AWG-chat-20070703: Difference between revisions
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(New page: <pre> gwg: hello! eurie: morning j-lo has joined the channel gwg: comment va la bataille avec les limaces? 8:30 AM pascale: plutot bien! les oiseaux ont gagne et mange toutes les fraises g...) |
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Latest revision as of 18:46, 8 April 2014
gwg: hello! eurie: morning j-lo has joined the channel gwg: comment va la bataille avec les limaces? 8:30 AM pascale: plutot bien! les oiseaux ont gagne et mange toutes les fraises gwg: ah non! sacre bleu gwg: hier soir, il pleuvait, et il y avait beaucoup de limaces rama has joined the channel gwg: je les ai tue sous mes chaussures pascale: ah oui> j'en ai attrape quelques unes, et je les ai noyees dans de l'eau salee rama: gwg- please translate gwg: last night it was raining and there were loads of slugs around gwg: I killed them under my shoes j-lo: yeah, it's been a good year for slugs and snails so far 8:35 AM j-lo: i feed them to my chickens gwg: il ya avait aussi des escargots, et je les ai lancee dans la rue eurie: does anyone know if donghui and val are around? eurie: ben is out of town eurie: what about chris? sjcarbon: talked to him last night before he left sjcarbon: not in yet sjcarbon: lemme take a look j-lo: you throw the snails into the road? gwg: or into my neighbours garden, depending on my mood pascale: that's really evil ! cjm has joined the channel gwg: well, they only have flowers and stuff, so they don't mind, I'm sure j-lo: I saw Val earlier - lemme email her... gwg: I have to protect my crops! pascale: bien sur! 8:40 AM eurie: i'm sure this isn't the last time we'll talk about mapper and finder. eurie: nice work in getting those set up and integrated into the rest of AmiGO, Seth and Amelia j-lo: yeah - looks really good gwg: that was Seth, not me sjcarbon: stole all of amelia's front stuff sjcarbon: some work still needs to be eurie: ok, i take that back then - no compliments for you amelia. sjcarbon: done in back to fully integrate it gwg: I feel much better now Eurie! gwg: who is chairing today? eurie: so should we talk about some features we'd like implemented on finder and mapper? eurie: me sjcarbon: let's talk! eurie: Seth, do you want to start out with finder or mapper? sjcarbon: I'd rather fish for what people like in other implementations sjcarbon: oops sjcarbon: parsed that wrong sjcarbon: mapper 8:45 AM gwg: as in map2slim? sjcarbon: yes eurie: I like the ability to choose one ontology and the specific organism annotation set eurie: I like the options you have now - choose an existing slim or upload your own slim as well as uploading your own gene_assocation file gwg: sorry, do you have the URLs of those two other implementations? I've lost the email between here and my work computer rama: I also like the ability to upload a slim in OBO format rama: http://go.princeton.edu/cgi-bin/GOTermMapper rama: SGD's - rama: http://db.yeastgenome.org/cgi-bin/GO/goTermMapper\ rama: Sorry, there is a slash at the end. gwg: thanks Rama! 8:50 AM eurie: Are all the slim sets that are in the OBO file (using the category tag, I think?) loaded into AmiGO? gwg: they're all in the database, yes eurie: cool - so could all those be available from the mapper? sjcarbon: i suppose once the backend is cleaned up from where it is now j-lo: we should definitely do that gwg: the current mapper doesn't work in a very efficient way, it parses an ontology file plus whatever goslim you upload gwg: so it doesn't run off the database at all gwg: did anyone have a look at the options available here: http://toy.lbl.gov:9006/cgi-bin/amigo/goslimmer.cgi eurie: this wasn't working for me this morning gwg: no, I am half-way through uploading various files at the moment unfortunately! eurie: never mind - i can see it now 8:55 AM gwg: the main difference is that you can upload a list of terms or an ontology file gwg: you can also upload a list of gene products and it will use the data from the database gwg: or you can upload your own association file gwg: It's only a partial implementation at the moment because I didn't know how useful or otherwise that would be gwg: