HCLSIG/PharmaOntology/Meetings/2009-02-05 Conference Call

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Conference Details

  • Date of Call: Thursday February 5, 2009
  • Time of Call: 12:00pm Eastern Daylight Time (EDT), 17:00 Greenwich Mean Time (GMT), 18:00 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: 42572 ("HCLS2").
  • IRC Channel: irc.w3.org port 6665 channel #HCLS2 (see W3C IRC page for details, or see Web IRC)
  • Duration: ~1h
  • Convener: Susie


  • Review submitted use cases
  • Review submitted ontologies
  • Define next steps


Attendees: Elgar, Elizabeth, Matthias, Gwen, David Statham, David Sedlock, Mark, Sam, BI, Joanne, Christi, Susie

Regrets: Claudia, Holger, Bosse

D. Statham has been nominated as the scribe.


D. Statham: - (Millennium) growing problem of siloed data stores, begun to look at semantic technologies to see if they can help to address this issue. I think here we are primarily looking at RDF.

Mark Musen - Stanford - Ontologies - technology to support development of new ontologies.

D. Sedlock - Research and Development systems (Millennium) - Personalized Medicine, Pharmacogenomics, Want to keep up with technologies that may help in this area.

Susie - OWL vs RDFS.


First Item: Susie: Summary of why we want to do this. Compound Centric vs Patient Centric. Need to move toward tailored therapeutics and must become patient centric. Health care and pharma moving closing together. Patient centric business model use cases for Ontologies. Important to build applications that use these ontologies and work in a timely way to ensure value. Common way to exchange data and ideas in pharma collaborations.

D. Sedlock - Question re focus of group. Is it specific to ontology development or application of ontologies within a specific setting? New software development? 

Susie - Focus to be able to answer questions regarding data that is siloed. But want to focus on something that will prove effectiveness of ontology.

Second Item: Use Cases Christi and Elizabeth have done work and is documented on the Wiki. Its up on:


Christi - Translational Medicine use case. Views based approach. Can folks add to the various roles and what questions would be asked by a someone in that role.

Susie - Ways about thinking about use cases - what do we want to accomplish, cluster by roles. Group should look at these questions and refine and add to them.

D. Sedlock Question – Most views apply to other targets\disease areas – is there need to make the Parkinson’s use case generic? Target specific ontologies?

Christi – Parkinson’s is only mentioned to give credit. They should be generic and span diseases. Want to create the ontology at a higher level, and if we have specific cases we can drill down into those.

D. Statham – Have folks looked at the existing ontologies such as what is in OBO? There is a spot up on the Wiki for folks to add in existing ontologies.

Mark – OBO Foundry has stuff we may be able to leverage but nothing that is comprehensive that we can use.

Joanne – May make recommendations back to OBO to extending existing Ontologies.

Mark – Wouldn’t commit to this until we clarify our domain, translational medicine is ripe for ontology creation.

Susie – We must define what we want to do from a use case perspective, but at the same time collect ontologies that may be of use.

Elizabeth – Disease posting on Wiki. Alzheimer’s focused. Can anyone help expand the use case. Developed a knowledge base\web site that categorizes genes, proteins, hypothesis using RDF. What are hot topics in AD. Discussed various sources of data that could be minded to improve.

Gwen – The specific use case allows us to sample various databases and actually see the relationships created, and challenge an Ontology. Will it help answer the questions that we are asking?

Susie – Noticed this issue when reviewing the use cases. Specific use cases are of value but more excited about generic use case. Decision to continue to have two threads of use cases. Action item to examine these use cases for the group. Can each member go back and ask/interview their organizations.

Third Item: Existing resources. Patient and Disease centric model and list of ontologies exist. Susie reviewed the list of Ontologies that we have listed that we may be interested in. Can folks help to build up this list.

Joanne - Can we call out requirements for an ontology and then look to see what ontologies meet these needs. Domain, Terms of Domain, Ontologies that may contain these Domains. Drill down in concepts of interest or what the ontologies include? Use the use cases to fill in what someone in that role is interested in and what particular ontologies may be of use, market opportunities.

Joanne - Can we updated the Wiki page to make it more clear what we are looking for to encourage folks to add information?

Joanne - Can we get more people to participate? Assign concrete tasks, provide mechanism to facilitate participation – contact Susie? How can we bring in more people? Should we assign action items? Allow folks a few weeks to digest use cases and then assign action items?

Elizabeth – Opportunity to create questions using the AD information into the views.

Susie – Will try to get permission to use Lilly’s ontology, adding @ signs to wiki, and changing title of Parkinson’s use case, will examine CPR ontology.

Mark – Will review our ontology list to see if we are missing anything

Elgar - Will review use case.

Statham – Examine use cases, ontologies

Sedlock – Examine use cases, applications in the translational medicine\commercial space.

Sam – Just left..backround reading semantic web.

Joanne – Examine the role section and enhance

Sedlock – where is the list of members of this forum. Susie – we may need to start a section on the wiki for this. Sedlock – create survey that we could complete that would give bio’s so we can work with each other offline. Susie – lets look into this at next weeks meeting.