OE IRC 2Nov06

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tberardi has joined the channel
tberardi: Good morning everyone!
jrichter: Hi.
tberardi: Did you get my testing report, John?
jrichter: Let me check...
5:30 PM
pfey: Hello
tberardi: Hi Petra!
jrichter: Oh yeah, I got it.
MelissaH has joined the channel
tberardi: Great.
MelissaH: Hi there.
jrichter: Should we start?
hjd has joined the channel
midori: might as well; I don't know who else is coming
hjd: sorry I;m late; had to punch a few people out at my bank
midori: can you come punch out people at the banks here too?
hjd: missing paycheck autodeposit
jrichter: I thought that by this time of year there were no remaining vestiges of civilization in Bar Harbor. Haven't you dug into your ice forts by now?
hjd: actually, it was 55F yesterday
pfey: wait a day..
hjd: but last sunday we had 60mph winds
pfey: 36 here today!
hjd: F or mph?
pfey: F
pfey: and 25 mph
hjd: BTW, alex will not be joining today I think
jrichter: Do we have any sort of agenda?
midori: The only thing I had was reports on 1.1 beta testing.
5:35 PM
jrichter: It seems to me that most people haven't had time to tackle their assignments, or they're held up waiting for me to issue a bug fix.
midori: Well, the floor's open for anything else, if anyone has anything.
hjd: I've tested the graphviz stuff and could save in all formats ok
jrichter: I've got two quick announcements:
j-lo has joined the channel
jrichter: 1) We've registered oboedit.org, and I'll have a server soon.
midori: way hey!
jrichter: So if people have ideas of stuff they'd like on that site (besides the obvious) we should talk about that.
jrichter: 2) obo2obo now can run OSL scripts.
midori: what's OSL?
midori: (I'm sure you saw that coming.)
jrichter: OBO Scripting Language. See the User's Guide for details.
jrichter: If you are willing to do a little scripting, you can do amazing bulk transformations on your ontologies.
MelissaH: please transform mine.
jrichter: Umm... into what?
MelissaH: anything else?!!!>??
kchris has joined the channel
jrichter: Disclaimer: OSL cannot resolve major career crises or personality problems.
MelissaH: bummer.
kchris: sorry I'm late, traffic accident on my route today 
midori: hey, I can transform your ontology into free disk space on the unix command line 
jrichter: There are some example scripts in the latest user's guide that show the kind of thing it can do. One example script changes all spaces in term names into dashes, for example.
5:40 PM
tberardi: John, wrt the user's guide:
midori locates the relevant bits of documentation ...
tberardi: if we find areas that need updating/addition
tberardi: do we do that (if so, how?)
tberardi: or will you take care of it?
jrichter: I'll take care of it, unless it's a huge amount of work.
jrichter: (like adding several new sections)
midori: Another question about the user's guide: how does the search work?
jrichter: You mean when you bring up the user's guide from inside OBO-Edit?
midori: yep.
Alex_MGI has joined the channel
midori:  I just tried to search for "script" (looking for the OSL documentation), and there was only one hit, in the "Getting OBO-Edit Started" section ... but !script
hjd: hey alex; didn't think you'd make it
midori: ... oops ... 
Alex_MGI: I spaced out over lunch.
jrichter: I actually don't really know how the help search works. The User's Guide is displayed by a pre-fab component from the JavaHelp system. I think it's doing some kind of keyword search.
midori: that should be: the string "script" appears plenty of times in the obo2obo section, so I don't see why those occurrences weren't found.
5:45 PM
jrichter: Maybe there's something wrong with the index - the help system's index needs to be manually built, and it could be that the script I use is broken. I'll look into this today.
jrichter: Would you like to file a bug report, Midori?
midori: (So for "how does it work?" you could read "why didn't it find what I was looking for?")
midori: um, sure, bug report ...
jrichter: I also had a question for the WG...
jrichter: I've got a few pending requests for filtering/rendering in the Graph Viewer Plugin. It's several days worth of work to get this to work properly. I'd like to punt this until OBO-Edit 2.0, but if people think it's really urgent, I can address it now.
