OE Webex 30Sep08

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09/30/2008 09:36:04 AM from Amina Abdulla : I had to start the meeting again 09/30/2008

09:36:08 AM from David OS : ahhhh...

09/30/2008 09:36:09 AM from Nomi Harris : Oops!

09/30/2008 09:36:14 AM from midori : ... meeting ended on me, but I went back to the go webex site and found the new one.

09/30/2008 09:36:24 AM from Amina Abdulla : I sent out an email to the working group

09/30/2008 09:36:37 AM from jendeegan : and now Nomi is herself.So problem solved.

09/30/2008 09:36:40 AM from Amina Abdulla : Midori: any chance you saved the chat?

09/30/2008 09:36:44 AM from Amina Abdulla : or anyone else

09/30/2008 09:36:54 AM from jendeegan : sorry, it ended too suddenly.

09/30/2008 09:36:58 AM from midori : sorry, I didn't have a chance before it ended

09/30/2008 09:36:59 AM from Nomi Harris : Sorry about that.

09/30/2008 09:37:02 AM from Amina Abdulla : I didn't get that option since the host logged out

09/30/2008 09:37:08 AM from Nomi Harris : I didn't realize I had stolen host status from Amina.

09/30/2008 09:37:19 AM from jendeegan : shall we rerun what was said then?

09/30/2008 09:37:25 AM from jendeegan : just to save time.

09/30/2008 09:37:36 AM from Nomi Harris : If you like.

09/30/2008 09:37:45 AM from Nomi Harris : I'm going to grab my tea from the kitchen.

09/30/2008 09:37:48 AM from Amina Abdulla : Yeah - So I was talking about the autocommit and xps save bugs

09/30/2008 09:38:17 AM from Amina Abdulla : David: do you usually use the intersection editor?

09/30/2008 09:38:47 AM from Chris Mungall : David does all xp editing by hand e.g. in emacs..

09/30/2008 09:38:55 AM from Chris Mungall : or scripts

09/30/2008 09:38:56 AM from David OS : I've mainly been diong XPs by scripting - and occassionaly by hand

09/30/2008 09:39:17 AM from Amina Abdulla : Jen: did you want to talk about the bug reports on the intersection editor you posted

09/30/2008 09:39:32 AM from jendeegan : no thanks.

09/30/2008 09:39:41 AM from jendeegan : I just put them all in from our meeting with Chris.

09/30/2008 09:39:42 AM from David OS : Pronmise to test XP editor and XP tab more thoroughly on the new release

09/30/2008 09:39:47 AM from jendeegan : unless you have questions.

09/30/2008 09:39:47 AM from Amina Abdulla : o ok - sorry I thought further details were for the meeting

09/30/2008 09:40:09 AM from jendeegan : ah, no, but I think you might want to ask us some things as you reach each one.

09/30/2008 09:40:10 AM from midori : only if you have any questions about any of them

09/30/2008 09:40:15 AM from Amina Abdulla : Not yet - as I haven't used the intersection editor

09/30/2008 09:40:17 AM from jendeegan : you could just write as you get to them though.

09/30/2008 09:40:31 AM from jendeegan : It might be overwhelming to get the whole lot at once.

09/30/2008 09:40:32 AM from Amina Abdulla : Right

09/30/2008 09:40:37 AM from jendeegan : great

09/30/2008 09:40:45 AM from Amina Abdulla : They seemed like easy fixes though

09/30/2008 09:40:59 AM from Amina Abdulla : I'll get back on that

09/30/2008 09:41:03 AM from jendeegan : Sorry for getting behind on my SF item commenting. I'm nearly caught up though.

09/30/2008 09:42:03 AM from Amina Abdulla : Chris: Jen put in a request for the semantic parser suppress

09/30/2008 09:42:29 AM from Chris Mungall : can u post the tracker url here?

09/30/2008 09:42:38 AM from Amina Abdulla : Should I just gray it out and leave it in there - and have a way of activating through config

09/30/2008 09:42:59 AM from jendeegan : The idea was to remove it from the menu altogether

09/30/2008 09:43:05 AM from Amina Abdulla : https://sourceforge.net/tracker/?func=detail&atid=418257&aid=2137953&group_id=36855

09/30/2008 09:43:06 AM from jendeegan : we just need that tool on the command line.

09/30/2008 09:43:41 AM from Chris Mungall : It is still potentially useful in interactive mode to anyone editing GO

09/30/2008 09:44:08 AM from Chris Mungall : however, if it is hidden by default in the 2.0 release that's fine.

09/30/2008 09:44:24 AM from jendeegan : It will get us to the release faster too.

