OE Webex 12Jul07
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July 12, 2007 5:29:46 PM from Jen Deegan� to All Attendees: Hi July 12, 2007 5:30:17 PM from melissa� to All Attendees: Hi Jen, Hi Erika! July 12, 2007 5:31:11 PM from Erika� to All Attendees: Hi girls! July 12, 2007 5:31:24 PM from Midori Harris� to All Attendees: hi! July 12, 2007 5:31:43 PM from melissa� to All Attendees: Hi, how are you all? July 12, 2007 5:32:12 PM from Jen Deegan� to All Attendees: Fine thanks July 12, 2007 5:32:15 PM from Jen Deegan� to All Attendees: You? July 12, 2007 5:32:18 PM from Erika� to All Attendees: very well thanks July 12, 2007 5:32:30 PM from Erika� to All Attendees: here in Italy it is the time for aperitive July 12, 2007 5:32:40 PM from melissa� to All Attendees: we should all be so lucky! July 12, 2007 5:32:44 PM from Erika� to All Attendees: beer or wine ;-) July 12, 2007 5:32:50 PM from Jen Deegan� to All Attendees: In the lab? July 12, 2007 5:32:56 PM from Jen Deegan� to All Attendees: Cool! July 12, 2007 5:32:56 PM from Erika� to All Attendees: or the red drink that Jen tried klast time July 12, 2007 5:32:58 PM from melissa� to All Attendees: its oatmeal time here.... July 12, 2007 5:33:18 PM from Jen Deegan� to All Attendees: I have a pie in the oven July 12, 2007 5:33:29 PM from Erika� to All Attendees: mmmmh! July 12, 2007 5:33:57 PM from melissa� to All Attendees: Hi John July 12, 2007 5:34:05 PM from John Day-Richter� to All Attendees: Hi. July 12, 2007 5:34:11 PM from Jen Deegan� to All Attendees: I can't change to all participants yet July 12, 2007 5:34:17 PM from Midori Harris� to All Attendees: same here July 12, 2007 5:34:17 PM from John Day-Richter� to All Attendees: I'm going to have to log out and back in; it doesn't think I'm the host. July 12, 2007 5:34:29 PM from Jen Deegan� to All Attendees: oh righty July 12, 2007 5:34:32 PM from John Day-Richter� to All Attendees: That's probably why. July 12, 2007 5:38:56 PM from Erika� to All Attendees: can you change to all partecipants now? July 12, 2007 5:39:02 PM from Erika� to All Attendees: I cannot July 12, 2007 5:39:24 PM from Midori Harris� to All Attendees: We're still missing our host ... July 12, 2007 5:39:25 PM from Jen Deegan� to All Attendees: Me neither July 12, 2007 5:39:33 PM from Jen Deegan� to All Attendees: I shouldn't think it matters July 12, 2007 5:39:53 PM from Jen Deegan� to All Attendees: Except probably no one can share any applications July 12, 2007 5:40:16 PM from Jen Deegan� to All Attendees: Oh yes John's still not back. I thought he was for a minute there. July 12, 2007 5:40:23 PM from hurdil� to All Attendees: hi everyone; I will have to leave in about 1/2 hour as we are hosting an RGD visit July 12, 2007 5:40:30 PM from Jen Deegan� to All Attendees: Hi Harold July 12, 2007 5:40:38 PM from Jen Deegan� to All Attendees: How's it going there? July 12, 2007 5:40:49 PM from hurdil� to All Attendees: cold and wet July 12, 2007 5:40:53 PM from Jen Deegan� to All Attendees: Oh dear July 12, 2007 5:40:54 PM from Jen Deegan� to All Attendees: same here July 12, 2007 5:41:00 PM from Jen Deegan� to All Attendees: How's your new office? July 12, 2007 5:41:01 PM from melissa� to All Attendees: so lucky, we've had 104 July 12, 2007 5:41:14 PM from Jen Deegan� to All Attendees: I must admit I'm enjoying the cool summer July 12, 2007 5:41:23 PM from hurdil� to All Attendees: our move to new offices has been postponed indefinitely July 12, 2007 5:41:37 PM from Jen Deegan� to All Attendees: why? July 12, 2007 5:41:42 PM from John Day-Richter� to All Participants: Sorry that took so long. Quite an ordeal, actually. July 12, 2007 5:41:48 PM from Jen Deegan� to All Attendees: welcome back July 12, 2007 5:42:13 PM from Jen Deegan� to All Participants: welcome back again July 12, 2007 5:42:22 PM from John Day-Richter� to All Participants: Are we ready to get started? July 12, 2007 5:42:26 PM from Erika� to All Participants: yes July 12, 2007 5:42:26 PM from Midori Harris� to All Participants: yup July 12, 2007 5:42:32 PM from Jen Deegan� to All Participants: yup July 12, 2007 5:42:40 PM from melissa� to All Attendees: you betcha July 12, 2007 5:42:47 PM from hurdil� to All Attendees: da July 12, 2007 5:43:05 PM from John Day-Richter� to All Participants: Okay, I want to ask a little advice about priorities... July 12, 2007 5:44:28 PM from John Day-Richter� to All Participants: We're launching a new project at Berkeley that will ultimately allow annotators to request a new term from the GO, and begin to annotate against a new term id immediately. But, if their new term request gets rejected, there will be quick and clean recovery methods so that they can salvage their annotations and move them to another GO term... July 12, 2007 5:45:10 PM from John Day-Richter� to All Participants: This project requires some new software from me, particularly some utilities that can do automatic