
07/15/2008    10:14:41 AM    from Nomi Harris:	Thanks for offering to work on the reorg--I'm happy to help as needed.
07/15/2008    10:14:52 AM    from midori:	Karen E uses the reasoner in real time to edit SO, and it looks way bizarre with the reasoner off. Get the file so-xp.obo from the SO site.
07/15/2008    10:14:58 AM    from Amina:	yeah that would be helpful David
07/15/2008    10:15:28 AM    from Nomi Harris:	By the way, I was able to load and save the latest gene_ontology_edit.obo without fatal errors, so I think Amina's trouble with that might be due to changes she's made while working on the filtered save bug.
07/15/2008    10:15:47 AM    from Nomi Harris:	(Changes in her local copy of OBO-Edit, not committed to svn.)
07/15/2008    10:16:05 AM    from Amina:	thanks for the tip Midori - I did plan on use using SO for the - "Using the reasoner in repair mode section"
07/15/2008    10:16:50 AM    from Nomi Harris:	Maybe we can use SO for all the reasoner examples.
07/15/2008    10:17:13 AM    from midori:	Check with Chris to make sure, but I *think* Karen doesn't use "repair mode" with SO; repair is what Chris envisions for GO, and in that scenario we wouldn't necessarily have the reasoner on during editing.
07/15/2008    10:17:43 AM    from Amina:	I'll give it a shot - Don't know if I'll have time this week though
07/15/2008    10:18:09 AM    from midori:	Re fatal error: there were some ± characters in the GO:0008467 def a while back, but I removed them on June 17th, and the change propagated to gene_ontology_edit.obo the next day.
07/15/2008    10:18:31 AM    from Amina:	Chris should be back mid next week which is when I'll get back too
07/15/2008    10:20:16 AM    from Amina:	I got that version of GO from the OBO website
07/15/2008    10:21:51 AM    from Amina:	http://obofoundry.org
07/15/2008    10:22:16 AM    from Amina:	midori - is it possible that its not updated here
07/15/2008    10:22:40 AM    from David OS:	Hi all. Have to go catch a train.  See you next week.  David
07/15/2008    10:22:48 AM    from Nomi Harris:	Thanks for coming, David.
07/15/2008    10:22:49 AM    from Jen Deegan:	bye
07/15/2008    10:22:50 AM    from Amina:	bye David
07/15/2008    10:23:01 AM    from midori:	I tohught it was updated pretty frequently, and now it says "last changed" today, and links to yesterday's version ... so I don't know.
07/15/2008    10:23:09 AM    from Nomi Harris:	I will investigate.
07/15/2008    10:23:18 AM    from midori:	Once again, Chris is the one to ask.
07/15/2008    10:24:21 AM    from Nomi Harris:	Are we done for today?
07/15/2008    10:24:22 AM    from Amina:	I'll check with him - thanks
07/15/2008    10:24:35 AM    from Jen Deegan:	I don't have anything else.
07/15/2008    10:24:43 AM    from midori:	I don't have anything else either.
07/15/2008    10:24:49 AM    from Nomi Harris:	Ok, see you all next week!
07/15/2008    10:24:53 AM    from Karen:	I don't know how often the OBO site updates from the cvs, but you should be able to get the most up-to-date GO file  from the GO ftp site directly. I think our ftp site is set up to update at least 1x/hour
07/15/2008    10:24:56 AM    from Nomi Harris:	(Except Amina, who will be away.)
07/15/2008    10:24:58 AM    from Amina:	I won't be here next tuesday
07/15/2008    10:25:25 AM    from Nomi Harris:	Bye!
07/15/2008    10:25:28 AM    from midori:	bye
07/15/2008    10:25:33 AM    from Amina:	I'll be working on my documentation pages next week - should have those done and submitted once Chris reviews them