area51.slashnet.org has activated the following mode : No External Message
area51.slashnet.org has activated the following mode : Only Operator Change Topic
5:25 PM
kchris has joined the channel
5:30 PM
jclark has joined the channel
j-lo has joined the channel
j-lo: hello
jrichter has joined the channel
jrichter: Hey, folks.
tberardi has joined the channel
kchris: Hello
tberardi: Hi, sorry I'm late.
jclark: hello
jclark: Midori said to tell you that she's going to be a bit late but is leaving her chat window open to get the transcript.
jrichter: Okay.
jclark: shall we start?
jrichter: Sure. Are you in charge, Jen?
jclark: sort of
jclark: I don't have the agenda though
jrichter: Ahh... then I'll do my items first, and then Midori can add on any when she arrives.
jclark: good-oh
5:35 PM
jrichter: Item 1: John's status report:
jrichter: a) The paper
jrichter: It looks like we've finally got it ready to go. Once I integrate Jane's edit, it's ready to submit. Unless there are objections from those assembled, I'm going to submit it today. Is that okay?
kchris: good with me
jclark: yes
jrichter: b) OBO-Edit Documentation
jrichter: It turns out that the new features in OBO-Edit require a LOT of new documentation. I'm going to have to rewrite the entire "Customizing OBO-Edit Section", and the documentation will require extensive proofreading and testing to make sure its comprehensible. I'm thinking I've got at least 2 weeks of work here.
jclark: That was my section wasn't it?
jclark: I'll take a look
jrichter: Excellent!
jrichter: I'd like people to send me their favorite OBO-Edit layout. It would be nice to have a bunch of example layouts for users to try.
jclark: is the plan that you write it and I read it and see if I can make all the stuff work?
tberardi: I like and use Jen's layout.
jrichter: That's right, Jen.
jclark: I'll make an improved one with the new gadgetry
jrichter: Excellent! I think you'll be impressed.
jclark: I checked and I am already
jrichter: Since we have 2 weeks, does anyone have a tutorial they'd like to add to the documentation (maybe based on an email you wrote or something)...
jrichter: ?
5:40 PM
kchris: I still use the default, but would really be happier if I found the instructions Midori gave me for using a layout that allowed resizing the query results window
hjd has joined the channel
tberardi: Is there something in the documentation now about finding is_a orphans?
tberardi: If not, that would be handy.
kchris: For tutorials, we did talk about the idea of providing instructions for doing a query where you limit to one ontology, e.g. only function, I still can't remember how to write that query
jrichter: Hmm... maybe a better way to do this is to solicit the working group list for "Frequently Asked Questions" like "How do you limit a search to a single ontology"
jrichter: People on the list can compose answers, and I'll pick up the slack on any remaining unanswered questions.
jrichter: Does that sound good?
j-lo: yep
jrichter: Moving on to c) OBO-Edit 1.1 Last Minute Features
jrichter: As I was writing some documentation for the layout customization section, I was stunned by how hard it was to use the layout editor. It's highly intolerant of errors, and it's impossible to tell where your mistake is if there's a problem with the layout..
jrichter: The worst part is, all that error information exists, it's just not being displayed.
jclark: funky
5:45 PM
midori: Hi guys ... finally here for real.
jclark: how's the cat?
midori: do you really wanna know? :P
jrichter: I'd like permission to update that part of the Configuration Plugin to display line numbers in the layout editor, and I'd like to add a panel that will show you any errors (with the associate line number) if you try to enter a bad layout.
jclark: yes
jclark: good idea
midori: permission? nay, I grant encouragement!
jrichter: (BTW: I've already dropped in a new editor component that does syntax highlighting and automatic tabbing)
jrichter: Cool!
jrichter: Two more things on my agenda:
jrichter: 2) The install4j installers:
jrichter: I know the popup messages are annoying, but did the new installer system work well for everyone?
midori: I haven't tested it yet ...
kchris: nor I
hjd: I had no problem with beta 5 install
jclark: it works for windows
jrichter: And no memory problems?
midori: the platform-independent beta5 opens & loads GO nicely ...
hjd: I've loaded up to 5 ontologies simulataineously, and it seems to work ok
jclark: oh, actually now you mention it I used the platform independent version
hjd: I'm using the mac installer version
jrichter: It sounds like Harold's the only one who uses the installers. Please give the installers a try on your platform; I think the problems have been solved. If everything works well, I can get money to buy the program.
