OE IRC 25May06
jrichter: Never mind.
jrichter: We should wait a few minutes before we start; I think Karen intends to be here.
Alex_MGI: Harold will be joining too.
midori: Amelia has deserted us for a gig in London.
Alex_MGI: What's her gig?
midori: I assume her band is playing, but she didn't say where.
Alex_MGI: John, did you see my recent bug posting?
MelissaH: Hi everyone.
jrichter: Since last night? Let me look.
Alex_MGI: About an hour ago or so.
jrichter: Hmm. I'll look at that as soon as we're done.
jrichter: I think the gang's all here now. Should we start?
Alex_MGI: Midori, do you have an agenda?
midori: hmmm, that question could be taken out of context
jrichter: YES, MIDORI! We'll join Amway! Jeez.
midori: But on a more serious note, the main thing for today is to make sure OBO-Edit is ready to release (or get a handle on anything else it needs).
Harold: me: harold transporting in
midori: is there any intelligent life here?
kchris: Well, I'm here, someone else can comment on the intelligent life part
jrichter: As far as a release goes: I tried to address everyone's concerns in last night's release. Alex has submitted a new bug, but we're trying to diagnose it right now.
midori: OK, let's review ... if I recall correctly, three of us have sent our sign-off emails. Everyone else has a few hours left; the deadline is midnight (in whatever time zone you're physically in right now).
jrichter: And we determined that a lack of a signoff email will be taken as a go-ahead, right?
kchris: yes, we did agree to that
midori: yes indeed.
jrichter: And, as of this moment, are the signed-off folks happy with the bug fixes in beta23?
kchris: I was trying to download b23 just now, but am getting the SF down for maintenance page. I'll download and test after this chat
jen: I found out why my computer was running slow by the way. It wasn't obo-edit.
rama: What was it? I have the same problem.
midori: Let's see ... I've checked the ID manager plugin; all is well there.
jen: my trash was so fully that the entire hard drive had filled up. 30,000 items.
jrichter: Rama - The first thing to do is make sure that the reasoner is turned off. That's the number one most common cause of slow OBO-Edit behavior.
kchris: Seems like a good item to add to the nascent FAQ
rama: I see. John, yes, I saw that on the email thread (the reasoner thing)
midori: I'll just check the compound filter thing now ...
rama: Should it be turned off as a default?
jrichter: It is turned off as the default. But once you turn it on, OBO-Edit remembers the setting.
rama: Okay, sorry I missed that part.
jrichter: Did we decide that the FAQ will wait until the next major OBO-Edit release, or are we going to try to squeeze that in now?
midori: I think it can wait ...
J-Lo: sorry - I'm really late! Didn't realise the time
kchris: I think it can wait, just wanted to put it on the list of things for the FAQ when we do it.
jrichter: I'll do that right now.
jrichter: Regarding the docs - I went ahead and changed "Properties" to "Relations" whereever I could. Some of it was done with a brute search-and-replace, so there may be problems as a result. Please keep your eyes peeled.
kchris: Cool! I reread the Structural Editing section with an eye out for that.
ranjana: I had a question--is the user guide in beta23 complete?
jrichter: It should be.
midori: OK, I've tested the compound/not compound search problem (anyone who doesn't know what I'm talking about can look at SF item 1494304 in the bug tracker). It's much better now, and my sanity shall have a fighting chance
jrichter: Note that the way I fixed that problem, if you have a complex search set up, and you accidentally turn off compound searching, you'll lose all that setup work.
MelissaH: sourceforge is down right now for me.
J-Lo: it's been on and off all day
jrichter: Me too. But click the "status" link and chuckle as sourceforge reports all services "Online".
kchris: I got that too a couple minutes ago, but it looks like SF has just come back up
jrichter: As a larger issue, we may need to move off of sourceforge as a project. The constant outages have been a major headache these last few weeks.
jrichter: But that's for the whole consortium to discuss.
midori: I can live with that [losing compound search info if I'm reckless enough not to save the filter]-- it's not that easy to turn compound filtering off by accident. And it's much less annoying than getting search results that don't make sense. Might want to add a warning to the user guide, tho.
jrichter: I don't know if it's necessary. I think novice users will expect that kind of behavior. It's the entrenched users (us) that will be surprised.
jen: I never turn compound filtering off anyway. I couldn't work without it.
midori: ok; ;no big deal
jrichter: Okay - tonight's the signoff deadline, so-
midori: My outstanding issues fall into two categories:
Harold: My signoff will be in the (e)mail
jrichter: I'm going to shoot for beta24 to be the last beta version. I'll try to incorporate Karen's new documentation edits she sent last night, fix Alex's bugs, and release!
jrichter: But Midori's outstanding issues are...?
