AmiGO-chat-8May07

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 donghui has left the channel pascale: bye pascale has quit the server sjcarbon: bye gwg: see yas all gwg has quit the server saying: Quit: Goodbye cruel world! sjcarbon has quit the server saying: Quit: Leaving ben: l8r ben has left the channel