OE IRC 12July06

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The further adventures of the OBO-Edit Working Group! This week's exciting episode: "Cross Product Doublecross!" with special guest star Chris Mungall.

Alex_MGI: So who has the agenda?

cjm: Yup! This is my first time on IRC since those sanger apollo IRC chats back in the day...

midori: nobody did one [agenda], as far as I know ...

jrichter: I don't think we have an official agenda this time around, so I'll give a summary of what I'm doing, and then people can air any issues they want to discuss...

Alex_MGI: okay

cjm: sounds good

jrichter: After I wrote up a more detailed outline for the paper last week, I haven't done any further work on the paper. So, you know, insert a sad face.

midori: :(

gwg: is that the effect of my joining the channel? ;)

midori: nope, just lucky timing ;)

jrichter: But the good news is that I have been working on OBO-Edit 1.1 feature requests, and I've gotten the no-commit-button thing working in a prototype-y way.

gwg: excellent!

cjm: john, can you send me the outline (I am on the wg digest which I think scrambles attachments)

Alex_MGI: Will 1.002 be released now?

jrichter: I actually haven't sent the outline out to anyone yet (hence the "no further work comment"). I'll try to send out an outline tomorrow.

jrichter: In OBO-Edit 1.1, there won't be one big monolithic text editor. Every different editing component will be independent, so you will have a lot more freedom in how you set up the interface.

jrichter: Alex - Everyone in the 1.002 debug group has signed off, so if there are no complaints from folks here, I'm going to do the release as soon as we're done.

jrichter: That's the other thing I've done - OBO-Edit

Alex_MGI: Great

gwg: have you solved the all-important icon issue?

jrichter: 's cvs repository is now branched, so I can fix bugs in an old version without messing up the working version.

jrichter: GWG - I saw your email, you wily little minx. I'm going to incorporate your new icons as soon as possible. But they probably won't make it in until version 1.1.

gwg: it's OK, I can wait... I guess

gwg: (sob)

jrichter: Any issues that folks want to discuss? I think Chris might have things to say about x-products...

J-Lo: erm - beta testing?

jrichter: You came in immediately after I said that everyone has signed off, so I'm doing a release today.

J-Lo: oh - okay!

cjm: I think I've said my xp interface stuff on the wg list. i'd like to hear others opinions though too

J-Lo: I haven't actually used it yet, so I'm afraid I don't have an opinion...

Alex_MGI: Me neither.

Alex_MGI: Too bad Karen isn't here.

jrichter: I wonder if there's some kind of project we can take on within the WG where everyone could work on a few x-product terms. That way we can have the OBO-Edit elite improving the interface before our less patient users are forced to have a go of it.

J-Lo: that's a good idea

gwg: we might be able to do some with the pamgo stuff, jane

J-Lo: Michael has someone called George who will be using xprod plugin v. soon too

J-Lo: called George working for him (!)

jrichter: Ha!

cjm: That's George Gkoutios who does PATO. cc me on any emails with him John since this is important for cbio

jrichter: You bet.

J-Lo: he wanted someone to teach him how to use the plugin

cjm: The PATO cases are unusual though

jrichter: It's in the user's manual, or he can email me directly. I don't think I've gotten any emails from him yet.

J-Lo: i told him to email the OE WG list

J-Lo: it was only today so he probably hasn't done much yet!

jrichter: As far as the WG goes, do we need to make this a formal testing effort, or can we just say "make some cross products if you have a need, and report back?"

J-Lo: gwg and I will try it out next week with the new pamgo terms...

jrichter: Let's call that an action item.

jrichter: Anything else to discuss, then?

cjm: can you give an example of a pamgo xp term?

J-Lo: erm - carbohydrate catabolism in other organism

J-Lo: does that work as a xp?

Alex_MGI: Is that an internal xp?

