OE Webex 18Nov08

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We lost the first half of the meeting due to webex issues. The discussion mainly revolved around wiki organization. Here's the second part of the meeting:

11/18/2008 09:49:45 AM from Amina Abdulla : works?
11/18/2008 09:49:48 AM from David OS : That's better!
11/18/2008 09:50:01 AM from Amina Abdulla : great!
11/18/2008 09:50:08 AM from melissaH : hi, I'm alive!
11/18/2008 09:50:12 AM from Amina Abdulla : I've never seen that happen
11/18/2008 09:50:14 AM from David OS : Me too!
11/18/2008 09:50:17 AM from Jen Deegan : Welcome!
11/18/2008 09:50:18 AM from midori : hi melissa!
11/18/2008 09:50:34 AM from Jen Deegan : so xrefs?
11/18/2008 09:50:57 AM from melissaH : so there is a page about how to specify what your xrefs mean, its here:
11/18/2008 09:51:13 AM from melissaH : http://obofoundry.org/wiki/index.php/Mappings
11/18/2008 09:51:39 AM from melissaH : basically, in many cases the xrefs stand in an is_a relation to the other ontology and we'd like to be able to specify this in the metadata
11/18/2008 09:52:13 AM from Jen Deegan : how do you mean 'in the metadata'? Do you mean as a line in the obo stanza?
11/18/2008 09:52:17 AM from melissaH : there are other ways to specify this though
11/18/2008 09:52:21 AM from melissaH : yes
11/18/2008 09:52:29 AM from melissaH : in the header data
11/18/2008 09:52:34 AM from David OS : Why don't you just use an xref defintion?
11/18/2008 09:52:41 AM from David OS : sorry XP def
11/18/2008 09:52:48 AM from Jen Deegan : like a general dbxref?
11/18/2008 09:53:07 AM from melissaH : well, I suppose we could, but it would apply to almost all our terms and we'd have to maintain two version of our ontology
11/18/2008 09:53:20 AM from David OS : intesersection_of: is_a thingy from another ontology
11/18/2008 09:53:25 AM from Jen Deegan : yes
11/18/2008 09:53:35 AM from David OS : intersection_of: part_of Zfish
11/18/2008 09:53:35 AM from melissaH : so I kinda want to make a global xp definition
11/18/2008 09:53:41 AM from Jen Deegan : do you mean that all the terms would link to one term in another ontology?
11/18/2008 09:54:01 AM from Jen Deegan : that's like when we talked about all process terms being is_a process from the bfo ontology.
11/18/2008 09:54:12 AM from melissaH : so every term with an Xref to a particular ontology would be specified to have a particular relationship to the term in the other ontology
11/18/2008 09:54:17 AM from Jen Deegan : Did you have a plan for that Midori?
11/18/2008 09:54:17 AM from melissaH : yes exactly jen
11/18/2008 09:54:31 AM from melissaH : (wasn't there but its the same thing)
11/18/2008 09:54:54 AM from Jen Deegan : Midori and Chris were talking about this before.
11/18/2008 09:54:57 AM from midori : Jen - do you mean a plan for the GO-BFO thing?
11/18/2008 09:55:14 AM from Jen Deegan : yet that's right. I wasn't quite clear on where you planned to put that mapping line.
11/18/2008 09:55:26 AM from Jen Deegan : I wondered if your plan might work for Melissa.
11/18/2008 09:55:27 AM from melissaH : Chris has been hacking this type of info, but with more users we'd like to have this info in the file
11/18/2008 09:55:39 AM from midori : If so, it was Chris who was going to produce the one-line mapping file. I don't know where he was going to put it, or whether he's done it yet.
11/18/2008 09:55:50 AM from David OS : I think its better to use regular OBO relations if we can. This makes it much easier to work with the ontologies in other software.
11/18/2008 09:55:56 AM from Jen Deegan : Ah! I'm right up to date in my confusion then.