09/30/2008 09:44:27 AM from midori : iirc we decided it wasn't worth delaying the 2.0 release to get it working better

09/30/2008 09:44:28 AM from Amina Abdulla : ok - same for Intersection Editor?

09/30/2008 09:44:38 AM from jendeegan : that was the plan

09/30/2008 09:44:43 AM from Chris Mungall : yep

09/30/2008 09:44:51 AM from jendeegan : also matrix editor I think?

09/30/2008 09:44:56 AM from jendeegan : was that right?

09/30/2008 09:44:57 AM from midori : yes

09/30/2008 09:45:00 AM from jendeegan : great

09/30/2008 09:45:14 AM from Amina Abdulla : ok

09/30/2008 09:45:20 AM from David OS : But we should have intersection tab in text editor working OK - yes?

09/30/2008 09:45:27 AM from midori : matrix editor would get more attention after release, cos it would be useful

09/30/2008 09:45:38 AM from Amina Abdulla : yeah

09/30/2008 09:45:46 AM from Amina Abdulla : thats fixed

09/30/2008 09:45:49 AM from Chris Mungall : David - absolutely, the xp/intersection tab in the text editor is vital

09/30/2008 09:46:09 AM from David OS : Good - just checking. Easy to get confused between different editor names...

09/30/2008 09:46:38 AM from Amina Abdulla : There was question regarding the "*" that shows up in the Text Editor tabs - that signifies - has information

09/30/2008 09:47:03 AM from David OS : Matrix editor is distinct from intersection editor? or same?

09/30/2008 09:47:26 AM from midori : I've noticed that the * doesn't always update immediately.

09/30/2008 09:47:34 AM from Chris Mungall : distinct!

09/30/2008 09:47:35 AM from Amina Abdulla : distinct

09/30/2008 09:47:53 AM from Amina Abdulla : the matrix editor is the Cross-Product Matrix Editor

09/30/2008 09:48:06 AM from Amina Abdulla : Midori: I'm working on that too

09/30/2008 09:48:10 AM from Nomi Harris : It seemed like sometimes the * was just wrong, even if you hadn't done any edits.

09/30/2008 09:48:30 AM from melissaH : yeah, sometimes there is a * and no data, and vice versa. I put in a bug

09/30/2008 09:48:46 AM from melissaH : (I acutally use a lot)

09/30/2008 09:48:59 AM from midori : it is handy

09/30/2008 09:49:04 AM from Amina Abdulla : really? It seems to work ok for me - shows up only when I've added any info

09/30/2008 09:49:30 AM from melissaH : haven't checked on recent versions...i'll update the bug when I do

09/30/2008 09:49:40 AM from Nomi Harris : When I looked into it briefly (didn't actually try to fix it) I found plenty of cases where the * was wrong (missing when info was there or present when there wasn't info)

09/30/2008 09:49:55 AM from Nomi Harris : That was a few months ago.

09/30/2008 09:50:06 AM from midori : I don't think I've seen the kind of errors that Melissa has, but it's possible I just wasn't paying enough attention.

09/30/2008 09:50:12 AM from Amina Abdulla : I had a problem getting it to update right-away, not after I clicked on another term and came back

09/30/2008 09:50:27 AM from midori : me too

09/30/2008 09:50:28 AM from melissaH : mine was wrong from the start- even with no editing

09/30/2008 09:51:13 AM from melissaH : hey related question- we are adding synonym categories like GO- broad, narrow, related, exact. but we still have a different type- PLURAL. should we continue doing it this way?

09/30/2008 09:51:42 AM from melissaH : -it was on the synonym tab that I noticed the * problem

09/30/2008 09:51:42 AM from midori : the broad/narrow-exact business is synonym scope

09/30/2008 09:51:58 AM from midori : Plural sounds like a perfectly sensible synonym category.

09/30/2008 09:52:26 AM from Chris Mungall : ZFA implements this correctly, you're good

09/30/2008 09:52:38 AM from melissaH : ?

09/30/2008 09:52:41 AM from melissaH : good at what?

09/30/2008 09:53:02 AM from melissaH : our plan? or existing plural types?

09/30/2008 09:53:33 AM from melissaH : OE2 doesn't support both scope and categories for synonyms

09/30/2008 09:53:52 AM from midori : That's a problem with OE2, then.

09/30/2008 09:53:58 AM from midori : Is there a bug report?