J-Lo: oops - I haven't fixed that walkthrough yet...
midori: 1) Has anyone tested cross-products?
midori: 2) User guide edits, some of which Jane and John have just mentioned
J-Lo: i'll do mine right after the chat
jen: mine are all fixed
jrichter: Karen Eilbeck and Chris M. have been using cross-products for months now. I'm pretty sure they work well.
Harold: I was hoping for David to test x-products, but he couldn't squeeze it in.
midori: John - just as a formality (or, if you prefer, for CYA), could you ask one of them to drop a line to the wg list saying cross-products work?
jrichter: I think we should do our own testing too, but I'll email Karen.
kchris: I'll see if I can give it a go today. I have something for which it might be good to know how to do. It'll test out the documentation too
midori: I had a very brief stab at it, but soon realized that I don't really understand what I'm doing ...
MelissaH: me too!
kchris: I'm not sure I do either!
midori: (might mean documentation edits ... I'll be interested to see what Karen C thinks)
jrichter: If only there were some sort of, how do you say, "document" that could explain it...
jrichter: Midori - Can you conjur up some deadlines for this testing and final round of documentation edits? I want to get this mutha out the door.
jrichter: (conjure - not conjur)
midori: Well, Release Day is still June 1st. How long before that do you want to hear from us?
kchris: As an FYI, Monday is a holiday in the US, so anything I don't get done today or tomorrow won't happen till Tuesday.
jrichter: It depends on you. The only important thing to me is that there are no untested bug fixes in the official release. OBO-Edit 1.001 needs to be exactly the same as the last beta, just with a different version number.
midori: Monday's a holiday here too, and I've got tomorrow off, so I won't be able to do much testing at all!
midori: I'll see what I can squeeze in tonight ...
jen: can the people still at work maybe test today?
kchris: I'll test today. I even have a real edit to do, and I'll give cross products a stab.
midori: If we have to, we can rely on Chris and Karen E's cross-product work.
MelissaH: I'll be obo-editing all day today.
jrichter: To me, the documentation schedule is much more important. We've got docs from Jane still coming, and potentially new cross product docs. Has everyone sent me their documentation edits?
midori: (tho it'll be even better if we can do some ourselves, of course)
Alex_MGI: yes for me.
MelissaH: I can try some cross products testing today too.
midori: Doc edits: I have, and I WILL check over my sections again tonight, even if I don't get around to anything else.
kchris: Yes for me as well. We'll see if attempting to do cross products from the documentation leads to some suggestions there.
J-Lo: no for me on doc edits - I'm slack aren't I?
midori: 'fraid so ...
J-Lo: will do tomorrow - promise
jrichter: If you have documentation edits, I'd love it if you just committed them straight to cvs. It's faster for both of us. Just send me an email saying you're doing it, so I know to update my copies.
J-Lo: okay - will do.
kchris: I don't know how to commit to the SF cvs, so I'll need instructions on that if you want me to do it that way.
jrichter: Take a look at the instructions on the CVS link in sourceforge to check out the CVS repository. The docs are in the go-dev/java/oboedit/docs section of the repository.
jrichter: Make your edits, and do a "cvs commit".
jrichter: That should be all it takes.
midori: One documentation thing: is there anything yet on the active ID profile bit (from my email)? And if not, should I add it, even tho it's not in any of the sections assigned to me?
kchris: OK, I'll try that.
jrichter: Midori - I didn't know exactly what you wanted. The documentation does say that your currently selected profile is the one that's used for generating ids. How would you like to call that out more explicitly?
midori: I guess what I'm after is to spell out the implication (which is, well, implicit now) that you must choose the desired profile BEFORE adding a term.
jrichter: If you have specific ideas, I'd love it if you went ahead and committed the changes. If you don't have time, I'll take a stab at it.
midori: OK, one way or another I'll drop you an email.
kchris: I can add a bit on this to the "Adding New Terms" section as well, so that people see right in that section that they may want to check on their ID profile BEFORE adding a new term. Right now it just links to the ID docs
jrichter: (Karen - An additional word of warning about cvs commits: When you commit, it asks you to type in a comment on your edits. On most systems, it uses vi as the editor for those comments. If you hate vi like I do, you'll want to issue the command "export EDITOR='emacs -nw'" before you do a cvs commit, so that you use emacs instead)
midori: Karen - That would be great -- and may be enough to achieve my desired effect. I'll have a look at the ID generation section anyway, tho.
kchris: Thanks for the tip John. I DO hate vi as much as you do!
jrichter: Okay, here's a suggested schedule: All documentation edits are due by May 30th. A final beta release will be made on the evening of the 30th. On the 31st, we do last minute testing, and I'll be doing up-to-the-minute bug fixes until then. We release at midnight June 1.
midori: (vi haters unite! I set my editor to emacs all the time.)
midori: Sounds good.
