HCLSIG/Meetings/2009-02-05 Conference Call

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Conference Details

  • Date of Call: Thursday February 5, 2009
  • Time of Call: 11:00am Eastern Daylight Time (EDT), 16:00 Greenwich Mean Time (GMT), 17:00 Central European Time (CET)
  • 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: 4257 ("HCLS").
  • IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC)
  • Duration: ~1h
  • Convener: Scott, Susie

Agenda

Minutes

Agenda: • Task force updates • Mark Wilkinson presentation • F2F • New SPARQL Working Group

  • Attendees:
  • Christi, Egon, Eric P, Helen C, Jesse, Matthias, Michel, Scott, Susie, Mark Wilkinson, Oliver, Marco
  • Notes:
  • <cdenney> Scott: BioRDF in mode of getting a demo for C-SHALS; function inference; virtuoso instances – some interest in federating across databases; getting together next week
  • <cdenney> Matthias: described the aTag project
  • <cdenney> Helen: COI update - a few last tasks to tell the story. Majority can be ready by C-SHALS
  • <cdenney> Susie: Linking Drug Data - submitting paper to WWW workshop; clinicaltrials.gov, diseasome, Dailymed, DrugBank are now linked
  • <cdenney> Susie: defining use cases with these data sets for the paper
  • <cdenney> Susie: working to get paper finished and submitted by Tuesday
  • <cdenney> Susie: Pharma Ontology - call scheduled a couple of weeks ago and also today after this call.
  • <cdenney> Susie: looking to create high-level patient centric model; first call was to guage interest
  • <cdenney> Susie: participation from 8 pharma, academic groups
  • <cdenney> Susie: deciding on the focus
  • <cdenney> Susie: basing use case on Christ's Translational Medicine use case that builds on work Don Doherty
  • <cdenney> Matthias: Scientific Discourse - coordinating; no major milestones
  • <cdenney> Susie: They have integrated SWAN with SIOC
  • <cdenney> Susie: Now exploring integrating the experiment ontology that Lilly developed; how attributes related to experiment; discussion on how to integrate this.
  • <cdenney> Scott: Terminology - server that John Madden has running will be used rathen than getting linux machines
  • <cdenney> Scott: offering services of programmer he has
  • <cdenney> Scott: conversations about what can/cannot be viewed in SNOMED; may be best for terminology vs. linking into ontology
  • <mscottm> https://agfa.webex.com/agfa/j.php?ED=116104087&UID=1047458292&PW=a94de727223e43
  • <cdenney> Mark: Demo for Web 2.0 + Web 3.0 = Web 5.0?
  • <matthias_samwald> the slides are also attached to the wiki page at http://esw.w3.org/topic/HCLSIG/Meetings/2009-02-05_Conference_Call it seems...
  • <cdenney> Mark: Project for about the last year
  • <cdenney> Mark: left side of ontology spectrum is MESH, right side is informal user
  • <cdenney> Mark: division between formal and informal user
  • <ericP> fabulous distinction!
  • <marco> I'm afraid I (Marco) have to leave now, but I was lucky enough to have seen Mark's talk at SWAT4LS. Have fun and hear you soon!
  • <cdenney> Mark: Frames (Properties) is a key division area
  • <cdenney> Mark: the likelyhood of being right pops up at the Frames (Properties) area
  • <cdenney> Mark: Semantic web cannot be on the left of the line, must be on the right side of the line
  • <cdenney> Mark: SADI - Semantic ? ? ?
  • <cdenney> Mark: web services expose the relationship between gene and sequence
  • <cdenney> Mark: SHARE demo
  • <cdenney> Mark: will send out the web site
  • <cdenney> Mark: could answer query without a SPARQL endpoint
  • <cdenney> Mark: if there is no database, it slips to SADI to generate a database
  • <cdenney> Mark: can input data into a BLAST
  • <cdenney> Mark: Cardio Share demo - extends SADI to understand OWL classes
  • <cdenney> Mark: web services to resolve predicate
  • <cdenney> Mark: can define property pointing to an algorithm (e.g. increasingcreatinine)
  • <cdenney> Mark: ontology = query = workflow
  • <cdenney> Mark: and ontology = hypothesis
  • <cdenney> Mark: working with cardiac surgery data to duplicate outcomes research with OWL
  • <cdenney> Mark: works for NCBI or cases where we don't have SPARQL endpoints
  • <cdenney> Mapping between ontologies and web services? What is involved?
  • <cdenney> Mark: doesn't believe in traditional web services and XML schema; theirs are put http post to get a graph in return
  • <cdenney> Mark: these are pure post services
  • <cdenney> Mark: still working on the api for the registry and service writers
  • <cdenney> Mark: the WSDL could be an ontology with input (based on property restrictions) and output (based on property restrictions)
  • <cdenney> Mark: gives the biological relationship that the service uncovers
  • <cdenney> Mark: web service has to produce and consume RDF
  • <cdenney> Mark: (rather than XML schema)
  • <cdenney> Mark: we need to stop looking at legacy (XML) and move forward to RDF
  • <cdenney> Will NCBI and others be motivated to exchange via RDF?
  • <cdenney> Mark: give it 3-4 weeks; they will have a layer that generates connections
  • <cdenney> Mark: talk at C-SHALS about this
  • <cdenney> Susie: Lets all meet after the HCLS Tutorial at C-SHALS to discuss this further
  • <cdenney> Scott: F2F update
  • <mscottm> http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F
  • <cdenney> Scott: sign onto the link if you know that you are going.
  • <cdenney> Scott: need to register so we can make the best use of time... e.g. breakout sessions
  • <cdenney> Scott: edit the wiki and put your name down
  • <cdenney> Scott: new regulations to visiting the US
  • <cdenney> Scott: will mail the information for new procedures
  • <cdenney> Scott: arranging back-to-back w/ URI workshop
  • <cdenney> Scott: build confidence in common naming scheme
  • <cdenney> Scott: send e-mail if you are interested in joining this workshop

Live demo details (Thanks to Helen Chen!)

Topic: HCLS Date: Thursday, February 5, 2009 Time: 11:00 am, Eastern Standard Time (GMT -05:00, New York) Meeting Number: 704 859 986 Meeting Password: hcls

Please click the link below to see more information, or to join the meeting.

To join the online meeting 1. Go to https://agfa.webex.com/agfa/j.php?ED=116104087&UID=1047458292&PW=a94de727223e43 2. Enter your name and email address. 3. Enter the meeting password: hcls 4. Click "Join Now".

1 Minute Guide to IRC (Thanks to John Madden!)

  • If you do not have an IRC client installed on your computer, you can get one of the many free one (search "irc client" and your platform), or you can use a web-based client.

One possible web-based client you might try is Mibbit (http://www.mibbit.com/chat/). If you use mibbit, fill out the blanks like this: you need to click on "Server" (highlighted in red in png) to reveal the "Server address" field. NOTE: this meeting will use "hcls" channel, NOT "hcls2" as seen in the image.

(Note that I suggest using port 80 from mibbit. The W3C irc server supports this, and it neatly bypasses enterprise firewall issues that many users seem to be having with port 6667.)

Retrieved from "http://www.w3.org/wiki/HCLSIG/Meetings/2009-02-05_Conference_Call"
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