OE Webex 11Nov08

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11/11/2008 09:29:02 AM from midori: Hi Amina
11/11/2008 09:29:14 AM from Amina Abdulla: Hi Midori
11/11/2008 09:29:24 AM from Amina Abdulla: Hows it going
11/11/2008 09:29:28 AM from Amina Abdulla: Hi Jen
11/11/2008 09:29:29 AM from Jen Deegan: Hi!
11/11/2008 09:29:31 AM from midori: not a
11/11/2008 09:29:36 AM from Jen Deegan: That was tight. I just got home.
11/11/2008 09:29:39 AM from midori: oops
11/11/2008 09:29:41 AM from midori: not bad
11/11/2008 09:30:04 AM from melissaH: Hi there
11/11/2008 09:30:12 AM from Nomi Harris: Good morning
11/11/2008 09:30:20 AM from Amina Abdulla: Hi Melissa and Nomi
11/11/2008 09:30:23 AM from midori: I'm having a bit of troubly typing because the cat is competing with the laptop for my lap
11/11/2008 09:30:24 AM from David OS: Good evening
11/11/2008 09:30:35 AM from melissaH: hi David!
11/11/2008 09:30:44 AM from Amina Abdulla: Hi David
11/11/2008 09:30:48 AM from Jen Deegan: cats are keen on laptops aren't they?
11/11/2008 09:30:49 AM from David OS: Hey Melissa!
11/11/2008 09:31:07 AM from Amina Abdulla: Melissa I think you should be able to use OE2 as soon as the next release is out
11/11/2008 09:31:17 AM from melissaH: terrific!
11/11/2008 09:31:22 AM from Nomi Harris: My stupid cat woke me up at 5:45am.
11/11/2008 09:31:32 AM from melissaH: I've been there....
11/11/2008 09:31:39 AM from melissaH: yesterday in fact.
11/11/2008 09:31:50 AM from Amina Abdulla: I'll have b51 out later this week
11/11/2008 09:32:10 AM from Jen Deegan: great!
11/11/2008 09:32:20 AM from Amina Abdulla: All cat folks here? no dogs?
11/11/2008 09:33:09 AM from Amina Abdulla: ok moving on - I've been updating the wiki
11/11/2008 09:33:37 AM from Amina Abdulla: I think the discussions over the last few weeks concluded having a checklist on the wiki
11/11/2008 09:34:53 AM from Amina Abdulla: At the moment I'm going to host the latest docs on oboedit.org and the wiki too so that users who don't use svn can edit
11/11/2008 09:35:21 AM from Jen Deegan: do you mean the userguide?
11/11/2008 09:35:31 AM from Jen Deegan: won't they get out of sync?
11/11/2008 09:35:33 AM from Amina Abdulla: Yes the user guide
11/11/2008 09:35:47 AM from Amina Abdulla: There are ways to sync all the docs
11/11/2008 09:36:00 AM from Jen Deegan: secret cunning?
11/11/2008 09:36:04 AM from Jen Deegan: sounds good.
11/11/2008 09:36:07 AM from Jen Deegan: so we can edit either?
11/11/2008 09:36:27 AM from Amina Abdulla: Although it would be great to know how many users edit outside of svn
11/11/2008 09:36:54 AM from Jen Deegan: does anyone plan to do that? (show of hands)
11/11/2008 09:36:57 AM from Amina Abdulla: Yes ideally that should be possible
11/11/2008 09:37:41 AM from Jen Deegan: sounds like it won't be a big issue then.
11/11/2008 09:37:42 AM from Amina Abdulla: ok great - if noones editing the wiki it could just be a link from the website
11/11/2008 09:37:54 AM from Amina Abdulla: Hi Pankaj
11/11/2008 09:38:02 AM from pankaj: hi Amina and Everyone
11/11/2008 09:38:21 AM from melissaH: (I can use the svn, but may need a little help by having someone check formatting)
11/11/2008 09:38:24 AM from Amina Abdulla: I'll post the WG agenda on the wiki next week onwards
11/11/2008 09:38:29 AM from pankaj: Do we us ethe phone cpnversation or just the text
11/11/2008 09:38:40 AM from Jen Deegan: just text
11/11/2008 09:38:48 AM from Amina Abdulla: Ok Melissa we can double check that for you
11/11/2008 09:38:53 AM from midori: occasionally a demo
11/11/2008 09:38:57 AM from Jen Deegan: should we discuss Pankaj's question since he is here now?