updating of obsolete terms in annotation files and in multi-file ontologies... July 12, 2007 5:46:01 PM from John Day-Richter� to All Participants: This software will pop up a gui if a term refers to an obsolete term or the alt_id of a term, and ask the user how they want to deal with the problem... July 12, 2007 5:46:19 PM from John Day-Richter� to All Participants: So - I've got competing priorities. July 12, 2007 5:46:31 PM from John Day-Richter� to All Participants: 1) Fix show-stopping OBO-Edit 2.0 bugs July 12, 2007 5:46:33 PM from John Day-Richter� to All Participants: 2) Fix OBO-Edit 1.1 bugs July 12, 2007 5:46:52 PM from John Day-Richter� to All Participants: 3) Start experimenting with new complex filtering interfaces July 12, 2007 5:47:08 PM from John Day-Richter� to All Participants: 4) Write the obsolete/alt_id handling software July 12, 2007 5:47:18 PM from John Day-Richter� to All Participants: 5) Editing macros July 12, 2007 5:47:24 PM from John Day-Richter� to All Participants: 6) Any other new OBO-Edit 2.0 features July 12, 2007 5:47:50 PM from Jen Deegan� to All Participants: You can put the editing macros on hold as I have a perl script now that does the job. July 12, 2007 5:47:59 PM from John Day-Richter� to All Participants: That's good news. July 12, 2007 5:48:01 PM from Jen Deegan� to All Participants: if that is the search and replace thing at least. July 12, 2007 5:48:08 PM from John Day-Richter� to All Participants: Is it something we should publish? July 12, 2007 5:48:15 PM from Jen Deegan� to All Participants: eh? July 12, 2007 5:48:26 PM from John Day-Richter� to All Participants: Should we release your perl script to the larger community of editors? July 12, 2007 5:48:31 PM from Jen Deegan� to All Participants: oh I see July 12, 2007 5:48:39 PM from Jen Deegan� to All Participants: yes that would be sensible actually. July 12, 2007 5:48:40 PM from hurdil� to All Attendees: 2 > 1 >3 >4 July 12, 2007 5:49:07 PM from Jen Deegan� to All Participants: Yes I agree with Harold July 12, 2007 5:49:23 PM from melissa� to All Attendees: John, a question about the new term software. I know this is being developed for Phenote, but could this code be used as a module in other places, such as our curation interface? July 12, 2007 5:49:25 PM from John Day-Richter� to All Participants: I can't see what Harold's saying. Can everyone switch to "All participants"? July 12, 2007 5:49:42 PM from Jen Deegan� to All Participants: He said 2 > 1 >3 >4 July 12, 2007 5:49:50 PM from Midori Harris� to All Participants: I agree with Harold about 2>1>3>4 (which is the main thing he said) July 12, 2007 5:49:53 PM from Jen Deegan� to All Participants: Though I think 4 probably has to go higher July 12, 2007 5:50:33 PM from John Day-Richter� to All Participants: The main OBO-Edit 1.1 complaint is this damned dbxref library settings bug that I can't reproduce, right? July 12, 2007 5:50:40 PM from melissa� to All Participants: it does seem as though 2 and 4 are highest priority for most # of users July 12, 2007 5:50:51 PM from Midori Harris� to All Participants: Where 6 fit sin depends on which features -- I think we have to look at the outstanding requests, because they obviously won't all be the same priority as each other July 12, 2007 5:51:13 PM from Midori Harris� to All Participants: ... and therefore probably won't all be the same relative to 1-4 . July 12, 2007 5:51:42 PM from Jen Deegan� to All Participants: though I guess we can't do much with oboedit 2 until the bugs that stop testing are fixed July 12, 2007 5:52:11 PM from John Day-Richter� to All Participants: Can anyone summarize the OBO-Edit 2.0 bugs that prevent testing? July 12, 2007 5:52:14 PM from Karen R Christie� to All Participants: sorry I'm late, could someone give me a quick summary of what we're discussing now July 12, 2007 5:52:24 PM from Midori Harris� to All Participants: 1) Can't search July 12, 2007 5:52:31 PM from hurdil� to All Attendees: I can't search .. or at least, it currently searches everything, so it takes too long July 12, 2007 5:52:36 PM from John Day-Richter� to All Participants: Fixed July 12, 2007 5:52:36 PM from Jen Deegan� to All Participants: I'll mail the transcript to karen July 12, 2007 5:53:04 PM from Midori Harris� to All Participants: 2) Can't change default font, so I can't test cos I can't see the type! July 12, 2007 5:53:20 PM from John Day-Richter� to All Participants: ! July 12, 2007 5:53:34 PM from Midori Harris� to All Participants: addendum to search: after the long wait, any results I've gotten have been utter nonsense July 12, 2007 5:54:06 PM from John Day-Richter� to All Participants: Yeah - this is all related. The slow search + nonsense results are fixed. It had to do with a cache that wasn't getting cleared. July 12, 2007 5:54:24 PM from Erika� to All Participants: if I search for a term "regeneration in GO" I got loads of terms about 19000 