5:50 PM
jclark: okay
midori: downloading now ...
jrichter: The main problem to look for would be OutOfMemory issues.
jrichter: Last thing from me... 3) Webex status report?
jclark: we tried it on monday
jrichter: How's that going, Jen/Tanya?
jclark: it worked for me but not for jane or david
jclark: nto sure why
tberardi: We did three locations on Friday.
tberardi: Denver, Hinxton and Palo Alto.
tberardi: Prices:
tberardi: $38.50/month
tberardi: Voice options
tberardi: VoIP: 2 cents/min/person
jrichter: !
tberardi: 800 number: 20 cents/min/person
hjd: I've had a Webex with one person down in Boston (boston - bar harbor); Didn't know it does voice; does it do video too?
tberardi: 650 number (local for Palo ALto): 5 cents/min/person
tberardi: Yes, it does video with max 5 locations.
tberardi: the voice component is extra.
tberardi: VoIP is cheap but only 2 people max can talk at one time.
tberardi: Others have to wait for the host to pass the 'mike'
tberardi: the phone numbers let everyone talk at once
tberardi: but are more expensive
tberardi: For VoIP and for web meeting, max number of attendees is 200.
tberardi: Think that's enough info?
jclark: yes
jrichter: When are we getting an account?
jclark: the pricing seems problematic
tberardi: I do want to test VoIP with at least three locations.
tberardi: I have an account we can use now at Carnegie.
hjd: I just got a mike, so I'm game
jclark: Do you think if we paid more per month then the voice would be free?
tberardi: Do we need approval to get another one for GO purposes?
tberardi: I think this is the negotiated contract with Stanford as a whole.
tberardi: And we can't mess with it.
jclark: is that able to be opened up to the whole consortium?
5:55 PM
tberardi: I could get it here at Carnegie or Mike C. could get it at the Dept. of Genetics.
tberardi: Well, technically, no.
tberardi: The account goes to one person.
jclark: I think if we have to have a stanford person on every call then it will nto work
jrichter: No, it will nto.
tberardi: Right.
tberardi: It will not work.
jclark: should we find out the cost of a non stanford account?
tberardi: webex.com
jrichter: I know: $300/month.
tberardi: !!!
jrichter: That's why I was pushing convoq.com
jclark: and VoIP?
jrichter: VoIP is always pay per play, I think.
jclark: oh right
tberardi: We didn't have too much luck with convoq, though.
tberardi: (Jen, David and I tried.)
jclark: we need to write down all these costs so I can take them to the menagement call
tberardi: I believe I sent an email to you, Jen and John.
jclark: I think it has to be the $300 one so we can all use it
kchris: I've missed something, why do we need this?
tberardi: Did that disappear into cybervoid?
tberardi: Want to take that, John?
jclark: no actually, I have it, but we need to add on the requirements doc that john is writing
jrichter: It would be helpful for:
jclark: I hadn't managed to type that yet
jrichter: 1) These meetings
jrichter: 2) Webinars
jclark: online content meetings
jrichter: 3) Remote trainings of all kinds
jclark: management calls
tberardi: Harold: I'll email you separately to set up a test.
j-lo: and we want it for content meetings too
j-lo: quite urgently
jrichter: $300/month is WAY too much. There are cheaper solutions.
jrichter: I'm looking up a price breakdown now...
jclark: but do they work?
jrichter: megameeting does
tberardi: Would you like to try having a webex meeting for our next OBO-Edit meeting?