11/11/2008 09:39:23 AM from pankaj: would help
11/11/2008 09:39:39 AM from Jen Deegan: Are you able to contribute any developer time Pankaj?
11/11/2008 09:39:43 AM from Amina Abdulla: For todays meeting we have: 1) pankaj's email to the WG and 2) refactoring 3) new bugs
11/11/2008 09:40:08 AM from Jen Deegan: great, shall we do Pankaj's thing first?
11/11/2008 09:40:10 AM from midori: Can I also add 4) testing tasks?
11/11/2008 09:40:14 AM from Jen Deegan: true
11/11/2008 09:40:28 AM from Amina Abdulla: yes Midori thanks for bringing that up
11/11/2008 09:40:44 AM from pankaj: I will be hiring a person in next couple of months. If someone with plant background is in your sights, refer me . Otherwise I will ask Chih-Wei our coordinator to contribute. I will join as well
11/11/2008 09:40:54 AM from midori: (can carry most of #4 over to next week if we run short of time)
11/11/2008 09:41:33 AM from Jen Deegan: I'm just thinking that if you want features added to OBO-Edit soon then the best thing would be to get one of your developers to do it.
11/11/2008 09:41:43 AM from pankaj: sure.
11/11/2008 09:41:48 AM from Jen Deegan: since the project is open to community developers.
11/11/2008 09:42:01 AM from Jen Deegan: so we just need to discuss the details of the feature?
11/11/2008 09:42:18 AM from Jen Deegan: can you summarize again?
11/11/2008 09:42:32 AM from pankaj: Until I have teh fund arrived, I can't. But obviously yes. Right now we contribute to AmiGO development
11/11/2008 09:43:16 AM from pankaj: Yu want me to put the feature requenst here
11/11/2008 09:43:22 AM from Jen Deegan: WHen you have someone to work on OBO-Edit they can see how to start from here: http://wiki.geneontology.org/index.php/OBO-Edit
11/11/2008 09:43:24 AM from Amina Abdulla: Pankaj what is the timeline for this request and would be helpful if you could put it in the tracker
11/11/2008 09:43:42 AM from Jen Deegan: no if you could just summarize your request to start the discussion.
11/11/2008 09:43:45 AM from Amina Abdulla: Yes please put it on the feature requests section on sourceforge
11/11/2008 09:43:55 AM from pankaj: sure. It is a very high priority for us
11/11/2008 09:44:26 AM from Jen Deegan: we are very overloaded just now so it is unlikely that it can go in before OBO-Edit3 unless one of your developers does it. Would the others agree?
11/11/2008 09:44:56 AM from midori: maybe 2.1 or 2.2, instead of waiting for 3.0 ... but I agree, not 2.0
11/11/2008 09:45:04 AM from Jen Deegan: yes that sounds good.
11/11/2008 09:45:17 AM from pankaj: sounds good. when is 2.0 coming out
11/11/2008 09:45:27 AM from Jen Deegan: should we discuss the details of the proposal just now or wait until after release and get Pankaj back then?
11/11/2008 09:45:32 AM from Jen Deegan: we hope end of March.
11/11/2008 09:45:59 AM from midori: I'd say no new features in 2.0; the only "new" feature additions we should consider are any that are needed to match OE1 functionality.
11/11/2008 09:46:11 AM from Jen Deegan: yes that seems agreed.
11/11/2008 09:46:13 AM from Amina Abdulla: I agree with Midori
11/11/2008 09:46:29 AM from Jen Deegan:so we should perhaps call Pankaj back after OE2 is released to discuss this feature?
11/11/2008 09:46:39 AM from Jen Deegan: no sense taking up meeting time now?
11/11/2008 09:46:44 AM from pankaj: A bit late. But we will go ahead and start putting the taxon id in DBxref so that we don't lose track
11/11/2008 09:46:52 AM from Jen Deegan: that sounds good.
11/11/2008 09:47:05 AM from Amina Abdulla: Yes I believe setting a high priority on the feature request should be good for now
11/11/2008 09:47:07 AM from Jen Deegan: obviously if you can find developer time in your group you can add it before.
