HCLSIG BioRDF Subgroup/Meetings/2007-02-26 Conference Call
From W3C Wiki
- Date of Call: Monday February 26, 2007
- Time of Call: 11:00am Eastern Time
- Dial-In #: +1.617.761.6200 (Cambridge, MA)
- Dial-In #: +33.4.89.06.34.99 (Nice, France)
- Dial-In #: +44.117.370.6152 (Bristol, UK)
- Participant Access Code: 246733 ("BIORDF")
- IRC Channel: irc.w3.org port 6665 channel #BioRDF (see W3C IRC page for details, or see Web IRC)
- Duration: ~1 hour
- Convener: Susie Stephens, Vipul Kashyap
- Scribe: Joanne Luciano
- Review Action Items
- Identify subset of demo to implement
- Practicalities of the demo (e.g. live or recorded, size, storage) - all
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- ** Susie [email@example.com] has joined #BioRDF
- ** Susie @ericP
- ** Channel created on Mon Feb 26 15:14:07 2007
- ** BillBug [firstname.lastname@example.org] has joined #biordf
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<alanr> hi <vipul> hi
- ** Zakim [email@example.com] has joined #BioRDF
<alanr> oops <alanr> please do, susie <BillBug> SS: TBL started informatl SW gatherings in Jan 2007 - HCLS will piggy back and have an informal gathering connected with the next one(s).
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<RRSAgent> logging to http://www.w3.org/2007/02/26-BioRDF-irc <vipul> Zakim, this is BIORDF <Zakim> ok, vipul; that matches SW_HCLS(BioRDF)11:00AM <BillBug> SS: Hope at that meeting to bring a comprehensive list of current BioRDF data sources + comprehensive sense of the UCs (SS+VK) - focus on explicitly tying the two together <alanr> bill, I think I recognize your heavy breathing on the audio :) <Zakim> + +1.617.993.aaaa <BillBug> SS: explore workflow required to bring the BioRDF stores into play to address focussed/microdomains within the Use Case. <alanr> zakim, who is on the call? <Zakim> On the phone I see Susie, Vipul_Kashyap, John_Barkley, Bill_Bug, Alan, June_Kinoshita, +1.617.993.aaaa <alanr> zakim, 993.aaaa is Joanne_Luciano <Zakim> sorry, alanr, I do not recognize a party named '993.aaaa' <Zakim> +Kei_Cheung <alanr> zakim, 1.617.993.aaaa is Joanne_Luciano <Zakim> sorry, alanr, I do not recognize a party named '1.617.993.aaaa' <alanr> zakim, Joanne_Luciano 993.aaaa <Zakim> I don't understand 'Joanne_Luciano 993.aaaa', alanr <alanr> zakim, Joanne_Luciano is 993.aaaa <Zakim> sorry, alanr, I do not recognize a party named 'Joanne_Luciano' <Zakim> - +1.617.993.aaaa <BillBug> mute me <alanr> http://www.w3.org/2005/rules/wg/wiki/UsingZakim <vipul> Timing? <BillBug> Zakim, mute me <Zakim> Bill_Bug should now be muted <vipul> Date and time for the earlier meeting? <BillBug> SS+VK: will there be a callin number for March 13 gathering? Getting together prior to that too - later this week/early next <BillBug> VK: Callin number? <BillBug> Group agrees - get together earlier - MIT? Partners( exit 18 on 95)? - MGH (SWAN team) - or Harvard Campus (60 Oxford St.) - Alan will try to get an MIT room -since time is short. <Zakim> + +1.617.384.aabb <BillBug> Monday 3/5 - tough for June - need SWAN folks (Tim/Marco/Paolo) since SWAN will be playing a role in the demo <BillBug> TC: BioRDF folks asked for SWAN in RDF - still true? <BillBug> AR: We're depending on it <BillBug> TC: Monday 3/5 - could meet at Oxford St. - room will have phone - TC supply some food <alanr> healthy food please <BillBug> TC: search nauty/nice list to choose food for individuals. <BillBug> TC: has parking - garage right there - underground - see signs - say "SWAN" - go out front door - take L & L - past construction site. <BillBug> SS: Monday, 3/5 - 11:30 - lunch, parking, white board, projector, web casting + belly dancing. <BillBug> AR: Salad + Fruits for Alan. <BillBug> June: Near Peabody museum. <BillBug> TC: Oxford btween Hammond & Wendel. <BillBug> SS: for parking - look to TC IIC invitations <BillBug> SS: TC will send info to SS - she will compile and send to all. <BillBug> Zakim, unmute me <Zakim> Bill_Bug should no longer be muted <alanr> http://sw.neurocommons.org/map.html <alanr> http://prefuse.org/ <BillBug> AR: look at Prefuse.org & GoogleMap Allan Brain Atlas example <BillBug> SS: Look at latest version of the Use Case - what is that? - Is it in the Word file? - yes - June having trouble attaching to Wiki - SS will post <BillBug> JB: Date on document February 19th. <BillBug> AR: Could SWAN RDF for Hypotheses by next week? <BillBug> TC: No - can have in old format - want to give BioRDF the NEW stuff - won't have the SW ready until 3/6. Will bring old hypotheses for visual review - using SWAN 0.1 ontology (new with be SWAN v1.0 ontology) <BillBug> AR: BrainPharm? <BillBug> KC: Have an old version - in process of converting SenseLab data into RDF - data more in-line with CURRENT PD-AD Use Case - will have some time next week.
