AmiGO-chat-13Feb07

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gwg: OK, let's go then. Ben is first up with the report on amigo.geneontology.org

hitz: OK, stuart is having some trouble with some maintenance db copying scripts

hitz: he would like until next tuesday to get it all squared away.

hitz: I don't like to anhoy him because he's the system admin.

hitz: any problems?

gwg: I don't think so

gwg: anyone?

hitz: good, next item

rama: nope

gwg: GO loading refactor item

hitz: just a note that I am writing specs for speeding up the go loading. On page, if this kind of thing is interesting to you.

gwg: the link is on the wiki

hitz: thx amelia, typing too fast

gwg: excellent! next item is the requests for the June AmiGO release

gwg: working groupers, have you all been wracking your brains to think of things to ask for?

hitz: there is some disucssion in the talk section, but I find (and maybe Chris will agree/disagree) that the talk pages are not that cool. Better to discuss by email

gwg: ok, cool Ben.

gwg: have people had a look at the feature requests tracker to see what's in there and if there's anything they want to add?

cjm: Ben: I agree. It's

cjm: oops

cjm: nevermind

susan has joined the channel

gwg: AmiGO request tracker url: https://sourceforge.net/tracker/?func=browse&group_id=36855&atid=494390

gwg: hi susan, we are just talking about the new feature requests for amigo

gwg: well, I'm talking mainly

susan: ok sorry I'm late

gwg: so there are no new requests from anyone?

gwg: could you canvass your colleagues and see if they have any requests?

hitz: ok

pascale: sure

susan: ok

eurie: Are there any requests already on the tracker that you really really want?

donghui: will do

gwg: at the moment, there are a number of little fixes, and then the main concerns are sorting results

donghui: I want that feature too

gwg: and a few modifications to the blast search

pascale:

gwg: from what has come in on the mailing list recently, it sounds as if data downloads is also something that users want

cjm: I think people want more data download options, but . this will require a couple of additions to go-perl that Seth and I are working on. We can put in a request for this as a placeholder

susan: I agree

gwg: (the gohelp mailing list that is)

rama: How about searching by kingdoms?

gwg: I think that the best course of action might be for the AWGers to see if they can think of any further feature requests, or see if their colleagues have any, and then we can prioritize what will be done for the June release

hitz: that one is trickier because it requires change to db schema

hitz: (re: search by kingdom)

sjcarbon: species is already in the database--couldn't we just have kingdom groups?

gwg: perhaps the next AWG meeting in two weeks time could be used for prioritization

rama: okay, is there a plan to do it later than June

cjm: seth: people may want kingdom, order, family, phylum, genus, ...

sjcarbon: fair enough

pascale: did we not discuss using the NCBI structure to do this?

pascale: is that possible?

gwg: I think the species question is definitely an AmiGO 2.0 thing as we'll have to integrate a taxon tree into AmiGO

hitz: I thnk the NCBI taxonomy file is parsed to get the species file, but I think we should leave this to 2.0

pascale: ok

cjm: Changes to the schema aren't so hard - there is a standard way of storing a taxonomy tree in a SQL database. There would also be places in the API that would need hooks added, this is the bulk of the work

cjm: Ben: the nodes but not the hierarchy is loaded

eurie: Pascale, why don't you put that in the tracker?

gwg: we've already got something in the tracker along those lines, I think...

gwg: there's definitely some rambling on the AmiGO big ideas page about it

cjm: (We can also generate an OBO file from the taxonomy and treat it just like an ontology. This has a lot of advantages. may be less efficient though, and would slow down loading)

rama: yes, we have it in the tracker already

eurie: got it - I had the filter set to "AmiGO 1.0" so only saw a subset of items.

hitz: chris - I agree its not hard, but I think it's an added complication given a load re-write. Ask me again in april

gwg: OK, so action item from that discussion: everyone to think of AmiGO feature requests before the next session, and add them to SourceForge. We'll prioritize what should be done at the next meeting

gwg: Seth, do you want to mention the work you've done? Is it ready for showing to the AWG, or do you want to leave it a while?

sjcarbon: some things are showable, some maybe should wait

gwg: the term finder?

sjcarbon: the termfinder kinda needs another component, which is what I completed

sjcarbon: a kind of file manager

sjcarbon: it will hook in to the slim and termfinder

sjcarbon: clients

sjcarbon: (at this point, the slim client is closer to completion than the termfinder)

gwg: slim as in map2slim?

sjcarbon: yes

sjcarbon: something will be working with that later today or tomorrow

gwg: OK, great. If you send the URL out, we can all try to find some bugs to keep you busy

eurie: how about the auto-complete options?

gwg: how about the autocomplete demo?

donghui: there is a demo already? great

gwg: Chris, Ben - we're just about done on the discussion front if you need to scarper

hitz: bye all

hitz has quit the server saying: Quit: Quitting!

rama: bye

sjcarbon: sorry-phone call for chris

sjcarbon: gully wants to talk

gwg: so is the autocomplete demo ready for action or are you still working on it?

sjcarbon: http://toy.lbl.gov:9002/cgi-bin/amigo2/autocomplete-client.cgi

sjcarbon: is the autocomplete demo

gwg: do you want people to have a go and tell you which they prefer?

