Semantic Technologies Meeting Minutes 12 April 2013

From PHUSE Wiki
Jump to: navigation, search

Date/time of call

Friday, April 12, 2013, 11:00 AM - 12:00 PM EST

Access Information

Call-in toll-free number (US/Canada): 1-877-668-4490 Call-in toll number (US/Canada): 1-408-792-6300 Access code: 595 644 192


First Name, Last Name Organization
Frederik Malfait IMOS Consulting
Michael Brennan Janssen Pharmaceuticals
Mitra Rocca FDA/CDER/OTS
Scott Bahlavooni Genentech
Dean Allemang Working Ontologist, LLC
Armando Oliva FDA/CDER/OTS/OCS
Boris Brodsky FDA/CDER/OPI
Bob Friedman
Chris Olinger
Geoff Low Medidata Solutions Worldwide
K McManus
Kirsten Langendorf
Marc Andersen
Steve Wong


1. Overview of the Semantic Technologies Workgroup

2. Presentation/discussion

3. Questions & Answers

Summary of Discussions

Scott provided an overview on the goals on this work group, aiming at learning semantic technology and to execute experiments to better understand the value of representing clinical trials in RDF, expectations from workgroup members, Key problems to address, logistics (posting of materials on the PhUSE wiki, and setting up a ListBox. There was no objection from the work group members to use these tools.

He provided an overview of the PhUSE wiki content for the Semantic Technology workgroup and recommended for members of this work group to register on the PhUSE wiki in order to add contents. Contents will be added by editing the “Discussion” tab. If the members have any questions, they can contact the co-leads for this project.

Michael Brennan mentioned that this wiki is a public forum and is not limited to the work group members only. The Project manager will also post a membership list and asked members to identify their background and interest.

Frederik continued discussing the project scope document and provided a summary from the PhUSE/FDA CSS March 2013 workgroup annual meeting. He discussed the need for the workgroup members to educate themselves and influence others in order to promote this technology better. He proposed developing a number of educational materials, esp. focusing on what this workgroup is trying to achieve. The workgroup needs to start to reach out to other stakeholders, for example NCI is publishing the thesaurus in OWL. BRIDG also has an OWL format. SHARE is going to be the pinnacle of semantic. Within W3C there is a workgroup focusing on healthcare and life sciences. One of the important areas of this project is to deliver and experiment. One of the key SW technologies is to link data using RDF. Represent CDISC standards in RDF. These are softer things, and later the team will plan and implement 3 pilots. One area is where the team can add value and deliver things is to develop ontologies for SDTM, ADaM and CDASH The workgroup members could take 3 clinical trials and place them in OWL and see how this technology works and the challenges.

Frederik proposed developing a catalogue of use cases: 1. Produce a model to represent CDISC standards 2. Develop checks for CDISC standards 3. An experiment to develop clinical data standards for a therapeutic area and how to represent this in RDF; how meta data or data could be linked. There is a need to add more meat to the flesh (add more detail to each use case), as the team moves forward.

In reference to timeline, Frederik recommended starting slow and then moving forward full speed. He proposed looking at existing materials and ongoing projects. Another area to focus is to see if the Semantic Technologies are ready for prime time or shaky and what is this technology good for. By the end of 2 months, build a catalog of use cases. These use cases do not need to be detailed. Prioritize the use cases and start working on them. He suggested minimizing the risk. If something fails, the workgroup would want to find it out as soon as possible. For each use case, there is a need to produce within 3 months. He was interested in finding out, how much people can commit; what this team can achieve, what are the objectives and timelines and the key product that this workgroup will deliver as a team.

Frederik recommended forming 3 sub-WG and various members are assigned to each workgroup: 1. Develop reading materials (Scott, Mitra, and Frederik) 2. Identify Web sites and Ontology Editors (Geoff Low, Marc and Bob) 3. Work on a Standard Slide deck and review the slide deck. (Frederik, Kirsten and Varia (Biogen))

Dean is conducting a Semantic Web Workshop in Karlsruhe, Germany on 23 May 2013.

Members of this group can contact Dean directly at for information about discounted registration.

The information for the course in the SW in May will it also posted on the wiki.

Action Items

Item Description Responsible Individual Due Date
Send out meeting minutes Mitra Prior to next meeting
Provide Listbox Training materials to the work group members Scott Prior to next meeting
Register on the PhUSE wiki (If not already a member) All Prior to next meeting
Increase participation by reaching out to other interested individuals and providing them with the work group schedule All Prior to next meeting
Establish a list for workgroup members, add affiliations, contact information (email) All Prior to next meeting
Post Dean’s Semantic Web Workshop Information in Karlsruhe, Germany on the PhUSE wiki Scott Prior to next meeting
Start reviewing the reading materials Scott, Frederik, Mitra One Month
Identify Web sites and Ontology Editors Geoff Low, Marc and Bob One Month
Work on a Standard Slide deck and review the slide deck. Frederik, Kirsten, Varia 2 Months

Next Meeting

The next weekly call will be held on Friday, April 19, 2013 from 11:00 to 12:00 PM EST.

Last revision by DanBoisvert,05/30/2013