July 12, 2007 5:54:42 PM from Erika� to All Participants: also with beta7 July 12, 2007 5:54:55 PM from John Day-Richter� to All Participants: It's fixed in (not yet released) beta8 July 12, 2007 5:55:05 PM from Erika� to All Participants: ok! thanks John July 12, 2007 5:55:05 PM from melissa� to All Participants: wonderful! July 12, 2007 5:55:35 PM from John Day-Richter� to All Participants: What about more showstoppers? There's something about settings not getting saved, right? July 12, 2007 5:56:31 PM from Midori Harris� to All Participants: Oh yeah, that may be related to not being able to change fonts ... memory setting changes don't get saved. July 12, 2007 5:56:59 PM from Midori Harris� to All Participants: Whatever I do via the configuration manager is disappearing into the ether when I juit O-E. July 12, 2007 5:57:32 PM from hurdil� to All Attendees: ok, I need to leave now. David tells me RGD calls' bye July 12, 2007 5:57:49 PM from Midori Harris� to All Participants: er, quit O-E July 12, 2007 5:57:55 PM from Midori Harris� to All Participants: bye, harold! July 12, 2007 5:58:20 PM from John Day-Richter� to All Participants: Did Harold say anything before he left? I still wasn't seeing any messages from him. July 12, 2007 5:59:01 PM from Midori Harris� to All Participants: just goodbye and that some RGD folks are visiting July 12, 2007 5:59:07 PM from John Day-Richter� to All Participants: Ok. July 12, 2007 5:59:33 PM from John Day-Richter� to All Participants: I'll fix these configuration problems today, make sure search is working, and issue a 2.0 release today. This needs to be testable. July 12, 2007 5:59:45 PM from John Day-Richter� to All Participants: Then I guess I'll move on to OBO-Edit 1.1 bugs. July 12, 2007 6:00:04 PM from John Day-Richter� to All Participants: Does anyone have any major 1.1 bugs they want to call to my attention? July 12, 2007 6:00:30 PM from John Day-Richter� to All Participants: (Like tracker items I should look at first) July 12, 2007 6:00:32 PM from Karen R Christie� to All Participants: not necessarily a bug, but we've had the no namespace problem again, we reallly need to do something to prevent that July 12, 2007 6:00:58 PM from John Day-Richter� to All Participants: Midori, didn't you write a verification check for that? July 12, 2007 6:01:04 PM from Midori Harris� to All Participants: yup July 12, 2007 6:01:07 PM from Jen Deegan� to All Participants: I'd really appreciate a fix on the autosave bug July 12, 2007 6:01:29 PM from Karen R Christie� to All Participants: then we need to put in place the procedure so that everyone for GO is using Midori's verification check July 12, 2007 6:01:36 PM from Erika� to All Participants: Sometimes OE shows me the bug window without any reason. I usually close the window and keep working and everithing works well July 12, 2007 6:01:52 PM from Jen Deegan� to All Participants: Also less urgently the graph viewer save image button July 12, 2007 6:01:59 PM from John Day-Richter� to All Participants: Erika - It's never for no reason. Whenever you see that you should send me the stderr file. July 12, 2007 6:02:14 PM from Erika� to All Participants: Ok John! I will do that July 12, 2007 6:02:44 PM from Midori Harris� to All Participants: did you get the one I sent today? July 12, 2007 6:03:12 PM from John Day-Richter� to All Participants: I've got nothing on the tracker... July 12, 2007 6:03:37 PM from John Day-Richter� to All Participants: But I do have your email. I haven't looked at it yet. July 12, 2007 6:04:16 PM from Midori Harris� to All Participants: OK; that email accompanied a comment I made on Karen's exception bug item, SF 1749367 July 12, 2007 6:05:16 PM from John Day-Richter� to All Participants: This looks interesting. I'll check this out too. July 12, 2007 6:05:34 PM from John Day-Richter� to All Participants: Should we move on to graph editing demo stuff, or are there any other issues we should discuss? July 12, 2007 6:05:51 PM from Jen Deegan� to All Participants: how should I share my script? July 12, 2007 6:05:56 PM from Jen Deegan� to All Participants: Via the obedit wiki? July 12, 2007 6:06:02 PM from Jen Deegan� to All Participants: or the editors wiki? July 12, 2007 6:06:03 PM from Karen R Christie� to All Participants: If we're going to handle putting in place a policy for the no namespace issue via email then I have nothing else July 12, 2007 6:06:32 PM from Midori Harris� to All Participants: oboedit makes sense, cos it'll be useful for any ontology (I presume) July 12, 2007 6:06:49 PM from Jen Deegan� to All Participants: Great, I'll do that then July 12, 2007 6:06:49 PM from John Day-Richter� to All Participants: Jen - I think maybe you ought to start a sourceforge release package for it. July 12, 2007 6:06:49 PM from Midori Harris� to All Participants: (that was for Jen) July 12, 2007 6:07:08 PM from Jen Deegan� to All Participants: I'm not sure