OE IRC 10Aug06

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5:20 PM
Alex_MGI has joined the channel
5:30 PM
jen has joined the channel
jen is now called Guest27418851
midori: can I still call you Jen? it's much easier to type ...
Guest27418851: hmm
Guest27418851: back in a bit
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jclark has joined the channel
jclark: better
5:35 PM
jclark: still there?
midori: Yep. I have no idea who else is coming.
Alex_MGI: Hi, just dragged Harold away from lunch.
jclark: well done
jclark: tanya is lost and needs the chat room settings
jclark: anybody have them to hand?
midori: just sent 'em
gwg: where's J-Lo?
5:40 PM
midori: She should be chatting from home any ol' time now ...
midori: Soooo anyway ... I emailed some topics ...
j-lo has joined the channel
gwg: speak of the devil!
j-lo: sorry!
tberardi has joined the channel
tberardi: Ha!  Made it!
midori: yay!
midori: This might be all we get ...
tberardi: No John?
tberardi: Harold is fixing his settings so he can join too.
midori: Haven't heard from him (i.e. John).
pankaj has joined the channel
karene has joined the channel
midori: Hi all! Shall we start?
tberardi: BTW, I haven't heard whether John got our gift certificate.  I did get the receipt from PotteryBarn so I'm pretty sure it was sent.
midori: Thanks for dealing with that, Tanya!
tberardi: No problemo.
karene: Did the baby arrive?
tberardi: Don't know.
5:45 PM
tberardi: Let's start!
midori: None of us has heard anything. For all we know they could be rushing to the maternity ward even as we chat.
gwg: my connection is being a little sporadic...
Alex_MGI: What can we talk about in John's absence?
gwg: or else no one's saying anything
midori: OK, agenda item 1: the paper. Thanks to those who have looked at it.
midori: Not sure how much else we can do on it in John's absence, though.
midori: Any comments?
pankaj: thanks for doing all teh good work. the MS looks great.
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tberardi is reading it right now 
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Alex_MGI: I read it and think its quite a good job.  I only took issue with the statement that biologists needed OBO-Edit because they can't handle other tools (like text-editors).
karene: GO would be really difficult to deal with in a text editor.
midori: I think it was other ontology-development tools that we were referring to 
Alex_MGI: Lots of biologists have good computer skills.
midori: ... And the important point is that OBO-Edit is biologist-friendly, no matter  what other tools are or aren't.
midori: Any more on the paper?
tberardi: Could just be "...biology domain experts to easily browse, search, and edit..."
5:50 PM
Alex_MGI: I think that's better, less prejudiced.
Alex_MGI: (speaking for my inner biologist)
midori: That's pretty much what Amelia's version has (it just arrived in my inbox less than an hour ago). We can tell John that there are votes for it.
midori: Are we ready to move on?
tberardi: Sounds like that's all for the paper. 
Alex_MGI: Fine with me.
j-lo: yep
midori: OK! Next item: the new beta. Has anyone done any testing?
tberardi: No, sorry.
Alex_MGI: no
jclark: I used the new layout
midori:  (All I've tried is starting it up and loading GO, which worked fine.)
gwg: I submitted one or two bug reports...
jclark: it's fun
jclark: the layout I mean
hjd: Yes, I've used it for the usual add term
hjd: However, I still can't get the graph viewer to work for me since 1.002
midori: graph viewer is ok for /me ...
5:55 PM
hjd: I'm sure something in a file has gotten corrupted, but I can't for the life of me see what
jclark: was greyed out for me
midori: hmmm ...
midori goes to fire up OBO-Edit
hjd: By not work, I mean that it pops up ok, but is totally blank (white). All paths ok, etc.
gwg: 'fraid I haven't used it with GraphViz...
jrichter has joined the channel
jrichter: Hi, folks. Sorry I'm late. I forgot.
gwg looks disapprovingly at watch
midori: We've been wondering if mini-John had arrived!!!
midori: Anyway, we've chatted about the paper; people like it. (Some more details in the transcript)
jrichter: That's good news. I imagine we're going with Chris's edits?
midori: Amelia did some further edits; I think her intro is an improvement.
jrichter: Sweet.
midori: She also put in some open-ended suggestions/questions that you should look at; fine with me if you act on 'em.
tberardi: Was there a decision not to refer to the extremely useful user's guide?
midori: It's mentioned briefly ... could put the current URL in if it's going to be stable (or redirect usefully). I don't mind.
midori: btw, Graph Viewer working fine in 1.1beta1 (sorry, Harold!)
jrichter: Of course, to go any further after you've read the paper you need to download OBO-Edit, and then you have the user's guide anyway...
