OEWG 20090317

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OBO-Edit Working Group, Tuesday March 17th, 2008 9.30 a.m. PST
Conference call details:
US: 1-888-727-6732
Outside US: 1-719-867-3417
pin: 601425

Agenda/Chair: Midori
Minutes: Harold
Attendees: Amina, Midori, Jen, Chris, Melissa, Colin, Karen, Tanya, Harold, Nomi

Action items carried over


  1. b56 expected on Thursday 3/19.
  2. [ 2642262 ] can't delete term dbxref b55 - DONE
  3. Add switch to "Default Edit" and "Default Verify" Layouts: https://sourceforge.net/tracker2/?func=detail&aid=2657452&group_id=36855&atid=418257 - CLOSED
  4. Search has hits but no hitlist (b52): https://sourceforge.net/tracker2/?func=detail&aid=2588958&group_id=36855&atid=418257
  5. b55 unstable with fly_anatomy_XP.obo: https://sourceforge.net/tracker/index.php?func=detail&aid=2637233&group_id=36855&atid=418257
  6. Option to turn off incremental reasoning In progress
  7. GraphViewer - asserted links should not require reasoner. DONE
  8. Investigate uncommitted text edit window showing up when not required. DONE
  9. Load error report display in load window: https://sourceforge.net/tracker/index.php?func=detail&aid=2513220&group_id=36855&atid=418257 - In progress
  • Midori
  1. will compose email about OE2 release to be sent out about one week before release, which is March 23rd.
    • DONE composing
  • Working Group:
  1. Documentation Jamboree
    • This coming Friday 13th March, everyone please look over the documentation for the section(s) that you tested. Post comments to the wiki.


  1. will find out whether it is possible to collaborate with or accept funding from Microsoft Research without affecting the free open source status of OBO-Edit, and will also discuss it at the GO managers' meeting tomorrow March 11th.
  2. will look into whether a verification check for obsolete terms referred to in consider and replace by tags will serve the purpose of making the list easy to obtain


  1. David will submit a feature request proposing that the Description field of the definition dbxref manager is no longer inserted into the saved file.
  2. David will look into it further to determine the exact nature of the relationship loading issue for FlyBase Harvard.


  1. Documentation jam on Friday March 13th. Everyone should look at the documentation for the sections they tested and other sections as well if possible and add comments to the wiki.

Tracker items to be reviewed by the working group

  • All items above priority 5


user.dict should persist between sessions and should be backed up before getting rid of the config folder.

Discussion items

Working group:

  • Documentation jamboree comments
  • OE usability
  • Any outstanding bugs that are critical and need to be fixed ASAP.
  • ID Fixer ideal location to post replaced_by and consider tags information for obsolete terms.
    • Jen - I have looked into this and the ID Fixer is quite broken. Currently it seems that it is meant to handle substitution tags that point to obsoletes, and to fix situations where there are two terms with the same id. Currently it does not do either of these things. Also it seems to have two menu items, which makes OE2 look cluttered. I would like to propose that we remove both these menu items for the release. Post release I would like to move the substitution tag function to the verification manager, and the duplicate id function to obomerge. Does anybody have any thoughts on this proposal?
  • I would like to propose that for the OE2 release the default search settings should be that only result count is shown and that the result count is not prefixed with 'search results'. This makes the tab top much shorter which is far more convenient. I have already had to expain at length to one novice user how to change this and I think it would save time if it was the default.

