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 #: + (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: • 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.)