jclark: ok right
jrichter: http://www.megameeting.com/web-conferencing-chart.html
jclark: we need to test options but it doesn't have to be this meeting
jclark: yes
hjd: was that $300 per one site, or each one? if one site is needed for starting, and everyone else connects in, that's $3600 per year, but what would it be saving in terms of travel costs?
jclark: john should we test that next?
tberardi: No, the cost is only associated to the host.
tberardi: Attending is free.
jrichter: That page I posted shows a comparison of the major products.
jclark: cool
jclark: John can we talk about this in a separate meeting? we need to get details
6:00 PM
jrichter: Okay, let's take this offline.
jclark: we also need to do more testing
jclark: cool
jclark: what's next?
jrichter: Any other agenda items?
j-lo: John - following the content meeting we had with David earlier this week, we have an urgent feature request
jrichter: !
j-lo: it's to prevent us re-using ids
j-lo: when we're editing a section of the ontology
midori: I don't remember any feature requests that I'd characterize as 'urgent'....
j-lo: parallel to the live ontology
midori: (we have a social workaround for the ID problem)
jclark: yes
hjd: ?
j-lo: well, that hasn't worked so far
jclark: what did you think oboedit was going to do jane?
jclark: true
j-lo: not sure
jclark: that's the tricky part
j-lo: perhaps assign temporary ids?
tberardi: What's the problem?
jclark: because it's when we merge files that the problem arises
jclark: it's when we edit two files in parallel
jclark: and use the same id twice
jrichter: Okay, here are the possible solutions:
jrichter: 1) Assign temporary ids that are scoped per-file. When a user does some kind of "sync" operation, all the temporary ids are resolved to real, global identifiers.
jrichter: Advantages: Easy to write, doesn't require network access
jrichter: Disadvantages: All the problems of id clashes have been shunted to the "sync" operation. If two people sync without communicating, we're still screwed.
jclark: I think we have to assume that we're oblivious of the id clash
6:05 PM
jrichter: 2) Create a simple ID server on geneontology.org. When a user requests an id, the server never, EVER gives out that id again.
jclark: that would be good
jrichter: Advantages: Works every time, no possibility for problems
jrichter: Disadvantages: We'd rapidly waste our id space, it would require network access to create terms
midori: I wouldn't bother with (1) then, because if communication works, we don't need it, and if communication fails it won't help.
jrichter: We may need some combination of 1 & 2, actually. The temporary ids could be used until the user can communicate with the id server.
j-lo: yes - sometimes it's useful to be able to edit offline
jclark: true
midori: What we thought of was to have obomerge cough up a warning if terms in the changed files share an ID but not the term name.
jclark: that seems more straightforward to me
jrichter: That won't work.
jclark: oh
jrichter: OBO-Edit won't be able to tell if its an id clash or a name change.
hjd: wouldn't it be possible to just assign ranges, much like we do for entire Mods, but maybe split them per curator (mods's take care of assignment)?
midori: We'd get some "false positives" when we really just change term names, but I could live with that.
jclark: sometimes curators aren't bright enough to remember that they're editing two fiels concurrently
jclark: files
jrichter: Okay, it sounds like there are 2 proposals on the table:
jrichter: 1) Warnings for obomerge (easy)
midori: Harold - that's essentially what we decided to do pending any technical solution; we'd assign a range per meeting as well.
jrichter: 2) ID Server System (quite tricky)
midori: (for "we" read: Midori & David will be ID Range Czars)
jrichter: I can sneak 1) into the current release, but I think that 2) needs to wait OBO-Edit 1.2, if we can. Otherwise we're going to have delays.
kchris: To me, the fact that the ID server system is tricky means that it is probably not a good use of our time currently
j-lo: can we just do 1 then?
