AmiGO-chat-August1407

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Revision as of 08:21, 14 August 2007 by Hitz (talk | contribs) (New page: ben: OK. ben: I guess this is it. Only item is slim mapper. ben: URL? sjcarbon: http://toy.lbl.gov:9002/cgi-bin/amigo/map2slim.cgi 8:40 AM ben: well, there is 1 bug ben: Firefox 2.0 Mac O...)

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ben: OK. ben: I guess this is it. Only item is slim mapper. ben: URL? sjcarbon: http://toy.lbl.gov:9002/cgi-bin/amigo/map2slim.cgi 8:40 AM ben: well, there is 1 bug ben: Firefox 2.0 Mac OSX has 2 floating scroll bars about 3/4ths of the way down on the rhs sjcarbon: ! sjcarbon: lemme turn my mac on ben: ah, they are useful when you open [Display gene product filters] j-lo: I have a request from Matt j-lo: that when you add a load of GO ids as a slim, it can display them as an indented set val: did you make a decision about how IDs are handled? j-lo: so you can see the hierarchy sjcarbon: an indented set meaning just fancier whitespace? j-lo: yep val: I mean gene product IDs, sorry 2 questions at once 8:45 AM ben: another usefulness - ga files are typically gzipped. You get an error if you upload a gzipped gene association file sjcarbon: whitespace should not be an issue val: Matts request is difficult, how would you decide how to indent ? val: so he wants a complete graph as output? rama: Aren't we doing what Princeton does? Provide all GA files in a pull down? j-lo: we're doing that too j-lo: I don't think he wants a full graph, Val, just the terms you list val: I don't understand Matts reguest, sound like he just wants the graphical output rama: I think Matts request should be an enhancement- shd add to SF val: but if thety have multiple parents this will be like the Amigo 'view' ben: seth, are you debugging when you should be answering questions? sjcarbon: ben--i can add the questions are coming a bit fast sjcarbon: oops two thoughts ben: ok no more q's for a minute guys ben: I am running the sgd ga file vs. Plant slim ben: because that's the kind of guy I am sjcarbon: i can add the gzip if people find that helpful val: I still find the input confusing. sjcarbon: that's already written somewhere ben: seth - re: gzip, at least have it catch the exception. Low priority to actually have it unzip sjcarbon: i still need more information about exactly what matt wants 8:50 AM val: I can input pombe gen symbols cdc2,cdc25,act1 etc. j-lo: yeah - I'll check and get back to you! val: There is nothing in the output that tells me which org I have searched. val: When I click on the GO id link, I get the Amigo view for all genes annotated to this term, ben: my yeast-to-plant finished, took about 5 minutes (2800 terms, 6500 gps) val: not the list of genes I added sjcarbon: ben--you want an error for the gzipping specifically rather than a 'nothing found' error? val: I dont think that is too long, as long as the user knows it is running ben: I think this came up in a previous chat that I missed, but the distinction between #Inferred GPs and # Direct GPs is not obvious at all. ben: Also, I think people would like Pvalues sjcarbon: no pvalues in mapping ben: Also we need to think a little about what to do with root/unknown terms val: Ben, why dop you need P values for a slim? rama: How would you calculate pvalues for mappings val: they are just mapping up the tree? rama: I think counts makes sense sjcarbon: that should be term enrichment ben: well, never mind then ben: but why do we need 2 tools? val: also, don't understand direct vs inferred? val: They do differrent jobs? val: one is an inrichment tool, one is a slimmer ben: I actually DO understand direct/inferred, but it requires exposition, at least a click away. sjcarbon: direct is the most direct mapping in the slim while inferred is all of the ancestors in the slim rama: Val- ben direct annotations vs all rama: Sorry, I meant- ben meant Direct annotations vs All ben: users won't understand the why or how about the difference between direct/inferred. sjcarbon: ben we can add help to the column description val: it shouldn't be inferred. These aren't inferred val: it should be INDIRECT ben: Also - this is a little curious, "inferred" GPs to root terms should be 100%? val: No actually Rama is correct, it should be direct vs ALL ben: in my sgd->plant slim I get 100% CC, 99.3% MF, 96.9% BP rama: At SGD, we just should the genes mapped to the GO slim. We don't show the direct vs all 8:55 AM rama: I am really sorry. my typing is bad today val: I don't think we should allow direct/indirect for slimming, it doesn't make sense. It should be ALL always j-lo: I agree ben: yeah, actually, the whole point of the slim (one of them) is that we don't give a fig about the ontologoical structuremcgimmick rama: I meant At SGD, we just *show* ben: so I would just dump inferred/indirect ben: unless you can show it graphically. j-lo: yep ben: which would be an enhancment val: I don't even think it is needed graphiclly, if they want to look at this they want and enrichemtn tool, not a slimmer rama: I think it is confusing to show direct