what a sourceforge release package is July 12, 2007 6:07:18 PM from Midori Harris� to All Participants: Karen - I'll send my verify.xml to the oboedit list and anyone else that I know of who edits GO July 12, 2007 6:07:45 PM from John Day-Richter� to All Participants: Go to Admin -> File Releases and create a new pacakge. Follow the instructions to upload your script as release 1.0 July 12, 2007 6:07:54 PM from Midori Harris� to All Participants: Jen - another option is to check it in to GO CVS, in go/software/utilities July 12, 2007 6:07:58 PM from John Day-Richter� to All Participants: Then email gofriends (or something) and tell everyone about it. July 12, 2007 6:08:10 PM from Jen Deegan� to All Participants: Oh yes that's a good idea July 12, 2007 6:08:13 PM from John Day-Richter� to All Participants: You should ALSO check it into CVS. July 12, 2007 6:08:23 PM from Jen Deegan� to All Participants: I'll put it in utilities in cvs July 12, 2007 6:08:48 PM from Jen Deegan� to All Participants: I'll put the instructions on the oboedit wiki July 12, 2007 6:09:08 PM from Jen Deegan� to All Participants: Can I do another one too? July 12, 2007 6:09:15 PM from Jen Deegan� to All Participants: I have two scripts that I use with oboedit. July 12, 2007 6:09:39 PM from John Day-Richter� to All Participants: You can zip 'em up as a single package when you release them. Maybe call it 'Curator Utilities' July 12, 2007 6:09:52 PM from Jen Deegan� to All Participants: Gosh. July 12, 2007 6:09:54 PM from Jen Deegan� to All Participants: Ok July 12, 2007 6:11:01 PM from John Day-Richter� to All Participants: On to the demo, then? July 12, 2007 6:11:19 PM from Jen Deegan� to All Participants: Yes July 12, 2007 6:12:22 PM from John Day-Richter� to All Participants: Today I wanted to do more on how to use the graph editor + the reasoner to browse the ontology. July 12, 2007 6:12:44 PM from John Day-Richter� to All Participants: I'm going to disable global selection on the ontology editor panel first... July 12, 2007 6:13:06 PM from John Day-Richter� to All Participants: Now when I select something in the editor panel, it doesn't affect the rest of the program. July 12, 2007 6:13:31 PM from Midori Harris� to All Participants: what's the advantage of doing that? July 12, 2007 6:13:45 PM from Jen Deegan� to All Participants: This might be a good time to press start recording if it isn't greyed out for you john July 12, 2007 6:13:56 PM from John Day-Richter� to All Participants: Ok. July 12, 2007 6:15:04 PM from John Day-Richter� to All Participants: If you want to display an unrelated collection of terms in the graph editor, you can just drag them from an ontology editor panel. The global selection needs to be off for this to work properly (otherwise you'll get unwanted results when you click a term as you start to drag) July 12, 2007 6:15:50 PM from John Day-Richter� to All Participants: The terms I dropped all appeared in the graph editor. July 12, 2007 6:16:24 PM from John Day-Richter� to All Participants: Notice that when I just dropped that last term, TWO terms appeared. July 12, 2007 6:16:52 PM from John Day-Richter� to All Participants: That's because when you drag from the ontology editor panel, you aren't really dragging a term - you're dragging a link. The graph editor panel is showing both the parent and child of the link I dragged, which is why two terms appeared. July 12, 2007 6:17:25 PM from John Day-Richter� to All Participants: Also, notice the dotted line between "cryptic_splice_etc" and "consequences_of_mutation" July 12, 2007 6:18:10 PM from John Day-Richter� to All Participants: That's there because there's no direct connection between those two terms, but the reasoner always tries to draw all links (explicit or implied) between visible terms. July 12, 2007 6:18:34 PM from John Day-Richter� to All Participants: Hover the mouse over an implied link to see how the reasoner discovered it. July 12, 2007 6:19:34 PM from John Day-Richter� to All Participants: In the ontology editor panel, there needs to be a path to a term for it to be visible at all. July 12, 2007 6:19:40 PM from John Day-Richter� to All Participants: That's not the case in the graph editor panel. July 12, 2007 6:19:49 PM from John Day-Richter� to All Participants: You can hide or show anything you want. July 12, 2007 6:20:40 PM from John Day-Richter� to All Participants: If you use the ontology editor panel and the graph editor together, you can get some pretty powerful browsing and visualization behavior. July 12, 2007 6:20:57 PM from John Day-Richter� to All Participants: Any questions so far? July 12, 2007 6:21:06 PM from Jen Deegan� to All Participants: No July 12, 2007 6:21:25 PM from John Day-Richter� to All Participants: Okay, I'll keep going. July 12, 2007 6:21:26 PM from Midori Harris� to All Participants: nothing more specific than "what's going on" ... which is really my problem July 