6:10 PM
jclark: I think 1 is best
j-lo: every big content change we've done has had this id problem, it's a huge time waster
jrichter: Sure. I think the ID server idea is good, though. It deserves a place on the feature request tracker. Suzi has been begging for something like this for about 2 years.
midori: We need the non-technological aspects of ID management anyway, so I'd make 1 the priority ... maybe not even do 2 if we turn out to get on OK wit 1 plus aggressive ID range management by humans.
kchris: I completely agree with Midori
jclark: me too
jrichter: So voted. I'll add name warnings into obomerge.
midori: (fine to do 2 somewhere along the line if we or other O-E users need it later, but I don't feel the need right now)
j-lo: is that equivalent to the sync function john?
tberardi: (BTW, I just tried the Windows installer and it worked well. OBO-Edit opened and I was able to open the ontology without a problem. The pop-ups were a little annoying though so I ended up just clicking on 'Yes to all.')
jrichter: Jane - no. This would just tell you if two files you're trying to merge reuse an id with a different name.
midori: I've tested the Mac installer -- fine for installing, starting up, and loading GO.
jrichter: Should I go ahead with the temporary id feature too?
jrichter: Or was that voted down?
j-lo: I'd prefer the sync idea - I thought that was the vote
jclark: I don't think we need that
j-lo: I do because the obomerge method will still require hand assigning ids when things go wrong
midori: I agree with Jen. I think we've had problems in the past because we didn't manage ID ranges well.
kchris: couldn't you effectively create a temporary ID anyway, just by changing the name space?
6:15 PM
jclark: if obomerge shows duplicate ids we have easy ways to deal with that
jrichter: No! Namespaces don't effect ids!
midori: Karen - we can and do, but ... what John said.
jclark: eh?
j-lo: they're not that easy Jen!
kchris: sorry, I meant the prefix that is part of the ID
jclark: I have fixed one before
jclark: I have a script from Midori
midori: we'd like to be able to just do find/replace to convert temporary prefixes to GO:
jrichter: You know, now that I think about it, I may be able to get a more sophisticated behavior out of obomerge if I'm very, very tricky.
jrichter: Jane - would it be okay if obomerge just reassigns clashing ids?
j-lo: yes
jclark: yes that would be good
midori: reassigns them to what?
jclark: it could ask for a new range
tberardi: Midori, does anyone still fill in the go_numbers file?
midori: ... and we would need to be able to tell obomerge which file keeps its IDs
jclark: I do
j-lo: what about name changes though, John?
j-lo: won't it give them new ids?
kchris: automatic reassignment seems possibly problematic to me, based on the fact that someone, Midori?, already mentioned cases where it is just a name change
midori: Tanya - Jen does, and one of my action items from this week is to bring the rest of it up to date.
jclark: true
jrichter: Now that I think about it more, there's a way I can tell the difference between name changes and new term creation.
jclark: wouldn't it just be better if obomerge just listed the problematic ids and names?
jrichter: Best of obomerge could fix them too, optionally. Then we solve everyone's problem.
tberardi: That would certainly be a useful first step. (What Jen said.)
j-lo: I'd like it automatic
midori: could we try it with just step 1 first?
midori: automatic worries me more, actually ...
jclark: me too
kchris: automatic worries me a lot
6:20 PM
j-lo: doesn't worry me at all!
jrichter: It's equally easy to write either version, I think. Detecting the problem is a lot harder than fixing it.
jrichter: How 'bout I write the full featured version, with automatic reassignment, but we leave the reassignment features undocumented.
j-lo: okay
jrichter: A task force will go about the task of seeing whether the reassignment features are useful and safe.
jclark: sure
jclark: good idea
kchris: instead of automatic reassignment, could it bring them up with some sort of yes/no checkboxes
midori begins to suspect that j-lo is just angling to be relieved of file-merging duty ...
jclark: file merging does suck quite a lot
midori: agree with j, j, & k
tberardi: I was wondering about that.
jrichter: Karen - it probably couldn't, because obomerge is meant to be a non-interactive script.
j-lo: \j-lo never wants to do that again!