MelissaH: One of the requests was mine
MelissaH: to make the Graphviewer have similar behavior to the DAGviewer
MelissaH: eg. local button
midori: My opinion: those features would be really cool and useful, but I'm not actually impeded by their absence. So I'm willing to wait for 2.0.
MelissaH: anyone else want this?  the graph viewer is useless for me until implemented.
jrichter: Yeah. I looked over the code today, and I might be able to get a "local" button working in a day. Anything more complex will take a lot longer.
j-lo: Fine by me if we wait until 2.0
5:50 PM
hjd: Actually, I'm not in a rush for a change. I'm satisfied with how it works now, at least for my needs.
jrichter: Melissa: Is the problem that the non-transitive relationships clutter the display too much?
midori doesn't want to deprive anybody who does need the graph viewer features ...
MelissaH: If no one else is needing this, then no hurry.
jrichter: How 'bout this: I'll see if I can get a "local" button working today. If it takes more than a few hours, I'll give up and we'll put this on hold until 2.0. Does that work?
MelissaH: yep, fine by me.
midori: fine with me
jrichter: One more question:
jrichter: Jane submitted a bug about the verification plugin throwing out bad warnings because of filenames in comments and definitions.
jrichter: OBO-Edit thinks that the period in the filename is a full stop in a sentence, and complains about caps and spacing.
jrichter: Jane suggested that we fix this by allowing users to input a list of phrases to ignore -
5:55 PM
jrichter: But the problem is that this seems like a lot of work, and it's work that everyone who uses an ontology would have to duplicate.
jrichter: Here are two other possible solutions:
hjd: Could perhaps we have soemthing that just checks whaever was edited during the session?
jrichter: 1) Don't complain if there is a period immediately followed by a lower-case letter
jrichter: 2) Establish some convention to set filenames apart from the rest of the text: ie enclose them in quotes, or precede them with file: or something
jrichter: Do any of these sound okay?
gwg: I like 2 myself
j-lo: it's not just filenames
Alex_MGI: I the second as well.
Alex_MGI: like
j-lo: sometimes there's a period in chemical names
j-lo: and spliceosomal components too I think
gwg: the number of those is pretty small, though
midori: hmmm ... (1) would give false negatives -- e.g. it'd miss it if you forgot the space between sentences
MelissaH: and anatomical parts
Alex_MGI: The problem is that we may not want the markup needed to appear in all contexts.
j-lo: I vote 1
Alex_MGI: Like browsers.
jrichter: Midori: It would only give a false negative if you forgot a space AND forgot to capitalize.
MelissaH: I vote 1 also.
kchris: I like 1 as well.
gwg: I can quite easily imagine people forgetting the space and the capital letter...
Alex_MGI: Perhaps 1 is better then.
gwg: I think I've seen it, too!
midori: it's been known to happen ...
j-lo: it'd be pretty unlikely you'd forget the space AND the capital
j-lo: surely
6:00 PM
jrichter: I could make the behavior user configurable, I guess.
gwg: maybe that's the best thing? then you can change it depending on how much you trust the other people editing the ontology 
jrichter: Okay. I'll put that on my to-do list.
j-lo: great. I love the new verification plugin btw
jrichter: Cool. It'll get even better in OBO-Edit 2.0, where you can write your own verification scripts.
midori: On a tangent, but related, I've been thinking about whether it would be useful to be able to tell the verification plugin to ignore specific things that we know are OK ... for example, it throws up the repeated-word warning for lots of defs that really are about MAP kinase kinases. Would the script-writing ability deal with these?
j-lo: it can do that
j-lo: already
j-lo: look in the configure settings
tberardi needs to duck out, sorry!
jrichter: Scripts would only allow you to add new verification checks. The existing ones are immutable, I'm afraid.
jrichter: But Jane is right, you can fix that particular problem.