Meeting chat transcript

03/17/2009 08:27:50 AM from Harold:Hi Amina
03/17/2009 08:30:35 AM from Amina Abdulla:Hi Everyone
03/17/2009 08:30:48 AM from Amina Abdulla:We're on the phone
03/17/2009 08:31:31 AM from Amina Abdulla:Hi Colin
03/17/2009 08:31:39 AM from Harold:my connection echos very badly; just me, so I'll try to follow here
03/17/2009 08:31:41 AM from Amina Abdulla:We're on the conference line
03/17/2009 08:31:47 AM from Harold:and read minutes when they become avaiilable
03/17/2009 08:32:27 AM from Amina Abdulla:ok you were in charge of the minutes
03/17/2009 08:32:33 AM from Colin Batchelor:Hello Amina
03/17/2009 08:32:51 AM from Harold:Ican't be in charge of minutes as I won't be here long
03/17/2009 08:32:53 AM from Amina Abdulla:I'll do the minutes today :)
03/17/2009 08:33:16 AM from melissaH:shall we hang up and try again?
03/17/2009 08:33:18 AM from Amina Abdulla:Colin do you have the GO conference call details?
03/17/2009 08:33:18 AM from Harold:I'm going to try connecting through skype
03/17/2009 08:33:25 AM from Amina Abdulla:ok - will re
03/17/2009 08:33:32 AM from Amina Abdulla:initialting the call help?
03/17/2009 08:33:40 AM from Colin Batchelor:I've dialled in but there are horrible noises.
03/17/2009 08:34:04 AM from Jen Deegan:are we on the phone line today?
03/17/2009 08:34:08 AM from Amina Abdulla:yes
03/17/2009 08:35:10 AM from Harold:can't do it through skype (no routes found)
03/17/2009 08:35:21 AM from midori:I'm glad I programmed the number into my office phone :P
03/17/2009 08:36:13 AM from Chris Mungall:hang up one by one til we figure out who is causing it
03/17/2009 08:36:23 AM from Amina Abdulla:Who hasn't hung up yet?
03/17/2009 08:36:26 AM from midori:I'm out.
03/17/2009 08:36:28 AM from Jen Deegan:it's not me as there was no echo with me
03/17/2009 08:36:32 AM from Colin Batchelor:I haven't hung up yet.
03/17/2009 08:36:42 AM from Jen Deegan:was it when Amina joined?
03/17/2009 08:36:48 AM from Harold:aha!
03/17/2009 08:36:49 AM from midori:I could hear echoes and other noises; no idea if I was causing any of it.
03/17/2009 08:36:51 AM from Colin Batchelor:OK, hung up now.
03/17/2009 08:37:00 AM from Amina Abdulla:I didn't have echo when I came in
03/17/2009 08:37:05 AM from Jen Deegan:who is still on?
03/17/2009 08:37:09 AM from melissaH:melissa
03/17/2009 08:37:10 AM from Nomi Harris:I just hung up
03/17/2009 08:37:11 AM from Chris Mungall:i ams till on
03/17/2009 08:37:12 AM from Amina Abdulla:I was the first caller and then hung up and called in
03/17/2009 08:37:15 AM from midori:Someone should report this to Judy so she can pursue it with the ReadyConference people.
03/17/2009 08:37:17 AM from melissaH:hung up and called back in. still echos
03/17/2009 08:37:18 AM from Karen:I'm still on
03/17/2009 08:37:27 AM from Jen Deegan:is anybody skypng in?
03/17/2009 08:37:31 AM from Karen:just hung up
03/17/2009 08:37:41 AM from Jen Deegan:still echo
03/17/2009 08:37:48 AM from Harold:I tryied skyping to the readycall number but it own't work
03/17/2009 08:37:51 AM from midori:I was phoning ...
03/17/2009 08:37:57 AM from Jen Deegan:I'm on phone
03/17/2009 08:38:02 AM from midori:Harold - it ought to work! Jen and I have done it.
03/17/2009 08:38:04 AM from Colin Batchelor:I was on the phone.
03/17/2009 08:38:06 AM from Jen Deegan:chris is echoing for me
03/17/2009 08:38:09 AM from Tanya:me t00
03/17/2009 08:38:10 AM from midori:hrrumph
03/17/2009 08:38:12 AM from melissaH:me too
03/17/2009 08:38:14 AM from Amina Abdulla:Is anyone calling in from skype or a speaker phone?
03/17/2009 08:38:17 AM from Jen Deegan:I didn't hear amina echo
03/17/2009 08:38:20 AM from Harold:That's what I thought;
03/17/2009 08:38:32 AM from Harold:but it said no route available
03/17/2009 08:38:42 AM from Jen Deegan:should we try that website we had last week?
03/17/2009 08:38:42 AM from Chris Mungall:i hung up
03/17/2009 08:38:51 AM from midori:I used a phone that has a speaker phone option, but I wasn't using the speaker mode.
03/17/2009 08:39:05 AM from melissaH:still echoing after chris hung up, I've hung up now too
03/17/2009 08:39:09 AM from Jen Deegan:http://clackpoint.com/
03/17/2009 08:39:14 AM from midori:(and I hung up ages ago)
03/17/2009 08:39:26 AM from Jen Deegan:it gave me better sound quality than the phone
03/17/2009 08:39:33 AM from Harold:room number?
03/17/2009 08:39:40 AM from Jen Deegan:601425
03/17/2009 08:39:47 AM from Amina Abdulla:Heres the agenda for today: http://wiki.geneontology.org/index.php/OEWG_20090317
03/17/2009 08:39:49 AM from Jen Deegan:just a thought
03/17/2009 08:39:54 AM from Amina Abdulla:Are we moving to clackpoint?
03/17/2009 08:40:12 AM from Jen Deegan:could do
03/17/2009 08:40:17 AM from Jen Deegan:just to see if it is better
03/17/2009 08:40:23 AM from Jen Deegan:this phone does not seem to be working
03/17/2009 08:40:28 AM from Amina Abdulla:Guys, lets give our conference line another shot - the folks on right now don't have echo
03/17/2009 08:40:33 AM from Jen Deegan:several people are in clackpoint
03/17/2009 08:40:48 AM from Chris Mungall:wait, who is still on?
03/17/2009 08:40:54 AM from Amina Abdulla:I'm on
03/17/2009 08:41:17 AM from Amina Abdulla:Taniya's here
03/17/2009 08:41:19 AM from Chris Mungall:did we determine whos phone was causing it?
03/17/2009 08:41:35 AM from Amina Abdulla:Taniya and me are here and don't have echo
03/17/2009 08:41:37 AM from Chris Mungall:it was still echoing after i hung up apparently
03/17/2009 08:41:46 AM from Chris Mungall:so it was someone who hung up after me