and All. We shd list all genes that map to a GO slim term sjcarbon: rama--couldn't that get rather large and confusing? j-lo: what's the alternative? val: SO do we agree, ditch direct show ALL sjcarbon: already ditched j-lo: great val: It needs to be ALL, that is what the tool is for, val: great ben: duh rama: Thanks Val. That is exactly the point ben: I get it now ben: but why is "cellular process" in the Plant slim... (plz. don't answer here) rama: Ben, please send mail to TAIR curator j-lo: Shall we discuss gene ids? val: please ben: and we need to handle root terms specially ben: otherwise they will always all be 100/100/100% ben: we had this problem at SGD val: I think there was an earlier mail to only show the output for the terms in the slims, not for all their parents too, this would solve this 9:00 AM rama: do all the slims have the root terms listed. I know SGD does ben: unless people put the root terms in their slims sjcarbon: only slim terms are displayed now val: Although I am getting the same problem Ben pointed out so it could be a bug. val: Ah so the yeast slim contains the root nodes? rama: yes val: OK, ben: OK, gene ids? Can someone summarize the Q/issue for me/ ben: ? j-lo: I can try val: Did you see the e-mail, it was quite long, I'll have a go val: you GO jane j-lo: when people input their gene list into the mapper j-lo: it may be in any of several formats j-lo: some of which have name redundancy bewteen and within species j-lo: also, so genes may simply not be in the database ben: val - I just got back from vacay j-lo: so how should AmiGO handle this? pasc_g has joined the channel ben: got it. The fundamental job of bioinformatics val: With GO term mapper and GO term finder you preselect your organism, this reduces the problem partially. j-lo: heh - yep! ben: I suggest we do not attempt to solve this problem in general for the next amigo release 9:05 AM rama: the interface will show an intermediate page with IDS that it can find with an option to either move on or go back and fix rama: Sorry, typo- I meant 'IDS it cannot find' val: Sounds sensible ben: there are two variants of this: val: but you should also be able to preselect your organism ben: 1) abort function, and query user ben: 2) just passthough with message that some IDs could not be mapped uniquely rama: yes, the intermediate page should say that those IDS were not valid for that species donghui has joined the channel val: Most of the probelms would go away if people were encouraged to use the systemtic identifiers for their species (as most users do with any geneome wide data). ben: or uniprot ids val: Most problems occur becasue we are allowing cdc2 cdc28 etc val: I don't think Term mapper allows this, it expects systemtic identifiers val: (I meant he princeton version) 9:10 AM ben: going back to 1) vs. 2) above, the "correct" answer is some non-linear function of the number of "whiffs" in your input file ben: although since (for a large number of input genes) these apps take a while anyway - mabye we can split the different. ben: User hits "go" - sent to intermediate page which j-lo: Ben, I'm not sure I understnad what you're saying ben: a) lists IDs that could not be mapped j-lo: ah - okay - yes ben: b) says "working......" with a status bar ben: c) a big ol' red ABORT button if user decides the number of whiffs is too large sjcarbon: asynchronous will be hard/take time sjcarbon: also, the mapping is the time consuming part j-lo: we thought an intermediate page, and the user can assess the 'whiffs', and then alter their input file and rerun, or just continue j-lo: mapping? ben: if mapping takes time, then just always stop and ask. rama: keep it simple. Provide the intermediate page and force the user to make a decision ben: Also, is that also true for term enrichment? sjcarbon: that is fine, and can be added once the session stuff that amelia is working on is completed ben: It doesn't have to be asynchronous.... if the intermediate page is the app that actually submits a (valid) gene list to the mapper... 9:15 AM sjcarbon: am i correct that you want to have a job running in the background while the user decides if they want to abort? sjcarbon: that will depend on the session stuff ben: I see... sjcarbon: either way ben: not if they just hit the "stop" and "back" buttons on their browser! j-lo: so what would the user see? ben: I wonder how hard that would be to emulate in j/s sjcarbon: j/s? ben: ANYWAY.... I have a hard 9:22 PDT dead line, and I am chair, so lets wrap up ben: javascript ben: we all agree that we need an intermediate page ben: we all all agree not to solve ID mapping problem in general rama: yes val: yep j-lo: I'm to get more details about Matt's request ben: details left to seth to implement in a timely manner j-lo: and we're losing the All/direct options for just ALL ben: anything else? 9:20 AM j-lo: yes? rama: yes j-lo: cool ben: it would be great to have a working beta, with some solid examples for the interactome meeting in UK at the end of the month. ben: we are doing a go demo/tutorial ben: ok, meeting closed. have a nice day/night all