09/30/2008 09:54:05 AM from melissaH : yes- lemme find it

09/30/2008 09:54:39 AM from Chris Mungall : melissa - yes you should continue doing it this way

09/30/2008 09:54:44 AM from melissaH : 2020766

09/30/2008 09:55:00 AM from midori : https://sourceforge.net/tracker/index.php?func=detail&aid=2020766&group_id=36855&atid=418257

09/30/2008 09:55:11 AM from melissaH : ok, will do.

09/30/2008 09:56:05 AM from Chris Mungall : this bug should be fixed before release

09/30/2008 09:56:22 AM from Nomi Harris : Is it a bug, or a feature not yet implemented?

09/30/2008 09:56:29 AM from Nomi Harris : (Not that it really matters.)

09/30/2008 09:56:35 AM from melissaH : so are the four "scopes" of a singular type or is that just implicit?

09/30/2008 09:56:53 AM from midori : From our point of view, bug, because it's a loss of OE1 functionality

09/30/2008 09:57:01 AM from melissaH : I think it was a feature that was never brought over from OE1

09/30/2008 09:57:09 AM from midori : Scopes and types are orthogonal.

09/30/2008 09:57:12 AM from melissaH : :-)

09/30/2008 09:57:28 AM from midori : I have the bug report open -- want me to up the priority?

09/30/2008 09:57:42 AM from melissaH : sounds good to me

09/30/2008 09:57:51 AM from Amina Abdulla : sure midori

09/30/2008 09:57:52 AM from David OS : Can someone explain the difference between synonym scope and synonym category?

09/30/2008 09:58:40 AM from Chris Mungall : scope = EXACT/NARROW/BROAD/RELATED type=user defined list

09/30/2008 09:58:57 AM from jendeegan : type would be something like our stuctured synonyms

09/30/2008 09:58:58 AM from Chris Mungall : a synonym always has scope and optionally type

09/30/2008 09:59:18 AM from Chris Mungall : types can optionally be defined to imply scope

09/30/2008 09:59:39 AM from David OS : So thie disintinction is really just operational?

09/30/2008 10:00:12 AM from melissaH : so for example- in anatomy ontologies we need plural synonyms, these go in with a type definition in the header as type PLURAL

09/30/2008 10:01:39 AM from melissaH : I guess we haven't yet defined any as PLURAL + scope, but chris' point is that that would be useful

09/30/2008 10:02:42 AM from David OS : OK. Guess this will be one for future OBO meeting debate... So. Won't push it further here.

09/30/2008 10:03:33 AM from melissaH : ok sounds good.

09/30/2008 10:03:47 AM from melissaH : I have to run to another meeting- thanks everyone

09/30/2008 10:03:58 AM from David OS : Bye Melissa

09/30/2008 10:04:02 AM from midori : good to see you again!

09/30/2008 10:04:05 AM from Chris Mungall : bye!

09/30/2008 10:04:09 AM from Amina Abdulla : bye mellisa

09/30/2008 10:04:19 AM from harold : bye

09/30/2008 10:04:36 AM from Nomi Harris : bye Melissa

09/30/2008 10:05:51 AM from Amina Abdulla : Are any of the editors currently using OBO Merge

09/30/2008 10:06:00 AM from jendeegan : no

09/30/2008 10:06:04 AM from Amina Abdulla : from the GUI or command line

09/30/2008 10:06:08 AM from jendeegan : I used it a while ago, but not that recently

09/30/2008 10:06:21 AM from David OS : No - but I'm about to train up a new editor this week - so expect to be using it soon.

09/30/2008 10:06:35 AM from midori : I don't have to use it very often; last time I did was about six weeks ago (or so).

09/30/2008 10:06:39 AM from jendeegan : Why do you ask?

09/30/2008 10:06:41 AM from Amina Abdulla : ok - theres a problem with merging obsoletes

09/30/2008 10:06:46 AM from jendeegan : ah, yes

09/30/2008 10:06:47 AM from midori : That's when I put in the bug report about losing tags.

09/30/2008 10:06:50 AM from Amina Abdulla : I'm not convinced I've fixed it

09/30/2008 10:06:58 AM from jendeegan : should we test?

09/30/2008 10:07:08 AM from Amina Abdulla : Chris maybe I can discuss this with you later this week

09/30/2008 10:07:32 AM from jendeegan : testing obomerge is hard so do let us know if you think there may be issues. Better to know that we've to look.

09/30/2008 10:07:35 AM from Chris Mungall : ok

09/30/2008 10:07:47 AM from Amina Abdulla : I was wondering if this bug was always present and went unnoticed

09/30/2008 10:07:50 AM from midori : We can test anything we know how to use, even if we wouldn't otherwise need to use it for whatever editing we're doing.

09/30/2008 10:08:04 AM from jendeegan : yes I that would be right. We didn't use to have the consider tags.