03/17/2009 08:42:00 AM from Karen:so are we trying Clackpoint, or going back to the conference line?
03/17/2009 08:42:01 AM from Amina Abdulla:Colin is here too
03/17/2009 08:42:05 AM from Jen Deegan:http://clackpoint.com
03/17/2009 08:42:08 AM from Jen Deegan:it is working better
03/17/2009 08:42:31 AM from Jen Deegan:if you type 601425 in the room box at the top and hit return at the top then you get let in to the chat
03/17/2009 08:42:38 AM from Jen Deegan:then you click call to talk to us
03/17/2009 08:42:49 AM from Jen Deegan:there are several of us talking there already
03/17/2009 08:43:44 AM from Amina Abdulla:Chris
03/17/2009 08:43:57 AM from Amina Abdulla:the meeting has moved to clackpoint
03/17/2009 08:44:59 AM from Jen Deegan:UK people can also call 0845 5270723 if it is preferred
03/17/2009 08:49:05 AM from Karen:we're almost 20 minutes into the "meeting" and have only played around with audio technicalities
03/17/2009 08:49:15 AM from Karen:maybe we should just do Webex chat
03/17/2009 08:49:27 AM from midori:works for me!
03/17/2009 08:50:52 AM from midori:http://wiki.geneontology.org/index.php/OEWG_20090317
03/17/2009 08:57:23 AM from Jen Deegan:ok back to webex
03/17/2009 08:57:24 AM from Tanya:I'm back
03/17/2009 08:57:45 AM from Amina Abdulla:back too
03/17/2009 08:57:55 AM from Jen Deegan:I'm back
03/17/2009 08:58:06 AM from Jen Deegan:let's get the heck on with the discussion shall we?
03/17/2009 08:58:13 AM from Tanya:thirty minutes to go
03/17/2009 08:58:14 AM from midori:Now, we were going to get the coding update from Amian,
03/17/2009 08:58:16 AM from Karen:yep
03/17/2009 08:58:17 AM from Amina Abdulla:should we give the conference line a quick shot in the essense of time
03/17/2009 08:58:20 AM from midori:er, Amina,
03/17/2009 08:58:22 AM from Jen Deegan:no
03/17/2009 08:58:24 AM from Amina Abdulla:ok
03/17/2009 08:58:34 AM from midori:and documentation updates from anyone who has done any
03/17/2009 08:59:00 AM from Jen Deegan:other than those reported on the list
03/17/2009 08:59:04 AM from Colin Batchelor:OK, I've got as far as http://wiki.geneontology.org/index.php/OBO-Edit:_Help_document_OBO-Edit_2 but I don't know where, for example, Loading_a_History_File.htm is...
03/17/2009 08:59:05 AM from Amina Abdulla:I'm working on the option to turn off incremental reasoning
03/17/2009 08:59:09 AM from Nomi Harris:I can do some testing this week if that would be helpful
03/17/2009 08:59:17 AM from Jen Deegan:that would be great
03/17/2009 08:59:19 AM from midori:I think we should resume using Webex chat for these meetings -- it's been by far the most reliably technology since we stopped using IRC.
03/17/2009 08:59:25 AM from Jen Deegan:me too
03/17/2009 08:59:25 AM from Nomi Harris:I agree
03/17/2009 08:59:31 AM from Karen:works for me
03/17/2009 08:59:35 AM from Jen Deegan:the phone line has not had good sound quality for me
03/17/2009 08:59:38 AM from Jen Deegan:text is better
03/17/2009 08:59:41 AM from midori:Nomi- testing this week would be excellent.
03/17/2009 08:59:50 AM from Amina Abdulla:The phone line works well for all the GO calls, doesn't it?
03/17/2009 09:00:04 AM from Jen Deegan:yes but they have fewer people I think
03/17/2009 09:00:08 AM from midori:It usually has, but today was pretty bad.
03/17/2009 09:00:14 AM from Jen Deegan:we had quite a number and some echoers this week
03/17/2009 09:00:19 AM from Amina Abdulla:Todays problem was caused due to someone calling in
03/17/2009 09:00:24 AM from Jen Deegan:yes
03/17/2009 09:00:30 AM from Tanya:did b56 come out?
03/17/2009 09:00:41 AM from Jen Deegan:yes, we need to test b56 before signing off
03/17/2009 09:00:51 AM from midori:Thanks, Tanya. Let's stay on the subject of OBO-Edit.
03/17/2009 09:00:52 AM from Amina Abdulla:Not yet Taniya - I'd like to get done with some of the things I'm working on
03/17/2009 09:00:52 AM from Jen Deegan:I have done it from source but others have not yet seen it
03/17/2009 09:01:22 AM from Jen Deegan:we need to have it out fairly soon so it can be properly tested before signogg
03/17/2009 09:01:26 AM from Jen Deegan:signoff :-)
03/17/2009 09:01:26 AM from Amina Abdulla:Colin - you had a question on documentation, right?
03/17/2009 09:01:37 AM from midori:http://wiki.geneontology.org/index.php/OBO-Edit:_Help_document_OBO-Edit_2
03/17/2009 09:01:39 AM from Amina Abdulla:Yes - Sure.
03/17/2009 09:01:50 AM from midori:there's a link to the subversion repository on that page
03/17/2009 09:01:58 AM from Colin Batchelor:Ah! Found it---it's on the SVN! Will have a proper look now.
03/17/2009 09:03:26 AM from Amina Abdulla:Colin - we have tested OE with cmo-xp - I wasn't able to replicate the crash
03/17/2009 09:03:43 AM from midori:Harold says he'll update the wiki to show which pages he's worked on (sent to Amina)
03/17/2009 09:03:56 AM from Colin Batchelor:I don't know of a good way of reproducing it---I'll see whether it happens again with b56.
03/17/2009 09:04:05 AM from Colin Batchelor:Very frustrating.
03/17/2009 09:04:13 AM from Amina Abdulla:I sent you an email with the things we could look into
03/17/2009 09:04:24 AM from midori:I had similarly weird things in earlier betas, but 55 has been good to me so far.
03/17/2009 09:04:37 AM from Karen:I'm not sure which wiki page is the right place to record documentation editing, etc.
03/17/2009 09:04:50 AM from Amina Abdulla:I'd liek to know your system configuration and the memory allocation to OBO-Edit
03/17/2009 09:05:02 AM from Colin Batchelor:1024 M to OBO-Edit.
03/17/2009 09:05:12 AM from Amina Abdulla:ok great - We can test it in b56