J-Lo: yep

gwg: yup

cjm: this would be an odd one - would the differentium be "occurs_in other_organism"?

gwg: yup

cjm: hmmmmmmm

jrichter: other_organism is one of those strange terms, like "host". It's like an ontology equivalent of a pronoun

gwg: there are going to be a load of terms which will be a biological process occurring in another organism

gwg: or regulation of a biological process in another organism

jrichter: Is there some more specific way to describe that "other_organism"? Maybe with reference to its relationship to the implied "this_organism"?

jrichter: (I can rephrase that, if necessary. It's almost unreadable)

cjm: we discussed this at the content mtg in tigr. ok. so the xp would be with the CC term 'external'?

gwg: it's usually going to be 'xxx process in host' or 'xxx process in symbiont'

gwg: yup (to chris)

J-Lo: I don't know if that will work

J-Lo: the term is 'extracellular' - not 'extraorganismal'

cjm: given that these will be controversial we may want to make some other xps the first ones that are public. what about the CC ones Karen has been doing? Also the BP-CL ones should be ready for viewing by the general GOC soon

gwg: i don't think these terms are going to be particularly controversial - they're just fleshing out concepts we already have

Harold: Or BP X MF

J-Lo: yes, but the xprods might be!

gwg: but there may be other more suitable candidates for showing to the general population...

J-Lo: Midori's doing some cc ones too i think

Harold: Since I'm curently working on a pathway project, I could try some process and function, like Citric Acid Cycle x the enzyme activities that comprise it

J-Lo: they're not really xprods though are they Harold?

cjm: the xps shouldn't be controversial if they reflect the definitions. however, if we go public with the xps people's attention will be focused on the terms themselves... but use the xp editor by all means if you're doing these terms anyway and it makes things easier

cjm: yes, this sounds like MF-BP cross-ontology links. if citric acid cycle can be defined entirely by its MF enzymatic constituents then it's a candidate for an xp

Harold: to j-Lo: wouldn't any cross between orthologous ontologies be a x-product?

J-Lo: i don't know!

gwg: if we do MF-BP, aren't we going to get into that debate about function again?

cjm: we should probably put an xp page on the wiki. the way we have been using the term, an xp is basically telling the computer the definition of the term based on a base term and it's relationships to other terms; eg cysteine biosynthesis = biosynthesis (BP)\ WHICH outputs cysteine (chebi)

gwg: do you want to move over the other xp wiki stuff?

cjm: Jane, aren't you working on the MF-BP links?

J-Lo: erm - not really...

cjm: yes, I should probably do that

cjm: well it sounds like Harold is.... Harold? Are there more details on this pathway project?

jrichter: Harold may have wandered off. Sometimes the Jax folks just leave their IRC clients on record and go have a coffee...

Alex_MGI: Really?

Harold: it's something me and a couple of intrens are looking at: the reprenstation of pathways from the defintiions of the enzyme activities.. and it's a coke

gwg: I will be doing some BP stuff soon involving metacyc pathways, and I would like to capture as much info as possible, including the MF / BP relationships

J-Lo: it gets very complicated with the whole species specificity thing

gwg: that's if the AmiGO working group can be galvanised into action so I can finish the mock ups... :S

cjm: Anything I can do to help the amigo wg move along?

jrichter steps away for a moment

cjm: jlo - species specificity does make it hard. but following on from our sensu discussion it may be easier if you differentiate by the functional parts (or whatever we call them) - then the BP-MF links will be true by definition?

gwg: I think everyone's busy at annotation camp at the moment, so maybe they'll all be back in action again next week

cjm: ok

J-Lo: possibly - I think we need more discussion though

gwg: I think Chris is correct on that, as long as we define things by their constituent parts

J-Lo: who's chairing this meeting?

J-Lo: we're a bit off-topic!

gwg: John, maybe?

J-Lo: I think John's gone

jclark: I think he went away

gwg: I don't think there are enough people here for it to be a big problem that we're a little off topic...

jrichter comes back

Alex_MGI: I'll just go get some coffee.

jclark: Should we have a show of hands for who's still here?

jrichter raises his hand


cjm: me

J-Lo raises her hand

jclark raises hand

gwg raise hand

gwg can't speak English, it seems

Alex_MGI: I don't know how to type in italics...

gwg: forward-slash and then "me", then type your message

jrichter: Are there any specific OBO-Edit topics before we plunge back into XP minutia?