6:05 PM
midori: OK, cool. What about the captial-letter and whitespace warnings? The comments that mention terms from fly_anatomy.ontology fall afoul of both ...
jrichter: Wait, didn't we just address that?
gwg: Midori probably wasn't listening 
j-lo: yes - that's what we were talking about...
midori: Did we include sentences that don't start with a captial letter on purpose? There are a few.
jrichter: Why would that happen?
j-lo: mRNA
jrichter: Bugger!
jrichter: How serious a problem is this? I've thought of a way to fix this, but it's several days worth of work.
kchris: Surely we can rephrase sentences slightly so that it is not necessary to start sentences with the word mRNA, or others like that. 
j-lo: can't we just have an add words to ignore option too?
Alex_MGI: Is there any set of words like 'mRNA' that could be specifically excluded?
6:10 PM
hjd: I just tried adding them to the exclude list now; seems to work
j-lo: that's just repeated words to ignore I think
jrichter: Jane's right.
hjd: Right, it just flaged the mRNA stuff anyways
jrichter: Okay, so we need to maitain a list of words that can legally appear at the beginning of a sentence in lower case.
jrichter: How important is this? Should I fix this now, or wait until the next release?
Alex_MGI: There can't be that many.
j-lo: it's mostly RNA types
midori: There are also some abbreviations ... what did we decide to do about 'vs.', 'e.g.', 'etc.', ... er ... etc.? The plugin flags 'vs.' 
midori: (tho there's only one def that uses 'vs.', so we could just change ti)
6:20 PM
j-lo: ncRNA, rRNA, snRNA etc
kchris: It also seems like we could just rewrite the sentences to avoid starting them with those  words.
jrichter: It'll be up to the user to configure their list of ignore words. Different ontologies will have different needs.
gwg: can't vs. just be reworded? It's a horrible word to have in a def!
jrichter: There's a configuration file for this... hold on.
kchris: like versus
jrichter: Never mind. It looks like it's hard-coded.
jrichter: I can add vs. to the list.
MelissaH: is there help doc info about the verification plugin?  I can't seem to find it.
gwg: let's just remove vs. from the defs
j-lo: I agree!
gwg: let's change it then
jrichter: Melissa: it looks like I haven't written any of these docs yet. <sigh>
MelissaH: sorry. :.(
jrichter: Does anyone have an on-staff tech writer that could be lent to this project?
j-lo: I wish!
jrichter: Do you think the consortium would hire one? If a bunch of projects could use a tech writer, maybe we could share one.
hjd: We do for our site web-help, , but she's never looked at this program
j-lo: Maybe - it'd certainly free up more of your time, John
jrichter: My wife used to do tech writing, and she's looking for part-time work...
j-lo: Shall we ask on the managers call on Wed?
jrichter: Yeah. I'm becoming concerned about the amount of time I spend working on docs for OBO-Edit. Just setting up screenshots takes forever.
MelissaH: John, one more issue with the verification.  right now, we have a lot of links in the form:
jrichter: Jane - I'd like you to ask, if you could.
j-lo: Will do.
midori: I just lost network ... what did I miss?
kchris: Midori: discussions about whether we could get access to a tech writer for OBO-Edit documentation
midori: aha - lots of comments just came; I may have everything after all.
midori curses ntl yet again ....
midori: tech writer idea sounds worth following up.
j-lo: Melissa?
MelissaH: <ahref='http://zfin,org/cgi-bin/ZFIN_jump?record=ZDB-PUB-961-14-576'>kimmel et al,1995.</a>
midori: that def with 'vs.' was (unfortunately) one I added, so I'll reword it.
MelissaH: I know the best place for these jump refs is not in the def, but thats where they are now. I get over a thousand errors.
jrichter: The problem is probably with the period after 1995. The verification check ignores periods that appear as part of a valid URL.
Alex_MGI: Not to mention that the URL has a comma where a period should be.