03/17/2009 09:05:22 AM from midori:Amina suggested the testing task list, but there's also the "help decument OE" page that I just linked above, which is more specifically about documentation.
03/17/2009 09:05:26 AM from Amina Abdulla:Karen - the page Midori is referring to
03/17/2009 09:05:27 AM from Colin Batchelor:Otherwise java 1.5.0_17. Nothing peculiar, other than Windows.
03/17/2009 09:05:46 AM from midori:I've upt most of my comments on the documentation page.
03/17/2009 09:05:50 AM from Karen:OK, will add my comments to the page Midori linked earlier
03/17/2009 09:06:30 AM from Amina Abdulla:ok - I'll incorporate your changes Karen
03/17/2009 09:06:45 AM from Karen:thanks
03/17/2009 09:06:50 AM from Amina Abdulla:http://sourceforge.net/tracker2/?func=detail&aid=2504817&group_id=36855&atid=418257
03/17/2009 09:07:12 AM from midori:I haven't done much with the dictionary; sorry
03/17/2009 09:07:15 AM from Amina Abdulla:This bug was fixed in b55 - I'm wondering if anyone else is experiencing this
03/17/2009 09:07:36 AM from Karen:I also have a question about something in the GE, when there's a good moment
03/17/2009 09:07:49 AM from Amina Abdulla:ok - we can skip it for now if nooone else has worked with dictionaries
03/17/2009 09:07:53 AM from Amina Abdulla:Go ahead Karen
03/17/2009 09:08:13 AM from Karen:I noticed that the first icon in the GE toolbar is called the "drag and drop" tool
03/17/2009 09:08:16 AM from Nomi Harris:I will test dictionaries this week
03/17/2009 09:08:29 AM from Karen:but it doesn't let you drag and drop individual terms
03/17/2009 09:08:34 AM from melissaH:me too- having some other verification problems
03/17/2009 09:08:53 AM from Karen:I was wondering if I'm seeing odd behaviour or if it is just misnamed
03/17/2009 09:09:16 AM from Amina Abdulla:I'm testing it right now
03/17/2009 09:09:22 AM from Jen Deegan:there are a few bugs in the graph editor
03/17/2009 09:09:31 AM from Jen Deegan:I noted them but didn't think they were show stoppers
03/17/2009 09:09:31 AM from Karen:
03/17/2009 09:09:47 AM from Karen:I'm not sure if that's a bug, I think the icon is just misnamed
03/17/2009 09:09:48 AM from Jen Deegan:some of the buttons at the top I noticed didn't do what they said they did
03/17/2009 09:10:01 AM from Jen Deegan:I think delete didn't work for me#
03/17/2009 09:10:10 AM from Karen:if you drag, you recenter the graph, which is probably the desired behaviour
03/17/2009 09:10:33 AM from Karen:if the google-like moving of the graph is what we want, maybe the first icon should be renamed the "select" tool
03/17/2009 09:10:55 AM from Karen:and then we can just change the explanation to fit what it is actually doing
03/17/2009 09:11:10 AM from Jen Deegan:select would be better
03/17/2009 09:11:14 AM from Tanya:I agree - I see what you mean Karent
03/17/2009 09:11:17 AM from Tanya:Karen
03/17/2009 09:11:27 AM from Karen:delete worked for me several times, but then stopped :(
03/17/2009 09:11:38 AM from Amina Abdulla:Well the google-like moving works by itself
03/17/2009 09:11:49 AM from Amina Abdulla:You don't need drag and drop for that
03/17/2009 09:11:51 AM from Tanya:I can't drag and drop a term on another
03/17/2009 09:11:59 AM from Tanya:but I can access the right click menu
03/17/2009 09:12:02 AM from Tanya:for those actions
03/17/2009 09:12:13 AM from Jen Deegan:what OS are you on?
03/17/2009 09:12:13 AM from Amina Abdulla:It doesn't seem to be working - I'll look into it
03/17/2009 09:12:23 AM from Amina Abdulla:Has this feature worked in the past?
03/17/2009 09:12:33 AM from Tanya:me?
03/17/2009 09:12:39 AM from Jen Deegan:do you have the select button selected?
03/17/2009 09:12:41 AM from Jen Deegan:yes
03/17/2009 09:12:44 AM from Karen:I only remember this icon behaving as a select, not as drag and drop
03/17/2009 09:12:45 AM from Tanya:OS X 10.5.6
03/17/2009 09:12:57 AM from Tanya:yes, I have the select button selected
03/17/2009 09:13:01 AM from Jen Deegan:what do you expect drag and drop to so?
03/17/2009 09:13:17 AM from Amina Abdulla:There is a comment in the codebase saying - Uninstalled drag & drop behavior
03/17/2009 09:13:27 AM from Amina Abdulla:which explains why its not doing anything
03/17/2009 09:13:27 AM from Tanya:if I highlight a term and drag it onto another, I expect to make a link between the two
03/17/2009 09:13:31 AM from Tanya:that I can specify by type
03/17/2009 09:13:33 AM from Tanya:aha!
03/17/2009 09:13:34 AM from Karen:mousing over the drag and drop icon says it will create links between terms
03/17/2009 09:13:37 AM from Amina Abdulla:Yes thats right Tanya
03/17/2009 09:13:51 AM from Amina Abdulla:Good sopt Karen
03/17/2009 09:13:58 AM from Amina Abdulla:spot
03/17/2009 09:13:58 AM from Karen:but it doesn't do that, nor do I think it needs to, you can click the link creation icon for that
03/17/2009 09:14:08 AM from Jen Deegan:wouldn't you use the link creation tool?
03/17/2009 09:14:17 AM from Jen Deegan:agreement :-)
03/17/2009 09:14:25 AM from Tanya:the described middle mouse rubber banding thing works
03/17/2009 09:14:27 AM from Karen:that's my point, I think we should rename the first icon the "select" tool
03/17/2009 09:14:36 AM from midori:maybe that's why drag-n-drop was uninstalled
03/17/2009 09:14:50 AM from midori:renaming is a lot easier than changing its behavior
03/17/2009 09:14:53 AM from Jen Deegan:good thought
03/17/2009 09:14:53 AM from Tanya:I second that, Karen
03/17/2009 09:14:57 AM from Jen Deegan:me too
03/17/2009 09:15:01 AM from Amina Abdulla:Is there a need for a selection tool as such?