11/11/2008 09:47:17 AM from pankaj: will try
11/11/2008 09:47:20 AM from Jen Deegan: great
11/11/2008 09:47:21 AM from Jen Deegan: thansk.
11/11/2008 09:47:45 AM from Jen Deegan: Pankaj, would you note on the feature request that we are to call you back after release of OE2?
11/11/2008 09:48:02 AM from pankaj: sure I will copy the notes from here
11/11/2008 09:48:11 AM from Jen Deegan: brilliant, thanks for that.
11/11/2008 09:48:13 AM from Jen Deegan: what's next?
11/11/2008 09:48:36 AM from Amina Abdulla: I did some minor refactoring last week
11/11/2008 09:48:40 AM from Jen Deegan: great!
11/11/2008 09:48:43 AM from Jen Deegan: tell us all.
11/11/2008 09:49:12 AM from Amina Abdulla: I sent out the renaming proposal last week and the code should be more intuitive now
11/11/2008 09:49:33 AM from Jen Deegan: this was the category, subset, type stuff?
11/11/2008 09:49:40 AM from Amina Abdulla: It will certainly help developers looking at those components
11/11/2008 09:49:41 AM from Amina Abdulla: yes
11/11/2008 09:49:44 AM from Jen Deegan: great
11/11/2008 09:49:53 AM from melissaH: yes I was very happy about that
11/11/2008 09:50:00 AM from Jen Deegan: thanks for co-ordinating with us for the names on the GUI.
11/11/2008 09:50:09 AM from Amina Abdulla: I've been looking into profiling too and will post updates on that next week
11/11/2008 09:50:16 AM from Jen Deegan: great
11/11/2008 09:50:40 AM from Amina Abdulla: We have a copy of your kit now and if anyone else is interested we can request additional licenses
11/11/2008 09:50:58 AM from Jen Deegan: are they free?
11/11/2008 09:51:16 AM from Amina Abdulla: for open source projects yes
11/11/2008 09:51:28 AM from Nomi Harris: They let us have free licenses for everyone in BBOP in exchange for putting a YourKit blurb on our home page.
11/11/2008 09:51:40 AM from Jen Deegan: Could I have one? It would help diagnose the graphviz slowdowns.
11/11/2008 09:51:52 AM from Jen Deegan: oh that's great!
11/11/2008 09:51:54 AM from Nomi Harris: I don't think everyone in our group is using theirs, so we probably have a few extras that we could give Jen
11/11/2008 09:52:02 AM from Jen Deegan: brilliant, thanks.
11/11/2008 09:52:06 AM from Nomi Harris: I'll send out a note to the group.
11/11/2008 09:52:35 AM from Amina Abdulla: great thanks.
11/11/2008 09:53:58 AM from Amina Abdulla: Alright - sorry for the pause
11/11/2008 09:54:16 AM from Amina Abdulla: New bugs:
11/11/2008 09:54:56 AM from Amina Abdulla: I'm looking into david's bugs - Chris will be helping with the reasner bugs too once hes back
11/11/2008 09:55:27 AM from Amina Abdulla: does anyone have any odd bugs to discuss?
11/11/2008 09:55:51 AM from Jen Deegan: nothing more for me than is in the tracker.
11/11/2008 09:56:01 AM from David OS: cool - having descendant queries work in filtered saves would be great
11/11/2008 09:56:34 AM from Amina Abdulla: yeah I'm working on that one too.
11/11/2008 09:57:38 AM from Amina Abdulla: Moving on to testing - I'm putting up new release tasks on the wiki
11/11/2008 09:57:43 AM from David OS: Excellent. The other reasoner issues I can live with - although improved flagging redundancies would also help alot
11/11/2008 09:58:13 AM from Amina Abdulla:
The previous release tasks like a good model to follow
11/11/2008 09:58:13 AM from midori: The somewhat older testing list is here:
11/11/2008 09:58:14 AM from midori: http://wiki.geneontology.org/index.php/OBO-Edit_2.000_Testing_Tasks
11/11/2008 09:58:49 AM from Amina Abdulla: Yeah that needs to be updated
11/11/2008 09:59:52 AM from midori: For OE1 and in that earlier round of OE2 testing, we divided up the testing to ensure that every feature got tested by at least one wg member.