11/18/2008 09:56:05 AM from melissaH : well, these are still regular obo relations
11/18/2008 09:56:24 AM from David OS : But they won't be read by any other software
11/18/2008 09:56:40 AM from Jen Deegan : it sounds like we need to ask Chris this doesn't it?
11/18/2008 09:56:44 AM from melissaH : so maybe its a obo format issue then?
11/18/2008 09:56:52 AM from Jen Deegan : yes it sounds like it.
11/18/2008 09:57:16 AM from melissaH : alrighty well I'll bug him soon. I just didn't know if there was OE2 capabilities that I was unaware of.
11/18/2008 09:57:16 AM from David OS : No, I think its an ontology management issue: how to deal with ontologies that have terms that link to foreign terms
11/18/2008 09:57:23 AM from Jen Deegan : yes that too.
11/18/2008 09:57:28 AM from midori : And I'm not sure how much the GO plan would help Melissa and ZFIN, since the GO mapping is (or will be) literally one line saying that the biological process ontology root (creatively named biological_process) is_a BFO:[whatever the relevant BFO term is
11/18/2008 09:57:29 AM from Jen Deegan : but I think Chris has a plan.
11/18/2008 09:57:39 AM from Jen Deegan : ah
11/18/2008 09:57:47 AM from melissaH : yes its the same thing midori.
11/18/2008 09:58:06 AM from Jen Deegan : It's just a question of where to put the line and whether we can do it through oboedit
11/18/2008 09:58:12 AM from David OS : And I'd rather make relation explicit than leave them implicit in some xref subtype. Guess I should wait to hear what chris says though.
11/18/2008 09:58:13 AM from melissaH : ok, well I'll check in with him and make sure he replies to our WG.
11/18/2008 09:58:16 AM from melissaH : yes, exactly.
11/18/2008 09:58:31 AM from Jen Deegan : great, that's a plan then.
11/18/2008 09:58:32 AM from melissaH : the line makes the xrefs explicit.
11/18/2008 09:58:41 AM from melissaH : right now, they are actually undefined in many cases
11/18/2008 09:58:54 AM from melissaH : becuase they are used to mean all kinds of things
11/18/2008 09:58:55 AM from David OS : 'fraid I have to go soon.
11/18/2008 09:59:38 AM from David OS : Amina - can I ask quickly whether you've made any progress on the XP commit bug
11/18/2008 09:59:39 AM from David OS : ?
11/18/2008 09:59:56 AM from Amina Abdulla : In a weird way it works for me
11/18/2008 10:00:13 AM from Amina Abdulla : Im trying to investigate the intermittent behaviour
11/18/2008 10:00:32 AM from David OS : It never works first time for me. On any computer. Have you tired using my anatomy AO?
11/18/2008 10:00:51 AM from Amina Abdulla : No - where can I find that
11/18/2008 10:00:54 AM from Amina Abdulla : oh wait
11/18/2008 10:01:07 AM from Amina Abdulla : its on the bug report I think
11/18/2008 10:01:30 AM from David OS : Yep. Your password to our trac should work to give you access.
11/18/2008 10:01:49 AM from David OS : OK - really have to go now. See you!
11/18/2008 10:01:58 AM from midori : bye david
11/18/2008 10:02:03 AM from Jen Deegan : I thought of something to tell you Amina.
11/18/2008 10:02:06 AM from Amina Abdulla : Right. bye David
11/18/2008 10:02:22 AM from melissaH : bye!
11/18/2008 10:02:24 AM from Amina Abdulla : Yes Jen..
11/18/2008 10:02:29 AM from Jen Deegan : I managed to get the 'discard uncommitted edits' dialog to show consistently.
11/18/2008 10:02:35 AM from Jen Deegan : I wondered if that would be useful.