03/17/2009 09:15:09 AM from Jen Deegan:yes I think so
03/17/2009 09:15:12 AM from Karen:yes, it's useful
03/17/2009 09:15:18 AM from Jen Deegan:so we can select relationships or terms
03/17/2009 09:15:22 AM from Tanya:me too
03/17/2009 09:15:25 AM from Karen:exactly :)
03/17/2009 09:15:28 AM from Jen Deegan:which will then show in other components
03/17/2009 09:15:40 AM from Jen Deegan:but we need to update the tooltip and help guide
03/17/2009 09:15:54 AM from Jen Deegan:it's just like photoshop isn't it?
03/17/2009 09:16:11 AM from midori:I have another question about the editing interface -- this one is relevant to the GE and OTE
03/17/2009 09:16:40 AM from midori:There used to be a hotkey for merge, but it hasn't worked in OE2 for a long time.
03/17/2009 09:17:04 AM from midori:We can do without it, and I can update the documentation to remove references to it,
03/17/2009 09:17:25 AM from Amina Abdulla:I'll look into it Midori
03/17/2009 09:17:25 AM from midori:but it's still there in the hotkey toolbar.
03/17/2009 09:17:41 AM from Jen Deegan:perhaps it could be commented out from there until it is back?
03/17/2009 09:17:52 AM from Tanya:good idea
03/17/2009 09:18:05 AM from Amina Abdulla:I'll investigate and make the changes to the documentation if its not a quick fix
03/17/2009 09:18:09 AM from Karen:I sent Amina a revised version of the GE help yesterday and can send a new version for the "select" icon
03/17/2009 09:18:12 AM from midori:It's probably not worth fixing for the OE 2.000 release, so yes, I was going to suggest removing it from the menu.
03/17/2009 09:18:37 AM from Colin Batchelor:I've just been looking at my user.dict and it has words in it that b55 still flags as misspelt!
03/17/2009 09:18:47 AM from midori:not good.
03/17/2009 09:18:59 AM from Colin Batchelor:But I added those words in a text editor rather than patiently clicking on the hammer icon in OE.
03/17/2009 09:19:03 AM from Colin Batchelor:Should that matter?
03/17/2009 09:19:10 AM from midori:I thought not.
03/17/2009 09:19:16 AM from Amina Abdulla:No it should not
03/17/2009 09:19:26 AM from Jen Deegan:that's how I did the main dict file
03/17/2009 09:19:34 AM from Colin Batchelor:it's in the config folder that I/jen sent round with cmo-xp.obo
03/17/2009 09:19:37 AM from Amina Abdulla:Did you place your user.dict in the Oe config folder Colin
03/17/2009 09:20:00 AM from Colin Batchelor:It's in C:\Documents and Settings\batchelorc\Application Data\OBO-Edit2-beta
03/17/2009 09:20:07 AM from melissaH:the verification manager is also still finding things that have been fixed, like spaces, punctuation
03/17/2009 09:20:07 AM from Amina Abdulla:Are the words in the dict seperated by newline
03/17/2009 09:20:11 AM from Colin Batchelor:And when I add words with the hammer they appear in the user.dict
03/17/2009 09:20:21 AM from midori:yeah, sometimes line endings can catch you out
03/17/2009 09:20:32 AM from Colin Batchelor:Aargh---will have a look using Perl or something
03/17/2009 09:20:38 AM from Amina Abdulla:I don't think this is your config folder
03/17/2009 09:20:44 AM from Colin Batchelor:But emacs says --(Unix)-- at the bottom of the page.
03/17/2009 09:20:59 AM from Amina Abdulla:This is where the application is installed on windows
03/17/2009 09:21:00 AM from Jen Deegan:mine is in C:\Documents and Settings\Jennifer I Deegan\Application Data\OBO-Edit2-beta
03/17/2009 09:21:04 AM from Nomi Harris:Did you restart OE after editing your dictionary? If you hand-edit the file while OE is running, it might not see the additions.
03/17/2009 09:21:04 AM from midori:and it doesn't find any control-Ms in the file?
03/17/2009 09:21:14 AM from Colin Batchelor:No control-Ms.
03/17/2009 09:21:27 AM from midori:drat - there goes my idea.
03/17/2009 09:21:58 AM from Jen Deegan:colin can you send me your file?
03/17/2009 09:22:06 AM from Jen Deegan:if it's a windows thing it might happen for me too
03/17/2009 09:22:11 AM from Amina Abdulla:Yes Colin send it to me too
03/17/2009 09:22:16 AM from Amina Abdulla:I'll test it out
03/17/2009 09:22:27 AM from Amina Abdulla:Should'nt be a windowd issue
03/17/2009 09:22:42 AM from Colin Batchelor:Hmm. Doesn't seem to pick up any of the words in user.dict any more, sorry. But that seems more logical.
03/17/2009 09:22:54 AM from Amina Abdulla:Colin - Go to Config -> Configuration Manager -> User Settings
03/17/2009 09:23:00 AM from Nomi Harris:Colin, can you send your user.dict to the OEWG mailing list? I want to try it, too.
03/17/2009 09:23:19 AM from Amina Abdulla:There is an option over there to backup user.dict
03/17/2009 09:23:31 AM from Colin Batchelor:OK---where to?
03/17/2009 09:23:55 AM from Amina Abdulla:If you select that option it will open up a file browser window showing your OE config dir
03/17/2009 09:24:16 AM from Colin Batchelor:It's what I think it is.
03/17/2009 09:24:16 AM from Amina Abdulla:Please check if thats where you have been placing your own custom user.dict
03/17/2009 09:24:56 AM from Amina Abdulla:Hmm - if you stick to the naming convention - OE should be able to pick it up
03/17/2009 09:25:40 AM from Amina Abdulla:I'll take a look at it when you send it out.
03/17/2009 09:25:51 AM from Karen:I have a question about the reasoner with respect to the GE
03/17/2009 09:25:57 AM from Colin Batchelor:Have checked and that's where my custom user.dict is going.
03/17/2009 09:26:08 AM from Jen Deegan:Colin's user.dict is also not working for me
03/17/2009 09:26:11 AM from Amina Abdulla:Moving on - Jen did you want to comment on your action items