sjcarbon: i'd love that (sorry, half of my attention is trying to figure out why the demos worked last night when I left and are silent now)

val: working for me, cool

rama: Seth, you should post some instructions on how to test/what to expect...

rama: yeah, it is working for me too.

sjcarbon: the first seven and the last sevrn use the same algorithm, but are tied to a different set of widgets

susan: Fab!

gwg: Do you want to email everyone with the URL and some instructions? The people who aren't here can also comment then

gwg: Lovely.

gwg: Does anyone have any other business?

gwg: (AmiGO related business, that is)

gwg: going once

gwg: going twice...

eurie: wait...

sjcarbon: wait!

eurie: ha

gwg:

sjcarbon: i think eurie won

eurie: but I think you were louder, seth. =) do we have a time frame for the autocomplete comments?

gwg: comments to come in before the next AWG meeting

gwg: presumably the sooner the better, yes?

sjcarbon: it gets complicated; i'd like to have a discussion sometime about widgets and the like

pascale: can you explain what the number means on top of the list?

sjcarbon: as well as the algorithms

sjcarbon: that's the number of things returned

pascale: really? you only see the first ten or so then?

sjcarbon: yes

pascale: ok thanks

sjcarbon: also, the file manager is working again (i was having NFS problems)

rama: Please also explain what the 1,2,3,4 pull downs mean in each widget

rama: all in the email is fine.

gwg: seth, do you want to email about scheduling the discussion about widgets, algorithms and similar things? Will it be an AWG thing?

sjcarbon: just an id so we know which we're talking about

sjcarbon: the ones that start with a G are doing gene products, what the ones wothout are doing terms

donghui: what's the 'process' button for?

sjcarbon: something fun to press

donghui: i thought it should be 'auto'

sjcarbon: i'll remove it to avoid confusion

sjcarbon: http://toy.lbl.gov:9002/cgi-bin/amigo2/data-manager-client.cgi

eurie: we have some time now - should we do some discussion now?

sjcarbon: is a file manger for programs like map2slim

rama: eurie, you mean on autocomplete

eurie: for whatever seth wants to discuss

rama: Seth, your call

sjcarbon: is there other business?

gwg: no, I don't think so

sjcarbon: eurie?

gwg: nothing else on the agenda, anyway

eurie: me? no, my wait was only for the time frame for comments

sjcarbon: well, let's see what I can explain in ten minutes

sjcarbon: for a AmiGO2, it's becoming obvious that widgets (buttons, sortable tables, etc.) will be a time sink

sjcarbon: so we have the option of using a third-party widget set or going alone

sjcarbon: third-party will give us speed of application turn-araound, but decrease flexibility

sjcarbon: for example, in the autocomplete

sjcarbon: the top seven lines are from a third party

sjcarbon: and there is no real way to separate out the number of returned items from the actual returned tiems

sjcarbon: whereas the bottom severn are something i put together in an afternoon

sjcarbon: but never got around to completing (doesn't listen to mouse yet) because I ran out of time

sjcarbon: the issue in a nutshell

sjcarbon: until now, I've been rolling my own (sortable table)

sjcarbon: but there is definitely an argument for just grabbing someone else's

gwg: especially for stuff like tablesorting... there are a million sortable tables out there

sjcarbon: very few *fast* ones though

sjcarbon: which is why I went my own way in that case

donghui: autocomplete: sorry to interupt. i suppose the results are sorted by alphabetical order. If I am searching for a term 'kinase', I would like to see that term listed on the very top; followed by other terms. Is this reasonable?

gwg: I think someone else mentioned having the autocomplete results ranked by 'relevance'

sjcarbon: that would be algorithm "G2" i believe

susan: I'm confused isn't that a gene product one?

sjcarbon: yes, it is

val: will the results eventually be scrollabe?

sjcarbon: for 5000? i think that's a bad idea

sjcarbon: a lot of data to transfer

sjcarbon: if the autocomplete isn't quick, it probably will be more of an problem than anything else

gwg: and if your search query is vague to start with, it probably won't help

susan: with the second one how do you select something from the list? e.g. type methylation and you want to choose DNA methylation from the list - do you have to type the missing bit?

sjcarbon: for the second set (the second seven)?

susan: BBOP rather than Dojo

sjcarbon: up and down arrows and then tab or return

susan: doesn't seem to work for me

val: I see... i"m typing things like actin though...325 results and the most relevent aren't first. Perhaps there are other ways like prioritizing term banes above synonyms etc

val: yes BBOp is better

sjcarbon: sorry--this seems to be running pretty slow hammering on my little toy server

sjcarbon: susan: make sure that the cursor is flashing in the text box

gwg: perhaps people should test it over the next few days so they can get a feel for how the response would be when the entire AWG wasn't testing it!

susan: ahh got it - thanks

gwg: Shall we draw proceedings to a close? Our hour is pretty much up

gwg: I'll put the action items and the transcript on the wiki

sjcarbon: thanks

rama: great. Thanks Amelia for chairing the session

gwg: Next meeting is in two weeks time, the 27th

gwg: so see you all then!


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