6:00 PM
midori: true...
tberardi: Yeah, but it's nice to know up front that alot has been invested in developing a guide as opposed to being a trial and error kind of learning process.
midori: Do you have a phrase handy that we could pop in?
midori says, trying to get away with the lazy approach ...
tberardi: How about a sentence at the end of the intro. 
tberardi mulling over the wording
jrichter: Could we sneak it into the availability section? Have a "download" link and a "documentation" link?
tberardi: Good idea, though I think calling it "User's Guide" (vs. Documentation) might be better.
jclark: Ijust tried to test the new beta on my computer to see if graphviz works but oboedit wont start. I'll put a bug report in.
j-lo: can we make a sensible url for it though? One we're sure won't change?
jrichter: Make sure to include your stderr dump! It's the only way I can diagnose the "won't start" bugs.
gwg: it can always be a redirect
j-lo: that would be fine
midori: Re 'documentation' link - I suspect that may not fly with the editors; the abstract structure is prescribed. But we could try it ...
6:05 PM
gwg: I'm surprised that John hasn't registered obo-edit.org yet...
jclark: where do I get the stderr file on XP?
jrichter: It's going to be in the .oboedit subdirectory of your user directory (probably something like c:\documents and settings\Jen Clark\.oboedit)
midori: the current url is http://www.godatabase.org/dev/java/oboedit/docs/ (for the user guide, not anyone's stderr!  )
tberardi: How about "The included user's guide provides detailed information on both basic and more complex applications of the program."
jclark: That's good
jrichter: Where does that sentence go?
midori: last or next-to-last in the intro?
tberardi: At the end of the intro.
tberardi: (Amelia's revised version, or the existing one.)
midori: Any more on the paper (again)?
midori: We've also touched on the 1.1 beta, but only a few people have done anything so far.
tberardi: Not from here (really!).
jrichter: I'll add that sentence to Amelia's version this afternoon and send it around. I'll also see about registering obo-edit.org, and creating some redirects from there.
midori: most cool.
6:10 PM
midori: I have one more topic: the users meeting. OBO-Edit should have some sort of presence there, maybe a demo or talk.
Alex_MGI: That's makes sense.
jclark: yes
tberardi: I'm coming.
jclark: the people at the cns meeting were really keen on obo-edit
tberardi: Sounds like you (Jen) did a great job of demo-ing it.
jclark: we have several oboedit groupees now
jclark: ta 
jrichter: I'll be there. I'm happy to do a demo, although my demos usually enrage people with their lack of biological meaning.
midori: excellent.
jclark: we could do a short live edit
jclark: that winds people up no end
karene: I just set up a server at bbop for the SO domain. It was easy. Talk to  Seth.
tberardi: Jen could do an encore (sorry for volunteering you).
jclark: that's okay I got on okay last time
midori: (I'll be emceeing, so that'll keep me busy enough.)
jclark: John could talk and I could type
tberardi: (I can cheer.)
jclark: Yay!
jclark: Jane could show off some funky stuff too as she'll be there
midori: all righty then  can one of you submit an abstract?
jrichter: Probably better Jen if you talk and I type. I always want to do senseless edits. But we can figure this out offline.
jclark: ok
jrichter: Also: if people are excited about this, perhaps I should hang back from the demo. I'll have only been back at work about a week at that point.
6:15 PM
gwg: I bet you'll be raring to go, tho
tberardi: Take more time off!!!  (If you can.)
jclark: david will be at the meeting wont he? Maybe we could do the same double act
j-lo: I've got to do an AmiGO thing, but could probably help out some...
tberardi: The Punch and Judy Show, GO-style.
jclark: yes
jclark: Everybody shout 'part_of'!
jrichter: Well, I'll be there in any case. So, at worst, I'll hand presentation notes off to someone else.
midori contemplates the demands of her role as chair ...
jrichter: I'll stay in touch with Jen about the content of the demo.
jclark: Shall I ask david if he's up for that or does it seem to mad?
midori wonders if 'to mad' is a verb now 
tberardi: Isn't he doing some other thing too?
jrichter: I think it may not be necessary. I think I can pull this together.
jclark: ok
tberardi thinks midori is still high from the wedding - Congratulations!!!!!!
jrichter: The paper's a good outline for an overview presentation, actually.
hjd: John: that's a good point
midori is actually giddy from getting a book chapter sent out today - only 4.5 months late :P
j-lo says she'll win 50 quid if she says 'bum' on this chat
jclark: really?
gwg: Are we going to discuss the new OBO-Edit beta or is that about it for today? Just wondering if I can pick my car up from the garage)
jrichter: I had some real quick OBO-Edit questions...
gwg: go John!