03/17/2009 09:26:37 AM from Jen Deegan:which were they again...
03/17/2009 09:27:05 AM from midori:microsoft & verification ...
03/17/2009 09:27:15 AM from Jen Deegan:got it
03/17/2009 09:27:18 AM from Jen Deegan:was on wrong page
03/17/2009 09:27:43 AM from Jen Deegan:I have been given permission to go and talk to Satnam at Microsoft and I see him tomorrow at 9.45am
03/17/2009 09:27:48 AM from Jen Deegan:I will let you know all about it
03/17/2009 09:28:00 AM from Jen Deegan:verification check
03/17/2009 09:28:16 AM from Jen Deegan:Amina rightly pointed out that the check for obsolete substitution tags is in the ID fixer
03/17/2009 09:28:29 AM from Jen Deegan:it is also mean tto check for different terms having the same ID
03/17/2009 09:28:42 AM from Jen Deegan:I checked and both these features do not work for me
03/17/2009 09:28:57 AM from Jen Deegan:also the ID fixer seems to have two menu items that do slightly differnt things
03/17/2009 09:29:08 AM from Jen Deegan:I think it might be good to remove the menu items for the release
03/17/2009 09:29:19 AM from Tanya:is that why it says (beta - not yet working)?
03/17/2009 09:29:23 AM from Amina Abdulla:(@Colin: I just run OE with your user.dict - added words to it and no terms appear flagged)
03/17/2009 09:29:28 AM from Jen Deegan:then I propose that I put the check for obsoletes on subsitution tags into the verification checker
03/17/2009 09:29:36 AM from Jen Deegan:and put the duplicate id feature into obomerge
03/17/2009 09:29:36 AM from midori:no objection here - I've never tried to use it, and there wasn't anything like it in OE1
03/17/2009 09:29:39 AM from Jen Deegan:I'm done now
03/17/2009 09:29:46 AM from midori:I'm going to have to go in a minute here ...
03/17/2009 09:30:00 AM from midori:Karen - you had another question?
03/17/2009 09:30:06 AM from Amina Abdulla:Chris - has the ID fixer been working well for you?
03/17/2009 09:30:06 AM from Jen Deegan:does that proposal sound okay? ANy objections?
03/17/2009 09:30:11 AM from Tanya:yes, Jen - good proposal
03/17/2009 09:30:15 AM from Jen Deegan:oh good
03/17/2009 09:30:24 AM from Karen:I completely agree that I'd rather see the check for obsolete tags in the regular verification checks
03/17/2009 09:30:26 AM from melissaH:can we keep some type of manual check for duplicate ids on adding new terms and/or in the verification manager?
03/17/2009 09:30:28 AM from Jen Deegan:I have never seen it do anything, through repeated trials over the last year
03/17/2009 09:30:42 AM from Jen Deegan:currently terms with duplicate ids are not loaded
03/17/2009 09:30:45 AM from Jen Deegan:the first is dropped
03/17/2009 09:31:06 AM from Jen Deegan:so the loading mechanism would have to change
03/17/2009 09:31:27 AM from Jen Deegan:this was alway intended as a feature for obomerge for when we accidentally have duplicate ids
03/17/2009 09:31:31 AM from Jen Deegan:and obomerge is a separate app
03/17/2009 09:31:39 AM from Jen Deegan:calledfrom within a gui
03/17/2009 09:31:44 AM from Colin Batchelor:(@Amina: what do you mean by "no terms appear flagged"?)
03/17/2009 09:31:47 AM from Jen Deegan:but without involving the main file loading mechanism
03/17/2009 09:31:51 AM from Chris:I have not systematically tested the ID fixer, but it worked when I tried it, but I think it needs to be tested properly with the xps
03/17/2009 09:32:00 AM from Jen Deegan:what did it do for you?
03/17/2009 09:32:11 AM from Amina Abdulla:(@Colin: user.dict is recognized)
03/17/2009 09:32:15 AM from Jen Deegan:maybe it does something I don't knwo about
03/17/2009 09:32:57 AM from Amina Abdulla:(@Colin: try restarting OE - it worked for me without restarting - we can chat on skype after the meeting)
03/17/2009 09:33:05 AM from Jen Deegan:if there's time could we have a vote on this one? "I would like to propose that for the OE2 release the default search settings should be that only result count is shown and that the result count is not prefixed with 'search results'."
03/17/2009 09:33:24 AM from Jen Deegan:it give shorter tabs in the search results
03/17/2009 09:33:32 AM from midori:that's what OE1 does, so it would look familiar
03/17/2009 09:33:34 AM from midori:fine with me
03/17/2009 09:33:39 AM from Jen Deegan:oh good
03/17/2009 09:33:41 AM from Colin Batchelor:fine by me too.
03/17/2009 09:33:43 AM from Jen Deegan:I can fix that
03/17/2009 09:33:44 AM from Karen:I'd be fine with dropping "search results" from the tabs
03/17/2009 09:33:53 AM from melissaH:me too
03/17/2009 09:33:54 AM from Jen Deegan:action item for me
03/17/2009 09:34:04 AM from Amina Abdulla:Ok with me - the goal for this one was to differentiate between multiple search queries
03/17/2009 09:34:14 AM from Tanya:for me too
03/17/2009 09:34:15 AM from Amina Abdulla:I personally liked to see it that way
03/17/2009 09:34:21 AM from Jen Deegan:do people need to go?
03/17/2009 09:34:24 AM from Tanya:yes
03/17/2009 09:34:37 AM from midori:you can always restore it if you care to configure to see the extra info
03/17/2009 09:34:44 AM from Jen Deegan:yes that's what I thought
03/17/2009 09:34:46 AM from Amina Abdulla:Yeah thats right
03/17/2009 09:34:53 AM from Jen Deegan:easier for new users this way thought
03/17/2009 09:35:06 AM from midori:less change from OE1
03/17/2009 09:35:06 AM from Amina Abdulla:ok Great
03/17/2009 09:35:09 AM from midori:gotta go now
03/17/2009 09:35:10 AM from Jen Deegan:yay!
03/17/2009 09:35:13 AM from Jen Deegan:my midori
03/17/2009 09:35:15 AM from Tanya:me too
03/17/2009 09:35:17 AM from Amina Abdulla:Karen - did you have a question?