MelissaH: okey dokey.
Harold: with much florish!
kchris: (mine is too for my system )
jrichter: (By midnight June 1st, I mean late on the night of May 31st)
jrichter: We have 10 minutes. Any other topics, Midori?
midori: it'll be past midnight here!
J-Lo: the paper
jrichter: Midnight my time (Mountain).
midori: Any more on the release? If not, we could spend the last few minutes looking ahead to what we want in the next release ...
jrichter: Jane - good topic.
jrichter: Here's what I have to say-
jrichter: Suzi has told me that I need to write two OBO-Edit papers. She wants a short application review type thing very soon, and then a full-length publication by September.
jrichter: I think she would be very happy if the whole working group (or much of it) was involved in crafting one or more of these.
midori: Has she said anything about where to publish?
kchris: Where would these things get published?
Harold: BMC Bioinformatics?
midori: I'd go further than that, and say that helping with the publication(s) is clearly part of the wg's role.
jrichter: No word on where to publish. Do Midori, Jane & co have any ideas?
kchris: Sorry, I meant what journals are even appropriate to submit to?
jen: the tools page has lots of tools that have been published. We could find out where.
rama: yes, good idea Jen.
midori: I had a quirk nose around when Jane brought this up last week. BMC Bioinformatics is a strong contender; it's full of open access goodness and clearly does publish software papers.
jrichter: Let's get some volunteers to form a breakout group to research where we ought to publish.
jrichter: (Not it!)
jrichter puts his finger on his nose
midori: Bioinformatics (OUP) is another possibility. They certainly carry software articles; I'll have to re-check whether they do open access.
J-Lo: what about one of the Plos journals?
midori: ... hmmm, much as it pains me to say it, it lloks
Harold: There is Journal of Computational Biology, but I think that is certainly not open access
midori: (oops, hit return instead of backspace) ... anyway, it *looks* like I've turned myself into part of the where-to-publish sub-group.
jrichter: Thanks, Midori.
J-Lo: i'll help
midori: I'll see if I can find out whether PLoS Computational Biology would take a software write-up. If they would, it could be a good one.
midori: Thanks, Jane.
MelissaH: Melissa the broken record says, next priority following release should be user testing.
jrichter: Something I want to put out there - I'm not terribly excited about the overall OBO-Edit paper (it sounds a lot like the documentation all over again to me). I'd much rather do a more technical paper on the reasoner...
jrichter: I'd like to address Melissa's point -
midori: I also looked at Genome Biology ... will have to figure out whether it'd be open access, because they seem to open some article types but not others??
midori: Melissa - good thought
Harold: I think for Genome Biology, reaserach articles are open, but reviews are not; but this wouldn't be a research article either
jrichter: I think user testing has the potential to be a horrifying pain in the ass if we try to centralize it. User testing could require a huge amount of travel and planning for very little payoff. But -
midori: John - the world desperately needs a paper to cite when they talk about OBO-Edit. If a short application note thing would do, fine.
kchris: that's my recollection for Genome Biology too, but I don't know how this paper might be classified
J-Lo: perhaps we could just submit the documentation for publication?
J-Lo: what do you mean by user testing?
jrichter: Still on Melissa's point: If we use a distributed model, it could go very easily. I think the role of this group should be to come up with a user testing protocol, which each of the working group members could implement on a small scale in their own lab.
midori: Harold - that's why I'm not sure ... don't know whether O-E pub would count as research (even tho it's not), or a review (ditto), or something else.
jrichter: I think user testing means exposing new users to OBO-Edit and seeing how they react, and using that information to improve the interface.
MelissaH: Have john watch how people actually use the program.
J-Lo: oh, i see
MelissaH: yes, but not only new users, moderate and heavy users too.
J-Lo: can we hire people to do this sort of testing?
MelissaH: And users that use the program for different purposes too.
jrichter: But it can't be just me. That's my point. We need a way to do this without me being in the room. Otherwise I need to travel the world while my newborn baby sings "Cat's in the Cradle".
midori: several of us are at sites where we have a mix ...
MelissaH: we'll come visit the new baby.
jen: could you use vnc +skype?
kchris: You're supposed to be the one singing, it'll be a while before the baby does more than gurgle
MelissaH: I think that would work just fine, if we can deal with it.