6:20 PM
jrichter: 1) There was a suggestion that there be some personal dbxrefs that are automatically added to newly created definitions. But the need to have a definition AND def dbxrefs defined together is enforced right to the core of OBO-Edit. So I had to set things up so that a default definition is also added when a new term is created. Is this okay?
jclark: yes
j-lo: great
midori: sounds fine
jrichter: Cool.
jrichter: 2) For Jane: What is directly behind one's rear pants pockets?
gwg: er... could this be an option to turn on and off?
jrichter: Yeah, it's optional?
jrichter: !
j-lo: bum!
midori ponders the juxtaposition of the last few comments
jrichter: Well done Jane. And the new feature is totally optional.
gwg: wikkid!
jrichter: You'll also get warned if there are unedited default definitions sitting around.
tberardi: ...on your bum.
jclark: Does this go unedited on the wiki? 
gwg: that was a bit of a bum joke, Tanya 
tberardi: Gotta have some fun.
gwg: yup - and all the PIs read it
jclark: Yay!
jclark: Like they have time
midori: (unless suitable arrangements are made with those who edit the wiki ...)
j-lo has the 50 quid!!
jrichter: 3) It's turning out to be quite tricky to figure out what periods end a sentence, and which are being used for other purposes. What are the commonly used GO abbreviations, so I can treat them special?
Alex_MGI: Like they care.
gwg: e.g.
gwg: i.e.
midori: who's paying up?
jclark: I thought we didn't use those
jclark: I use for example
jrichter: (I'm also writing special cases for urls and numbers with decimals)
gwg: there aren't all that many actual abbreviations in defs
jclark: good point
jrichter: There are also several etc.'s in there.
hjd: Do any defs refer to an EC number?
gwg: don't think so...
6:25 PM
midori: yes, but they're in the dbxrefs, not the def text
jrichter: So we're fairly sure that e.g., i.e., and etc. are the only commonly used abbreviations?
jclark: it's only the number decimal points that I can think should be needed
hjd: some chemical names may have one somewhere (a period)
midori: we can double-check
gwg: I am 100% sure and would stake my life on it
gwg: er, not really...
jrichter: Is there a consistent way to know if we're looking at a chemical name with a period in it?
jrichter: (Without looking at a huge chemical dictionary?)
j-lo: probably
gwg: how many of said chemical names are there?
jrichter: Harold?
gwg: IIRC, the periods are in between numbers...
hjd: Not sure we have any, but I know some organics use a 1.2.3 nomenclature; we might not have any, but we might
gwg: I would just ignore words with a period in if they contain digits
jrichter: I'll give that a try.
jrichter: Anything else, or should we disband?
j-lo: shall we form a beta-test sub-group again?
midori: We covered everything I had.
hjd: I've just found this
hjd: def: "Catalysis of the reaction: Zn2+(out) = Zn2+(in), probably powered by proton motive force." [TC:2.A.5.1.1]
6:30 PM
j-lo: that's the dbxref
jrichter: That's fine.
hjd: hang on
midori: Good idea to have a testing group again -- maybe a bit bigger this time, since it's a more substantial version change.
jrichter: I think we should form a beta-test sub group for the next OBO-Edit 1.00X beta test. I think that the whole WG will need to weigh in on the 1.1 release.
j-lo: ok
j-lo: do we have a deadline?
j-lo needs deadlines
jrichter: I think we can go with the same model we used before. Once all the changes are in, I'll send out an email. People have 2 weeks to complain.
jrichter: I can't commit to a deadline, I'm afraid. The baby is sure to stir up my schedule in totally unpredictable ways.
j-lo: true
jrichter: If the baby waits until next week, I'll have another release out by Friday.
jrichter: This time with the much improved Verification Plugin.
j-lo: hurray!
jrichter: (Cool new feature: Create your own checks by building filters!)
j-lo: sounds great
midori: Anything else?
jrichter: Not from me. I'm ready to go.
jrichter: Midori, are you handling the transcript?
midori: can do
jrichter: Farewell, all.
gwg: see yas!
gwg has quit the server saying: Quit: Goodbye cruel world!
j-lo: bye - thanks for the winnings!
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6:35 PM
tberardi: Bye!  
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jrichter: bye.
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hjd: ok, I think we have some embeded ec numbers in some defs:
hjd: for example:
hjd: arsenate + reduced glutaredoxin = arsenite + oxidized glutaredoxinGlutaredoxin functions as the electron donor for arsenate reduction The electron flow therefore is ( NADPH -> glutathione reductase (EC: -> ) glutathione -> glutaredoxin -> arsenate reductase, i.eglutathione is reduced by glutathione reductase and glutaredoxin is reduced by glutathione