09/30/2008 10:08:28 AM from midori : ... which means we wouldn't have had a way to spot the problem

09/30/2008 10:08:28 AM from jendeegan : yes, I mean that the errors wouldn't necessarily leap out though.

09/30/2008 10:08:38 AM from Amina Abdulla : it seems like it never merged correctly (I know its a scary thought )

09/30/2008 10:09:01 AM from jendeegan : what did you think it did wrong?

09/30/2008 10:09:01 AM from Amina Abdulla : Yeah I'll send out details for testing too

09/30/2008 10:09:06 AM from jendeegan : thanks.

09/30/2008 10:09:07 AM from midori : For the merge I did, the loss of tags from obsoletes was the only problem.

09/30/2008 10:09:31 AM from jendeegan : yes me too.

09/30/2008 10:10:10 AM from Amina Abdulla : I've been testing with toy ontologies - it left out some obsolete terms too

09/30/2008 10:10:20 AM from Amina Abdulla : not just the consider and replaced_by tags

09/30/2008 10:10:29 AM from midori : I didn't lose any terms ...

09/30/2008 10:10:38 AM from jendeegan : I didn't either.

09/30/2008 10:10:52 AM from jendeegan : the diff would have showed that and I had only a small number of edits.

09/30/2008 10:11:26 AM from Amina Abdulla : ok - I'll send out an email once thats fixed

09/30/2008 10:11:37 AM from jendeegan : Thanks.

09/30/2008 10:12:05 AM from Amina Abdulla : Log4j has a couple of warnings that come up on startup

09/30/2008 10:12:34 AM from Amina Abdulla : Just wanted to let everyone know that its due to the common logging configuration for OE and Phenote

09/30/2008 10:12:46 AM from Amina Abdulla : I'll be removing that dependency soon

09/30/2008 10:12:52 AM from jendeegan : Great, thanks.

09/30/2008 10:13:26 AM from Amina Abdulla : and have seperate logging properties for both - bbop currently sets logging for both

09/30/2008 10:15:04 AM from Amina Abdulla : Jen: I've never used the Graphviz viewer - Do you think we can have a small demo

09/30/2008 10:15:10 AM from jendeegan : yes sure.

09/30/2008 10:15:12 AM from jendeegan : now?

09/30/2008 10:15:38 AM from Amina Abdulla : sure

09/30/2008 10:15:46 AM from jendeegan : okay, just a sec.

09/30/2008 10:15:57 AM from jendeegan : can you make me presenter?

09/30/2008 10:17:33 AM from jendeegan : was that the sort of thing you had in mind?

09/30/2008 10:17:42 AM from jendeegan : the set up instructions are in the help guide.

09/30/2008 10:17:43 AM from Amina Abdulla : Yeah - thanks

09/30/2008 10:17:46 AM from jendeegan : great

09/30/2008 10:17:49 AM from Chris Mungall : thanks

09/30/2008 10:17:54 AM from jendeegan : any specific questions?

09/30/2008 10:18:05 AM from Amina Abdulla : So its basically just for representation

09/30/2008 10:18:08 AM from Chris Mungall : have u tried it deep in the regulation graph?

09/30/2008 10:18:11 AM from jendeegan : yes that's right

09/30/2008 10:18:21 AM from Chris Mungall : does it suffer the infamous graphviz hairball effect?

09/30/2008 10:18:22 AM from jendeegan : if you click one of the terms it shows in the OTE.

09/30/2008 10:18:29 AM from jendeegan : :-)

09/30/2008 10:18:35 AM from jendeegan : It can do, but it's pretty good actually

09/30/2008 10:18:58 AM from jendeegan : the bubbles are always well spaced out and if the graph is too big I print it to a file and then view it elsewhere

09/30/2008 10:19:19 AM from Chris Mungall : does it respect filters or does it draw all relations? what about renderers? 09/30/2008 10:19:39 AM from jendeegan :

It shows all relatiions except disjoint, and it does not filter or render.

09/30/2008 10:19:43 AM from Chris Mungall : (I'm guessing it doesn't use renderers thatd be way too hard in grapohviz)

09/30/2008 10:19:50 AM from Chris Mungall : ok

09/30/2008 10:19:55 AM from jendeegan : maybe, I'm not sure

09/30/2008 10:20:04 AM from jendeegan : I mean I haven't thought about how hard it would be

09/30/2008 10:20:07 AM from Chris Mungall : thanks so much jen this is really useful oe1 functionality restored

09/30/2008 10:20:10 AM from jendeegan : I don't think it would be a disaster

09/30/2008 10:20:27 AM from jendeegan : Thanks. :-)

09/30/2008 10:20:42 AM from jendeegan : I think filtering would not be so hard

09/30/2008 10:20:47 AM from jendeegan : it's just processing a text file.