<BillBug> KC: Will new SWAN version of current Use Case be available? <BillBug> JK: Yes - and is working on narrowing the Use Case <BillBug> VK: Highlight UC focus/microdomain in RED (SS will wait until she receives that). <BillBug> BB OBO Phenotype Assertion - http://esw.w3.org/topic/HCLS/OntologyTaskForce/OboPhenotypeSyntaxExperiment <alanr> perhaps review http://www.telemakus.net/AD/ <alanr> q+
- Zakim sees alanr on the speaker queue
- Zakim sees alanr, vipul on the speaker queue
<BillBug> Zakim, mute me <Zakim> Bill_Bug should now be muted <Zakim> +[IPcaller] <BillBug> AR: demo - did Mattias translate NN? <BillBug> Zakim, unmute me <Zakim> Bill_Bug should no longer be muted <alanr> negotiation is nice, but not useful for demo at this point <Zakim> +Don_Doherty
- ** Don [Don@188.8.131.52] has joined #biordf
<BillBug> MS: no NN - just talked - no further <alanr> Imaging, querying by gene, browsing gensat. <alanr> Integration - demo query before mapping, query after mapping. <alanr> Query - specificity - do google, do sparql. <alanr> RDB - SQL then Sparql discovery, (ask classes, ask properties, look at a few simple queries) <alanr> Browsing - Show timeline, show graph, show table generated from same data <BillBug> JB & KC: Semantic Web - demonstrating benefits - document <BillBug> Zakim, mute me <Zakim> Bill_Bug should now be muted <Susie> http://esw.w3.org/topic/HCLS/HCLSIG_DemoHomePage_HCLSIG_Demo
- ** samwaldmatthias [email@example.com] has joined #BioRDF
<alanr> NN ontologies *were* here last week. Errors now :( http://braininfo.rprc.washington.edu/tools.html <BillBug> BB: I need to speak with Doug Bowden today (NN). I'll ask him about this <BillBug> JB: reviewed document - will tie more to Use Case <BillBug> JK: There are many types of Abeta - what structural properties <BillBug> Zakim, unmute me <Zakim> Bill_Bug should no longer be muted <BillBug> AR: Pull out the papers that define the entities - AR will represent them in OWL <alanr> not the papers - the definitions of the entities (clips from paper are ok) <alanr> re:NN I have two spreadsheets: NN2002.xls, NN2006MouseandRatNomenclatures.xls that I downloaded last week <samwaldmatthias> I looked at these spreadsheets some months ago.
<BillBug> JK: What import models of nerve cell physiology are important to AD? LTD? LTP? - those models point to specific neuronal properties - the models are the result of hypotheses about evidence. <BillBug> KC: SenseLab's ModelDB can provide a lot of info on the various molecular entities - channels, receptors <BillBug> BB: need 2nd messenger system too (pathways) <BillBug> JK: posited K+-Channle polymorphisms that are relevant to AD expression <BillBug> KC: look to SNP data sources for info on channel polymorphism - and SNPs associated with AD/PD <BillBug> AR: has worked on converting cell properties. <vipul> Susie: There was also an e-mail from Ivan asking for the presentors
<vipul> For the W3C track <BillBug> AR: some data to RDF-isize - would like MS to do this. <BillBug> MS: OK <BillBug> SS: Use BMC HCLS paper - submit to ISMB "highlighted papers" - 3/4 or 3/5 deadline. Do we all agree? <alanr> http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?taxid=9606&species_db=all&ev_code=aca&show_associat... <samwaldmatthias> http://www.iscb.org/ismbeccb2007/highlights/ <alanr> ion channels <BillBug> SS: Any other issues <BillBug> VK: Ivan asked for list of presenters - all of us? <BillBug> SS: deadline? <BillBug> VK: before 3/2 - Friday <BillBug> AR: Can we ask Ivan EXACTLY what he needs? Only the people presenting - or all participants? <BillBug> SS: Last year - one person's names on abstract (presenter) - could split across several people? Let's cogitate on this option? - makes sense that those who WILL DEFINITELY BE PRESENT in Banff to be included (and those who will not be there not on the paper). <Zakim> -Alan <Zakim> - +1.617.384.aabb
<Zakim> -Vipul_Kashyap <Don> http://sw.neurocommons.org/map.html
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<BillBug> SS: see you next monday - 3/5 - at SWAN/Harvard Oxford St. site - try to set up camera, phone, and desktop sharing <BillBug> SS: 11:30 AM EST <Zakim> -Susie <Zakim> -John_Barkley <Zakim> -Kei_Cheung <Zakim> -June_Kinoshita <Zakim> -Don_Doherty
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<Zakim> -[IPcaller] <Zakim> disconnecting the lone participant, Bill_Bug, in SW_HCLS(BioRDF)11:00AM <Zakim> SW_HCLS(BioRDF)11:00AM has ended <Zakim> Attendees were Susie, Vipul_Kashyap, John_Barkley, Bill_Bug, Alan, June_Kinoshita, +1.617.993.aaaa, Kei_Cheung, +1.617.384.aabb, [IPcaller], Don_Doherty
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