12, 2007 6:21:34 PM from John Day-Richter� to All Participants: Wait... what? July 12, 2007 6:22:18 PM from Midori Harris� to All Participants: I'm just having a terrible time getting my head around the graph editor. Mut I don't think we should hold up the participants who do get it. July 12, 2007 6:22:47 PM from melissa� to All Participants: (I feel the same way....) July 12, 2007 6:22:53 PM from John Day-Richter� to All Participants: No, we need to deal with this immediately, because I bet you aren't the only one having trouble. And if it doesn't make sense at first glance, I need to change it. July 12, 2007 6:23:41 PM from melissa� to All Participants: somehow it seems to make sense when John drives, but not when I do it myself. July 12, 2007 6:23:46 PM from Jen Deegan� to All Participants: It makes sense to me but that's because I've been trying to delete links in the graph viewer for about two years. July 12, 2007 6:24:11 PM from Jen Deegan� to All Participants: I'm a bit overwhelmed by the number of other things this does but I think I'll get used to them July 12, 2007 6:24:49 PM from Midori Harris� to All Participants: (miserable sodding webex just quit on me AGAIN. this is getting old.) July 12, 2007 6:25:03 PM from John Day-Richter� to All Participants: So, does it make sense what we're looking at right now? July 12, 2007 6:25:07 PM from Jen Deegan� to All Participants: Yes July 12, 2007 6:25:10 PM from Erika� to All Participants: yes July 12, 2007 6:25:15 PM from melissa� to All Participants: yes July 12, 2007 6:25:34 PM from Midori Harris� to All Participants: it's one term and one of its ancestors? July 12, 2007 6:25:35 PM from melissa� to All Participants: (midori I see you there twice, if it helps you troublshoot webex) July 12, 2007 6:25:58 PM from John Day-Richter� to All Participants: Yes, we're seeing a term and an ancestor. July 12, 2007 6:26:05 PM from Jen Deegan� to All Participants: I'll mail sandra and ask if she can look at the log right now. July 12, 2007 6:26:11 PM from Midori Harris� to All Participants: melissa - that's happened 3 of the 4 times I've been booted) July 12, 2007 6:26:21 PM from John Day-Richter� to All Participants: There's an is_a relationship between the two terms. July 12, 2007 6:26:25 PM from Midori Harris� to All Participants: ooh, now the extra me is gone July 12, 2007 6:26:51 PM from John Day-Richter� to All Participants: If I want, I can look at the whole is_a hierarchy above either of those terms, to help put it in perspective. July 12, 2007 6:27:17 PM from Midori Harris� to All Participants: Anyway, yes, I think I get it -- there are "in between" relationships that aren't shown in the graph? July 12, 2007 6:27:31 PM from John Day-Richter� to All Participants: There can be. That's what the dotted lines do. July 12, 2007 6:27:33 PM from Jen Deegan� to All Participants: John, can you invite this person to the meeting? Sandra.Schonenberger@webex.com July 12, 2007 6:27:42 PM from Midori Harris� to All Participants: Sorry, I was typing and didn't get a good look at what you selected in the pulldown. July 12, 2007 6:27:52 PM from John Day-Richter� to All Participants: Hold on... inviting someone, and then I'll redo that... July 12, 2007 6:28:41 PM from John Day-Richter� to All Participants: Okay. First, I'll hide everything but the current selection. July 12, 2007 6:29:38 PM from John Day-Richter� to All Participants: Now I'll show the is_a heirarchy for this term. July 12, 2007 6:29:47 PM from John Day-Richter� to All Participants: (Hmm... I'm getting a very long delay between when I send a message and when it appears on the screen) July 12, 2007 6:30:27 PM from Midori Harris� to All Participants: There's also a delay between when you say you'll do something, and when I see the movewent on the shared app. July 12, 2007 6:30:52 PM from John Day-Richter� to All Participants: I think the confusing thing about this view is that, unlike the term editor panel, you can navigate up or down. You aren't constrained by the way the ontology is rooted. July 12, 2007 6:31:24 PM from Midori Harris� to All Participants: Sorry, I don't even know what you mean by "navigate up or down" ... July 12, 2007 6:31:33 PM from Jen Deegan� to All Participants: me neither July 12, 2007 6:32:09 PM from John Day-Richter� to All Participants: In the ontology editor panel, you cannot choose an arbitrary term in the middle of the graph and say "show me all your ancestors". That doesn't even really make sense, given the fact that the ontology is displayed from the roots down. July 12, 2007 6:32:17 PM from John Day-Richter� to All Participants: Here, you can do that. July 12, 2007 6:33:25 PM from John Day-Richter� to All Participants: I think we might have more luck looking at the GO, since you're more familiar with that. July 12, 2007 6:33:31 PM from John Day-Richter� to All Participants: Can people stay 10 more minutes? July 12, 2007 6:33:34 