03/17/2009 09:35:17 AM from Jen Deegan:should we stop then?
03/17/2009 09:35:21 AM from Tanya:bye!
03/17/2009 09:35:24 AM from Jen Deegan:bye tanya
03/17/2009 09:35:24 AM from midori:thanks all - keep that documentation coming!
03/17/2009 09:35:25 AM from midori:bye
03/17/2009 09:35:33 AM from Amina Abdulla:bye Midori and Tanya
03/17/2009 09:35:41 AM from Karen:I have a question about the reasoner with respect to the GE
03/17/2009 09:35:44 AM from Amina Abdulla:Yes
03/17/2009 09:35:47 AM from Amina Abdulla:Go ahead
03/17/2009 09:36:10 AM from Karen:when I try to use the GE with the reasoner on, either OE2-b55 crashes,or it behaves as if I did not have the reasoner on
03/17/2009 09:36:32 AM from Karen:I was wondering what behaviour others see with the GE with the reasoner on
03/17/2009 09:36:39 AM from Chris:I have experienced crashes with the GE+Reasoner
03/17/2009 09:36:51 AM from Chris:not sure what you mean by behaving as if the reasoner was not on
03/17/2009 09:36:52 AM from Amina Abdulla:when you say behaves as if he resoner is not on - do you mean you cannot see the implied links?
03/17/2009 09:37:06 AM from Karen:particularly since the help actually suggests turning on the reasoner so that the GE will open up the full path to the root
03/17/2009 09:37:07 AM from Amina Abdulla:is this with GO?
03/17/2009 09:37:11 AM from Karen:yes with GO
03/17/2009 09:37:16 AM from Chris:if you are editing the plain GO with no xps, then there is not much for the reasoner to imply
03/17/2009 09:37:36 AM from Chris:the reasoner will tell you if you make a redundant link for example
03/17/2009 09:37:52 AM from Karen:by acting as if the reasoner is not on, I mean that teh last time I tried this, it would only open up one level of parents, not the full path to root
03/17/2009 09:38:16 AM from Karen:the previuos two times, it would open up the full path to root 1 or 2 x, and then crash
03/17/2009 09:38:17 AM from Chris:you mean when you click on a corner icon, or use the ancestors menu item?
03/17/2009 09:38:31 AM from Karen:click (not right click) the corner icon
03/17/2009 09:38:33 AM from Amina Abdulla:Is this when you say Show -> Roots
03/17/2009 09:38:38 AM from Amina Abdulla:for a selected term?
03/17/2009 09:38:43 AM from Karen:no, just click the upper right corner icon of the selected term
03/17/2009 09:38:44 AM from Chris:I think this has always been the behaviour.
03/17/2009 09:39:05 AM from Karen:the help makes a distinction in behavior for when the reasoner is on vs off
03/17/2009 09:39:13 AM from Karen:off: open up one set of parents
03/17/2009 09:39:40 AM from Amina Abdulla:The only time the upper right corner blue icon does not work is when all roots are displayed
03/17/2009 09:40:05 AM from Karen:on: open up full path to root
03/17/2009 09:40:29 AM from Karen:when all paths are displayed, the blue icon turns gray
03/17/2009 09:40:39 AM from Amina Abdulla:Sorry I meant parent there - not root
03/17/2009 09:41:00 AM from Amina Abdulla:When only the parent term is displayed the icon is gray
03/17/2009 09:41:54 AM from Karen:I'm not talking about when the icon is gray
03/17/2009 09:42:04 AM from Karen:when it is blue, with the reasoner off, it opens up 1 lvl of parents - good
03/17/2009 09:42:09 AM from Chris:I see. So you would like a way of iteratively showing all paths to the root. This seems useful. But AFAIK the GE has never worked this way. The corner icon always open up one level. i think it should continue to work this way, but the path expansion could
03/17/2009 09:42:21 AM from Karen:no, that's not where I'm going
03/17/2009 09:42:24 AM from Chris:be a new menu item
03/17/2009 09:42:27 AM from Chris:ok...
03/17/2009 09:42:51 AM from Karen:my point is that the help makes a big deal about the distinction in behavior with the reasoner on vs off
03/17/2009 09:43:07 AM from Karen:but if you actually turn the reasoner on, and use the GE, for me it crashes OE
03/17/2009 09:43:20 AM from Jen Deegan:that might be because I have misunderstood it based on clicking and watching what happens
03/17/2009 09:43:24 AM from Chris:OK, so that's a problem
03/17/2009 09:43:26 AM from Amina Abdulla:Yes that should not be highlighted
03/17/2009 09:43:42 AM from Amina Abdulla:the resoner required bit
03/17/2009 09:43:43 AM from Karen:it does work the way the help says with the reasoner on, but for me only once before crashing
03/17/2009 09:43:56 AM from Jen Deegan:oh I see
03/17/2009 09:44:09 AM from Jen Deegan:mine used to crash until I got a much faster computer
03/17/2009 09:44:26 AM from Amina Abdulla:Karen - this could be a memory issue
03/17/2009 09:44:31 AM from Jen Deegan:it used to be really bad before
03/17/2009 09:44:31 AM from Karen:my work computer is dual processer, though maybe I need to give OE more mem
03/17/2009 09:44:51 AM from Chris:I think I need to go and check the latest help docs.
03/17/2009 09:45:01 AM from Karen:since we've already decided the GE is somewhat experimental and doesn't necessarily need to be perfect for release
03/17/2009 09:45:05 AM from Jen Deegan:they are on the little question mark icon on the GE
03/17/2009 09:45:15 AM from Karen:maybe we can jsut update the help to warn people about the potential problem
03/17/2009 09:45:25 AM from Jen Deegan:it was actually the processor that made the difference for me
03/17/2009 09:45:27 AM from Amina Abdulla:Colin - Did you get OE to pick up your user.dict by any change - it works for me and should not be a windows issue
03/17/2009 09:45:29 AM from Jen Deegan:I did not up the memory