sorry, I think I've just replaced an important template file so the page isn't working right now! 9:00 AM j-lo has quit the server saying: Ping timeout jane has joined the channel pascale has quit the server saying: Ping timeout jane: (sorry - got booted out) jane: I like the ability to enter a flat list of GO terms as an alternative to choosing or uploading a full slim file jane: (sorry if we've already moved on to another topic!) gwg: yes, we were on to the metaphysics of ontologies gwg: anyway, I need to discuss with Chris and Seth about it, but I think ideally it's a lot easier for users not to have to have an OBO format GO slim to upload pascale has joined the channel eurie: I like how you've broken it up into sections. There are three essential inputs for mapper: (1) input list of genes to be analyzed. (2) go slim to be used as the terms to map to (3) the associations that are to be used for the mapping. Maybe the page should be split into these sections? jane has quit the server saying: Read error: Connection reset by peer gwg: I was also wondering about other possible presentation methods, e.g. a list of tasks gwg: so you could have 'create a mapping for all ontology terms using my input terms' gwg: 'map my GA file terms to a goslim' gwg: ... well, things like that, perhaps expressed more clearly 9:05 AM gwg: the thing with map2slim (and similar scripts / amigo options) is that there are a number of options available, but presenting them to the user in a comprehensible manner isn't always easy gwg: I think a list of 'tasks' would appeal to newbies, because it would make it clear for them, but then it might get annoying for seasoned users to have to take 'baby steps' gwg: what do people think? sjcarbon: i recall that people didn't much care for the ORB 'wizard' eurie: For this first release, I don't think we necessarily need to shoot for the moon - just present simple instructions rama: I agree jane has joined the channel gwg: it's trying to find a way to make it simple that's tricky, though! eurie: Section 1: required, input a list of genes to be mapped jane: (that was a power cut that time!) eurie: Section 2: Pick a slim set (default: one of the go slims in the OBO file; advanced, your own list of GOID) eurie: Section 3: Pick a gene association file to use for the analysis (default: the organisms in the database; advanced, upload your own gene_associations file) rama: Did we decide on one ontology vs all three at a time? jane: Section 1: or select an annotation file? 9:10 AM jane: people might want just an overview of annotation for a given species? eurie: yup, both rama's and jane's suggestions sound good too rama: Jane- your idea is great. won't it take a long time to compute it on the fly? rama: should we precompute and have that available? eurie: maybe that's a summary page we couldl have pre-computed each time the database is loaded? jane: GOA do that - they provide a pre-slimmed annotation set rama: Regarding users entering terms- what if an user enters a bunch of terms from all three ontologies jane: then it slims over all 3 ontologies? eurie: maybe we should limit to 1 ontology per run 9:15 AM rama: I don't know if it is going to be hard on the servers to do all 3 at a time rama: I agree with Eurie eurie: We've got ~15 minutes left. Is this enough initial thoughts for the next rendition mapper? should we move onto finder? Seth/Amelia? sjcarbon: moving on might be good for the time left eurie: ok - amigo's finder: http://toy.lbl.gov:9002/cgi-bin/amigo/termfinder.cgi eurie: princeton: http://go.princeton.edu/cgi-bin/GOTermFinder eurie: sgd: http://db.yeastgenome.org/cgi-bin/GO/goTermFinder eurie: i actutally really like princeton's "basic input" list rama: me too. 9:20 AM gwg: re: slimming over 1 vs 3 ontologies - it is quicker just to do it over 1 ontology, but it doesn't take all that long to do a slim down on all the terms in the ontology - if you choose the bottom option of the list at http://toy.lbl.gov:9006/cgi-bin/amigo/goslimmer.cgi, you'll see it is quick(ish) gwg: (sorry, took ages to type that reply!) rama: we should also change the title to Term enrichment analysis or something meaningful sjcarbon: choose a title and it will be