jclark: It's no fun
jrichter: You could run it in "warnings" mode, and then go ahead and do the merge if you aren't bothered by the warnings.
jclark: I did it about 16 times for the cns file
midori: oooh, I like John's latest suggestion!
jclark: there might be quite a lot of warnings
jclark: Could it list the terms in those warnings?
midori: 'tis the nature of the beast, I'm afraid ...
jclark: true
tberardi: (A way to get your heart racing while at the computer.)
jrichter: Jen - absolutely.
midori: good idea to have it show terms
jclark: That would be good
jclark: Then we'd know where we are
jclark: We can manually reassign and then merge
j-lo: it's the error-prone human fixing of said warnings that worries me
jrichter: Would it be useful to have a little command line utility called "reassignoboid" that would take a file and reassign an id in it?
jclark: We have a script that midori wrote
j-lo: it's so easy to introduce new problems when you're doing search and replace on the file
jclark: the script rocks
midori: tell me more, 'cos I suspect the answer (to John) is yes
jrichter: Usage:
jrichter: reassignoboid <oldid> <newid> <inputfile.obo> -o <outputfile.obo>
6:25 PM
midori asks in an aside to Jen - which script is that? I can't remember!
jrichter: or, if you're nasty:
jrichter: reassignoboid <oldidregexp> <replacementidregexp> <inputfile.obo> -o <outputfile.obo>
jclark: it take the obo file and a two column tab delimeted file with old id in first column and new id in second column and replaces
jclark: splendid
j-lo: would you have to do that for each id you've reused?
midori: oh, that one! using it on obo files is your adaptation; I wrote it for something else originally
jclark: oh right.
jclark: It's fantastic
jclark: I like it a lot
midori: j-lo - the regexp option would let you do a batch at once
jrichter: Jane - obomerge could do it automatically. You'd run this script if you wanted to change a specific id.
jrichter: I could write the script so that you could give it an unlimited number of oldid:newid pairs.
jclark: that would be good
midori: yup
jrichter: Should this be done for OBO-Edit 1.1, or wait until 1.2?
jrichter: (I think it's < 1 day)
midori: we'll use it as soon as it's available, so if it's quick , let's go for 1.1
jrichter: Okay, for OBO-Edit 1.1: obomerge improvements, reassignoboid script!
jclark: Yay!
midori: yay too
jrichter: I've got a fussy baby in my lap. Any other items?
jclark: can you tell me the path to the eclipse oboedit file so I can import from cvs?
jrichter: I'll post that on the developers wiki today.
jclark: ta
6:30 PM
jclark: nothing else for me then
jrichter: Oh! One more thing for the grammar cops.
jrichter: Is it a "User's Guide" or a "Users Guide"?
midori: for next time, we should report on 1.1 beta testing (which means I ought to do more testing in the meantime , if possible ...)
tberardi: Users' Guide
jrichter: (I think 1, on the "Farmer's Almanac Logic
tberardi: Well, are you addressing a single person or all users?
midori: User's Guide (for one user) or Users' Guide (for plural users)
jrichter: I'm addressing "The User"
tberardi: Then, 1.
jclark: User Guide?
midori: in that case, User's Guide
jclark: That would be a guide to users I suppose
jrichter: Good. Nothing changes then.
jrichter: I'm off to write some scripts and so on!
kchris: singular User's Guide seems file, it's a guide to the use who is reading it at the time
jclark: Good luck
tberardi: Keep me in the webmeeting loop. I'm happy to try the VoIP option, if we desire.
jclark: ta
tberardi: on webex.
jclark: yes
jrichter: Bye.
jclark: bye
midori: likewise on the web meeting front
tberardi: bye
j-lo: see ya
jrichter has quit the server saying: Client exited
jclark: cheerio
tberardi has quit the server saying: Quit:
kchris: bye
j-lo has quit the server saying: Quit:
jclark has quit the server saying: Quit: jclark