AmiGO-chat-8May07

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ben: I have a non-agenda item:
eurie: ok
ben: very quick - 
eurie: go for it
ben: for those not in the hub group - I have set up a cron job to send
ben: an email every (other) friday with a note about this meeting.
ben: The chair rotates, and the chair is supposed to assemble agenda/cancel meeting by monday evening pacific time.  Some more notes are on the wiki, but that's the jist of it.
rama: cool. thanks Ben
eurie: Thanks Ben
8:40 AM
eurie: Chris had emailed suggesting we review some web interfaces for downloading data
eurie: so we can do a survey before going whole-hog in implementing fancy downloading options for AmiGO
eurie: and see what the options are already out there
eurie: When we started thinking about how users might access the data, we put up a diagram of the work flow on the wiki
eurie: that shows at what points people might download data
eurie: http://gocwiki.geneontology.org/index.php/AmiGO_workflows
sjcarbon: one comment on that
sjcarbon: they should probably all go to the same node in the gragh for the sake of clarity
sjcarbon: how was these files?
sjcarbon: who has these files?
8:45 AM
eurie: Jane does - should we make an action item for Jane to have all arrows go to a single "output file" node?  
sjcarbon: that would be helpful--that way you don't have to have two graphs
ben: why is this necessary?
ben: is it clear to you that they are the same module?
rama: I agree. It is clear to me.
sjcarbon: not to be
sjcarbon: not to me
sjcarbon: if there was a need
sjcarbon: for different output modules, things would get confusing
sjcarbon: the point of the graph is to show states
eurie: Maybe the output should be more explicit - you'd never expect certain workflows to lead to a list of genes or an association file.
sjcarbon: yes, but they might all lead to the same output module
sjcarbon: the module would figure out what is appropriate
sjcarbon: in some cases anyways
ben: I guess if the spec diagram confuses seth, then it should be chagned
8:50 AM
sjcarbon: i'm easily confused
rama: okay
eurie: So would it help if there was just one yellow "output file" with all arrows pointing to it?
eurie: The current text is ok?
sjcarbon: it seems fine--i'm more than happy to make the changes if I could get the files
eurie: ok - still an action item for Jane - either send file to Seth or make changes to image when she returns
eurie: Are there any other questions about the workflows?
rama: Can we clarify/discuss what sort of comments we should provide after looking at these sites like Biomart etc?
eurie: Because we should refer back to these workflows as we look at other web based download tools
sjcarbon: um...
8:55 AM
eurie: Chris suggested BioMart, NCBI-Entrez for starters.  Are there any other websites we should look at?  Should we look at MOD specific ones as well?
eurie: Seth?
sjcarbon: umm...i just took a good long look at the graphs again--could you all please disregard everything i said about nodes. i understand now what jane was getting at. i blame society.
rama: let us start with these two and send other sites by email
eurie: Well, I'm not sure it's a good use of everyone's time if everyone looked at the same website doing the same things.
eurie: ok, no action item for Jane.  
eurie: I'm sure we won't be able to do every work flow on every site 
gwg: are there any sites people here regularly use to get data from that they can report on?
pascale: we use an implementation of biomart
eurie: but we can look at the site to get an idea of usability, features or tools that seem to help make things easier, etc.
eurie: Yeah, so if we a have a list of sites, we could divvy them up - one person take one site to evaluate.
eurie: and then report back at the next AWG meeting in 2 weeks time.
9:00 AM
eurie: Rama, does that answer your earlier question?
eurie: Is everyone ok with divvying up websites to evaluate?
gwg: I guess so, although if there are sites people already have expertise with, that would be good - save some work
rama: Thanks. yes
9:05 AM
rama: I think almost everyone is familiar with biomart
ben: there are several implementations of biomart however
ben: new vs. old
rama: i see
ben: either worm or fly has the old "filter" based one
pascale: ysee I know- we are still using the old one
pascale: we have that too 
ben: (you start with a big blob, and filter it down with sucessive searches)
pascale: yep
eurie: So it might not be worth evaluating the older version of BioMart that's implemented at Dicty?
pascale: I guess not; but I figured it may be easier for me to lok at biomart since I am familiar with it; although I have heard the new version is quite different
ben: ?  I thought the point was to evalaulte styles/paradigms, not actual software we would adapt?
ben: am I confused?
sjcarbon: i thought that we wanted to examine download options
9:10 AM
sjcarbon: we're about to have the ability to have a mess of them added quickly
sjcarbon: but we don't want to clutter the window or confuse users
sjcarbon: (and other usability stuff)
ben: right, so that we should look at BOTH old and new versions of biomart
sjcarbon: yes, anything with a different ui'
eurie: ok, so that was your point of brining up old vs. new biomart [I got confused as to why you brought it up Ben]
ben: so that we knew that we needed to check them both, not assign one person to "biomart"
eurie: so we have (1) old BioMart (implementation at Dicty) (2) new BioMart (3) NCBI-Entrez
rama: who has implemented the new biomart?
eurie: biomart.org
pascale: it's available from EBI, you can search EBI data
9:15 AM
rama: ho. Doh!
gwg: how about the EBI's SRS system? You must be able to download data from that
ben: I think we can safely skip SGDs...
eurie: EBI's SRS sounds good
9:20 AM
eurie: Maybe we should just start out with 4 
eurie: Volunteers?  I assume Pascale will do Dicty's BioMart?
rama: I can try SRS
pascale: sure 
ben: I could do EBI biomart
eurie: any takers for NCBI-Entrez Nucleotide?
gwg: I bet Jane would do volunteer if she were here
gwg: *would volunteer
ben: nice
rama: gwg, very nice
gwg: 
eurie: i'm trying not to volunteer since we already have 2 SGDdonghui? 
9:25 AM
donghui: sure I can do the entrez
eurie: cool - thanks!
gwg: I'll have a look at the download options at some non-bio sites and see if there's anything inspiring or revolutionary there
eurie: ok - so the task is to assess the usability of these interfaces for different types of data download we want for AmGO. 
eurie: sounds good, amelia
eurie: anything else?
rama: nope
9:30 AM
eurie: ok  - we're done then
rama: bye
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pascale: bye
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sjcarbon: bye
gwg: see yas all
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ben: l8r
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