PM from Midori Harris� to All Participants: ok July 12, 2007 6:33:37 PM from Karen R Christie� to All Participants: ok July 12, 2007 6:33:38 PM from melissa� to All Participants: sure July 12, 2007 6:33:44 PM from Jen Deegan� to All Participants: Do you think it would be easier to fit everything in the window if the boxes weren't so big? July 12, 2007 6:33:49 PM from Erika� to All Participants: I am sory I should go in 5 minutes July 12, 2007 6:33:54 PM from Erika� to All Participants: (sorry) July 12, 2007 6:34:01 PM from Jen Deegan� to All Participants: the test is small but the boxes take up a lot of space July 12, 2007 6:34:06 PM from Jen Deegan� to All Participants: text I mean July 12, 2007 6:34:54 PM from John Day-Richter� to All Participants: We can play with that. July 12, 2007 6:34:59 PM from Jen Deegan� to All Participants: great July 12, 2007 6:36:06 PM from John Day-Richter� to All Participants: OBO-Edit and Webex sharing are having a bit of a toxic interaction right now. Hopefully we can get this to work properly... July 12, 2007 6:36:31 PM from John Day-Richter� to All Participants: I'm in a very low-memory environment right now, so the reasoner might not be able to do the trick. July 12, 2007 6:36:53 PM from Midori Harris� to All Participants: GO's a lot bigger than SO ... July 12, 2007 6:36:59 PM from Erika� to All Participants: Guys I should go now! July 12, 2007 6:37:07 PM from Midori Harris� to All Participants: bye! July 12, 2007 6:37:08 PM from Jen Deegan� to All Participants: Bye Erika July 12, 2007 6:37:16 PM from Erika� to All Participants: I am sorry but I will read the webex transcipt July 12, 2007 6:37:21 PM from Erika� to All Participants: thanks July 12, 2007 6:37:23 PM from Erika� to All Participants: bye July 12, 2007 6:37:26 PM from melissa� to All Participants: bye July 12, 2007 6:38:20 PM from John Day-Richter� to All Participants: Okay, here's what I mean about being able to navigate up or down... July 12, 2007 6:38:51 PM from John Day-Richter� to All Participants: In the ontology editor panel, we just don't have the option to browse the parentage of "primary cell wall". We need the DAG Viewer to help us. July 12, 2007 6:39:05 PM from John Day-Richter� to All Participants: But in the graph editor... July 12, 2007 6:39:40 PM from John Day-Richter� to All Participants: And if we don't want to go just one step at a time... July 12, 2007 6:40:03 PM from Jen Deegan� to All Participants: Nice July 12, 2007 6:40:31 PM from melissa� to All Participants: I'm having a hard time seeing what you are doing to accomplish the changes.... webex is really choppy now July 12, 2007 6:40:39 PM from Midori Harris� to All Participants: Can you do the pulldown thing any slower? The menus just barely appear, and then vanish before I can see what you pick. July 12, 2007 6:41:00 PM from Jen Deegan� to All Participants: you can make johns screen bigger July 12, 2007 6:41:05 PM from John Day-Richter� to All Participants: Yeah. I'm going to hide everything but "primary cell wall". July 12, 2007 6:41:35 PM from Jen Deegan� to All Participants: do 'sharing' 'view' '100%' July 12, 2007 6:41:35 PM from Midori Harris� to All Participants: Jen - how? July 12, 2007 6:42:00 PM from John Day-Richter� to All Participants: Now I'm going to show all of "primary cell wall's" ancestors... July 12, 2007 6:42:36 PM from Jen Deegan� to All Participants: can you do that a bit slower again? July 12, 2007 6:43:17 PM from Jen Deegan� to All Participants: got it July 12, 2007 6:43:25 PM from Midori Harris� to All Participants: yes - finally! July 12, 2007 6:43:31 PM from Jen Deegan� to All Participants: 'show' is the thing we want July 12, 2007 6:43:44 PM from John Day-Richter� to All Participants: Okay, this is how ALL the ancestors look. Let's look at how the Graphical DAG Viewer wants to show it. July 12, 2007 6:44:46 PM from Jen Deegan� to All Participants: Cool! July 12, 2007 6:44:53 PM from melissa� to All Participants: ooohhhh July 12, 2007 6:45:02 PM from Jen Deegan� to All Participants: And the great thing is that you can now change the relatinships in that view July 12, 2007 6:45:13 PM from Jen Deegan� to All Participants: really cool! July 12, 2007 6:45:20 PM from melissa� to All Participants: develops from horizontal??!!??? July 12, 2007 6:45:21 PM from John Day-Richter� to All Participants: No, you can't. July 12, 2007 6:45:25 PM from Jen Deegan� to All Participants: no? July 12, 2007 6:45:38 PM from John Day-Richter� to All Participants: Sorry. The graphical dag view is read-only, but I can change that. July 12, 2007 6:45:45 PM from John Day-Richter� to All Participants: I thought it would be too confusing... July 12, 2007 6:45:52 PM from Jen Deegan� to All Participants: oh right July 12, 2007 6:45:53 PM from melissa� to All Participants: huh??? July 12, 2007 6:46:01 PM from Jen Deegan� to All Participants: I thought that that was the point of this July 12, 