https://wiki.geneontology.org/index.php?title=OE_IRC_12July06&feed=atom&action=historyOE IRC 12July06 - Revision history2024-03-28T09:09:19ZRevision history for this page on the wikiMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=OE_IRC_12July06&diff=6682&oldid=prevGirlwithglasses at 10:55, 3 August 20062006-08-03T10:55:18Z<p></p>
<p><b>New page</b></p><div>The further adventures of the OBO-Edit Working Group! This week's exciting episode: "Cross Product Doublecross!" with special guest star Chris Mungall.<br />
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<span style="font-weight: bold; color: blue">Alex_MGI</span>: So who has the agenda?<br />
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<span style="font-weight: bold; color: blue">cjm</span>: Yup! This is my first time on IRC since those sanger apollo IRC chats back in the day...<br />
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<span style="font-weight: bold; color: blue">midori</span>: nobody did one [agenda], as far as I know ...<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: 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...<br />
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<span style="font-weight: bold; color: blue">Alex_MGI</span>: okay<br />
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<span style="font-weight: bold; color: blue">cjm</span>: sounds good<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: 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.<br />
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<span style="font-weight: bold; color: blue">midori</span>: :(<br />
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<span style="font-weight: bold; color: blue">gwg</span>: is that the effect of my joining the channel? ;)<br />
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<span style="font-weight: bold; color: blue">midori</span>: nope, just lucky timing ;)<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: 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.<br />
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<span style="font-weight: bold; color: blue">gwg</span>: excellent!<br />
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<span style="font-weight: bold; color: blue">cjm</span>: john, can you send me the outline (I am on the wg digest which I think scrambles attachments)<br />
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<span style="font-weight: bold; color: blue">Alex_MGI</span>: Will 1.002 be released now?<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: 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.<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: 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.<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: 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.<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: That's the other thing I've done - OBO-Edit<br />
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<span style="font-weight: bold; color: blue">Alex_MGI</span>: Great<br />
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<span style="font-weight: bold; color: blue">gwg</span>: have you solved the all-important icon issue?<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: 's cvs repository is now branched, so I can fix bugs in an old version without messing up the working version.<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: 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.<br />
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<span style="font-weight: bold; color: blue">gwg</span>: it's OK, I can wait... I guess<br />
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<span style="font-weight: bold; color: blue">gwg</span>: (sob)<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: Any issues that folks want to discuss? I think Chris might have things to say about x-products...<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: erm - beta testing?<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: You came in immediately after I said that everyone has signed off, so I'm doing a release today.<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: oh - okay!<br />
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<span style="font-weight: bold; color: blue">cjm</span>: I think I've said my xp interface stuff on the wg list. i'd like to hear others opinions though too<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: I haven't actually used it yet, so I'm afraid I don't have an opinion...<br />
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<span style="font-weight: bold; color: blue">Alex_MGI</span>: Me neither.<br />
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<span style="font-weight: bold; color: blue">Alex_MGI</span>: Too bad Karen isn't here.<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: 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.<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: that's a good idea<br />
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<span style="font-weight: bold; color: blue">gwg</span>: we might be able to do some with the pamgo stuff, jane<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: Michael has someone called George who will be using xprod plugin v. soon too<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: called George working for him (!)<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: Ha!<br />
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<span style="font-weight: bold; color: blue">cjm</span>: That's George Gkoutios who does PATO. cc me on any emails with him John since this is important for cbio<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: You bet.<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: he wanted someone to teach him how to use the plugin<br />
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<span style="font-weight: bold; color: blue">cjm</span>: The PATO cases are unusual though<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: 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.<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: i told him to email the OE WG list<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: it was only today so he probably hasn't done much yet!<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: 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?"<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: gwg and I will try it out next week with the new pamgo terms...<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: Let's call that an action item.<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: Anything else to discuss, then?<br />
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<span style="font-weight: bold; color: blue">cjm</span>: can you give an example of a pamgo xp term?<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: erm - carbohydrate catabolism in other organism<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: does that work as a xp?<br />
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<span style="font-weight: bold; color: blue">Alex_MGI</span>: Is that an internal xp?<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: yep<br />
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<span style="font-weight: bold; color: blue">gwg</span>: yup<br />
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<span style="font-weight: bold; color: blue">cjm</span>: this would be an odd one - would the differentium be "occurs_in other_organism"?<br />
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<span style="font-weight: bold; color: blue">gwg</span>: yup<br />
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<span style="font-weight: bold; color: blue">cjm</span>: hmmmmmmm<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: other_organism is one of those strange terms, like "host". It's like an ontology equivalent of a pronoun<br />
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<span style="font-weight: bold; color: blue">gwg</span>: there are going to be a load of terms which will be a biological process occurring in another organism<br />