Harold: Yes, we should think about vnc, etc. as long as we keep the # of users down,
Harold: at one time
jen: it would only be two users so should work
jrichter: We could assist this process with VNC. But I'd like the sites to be in charge of rounding up testers, and coming up with a simple set of initial tasks.
Alex_MGI: I think experienced users other than John could observe novice users and report back to John as well.
jen: yes clearly. vnc might help john though
jrichter: Also, a huge obstacle to starting with OBO-Edit is not understanding what ontologies are in the first place. So we need some way of screening and/or educating users so that we don't waste time on that hurdle.
jrichter: What if we used part of a GO User's Meeting for this purpose!
rama: I don't know of any users who use oboedit other than GOC members-do you?
MelissaH: I have lots.
J-Lo: good idea John!
midori: hey, there'll be a User's Meeting in September!
Harold: At MGI, we have one using it for anatomy, another for a phenotype ontology
MelissaH: we could also do some user testing at the anatomy meeting in september
kchris: People at SGD are creating a phenotype ontology, but I don't know what they are using to edit/maintain it.
jrichter: Okay. I think we have a plan. We "teach users about OBO-Edit" during part of these meetings, and while that's going on, we observe users and ask them how to make the program better.
midori: Do the Cell Type people use it? I know the ChEBI crowd do, and we can pester them any old time.
MelissaH: I agree though, anytime there are a bunch of users in one place it would be great to take advantage.
Harold: I think rex c is doing something with a disease ontology?
MelissaH: yes, the cell group does use it.
ranjana: People at WormBase are using it for a phenotype and an anatomy ontology.
jrichter: And there's PATO, and all the OBO ontologies. So we have a fair amount of users.
J-Lo: InTact use it
J-Lo: they're at ebi
jrichter: One last thing before we run out of time:
midori: That leads me off on a bit of a tangent: John, do you know if there's a way to convert OWL to OBO? Or if anyone's working on such a beast?
pfey: Harold - John Osborne is doing the disease ontology - he is part of this group but broke his foot recently
midori: I'm asking because at least some MGED ontology users would love to be able to use OBO-Edit on it (maybe only for browsing).
jrichter: Midori - It can be done easily. The tricky part is translating weird little dialects of OWL (like Proteges) into the simplest version of OBO.
jrichter: Which brings me to my final issue:
Harold: petra, is /was he using obo-edit?
jrichter: How do people feel about a June 1st deadline for their "New Features I Want" report.
pfey: yes, he is
kchris: Too soon for me. I've been too busy testing and editing documentation to review all the feature requests. I'd like a little more time after the release goes out.
midori: I think I'll be able to make it ... I can at least come up with some preliminary thoughts.
J-Lo: you want us to submit new features by june 1?
MelissaH: ok with me
pfey: and we are doing a phenotype ontology
jrichter: How 'bout June 8th, then?
Harold: June 1 sounds good; how many things do we have for new feature requests already?
kchris: June 8th would be great.
Alex_MGI: I think we should rather look over the possible new features at the next IRC chat and discuss. You can pick some good ones to work on before then if you like.
jrichter: Actually, I already have. I'm researching graph-based editing.
jen: I like the idea of graph based editing
midori: Either date is non-ideal, but tolerable, for me (I'll be traveling a lot in mid-June).
Alex_MGI: Ideas for new features might come at any point, the question is really which new features to include on the next release.
Alex_MGI: Which we can discuss at the IRC chat in two weeks.
rama: Is there a date set for the next release?
Harold: Perhaps they can be broken down into classes based on ease of implimentation?
jrichter: No. But I think it should be no later than August 1st.
midori: Rama - not yet; we should choose a target date for that next release (but not etch it in stone).
jrichter: Harold - Good idea. I'll go through the new features list and comment on each.
kchris: That should certainly help us prioritize
jrichter: I declare this meeting way over time. It's time for the action item roundup!
jrichter: 1) Get documentation edits in by May 30th. Release June 1.
jrichter: 2) Midori & Jane will research publication options
jrichter: 3) Get your new feature report out by June 8th.
jrichter: 4) Think about how to get the most out of user testing at the GO User's Meeting
jrichter: Any others?
Harold: 1a, get beta 24 up by 30th for quick testing on 31th
jrichter: He's in Maine. You're lucky he can talk at all.
Harold: argh! 31rsted
Alex_MGI: We have trouble pronouncing r's in Maine.
jrichter: See you all on June 8th! (Although we should be prepared for an emergency June 1 chat, just in case something goes horribly wrong)
Harold: it means I'm slowing turning into "from here" and not "from away"
midori: you mean, "from heah, no"?
Alex_MGI: Or to celebrate.