done eurie: but go term finder is so catchy. gwg: but it sounds like a search engine! jane: How about 'find over-represented GO terms' jane: or 'enriched GO term finder' gwg: I think that sounds like areas of the ontology where we've got loads of detail rama: okay settling on a title is easy. Lets get to the options on the interface (sorry!) jane: I like the basic v/s advanced input sections too eurie: I like having the evidence code options - but maybe checkboxes? so you can see the full list? maybe people will start actually paying attention to them! 9:25 AM rama: checkboxes is a good idea jane: I think we should just have maybe three evidence codes options eurie: experimental, sequence-based, computational? jane: e.g. experimental, all manual, manual + electronic jane: yeah - exactly pascale: I like that too; I think AmiGO should also have that rama: can we say experimental and Non-experimental gwg: if we can decide on what to use, I can implement that pretty quickly gwg: in the main AmiGO, that is rama: we are combining type of evidence and type of annotation when we say experimental and manual etc. gwg: doesn't the new evidence code documentation split the evidence codes into three main groups? eurie: Possibly the separation of evidence codes into major sections should be brought up tot he greater GOC in order to make it consistent across the board rama: Yeap. 9:30 AM jane: how about we just have 'manual v/s manual+electronic' and then in advanced options allow people to choose specific evidence codes? rama: How about the results page for these interfaces rama: Sorry I moved on since we are out of time pascale: right, that seems like a big change jane: has anyone seen the new evidence code docs? rama: I have gwg: am looking at them right now gwg: they split evidence codes up into several categories: gwg: experimental evidence codes gwg: computational analysis gwg: author statement gwg: curator statement gwg: and automatically assigned jane: hmm - not very intuitive gwg: ( http://www-dev.yeastgenome.org/draftGO/go/www/GO.evidence.new.shtml ) gwg: no - I wouldn't have thought the author/curator divide would be all that interesting to people outside GO jane: I don't think those are good categories for AmiGO - they're almost as confusing as the evidence codes! gwg: how about experimental / computational / statement? eurie: ok, maybe this is a conversation we should have on the greater list - evidence code breakdown on evidence code docs and possibly transferring them to AmiGO. eurie: and we can influence some change. rama: I agree jane: me too gwg: moi aussi 9:35 AM eurie: sounds like there is enough food for thought for the next interface versions of finder and mapper? eurie: any specific actions items we want to extract from this meeting? gwg: yeah rama: How about results page? eurie: maybe that can be a topic for discussion for the next awg? rama: okay gwg: I did a little mock up of the mapper front page from Eurie's description: http://toy.lbl.gov:9006/cgi-bin/amigo/goslimmer.cgi gwg: or maybe we can discuss it on the mailing list (if it's not too controversial!) eurie: Sending it back around to the mailing list sounds good gwg: OK, perhaps I will email about it tomorrow? gwg: I also want people to test the new search to see if the relevant results it produces are relevant or not eurie: Since these tools are major leaps forward, Seth and Chris suggested sending these out to the greater GOC for comments once the AWG has come up with a version we like gwg: good idea 9:40 AM eurie: ok, we're all done here then? look forward to the discussion of mapper over email then gwg: I'm excited about it already! jane: ok gwg: before we all go eurie: yes? gwg: it's Jane's birthday tomorrow, so I'm sure you'd all like to join me in a (silent) rendition of 'Happy Birthday'! eurie: HAPPY BIRTHDAY!!! pascale: joyeux anniversaire jane! rama: Happy birthday Jane gwg: perhaps we can give her the bumps, too! rama: Bye gwg: see y'all on the mailing list pascale: ciao eurie: bye pascale has quit the server sjcarbon: bye gwg has left the channel sjcarbon has left the channel jane: thank you jane: (sorry, wasn't paying attention jane: see ya! rama has left the channel 9:45 AM