Alex_MGI: zfin,org
6:25 PM
j-lo: I think we need to make the verification plugin user configurable
j-lo: for this sort of thing
hjd: which is why it's chocking a browser
MelissaH: typo, couldn't get it paste.
hjd: choak
gwg: choke 
hjd: whatever!
jrichter: Okay, so we ALSO need a list of words that contain periods that should be ignored.
jrichter: I never got an answer - do we need these things fixed in this release? Are there so many warnings right now that they're useless?
j-lo: pretty much
Alex_MGI: I have to admit I find them annoying.
MelissaH: me too.
MelissaH: annoying too.
midori: Well, we can turn them off ... which I'm now doing for saves. But turning 'em off everywhere kind of defeats the purpose of having the plugin.
Alex_MGI: One may miss a real error in all the unnecessary warnings.
jrichter: Okay. I'll make this the new top priority. I'll see if I can add a button to the warning report that says "ignore this word in the future" or something.
j-lo: Perfect!
Alex_MGI: Good approach.
midori: that would be great!
MelissaH: hooray!!!
jrichter: Any other business?
hjd: I have been ignoring them.  I'd like them just to check what I've done, not everthing in the entire ontology
midori: p.s. once CVS finishes committing, GO will be 'vs.' -free 
6:30 PM
gwg: Phew! 
kchris: sorry I was late, but did we discuss a timetable for completing testing?
midori: no, but it's a good point, so let's do that now
hjd: (BTW, the requested id in the ref above apparently does not exist or no longer exists in Zfin)
jrichter: Wait, do people like Harold's suggestion? It's at least another day of work.
Alex_MGI: I do.
j-lo: Harold - once it's working properly we can fix eveything in GO and you won't see loads of errors
midori: me too
kchris: I could go with Jane's idea, get it working properly, fix the backlog, and then it effectively will be checking only new work
MelissaH: hmm thats not good.
midori watches CVS churn and grind, and tells gwg not to hold her breath
gwg exhales
j-lo: How come Melissa?
jrichter: Okay. Let's implement Jane's plan, and if we still have trouble, we'll implement Harold's plan.
MelissaH: no, that our link doesn't work.  not your idea!
MelissaH: those links get loaded into the database, it works from there.
jrichter: Back to a testing deadline...
jrichter: I think I'd like to make these chats once a week, so that we have some pressure to finish testing goals and turn over beta releases quickly.
jrichter: This *has* to be out the door by Dec 1st, but I want it done a lot earlier.
Alex_MGI: Do you need to add to the testing tasks?
6:35 PM
Alex_MGI: (I already did mine)
j-lo: We've been having content meetings on alternate Thursdays...but I guess we could move them
kchris: Do you mean once a week chats for the short term to get this out?
jrichter: Yeah.
gwg: alex, you can have my task if you want - i haven't had a chance to do anything because i've been working on amigo...
Alex_MGI: I'll take a look at it, Amelia.
gwg: mine is really fun and i think you'll enjoy it!   <-- winning smile
midori: John - More frequent chats for how long? It would be convenient if we didn't have to find a different time for the content chats.
jrichter: Just until the release is out, so until Dec 1 at the latest.
midori: OK, so that's only 2 sessions worth of conflicts. Not too bad.
MelissaH: looking at our testing wiki, only one cross out.  has no one done their tasks?
jrichter: As far as deadlines go, I'd like to make the testing deadline next Thursday.
jrichter: Some people have done their tasks, but the feature didn't work so they're waiting for a bug fix.
jrichter: If everyone's done their tasks by next Thursday, we'll know what works and what doesn't, and we'll set another interim deadline.
6:40 PM
j-lo: sounds good
MelissaH: ok, so when shall we chat?
jrichter: Next Thurs, 9:30 pacific?
j-lo: ok
kchris: OK by me
gwg: cya then
MelissaH: It was the GOcontent meeting conflict I was worried about.
jrichter: Great. Bye everyone.
midori: OK. Those of us who would also do the content chat will choose one to join, and catch up with the other via transcripts.
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midori: I'll send this transcript out as usualp
hjd: That's good for me too
MelissaH: ok, talk to you next week then.
jrichter: Thanks.
midori: ... er, as usual.
MelissaH: bye.
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