11/18/2008 10:02:50 AM from midori : oh yes, I've got something of the sort too
11/18/2008 10:03:05 AM from Jen Deegan : mine is in the oldest comment on this: https://sourceforge.net/tracker/index.php?func=detail&aid=2277324&group_id=36855&atid=418257
11/18/2008 10:03:34 AM from Jen Deegan : I thought it might help for detection of the bug.
11/18/2008 10:03:39 AM from Amina Abdulla : yes I've read the updated comments too
11/18/2008 10:03:44 AM from Jen Deegan : great :-)
11/18/2008 10:04:02 AM from midori : In my case I don't think disjoint was an issue. I put comments in my older pending-edits bug (hope you saw that)
11/18/2008 10:04:05 AM from Jen Deegan : I'm going to have a go at linking up the graphviz component to the new relationship loading thing.
11/18/2008 10:04:30 AM from midori : https://sourceforge.net/tracker/index.php?func=detail&aid=2142711&group_id=36855&atid=418257
11/18/2008 10:05:58 AM from Amina Abdulla : yeah thanks - this is turning out to be a menace - will look into it
11/18/2008 10:06:33 AM from midori : thanks
11/18/2008 10:06:56 AM from Jen Deegan : I've noticed that any bug that I investigate seem to come with a cluster of these dialogs. I'd love to know what's doing it.
11/18/2008 10:07:43 AM from Jen Deegan : is there anything else?
11/18/2008 10:08:04 AM from Amina Abdulla : Yeah it runs quiet deep since it delas with anything that requires commiting as you can imagine
11/18/2008 10:08:13 AM from Amina Abdulla : the autocommit has been buggy too
11/18/2008 10:08:33 AM from Amina Abdulla : I never heard back for the person who reported losing a days worth of work
11/18/2008 10:08:39 AM from Jen Deegan : by the way, would it be possible to forward on that license if there is one spare? For the profiling tool?
11/18/2008 10:09:00 AM from midori : I suspect that person was using OE1, cos OE2 does warn ...
11/18/2008 10:09:22 AM from Amina Abdulla : Yeah I didnt receive any volenteeres willing to give up their license so I'll just request an additional one
11/18/2008 10:09:55 AM from Jen Deegan : Thanks, that would be great. I've noticed graphviz redrawing frequently when it is not needed, so it would be good to look at that. I think it slows things down.
11/18/2008 10:09:56 AM from Amina Abdulla : yeah they reported the bug on OE2 though
11/18/2008 10:10:09 AM from midori : how odd ...
11/18/2008 10:10:28 AM from midori : the OE2 warning has always worked for me ...
11/18/2008 10:10:54 AM from Amina Abdulla : Great Jen. I'm going to decidate sometime to profiling too
11/18/2008 10:11:36 AM from Amina Abdulla : Any other items for today folks?
11/18/2008 10:11:51 AM from Jen Deegan : are you due to release soon? I think some other bug has crept into the tree viewer since I had it all working. I should fix it before release.
11/18/2008 10:12:06 AM from Jen Deegan : I think it's just an svn commit gone wrong.
11/18/2008 10:12:29 AM from Amina Abdulla : Yeah I was all set for one last week and had some bugs creep in too
11/18/2008 10:12:54 AM from Amina Abdulla : I promise the next one will be considerably better and worth the wait though
11/18/2008 10:13:13 AM from Jen Deegan : that sounds good then.
11/18/2008 10:13:32 AM from Jen Deegan : shall we wrap up? It seems as though we are out of topics.
11/18/2008 10:13:34 AM from melissaH : wonderful!
11/18/2008 10:13:51 AM from Amina Abdulla : Yeah. Thanks for coming everyone
11/18/2008 10:14:00 AM from Jen Deegan : Thanks for the meeting. It was great.
11/18/2008 10:14:03 AM from melissaH : thanks!
11/18/2008 10:14:04 AM from Jen Deegan : Bye!
11/18/2008 10:14:08 AM from midori : thanks & bye!
11/18/2008 10:14:15 AM from Amina Abdulla : Bye