11/11/2008 10:00:18 AM from midori: The GO managers have put me in charge of making sure the organized testing gets done. (lucky me)
11/11/2008 10:00:59 AM from Jen Deegan: did you want to try a round of testing again soon?

11/11/2008 10:01:11 AM from Amina Abdulla: Right - I'll put up a checklist on the wiki
11/11/2008 10:01:18 AM from Jen Deegan: ok
11/11/2008 10:01:37 AM from midori: Yes, I'd like to get more of the wg involved in testing soon.
11/11/2008 10:01:43 AM from Amina Abdulla: Midori do you have a plan for assigning the tasks
11/11/2008 10:02:02 AM from midori: Sort of ... but suggest refinements if you can!
11/11/2008 10:02:12 AM from Amina Abdulla: Yeah I think we should start testing b51 after the release
11/11/2008 10:02:42 AM from midori: Once Amina has the task list updated, I'll email the wg list asking everyone to look at it and volunteer for things to test.
11/11/2008 10:02:52 AM from Jen Deegan: sounds good.
11/11/2008 10:03:30 AM from midori: If we don't get enough volunteers I'll start cajoling people individually; I'l only drop tihngs in people's laps if all gentler approaches fail. ;)
11/11/2008 10:03:31 AM from Amina Abdulla: Yeah thats the best way to do it. Along with testing the person incharge should look at the user guide pages for that component too
11/11/2008 10:03:41 AM from midori: yup
11/11/2008 10:03:48 AM from Jen Deegan: good plan
11/11/2008 10:04:03 AM from Amina Abdulla: ok I have a feeling we might have some wiki editors then
11/11/2008 10:04:20 AM from melissaH: sounds good
11/11/2008 10:04:53 AM from Amina Abdulla: Any more items for today?
11/11/2008 10:05:06 AM from David OS: can I ask a v.quick question about the nascent OE manual on the svn?
11/11/2008 10:05:26 AM from Jen Deegan: just to mention that the verification manager should no longer show thousands of errors in the live file.
11/11/2008 10:05:29 AM from Amina Abdulla: Sure David
11/11/2008 10:05:40 AM from David OS: I've just updated it and there seems to be no TOC.html - making the index page pretty useless. Is this because it's changing so fast?
11/11/2008 10:05:46 AM from melissaH: I wanted to mention that Jim Balhoff is working on a synchronization tool based on OE2, so anyone interested in this might want to provide some input on the feature request
11/11/2008 10:06:11 AM from midori: oh yes, Jim emailed the wg list
11/11/2008 10:06:25 AM from Nomi Harris: The TOC is not in svn, it is made when you build (using ant or eclipse)
11/11/2008 10:07:00 AM from David OS: ahhh. Can I build if I've only checked out docs?
11/11/2008 10:07:12 AM from Nomi Harris: There is an XML page: OBO-EditTOC.xml
11/11/2008 10:07:43 AM from Nomi Harris: You will need build.xml (one directory above docs) to do the build.
11/11/2008 10:08:06 AM from Nomi Harris: Then, from the directory above docs, you can say "ant docindex"
11/11/2008 10:08:16 AM from David OS: OK. I have ant installed - so shouldn't be a problem. Cheers.
11/11/2008 10:08:41 AM from David OS: One other thing - can someone give me editing permissions on the wiki?
11/11/2008 10:09:02 AM from Jen Deegan: you just register a username.
11/11/2008 10:09:07 AM from Jen Deegan: it's all publically editable.
11/11/2008 10:09:12 AM from Nomi Harris: Does everyone know that if you add a new user guide page, you need to add it to several documents to get it to show up properly in the user guide?
11/11/2008 10:09:33 AM from Nomi Harris: And if you remove an obsolete page, there are places to remove references to it.
11/11/2008 10:09:45 AM from Jen Deegan: that's on the wiki, shall I get the link?
11/11/2008 10:09:53 AM from midori: yes please
11/11/2008 10:10:37 AM from Jen Deegan: http://wiki.geneontology.org/index.php/OBO-Edit:_Adding_to_the_OBO-Edit_help_guide
11/11/2008 10:10:53 AM from midori: thanks!
