OE IRC 10Aug06

From GO Wiki
Jump to: navigation, search
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
Guest27418851 has quit the server saying: Quit: Guest27418851
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.
gwg has left the channel
gwg has joined the channel
tberardi is reading it right now 
hjd has joined the channel
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 
jclark: 
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!
j-lo has quit the server saying: Quit: j-lo
6:35 PM
tberardi: Bye!  
jclark has quit the server saying: Quit: jclark
tberardi has left the channel
jrichter: bye.
jrichter has quit the server saying: Quit: Konversation terminated!
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:1.6.4.2) -> ) glutathione -> glutaredoxin -> arsenate reductase, i.eglutathione is reduced by glutathione reductase and glutaredoxin is reduced by glutathione