09/30/2008 10:22:12 AM from David OS : I'd use it if I could filter. Otherwise fly AO graphs are just too big

09/30/2008 10:22:26 AM from Amina Abdulla : Great - Thanks Jen

09/30/2008 10:22:42 AM from jendeegan : Any time. :-)

09/30/2008 10:23:32 AM from Amina Abdulla : Any more topics for today?

09/30/2008 10:23:47 AM from jendeegan : No I don't think so.

09/30/2008 10:24:05 AM from David OS : nope

09/30/2008 10:24:18 AM from midori : none here

09/30/2008 10:24:19 AM from jendeegan : would you like to see the file that would have to be filtered to make graphviz filtered?

09/30/2008 10:24:27 AM from jendeegan : I can email it or something.

09/30/2008 10:24:36 AM from Amina Abdulla : sure

09/30/2008 10:24:42 AM from jendeegan : okay, I'll do that.

09/30/2008 10:25:17 AM from Amina Abdulla : I was thinking - for our upcomming WG meetings - we could have a short demo each time

09/30/2008 10:25:23 AM from David OS : Hi Jen - could you send to me too. I'm inverstigating graph-viz for other purposes

09/30/2008 10:25:41 AM from jendeegan : Yes sure David. AMina, I think that would be great.

09/30/2008 10:25:46 AM from midori : Amina - John did something like that, and it worked pretty well.

09/30/2008 10:25:52 AM from Amina Abdulla : There are a lot of features that all the users don't know about or some cool tricks that users develop

09/30/2008 10:25:52 AM from jendeegan : Midori could maybe do the parent editor?

09/30/2008 10:25:58 AM from midori : ok

09/30/2008 10:26:01 AM from jendeegan : I could do obomerge GUI.

09/30/2008 10:26:12 AM from Amina Abdulla : Great!

09/30/2008 10:26:15 AM from jendeegan : I think we are all getting to grips with different bits, and this could be a good time.

09/30/2008 10:26:19 AM from Nomi Harris : Good idea, Amina.

09/30/2008 10:26:45 AM from jendeegan : we are able to record demos on webex

09/30/2008 10:26:52 AM from jendeegan : for others to see later.

09/30/2008 10:27:16 AM from Amina Abdulla : Yeah I'll look into some screen capturing video tools too

09/30/2008 10:27:33 AM from jendeegan : There's one built into webex

09/30/2008 10:27:41 AM from jendeegan : you just click 'start recording'

09/30/2008 10:27:45 AM from jendeegan : and off it goes.

09/30/2008 10:27:47 AM from Amina Abdulla : Webex never works right for me

09/30/2008 10:27:53 AM from jendeegan : oh dear.

09/30/2008 10:27:56 AM from Amina Abdulla : I'll give it a shot too

09/30/2008 10:28:08 AM from jendeegan : I'll send you the webex tech support contact details.

09/30/2008 10:28:22 AM from Amina Abdulla : Oh its ok Jen

09/30/2008 10:28:35 AM from jendeegan : When you record it takes everything on your desktop, not just what you're sharing.

09/30/2008 10:28:38 AM from Amina Abdulla : they don't support linux at all

09/30/2008 10:28:49 AM from jendeegan : oh, that's a shame.

09/30/2008 10:28:49 AM from Amina Abdulla : ok - great - I've never tried it

09/30/2008 10:28:58 AM from jendeegan : one of us could record for you.

09/30/2008 10:29:14 AM from Amina Abdulla : yeah it'll be good to have backup

09/30/2008 10:29:29 AM from jendeegan : Shall we potter off then?

09/30/2008 10:29:30 AM from Amina Abdulla : alright - Thanks for attending everyone

09/30/2008 10:29:46 AM from midori : thanks & bye

09/30/2008 10:29:48 AM from jendeegan : Thanks for the meeting. Cheerio.

09/30/2008 10:29:51 AM from Nomi Harris : Bye

09/30/2008 10:29:58 AM from David OS : Cheers. Bye

09/30/2008 10:30:01 AM from Karen : bye

09/30/2008 10:30:04 AM from Nomi Harris : Sorry about derailing the meeting earlier

09/30/2008 10:30:06 AM from Amina Abdulla : Bye everyone

09/30/2008 10:30:13 AM from Amina Abdulla : No problem Nomi

09/30/2008 10:30:21 AM from Nomi Harris : when I was being Amina's evil twin.