2007 6:46:25 PM from John Day-Richter� to All Participants: The graph EDITOR (left) can be used to change the relationships. The graph dag viewer (right) cannot. July 12, 2007 6:46:26 PM from Jen Deegan� to All Participants: I'm talking about the graph editor July 12, 2007 6:46:31 PM from Jen Deegan� to All Participants: yes that's fine July 12, 2007 6:46:34 PM from Jen Deegan� to All Participants: phew! July 12, 2007 6:46:36 PM from John Day-Richter� to All Participants: Okay, cool. July 12, 2007 6:46:39 PM from melissa� to All Participants: ok July 12, 2007 6:46:49 PM from John Day-Richter� to All Participants: Okay, before we go, lemme show a use case... July 12, 2007 6:47:56 PM from John Day-Richter� to All Participants: Let's say that we decide that actually, primary cell wall is_a envelope (an amazing new discovery!) July 12, 2007 6:48:34 PM from John Day-Richter� to All Participants: We can add "envelope" to our view on the left by dragging it from the ontology editor panel. July 12, 2007 6:49:12 PM from John Day-Richter� to All Participants: Now we can "draw" the new is_a relationship between primary cell wall and envelope. July 12, 2007 6:49:23 PM from John Day-Richter� to All Participants: First, we pick the link drawing tool... July 12, 2007 6:49:39 PM from John Day-Richter� to All Participants: Make sure that we have the right relationship type... July 12, 2007 6:49:58 PM from John Day-Richter� to All Participants: And click and drag between primary cell wall and envelope... July 12, 2007 6:50:26 PM from John Day-Richter� to All Participants: (There may be a long delay as the reasoner deals with this) July 12, 2007 6:50:54 PM from John Day-Richter� to All Participants: (In a machine with more than 500M of memory, it will be very quick) July 12, 2007 6:51:00 PM from Karen R Christie� to All Participants: John, will we still be able to edit relationships in the text ontology editor? July 12, 2007 6:51:12 PM from John Day-Richter� to All Participants: Our new link has been added! July 12, 2007 6:51:17 PM from Jen Deegan� to All Participants: Yay! July 12, 2007 6:51:31 PM from John Day-Richter� to All Participants: Karen - the ontology editor panel works exactly as it did before. July 12, 2007 6:51:50 PM from John Day-Richter� to All Participants: And you can drag between panels to do the kind of edits you're used to... July 12, 2007 6:52:21 PM from Karen R Christie� to All Participants: cool. while the graph based editing is cool is some ways, it seems slower than text based. I think I will love the graph-based view though for seeing all ancestors, not so easy sometimes in 1.1 July 12, 2007 6:52:48 PM from John Day-Richter� to All Participants: And I think you'll find it's faster, because you can choose to hide everything but what you want to work with. July 12, 2007 6:53:08 PM from Jen Deegan� to All Participants: I think we must all be spell-bound by it as we've gone 20 minutes over and no one has noticed. July 12, 2007 6:53:30 PM from melissa� to All Participants: john's a wizard, didn't you know?? July 12, 2007 6:53:32 PM from Midori Harris� to All Participants: who says we haven't noticed? July 12, 2007 6:53:37 PM from Jen Deegan� to All Participants: :-) July 12, 2007 6:53:38 PM from Karen R Christie� to All Participants: I'd noticed, I'd just agreed to stay a bit late ;) July 12, 2007 6:53:46 PM from Jen Deegan� to All Participants: Oh, it's just me then July 12, 2007 6:53:49 PM from John Day-Richter� to All Participants: I hearby release you from my thrall. July 12, 2007 6:53:59 PM from Midori Harris� to All Participants: we haven't *complained* because it's been interesting enough ;) July 12, 2007 6:54:14 PM from John Day-Richter� to All Participants: Next week, let's do more graph editing demos, and OBO-Edit should be in a condition where you can play along. July 12, 2007 6:54:15 PM from melissa� to All Participants: so seems that we all just need to practice a bit, and see if it becomes more intutive? also, maybe john can watch us play sometime July 12, 2007 6:54:24 PM from Jen Deegan� to All Participants: Yes that seems right July 12, 2007 6:54:26 PM from John Day-Richter� to All Participants: Remember, office hours Monday morning. July 12, 2007 6:54:37 PM from melissa� to All Participants: can anyone put their screen up on webex, or only the host? July 12, 2007 6:54:37 PM from Jen Deegan� to All Participants: Can I ask a quick question before we go? July 12, 2007 6:54:43 PM from John Day-Richter� to All Participants: You bet. July 12, 2007 6:54:48 PM from Midori Harris� to All Participants: Ah. I've been forgetting about office hours. July 12, 2007 6:54:54 PM from melissa� to All Participants: when are they again? July 12, 2007 6:55:05 PM from Jen Deegan� to All Participants: if I want to restore from autosave do I load my file then load the autosave file as a serial file load? July 12, 2007 6:55:14 PM from John Day-Richter� to All