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<span style="font-weight: bold; color: blue">gwg</span>: or regulation of a biological process in another organism<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: Is there some more specific way to describe that "other_organism"? Maybe with reference to its relationship to the implied "this_organism"?<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: (I can rephrase that, if necessary. It's almost unreadable)<br />
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<span style="font-weight: bold; color: blue">cjm</span>: we discussed this at the content mtg in tigr. ok. so the xp would be with the CC term 'external'?<br />
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<span style="font-weight: bold; color: blue">gwg</span>: it's usually going to be 'xxx process in host' or 'xxx process in symbiont'<br />
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<span style="font-weight: bold; color: blue">gwg</span>: yup (to chris)<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: I don't know if that will work<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: the term is 'extracellular' - not 'extraorganismal'<br />
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<span style="font-weight: bold; color: blue">cjm</span>: 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<br />
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<span style="font-weight: bold; color: blue">gwg</span>: i don't think these terms are going to be particularly controversial - they're just fleshing out concepts we already have<br />
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<span style="font-weight: bold; color: blue">Harold</span>: Or BP X MF<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: yes, but the xprods might be!<br />
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<span style="font-weight: bold; color: blue">gwg</span>: but there may be other more suitable candidates for showing to the general population...<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: Midori's doing some cc ones too i think<br />
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<span style="font-weight: bold; color: blue">Harold</span>: 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<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: they're not really xprods though are they Harold?<br />
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<span style="font-weight: bold; color: blue">cjm</span>: 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<br />
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<span style="font-weight: bold; color: blue">cjm</span>: 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<br />
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<span style="font-weight: bold; color: blue">Harold</span>: to j-Lo: wouldn't any cross between orthologous ontologies be a x-product?<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: i don't know!<br />
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<span style="font-weight: bold; color: blue">gwg</span>: if we do MF-BP, aren't we going to get into that debate about function again?<br />
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<span style="font-weight: bold; color: blue">cjm</span>: 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)<br />
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<span style="font-weight: bold; color: blue">gwg</span>: do you want to move over the other xp wiki stuff?<br />
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<span style="font-weight: bold; color: blue">cjm</span>: Jane, aren't you working on the MF-BP links?<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: erm - not really...<br />
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<span style="font-weight: bold; color: blue">cjm</span>: yes, I should probably do that<br />
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<span style="font-weight: bold; color: blue">cjm</span>: well it sounds like Harold is.... Harold? Are there more details on this pathway project?<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: Harold may have wandered off. Sometimes the Jax folks just leave their IRC clients on record and go have a coffee...<br />
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<span style="font-weight: bold; color: blue">Alex_MGI</span>: Really?<br />
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<span style="font-weight: bold; color: blue">Harold</span>: 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<br />
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<span style="font-weight: bold; color: blue">gwg</span>: 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<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: it gets very complicated with the whole species specificity thing<br />
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<span style="font-weight: bold; color: blue">gwg</span>: that's if the AmiGO working group can be galvanised into action so I can finish the mock ups... :S<br />
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<span style="font-weight: bold; color: blue">cjm</span>: Anything I can do to help the amigo wg move along?<br />
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<span style="font-weight: bold; color: blue">jrichter</span> steps away for a moment<br />
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<span style="font-weight: bold; color: blue">cjm</span>: 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?<br />
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<span style="font-weight: bold; color: blue">gwg</span>: I think everyone's busy at annotation camp at the moment, so maybe they'll all be back in action again next week<br />
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<span style="font-weight: bold; color: blue">cjm</span>: ok<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: possibly - I think we need more discussion though<br />
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<span style="font-weight: bold; color: blue">gwg</span>: I think Chris is correct on that, as long as we define things by their constituent parts<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: who's chairing this meeting?<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: we're a bit off-topic!<br />
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<span style="font-weight: bold; color: blue">gwg</span>: John, maybe?<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: I think John's gone<br />
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<span style="font-weight: bold; color: blue">jclark</span>: I think he went away<br />
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<span style="font-weight: bold; color: blue">gwg</span>: I don't think there are enough people here for it to be a big problem that we're a little off topic...<br />
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<span style="font-weight: bold; color: blue">jrichter</span> comes back<br />
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<span style="font-weight: bold; color: blue">Alex_MGI</span>: I'll just go get some coffee.<br />
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<span style="font-weight: bold; color: blue">jclark</span>: Should we have a show of hands for who's still here?<br />
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<span style="font-weight: bold; color: blue">jrichter</span> raises his hand<br />
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<span style="font-weight: bold; color: blue">Harold</span>: <br />
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<span style="font-weight: bold; color: blue">cjm</span>: me<br />
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<span style="font-weight: bold; color: blue">J-Lo</span> raises her hand<br />
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<span style="font-weight: bold; color: blue">jclark</span> raises hand<br />
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<span style="font-weight: bold; color: blue">gwg</span> raise hand<br />
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<span style="font-weight: bold; color: blue">gwg</span> can't speak English, it seems<br />