11/11/2008 10:10:54 AM from Jen Deegan: I messed it up first time so wikified Nomi's instructions.
11/11/2008 10:11:27 AM from Jen Deegan: may I mention the verfication manager?
11/11/2008 10:11:42 AM from midori: sure
11/11/2008 10:12:10 AM from Jen Deegan: when b51 comes out the verification manager should only flag two outstanding text errors that I wasn't sure how to resolve.
11/11/2008 10:12:29 AM from Nomi Harris: In GO, you mean?
11/11/2008 10:12:33 AM from Jen Deegan: this is because the dictionary, repeatable words, always lowercase words and period word are all now fully populated and loaded
11/11/2008 10:12:35 AM from Jen Deegan: yes
11/11/2008 10:12:38 AM from midori: out of curiosity, what are they?
11/11/2008 10:12:46 AM from Jen Deegan: question marks in the defs.
11/11/2008 10:12:46 AM from Nomi Harris: Cool. It will be nice not to see all those irrelevant "errors".
11/11/2008 10:12:55 AM from Jen Deegan: I wasn't sure what they were meant to be.
11/11/2008 10:13:22 AM from midori: I can have a look after the meeting ...
11/11/2008 10:13:24 AM from Jen Deegan: if people add new an excting words then I can add them to the dictionary file.
11/11/2008 10:13:30 AM from Nomi Harris: Are those files (lowercase words etc) going into the jar?
11/11/2008 10:13:36 AM from Jen Deegan: yes they should be
11/11/2008 10:13:43 AM from Nomi Harris: Good
11/11/2008 10:13:45 AM from Jen Deegan: they are in next to dictionary.dict
11/11/2008 10:13:55 AM from Jen Deegan: it all works when I run from Eclipse.
11/11/2008 10:14:11 AM from Jen Deegan: I hope it should also work after release.
11/11/2008 10:14:18 AM from Nomi Harris: S omeone should make sure that it works when you make and install a release (with your config directory wiped)
11/11/2008 10:14:33 AM from Amina Abdulla: I'll test it before I put up the installers
11/11/2008 10:14:44 AM from Jen Deegan: thanks.
11/11/2008 10:15:27 AM from Jen Deegan: It also now ignores repeated words that straddle the end of a sentence.
11/11/2008 10:15:45 AM from Nomi Harris: Great. That was on the bug tracker, right? Did you mark that bug completed?
11/11/2008 10:15:53 AM from Nomi Harris: It's always a nice feeling to close bugs.:-)
11/11/2008 10:16:02 AM from Jen Deegan: I actually just wondered that. I'll take a look.
11/11/2008 10:16:06 AM from Jen Deegan: true:-)
11/11/2008 10:17:44 AM from Jen Deegan: now closed.
11/11/2008 10:18:18 AM from Amina Abdulla: Should we end now? Does anyone have items for discussion?
11/11/2008 10:18:19 AM from Jen Deegan: would the silence suggest that we are done?
11/11/2008 10:18:25 AM from Jen Deegan: I'm done.
11/11/2008 10:18:49 AM from midori: No more from me until the testing task list is ready.
11/11/2008 10:18:58 AM from Amina Abdulla: ok great - Thanks for coming folks
11/11/2008 10:19:13 AM from melissaH: thanks for making OE better
11/11/2008 10:19:14 AM from Amina Abdulla: I'll work on that Midori
11/11/2008 10:19:17 AM from Jen Deegan: Thanks for the great meeting,:-)
11/11/2008 10:19:27 AM from pankaj: bye
11/11/2008 10:19:36 AM from Nomi Harris: Bye
11/11/2008 10:19:42 AM from David OS: Cheers. Bye.
11/11/2008 10:19:43 AM from midori: aside to Jen - I looked, and the ?s in the GO:0080014 def look like they're supposed to be there. I guess you could put "?-diol" in the allowed word list. Not sure what to do about the ? in quotes.
11/11/2008 10:19:45 AM from Jen Deegan: bye
11/11/2008 10:19:49 AM from Amina Abdulla: Thanks Melissa Bye all
11/11/2008 10:19:50 AM from midori: thanks and bye
11/11/2008 10:20:01 AM from Jen Deegan: okay thanks, I'll do that.
11/11/2008 10:20:04 AM from Amina Abdulla: Bye all