J-Lo: I don't know how to use the command line stuff

jclark: I used obodiff

jclark: it was really easy

jrichter: Is it broken? Or you can't get them to launch?

jclark: I can show you if you want

J-Lo: you mentioned something about a go slim command-line thing

jrichter: Yeah. You use the obo2obo command.

jrichter: obo2obo can apply any filter you want.

J-Lo: oh - I see now!

J-Lo: that was all

jrichter: Oh. Okay.

jrichter: We have 10 more minutes... Back to XPs?

gwg: yup

Alex_MGI: Is the general goal only to create xp for new terms, or will old terms be recast as xp's where appropriate?

cjm: both - we are in the process of recasting BP-CL xps

Alex_MGI: Are there already xp in the official gene_ontology.obo file?

cjm: Obol can be used to help with this

cjm: alex - not yet

cjm: did we resolve the issue regarding whether we will have a separate edit version of go.obo

jrichter: I don't know if we came to an official conclusion...

J-Lo: yes we did - we will have a separate version

cjm: This is how SO works. There is a so-xp.obo file which is Karen's primary version, it has lots of xps in it

J-Lo: I think that's sensible - my only concern was the main file being in OBO 1.0

cjm: I have lots of ideas about how the xp editor should work and i occasionally fire these off at random to the wg. is there a more structured way of going about this? perhaps the wiki can help here?

J-Lo: but I've got over that

jrichter: Chris - I think these work best as Feature Request items on sourceforge. That way, everyone will see them eventually.

jrichter: (When we do our next vote on new features)

cjm: ok

jrichter: You could also send out emails saying you added something, so interested people can take a look right away.

jrichter: 5 minutes left. Time to recap action items!

cjm: but it would also be good to have a wg wiki where some mockups could be inserted in a more visually pleasing way than the clunky sf interface

jrichter: That's true, but maybe we ought to just build these interfaces, release them in betas, and let the WG members decide what they like.

jrichter: The new text editor framework will make it a lot easier to demo new cross product editor ideas.

jrichter: Anyway, it wouldn't hurt to have a OE WG wiki page. We could create one on the main GO wiki.

Alex_MGI: John, how are you doing on the list of things to do you sent out for 1.1?

jrichter: You can check the Feature Request tracker to see what I've done so far. When I finish something, I change the status from "Pending" to "Closed" with a little comment.

gwg: I'm afraid that there's already a wiki page for the OE WG

jrichter: Whaaa?!

Alex_MGI: okay, are you feeling like you'll get it all done in time?

J-Lo: http://wiki.geneontology.org/index.php/Category:OBO-Edit_working_group

jrichter: Alex - Yes, if the paper demands are not too harsh. Most of it will get done, anyway.

Alex_MGI: great.

cjm: gwg - it needs linked from the front page! (in the main page not the sidebar) - never knew it was there

J-Lo: did you see the comments from Bioinformatics john?

gwg: it's in the software and utilities section

gwg: i'll do some fuller links on the front page tomorrow

jrichter: Jane - I did. Do we need to take any further action with them at this point?

J-Lo: I think it might be a good idea to tell them when to expect it

jrichter: Does Aug 13th sound realistic?

J-Lo: roughly

J-Lo: yes - it's only short isn't it?

J-Lo: I'll let them know.

jrichter: Thanks, Jane. I'm building in a lot of time for edits in that estimate. It may be done sooner.

jrichter: (But if Heather goes into labor early, all bets are off)

jrichter: Okay, action item time!

jrichter: 1) Jane & Amelia work on some XPs, report back on interface improvements

jrichter: 2) John sends a paper outline to the WG by Friday

jrichter: 3) John releases the official OBO-Edit 1.002

jrichter: 4) Chris posts cross product interface suggestions to Feature Request Tracker, mockups to OE Wiki

jrichter: Farewell, all. See you in 2 weeks!