HCLSIG BioRDF Subgroup/Meetings/2007-02-26 Conference Call

From W3C Wiki
Jump to: navigation, search

Conference Details

  • Date of Call: Monday February 26, 2007
  • Time of Call: 11:00am Eastern Time
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)
  • Dial-In #: + (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
  • AOB


  • ** Welcome to CGI:IRC 0.5.4 (2004/01/29)
  • ** Looking up irc.w3.org
  • ** Connecting to irc.w3.org [] port 6665

-irc.w3.org- *** Hello, you are connecting to irc.w3.org, the progress of your connection follows -irc.w3.org- *** If you experience problems connecting, you may want to check http://www.w3.org/Project/IRC/ -irc.w3.org- *** Looking up your hostname...

  • ** Welcome to the W3C IRC Network Susie
  • ** Your host is irc.w3.org[mcclure.w3.org], running version sor1.3.4
  • ** This server was created Thu Mar 6 2003 at 19:34:50 EST
  • ** sor1.3.4 oilmwsghOkcf Hbciklmnopstv
  • ** There are 90 users and 42 invisible on 2 servers
  • ** 1 operator(s) online
  • ** 69 channels formed
  • ** I have 79 clients and 1 servers

-irc.w3.org- Highest connection count: 162 (161 clients)

  • ** - irc.w3.org Message of the Day -
  • ** - 2/3/2006 10:01
  • ** -
  • ** - Welcome to the IRC server on irc.w3.org:6665.
  • ** -
  • ** - Note: this server is INSECURE; you should assume that anyone could be
  • ** - listening to anything you say here.
  • ** -
  • ** - This server is generally restricted to use by W3C staff and collaborators.
  • ** -
  • ** - If you are a W3C Staff member, please join the secure server on irc.w3.org:6667
  • ** -
  • ** - via an ssh tunnel.
  • ** -
  • ** - If you have any questions, see:
  • ** -
  • ** - http://www.w3.org/Project/IRC/
  • ** -
  • ** - or contact <sysreq@w3.org>.
  • ** -
  • ** - $Id: ircd.motd,v 1.6 2006/03/02 15:00:44 root Exp $
  • ** -
  • ** End of /MOTD command.
    • ** Susie [945701ac@] has joined #BioRDF
  • ** Susie @ericP
  • ** Channel created on Mon Feb 26 15:14:07 2007
  • ** BillBug [chatzilla@] has joined #biordf
    • ** vipul [aadff77d@] has joined #biordf
    • ** alanr [alanrutten@] has joined #biordf
 <alanr> hi
<vipul> hi
  • ** Zakim [rrs-bridgg@] 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).
  • ** RRSAgent [rrs-loggee@] has joined #BioRDF
<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

<vipul> q+

  • 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@] 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 [iuri@] 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
  • ** vipul [aadff77d@] has quit [Quit: CGI:IRC (EOF)]

<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

  • ** BillBug [chatzilla@] has quit [Quit: Chatzilla SeaMonkey|1.1/2007011110]
  • ** Don [Don@] has quit [Quit: Don]

<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

  • ** samwaldmatthias [iuri@] has quit [Quit: samwaldmatthias]