Participants: Office hours are 9-10, Pacific. July 12, 2007 6:55:21 PM from melissa� to All Participants: ok thanks July 12, 2007 6:55:21 PM from John Day-Richter� to All Participants: Jen - yes, although this changes in OBO-Edit 2.0 July 12, 2007 6:55:27 PM from Midori Harris� to All Participants: Mel - the host can make anyone the presenter. July 12, 2007 6:55:42 PM from Jen Deegan� to All Participants: It's just I crashed oboedit today after a 5 hour edit session July 12, 2007 6:55:48 PM from Jen Deegan� to All Participants: so I may need to know that tomorrow July 12, 2007 6:55:56 PM from melissa� to All Participants: it might be helpful to have a few of us play around and have you watch....then you can see what is intuitive and what is not... July 12, 2007 6:55:57 PM from Jen Deegan� to All Participants: or it might have straightened out over night July 12, 2007 6:56:37 PM from Jen Deegan� to All Participants: good idea to have john watch us use the graph editor July 12, 2007 6:56:47 PM from Midori Harris� to All Participants: I seldom go more than 15-20 minutes without saving ... been bitten by power cuts and other fun things ... July 12, 2007 6:57:05 PM from John Day-Richter� to All Participants: You'll love the new autosave. It works much better. July 12, 2007 6:57:08 PM from Jen Deegan� to All Participants: can we add the google maps style zoom ladder as a feature request fot the graph editor July 12, 2007 6:57:10 PM from Jen Deegan� to All Participants: ? July 12, 2007 6:57:19 PM from melissa� to All Participants: oh yessss! July 12, 2007 6:57:28 PM from Midori Harris� to All Participants: you know how the feature request tracker works ;) July 12, 2007 6:57:40 PM from Jen Deegan� to All Participants: oh yes I suppose so July 12, 2007 6:57:49 PM from Jen Deegan� to All Participants: is that okay for oboedit 2 then? July 12, 2007 6:58:01 PM from Jen Deegan� to All Participants: I mean to use the tracker. I shppose it is really. July 12, 2007 6:58:04 PM from Midori Harris� to All Participants: now we just have to remind Joh nto look at it ;) ;) July 12, 2007 6:58:17 PM from John Day-Richter� to All Participants: Ah, yes. We can add that, Jen. Can you suggest how I decide what is 100% and what is fully zoomed out? July 12, 2007 6:58:42 PM from Jen Deegan� to All Participants: I think fully zoomed out would be wehen you can see white space all round the terms currenntly showing July 12, 2007 6:58:53 PM from John Day-Richter� to All Participants: But unlike google maps, our world gets bigger and bigger as we add more terms to the view. July 12, 2007 6:59:01 PM from Jen Deegan� to All Participants: and zoomed right in would be when only two terms show in the vertical space July 12, 2007 6:59:14 PM from Jen Deegan� to All Participants: mayeb? July 12, 2007 6:59:18 PM from Jen Deegan� to All Participants: maybe I mean? July 12, 2007 6:59:51 PM from Karen R Christie� to All Participants: even if you can make the 'world July 12, 2007 7:00:01 PM from Jen Deegan� to All Participants: Shall I save the transcript? July 12, 2007 7:00:15 PM from Karen R Christie� to All Participants: bigger by adding more terms, it makes sens for the fully zoomed out view to be all terms currently in the graph editor July 12, 2007 7:00:29 PM from Midori Harris� to All Participants: jen - yes please! July 12, 2007 7:00:36 PM from Jen Deegan� to All Participants: good-oh July 12, 2007 7:00:45 PM from Jen Deegan� to All Participants: I checked and it works July 12, 2007 7:00:49 PM from John Day-Richter� to All Participants: Last thing: Who's coming to office hours on Monday? July 12, 2007 7:00:58 PM from Midori Harris� to All Participants: I agree that fully zoomed out = can see all the terms July 12, 2007 7:01:13 PM from Midori Harris� to All Participants: I'll try to remember office hours ... July 12, 2007 7:01:20 PM from melissa� to All Participants: I'll try to come too. July 12, 2007 7:01:22 PM from Jen Deegan� to All Participants: Haven't we gone home when your office hours start? July 12, 2007 7:01:34 PM from John Day-Richter� to All Participants: (I'll implement the zoom control this way, but I think you'll be surprised at how strange it is in practice) July 12, 2007 7:02:01 PM from Jen Deegan� to All Participants: If you have any better ideas then fire ahead July 12, 2007 7:02:12 PM from Jen Deegan� to All Participants: shall we call it a day now? July 12, 2007 7:02:26 PM from John Day-Richter� to All Participants: Yes. Bye everyone. I'll send out the transcript and recording. July 12, 2007 7:02:27 PM from Karen R Christie� to All Participants: yep, I need to move on to other things July 12, 2007 7:02:33 PM from Karen R Christie� to All Participants: bye July 12, 2007 7:02:35 PM from Jen Deegan� to All Participants: See you then. July 12, 2007 7:02:40 PM from Midori Harris� to All Participants: bye July 12, 2007 7:02:40 PM from melissa� to All Participants: thanks everyone