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<span style="font-weight: bold; color: blue">Alex_MGI</span>: I don't know how to type in italics...<br />
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<span style="font-weight: bold; color: blue">gwg</span>: forward-slash and then "me", then type your message<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: Are there any specific OBO-Edit topics before we plunge back into XP minutia?<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: I don't know how to use the command line stuff<br />
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<span style="font-weight: bold; color: blue">jclark</span>: I used obodiff<br />
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<span style="font-weight: bold; color: blue">jclark</span>: it was really easy<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: Is it broken? Or you can't get them to launch?<br />
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<span style="font-weight: bold; color: blue">jclark</span>: I can show you if you want<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: you mentioned something about a go slim command-line thing<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: Yeah. You use the obo2obo command.<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: obo2obo can apply any filter you want.<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: oh - I see now!<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: that was all<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: Oh. Okay.<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: We have 10 more minutes... Back to XPs?<br />
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<span style="font-weight: bold; color: blue">gwg</span>: yup<br />
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<span style="font-weight: bold; color: blue">Alex_MGI</span>: Is the general goal only to create xp for new terms, or will old terms be recast as xp's where appropriate?<br />
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<span style="font-weight: bold; color: blue">cjm</span>: both - we are in the process of recasting BP-CL xps<br />
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<span style="font-weight: bold; color: blue">Alex_MGI</span>: Are there already xp in the official gene_ontology.obo file?<br />
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<span style="font-weight: bold; color: blue">cjm</span>: Obol can be used to help with this<br />
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<span style="font-weight: bold; color: blue">cjm</span>: alex - not yet<br />
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<span style="font-weight: bold; color: blue">cjm</span>: did we resolve the issue regarding whether we will have a separate edit version of go.obo<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: I don't know if we came to an official conclusion...<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: yes we did - we will have a separate version<br />
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<span style="font-weight: bold; color: blue">cjm</span>: 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<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: I think that's sensible - my only concern was the main file being in OBO 1.0<br />
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<span style="font-weight: bold; color: blue">cjm</span>: 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?<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: but I've got over that<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: Chris - I think these work best as Feature Request items on sourceforge. That way, everyone will see them eventually.<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: (When we do our next vote on new features)<br />
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<span style="font-weight: bold; color: blue">cjm</span>: ok<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: You could also send out emails saying you added something, so interested people can take a look right away.<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: 5 minutes left. Time to recap action items!<br />
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<span style="font-weight: bold; color: blue">cjm</span>: 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<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: 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.<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: The new text editor framework will make it a lot easier to demo new cross product editor ideas.<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: Anyway, it wouldn't hurt to have a OE WG wiki page. We could create one on the main GO wiki.<br />
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<span style="font-weight: bold; color: blue">Alex_MGI</span>: John, how are you doing on the list of things to do you sent out for 1.1?<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: 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.<br />
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<span style="font-weight: bold; color: blue">gwg</span>: I'm afraid that there's already a wiki page for the OE WG<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: Whaaa?!<br />
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<span style="font-weight: bold; color: blue">Alex_MGI</span>: okay, are you feeling like you'll get it all done in time?<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: http://wiki.geneontology.org/index.php/Category:OBO-Edit_working_group<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: Alex - Yes, if the paper demands are not too harsh. Most of it will get done, anyway.<br />
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<span style="font-weight: bold; color: blue">Alex_MGI</span>: great.<br />
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<span style="font-weight: bold; color: blue">cjm</span>: gwg - it needs linked from the front page! (in the main page not the sidebar) - never knew it was there<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: did you see the comments from Bioinformatics john?<br />
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<span style="font-weight: bold; color: blue">gwg</span>: it's in the software and utilities section<br />
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<span style="font-weight: bold; color: blue">gwg</span>: i'll do some fuller links on the front page tomorrow<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: Jane - I did. Do we need to take any further action with them at this point?<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: I think it might be a good idea to tell them when to expect it<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: Does Aug 13th sound realistic?<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: roughly<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: yes - it's only short isn't it?<br />
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<span style="font-weight: bold; color: blue">J-Lo</span>: I'll let them know.<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: Thanks, Jane. I'm building in a lot of time for edits in that estimate. It may be done sooner.<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: (But if Heather goes into labor early, all bets are off)<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: Okay, action item time!<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: 1) Jane & Amelia work on some XPs, report back on interface improvements<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: 2) John sends a paper outline to the WG by Friday<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: 3) John releases the official OBO-Edit 1.002<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: 4) Chris posts cross product interface suggestions to Feature Request Tracker, mockups to OE Wiki<br />
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<span style="font-weight: bold; color: blue">jrichter</span>: Farewell, all. See you in 2 weeks!<br />
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[[Category:OBO-Edit_working_group]]</div>Girlwithglasses