03/17/2009 09:45:49 AM from Colin Batchelor:No, not even if I change the line endings to DOS line endings and restart :-(
03/17/2009 09:45:55 AM from Jen Deegan:Colin, did you say the verification checker would add words to that file?
03/17/2009 09:45:56 AM from Karen:I'm on a Dual 2 GHz PowerPC G5
03/17/2009 09:46:14 AM from Jen Deegan:that's a good machine
03/17/2009 09:46:39 AM from Jen Deegan:Amina, could it be the forward slashes hard coded? "org/oboedit/resources/user.dict"
03/17/2009 09:46:39 AM from Karen:and I still can't use the reasoner with the GE
03/17/2009 09:46:43 AM from Jen Deegan:we have back slashes in windows
03/17/2009 09:46:53 AM from Colin Batchelor:Jen: yes, but they're not honoured, so I have "electrophoresis" in twice!
03/17/2009 09:47:05 AM from Karen:how long do you have to wait for the reasoner to process? it takes minutes for me
03/17/2009 09:47:14 AM from Jen Deegan:nice
03/17/2009 09:47:36 AM from Chris:Karen - which reasoner
03/17/2009 09:47:49 AM from Amina Abdulla:Colin - I'll send you an email after testing this out some more.
03/17/2009 09:47:57 AM from Karen:they're all really slow for me
03/17/2009 09:48:06 AM from Jen Deegan:me too
03/17/2009 09:48:10 AM from Colin Batchelor:About 30 s for me on a dual-processor 3 GHZ Pentium, running the ForwardChainingReasoner and with 1024 M of memory.
03/17/2009 09:48:55 AM from Jen Deegan:took 25 seconds for me
03/17/2009 09:49:08 AM from Colin Batchelor:Amina - that's great. I should probably go home soon.
03/17/2009 09:49:21 AM from Jen Deegan:rule based reasoner 1024 M 2.53 dual core processor windows
03/17/2009 09:49:51 AM from Jen Deegan:how long does it take for you karen?
03/17/2009 09:49:53 AM from Chris:Karen you may need to up memory.
03/17/2009 09:49:54 AM from Chris:http://wiki.geneontology.org/index.php/OBO-Edit:Reasoner_Benchmarks#Results
03/17/2009 09:50:02 AM from Karen:I'm still waiting...
03/17/2009 09:50:07 AM from Jen Deegan:yoicks
03/17/2009 09:50:32 AM from Amina Abdulla:Any more items for today?
03/17/2009 09:50:39 AM from Jen Deegan:none from me
03/17/2009 09:51:01 AM from Colin Batchelor:None for today from me!
03/17/2009 09:51:10 AM from Karen:so, for the reasoner wrt GE, how 'bout if I just edit the help to make it clear that there may be issue using the reasoner with the GE
03/17/2009 09:51:28 AM from Jen Deegan:good idea
03/17/2009 09:51:32 AM from Chris:I think for the majority of day to day editing on GO without xps the reasoner isn't explicitly required. If there are sections of the docs that suggest otherwise point me to them, as I think there is still a lot of lingering confusion on this issue
03/17/2009 09:51:42 AM from Amina Abdulla:Yes
03/17/2009 09:52:11 AM from Jen Deegan:would the graph editor no longer need the reasoner if you changed it like you did the graph viewer?
03/17/2009 09:52:23 AM from Jen Deegan:to use the linkdatabase rather than the reasoned link database?
03/17/2009 09:53:02 AM from Karen:I' don't actually care if we change the behavior of the GE, I was just noticing that the help suggested something that doesn't seem to work well
03/17/2009 09:53:08 AM from Chris:Jen I think we should take this off-chat as I'm not following you
03/17/2009 09:53:13 AM from Amina Abdulla:Yes except that it needs to query the reasoned database to display implied links
03/17/2009 09:53:15 AM from Karen:I've always been fine with opening 1 lvl of parents at a time
03/17/2009 09:53:32 AM from Jen Deegan:okay we can do it offline
03/17/2009 09:53:36 AM from Chris:Amina: you don't get implied links if there are no xp definitions
03/17/2009 09:53:51 AM from Jen Deegan:did you want to talk on the phone. I can stay a bit longer
03/17/2009 09:53:56 AM from Amina Abdulla:oh I missed a section of that chat
03/17/2009 09:54:09 AM from Amina Abdulla:Alright everyone - thats for coming
03/17/2009 09:54:13 AM from Jen Deegan:bye then
03/17/2009 09:54:16 AM from Amina Abdulla:thanks!
03/17/2009 09:54:17 AM from Chris:bye
03/17/2009 09:54:19 AM from Amina Abdulla:Bye All
03/17/2009 09:54:20 AM from Karen:so 5 minutes for forwardChainReasoner
03/17/2009 09:54:21 AM from Colin Batchelor:Bye
03/17/2009 09:54:27 AM from melissaH:bye
03/17/2009 09:54:32 AM from Jen Deegan:AMina and Chris, did you want a quick chat on the phone?
03/17/2009 09:54:32 AM from Karen:bye
03/17/2009 09:54:32 AM from Nomi Harris:bye
03/17/2009 09:54:59 AM from Amina Abdulla:Yes
03/17/2009 09:55:03 AM from Jen Deegan:I'll call in
03/17/2009 09:55:09 AM from Amina Abdulla:Talk to you on the phone
03/17/2009 09:55:17 AM from Karen:Jen, I am actually not asking for a change in GE behavior
03/17/2009 09:55:27 AM from Amina Abdulla:Jen -
03/17/2009 09:55:39 AM from Jen Deegan:ok
03/17/2009 09:55:42 AM from Jen Deegan:no problem
03/17/2009 09:55:50 AM from Amina Abdulla:I think Karen just wanted to have the documentation changed
03/17/2009 09:55:54 AM from Jen Deegan:cool
03/17/2009 09:56:00 AM from Karen:yea, that's all
03/17/2009 09:56:06 AM from Jen Deegan:great. good to know
03/17/2009 09:56:16 AM from Jen Deegan:I'm on the phone now
03/17/2009 09:56:30 AM from Karen:which phone? should I call in too?
03/17/2009 09:56:49 AM from Jen Deegan:no it's okay, it's just that as I'm a developer now it's good touch base with amina dn Chris
03/17/2009 09:57:00 AM from Jen Deegan:we have to make an effort as I'm so far away
03/17/2009 09:57:05 AM from Karen:cool, just checking :)
03/17/2009 09:57:14 AM from Karen:bye
03/17/2009 09:57:20 AM from Jen Deegan:bye then

Demo /Tips/ Tricks

  • Jen: Searching for only obsolete terms

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