CTSA Ontology Workshop
- Venue: Hilton Garden Inn Orlando Airport, 7300 Augusta National Drive, Orlando, Florida 32822
- Date: February 11-12, 2013. Starting at 9am on Monday and finishing at 4pm on Tuesday
Draft schedule
9:00 Introduction
- Barry Smith: Limning the CTS ontology landscape
- Melissa Haendel: The eagle-i ontology
10:45 Coffee
11:00 Practical applications of ontology to support translational research Brief updates from:
- Warren Kibbe: Using Disease Ontology for mining medical records
- Yongqun He: OGMS, IDO and VO
- Rob Wynden: The HOM Health Ontology Mapper
12:00 Lunch
13:00 Existing initiatives to support consortium-wide data integration
- The ISF Integrated Semantic Framework
- Other IKCF initiatives
16:00 Close
9:00 Use of Ontologies to Support Evaluation of Translational Research
- Dagobert Soergel: Ontology-based resource and information tracking to support evaluation of translational research
10:45 Coffee
12:00 Lunch
13:00 Future planning. Mission of the CTS Ontology Affinity Group
- Identifying gaps in the CTS ontology Landscape
Principal Focus
The IKFC Clinical and Translational Science Ontology Affinity Group has been established to leverage the use of common ontologies to support different aspects of information-driven clinical and translational research? The focus of this meeting is to explore new uses of the common ontologies which are being developed in any case to support researcher networking and sharing of data, particularly in the evaluation of scientific research, and even more particularly in the evaluation of CTSA activities.
The proposal is that, when data are harvested from institutional sources, these data can be aggregated using common ontologies such as are maintained by the eagle-i and VIVO initiatives. As these data accumulate they can be compared at regular intervals for purposes of tracking and evaluation of research activities and generation of reports on research activities that can be filtered by type, location, or a temporally defined range.
Interestingly, the use of common ontologies will mean that the data that is harvested could also be exploited also for other purposes. First, they will make all research-relevant activities easily searchable in something like the way that publications databases such as PubMed and Google Scholar already make publications easily searchable. Second, they will make results of different sorts of research activities combinable, since the same ontologies will be used to annotate, for example, clinical studies, as are used to describe mentorship opportunities or patient outreach initiatives. Third, because common ontologies are being used, all of the information collected will discoverable not only be those working within the collecting institution, but also by individuals, institutions and software agents, on the outside.
Subgoals
The specific subgoals of the meeting are as follows (comments and suggestions welcome):
0. To devise a plan for creating an evolving inventory of projects across the CTSA Consortium that develop and use ontologies. The inventory needs to include information about the ontologies, their uses, the groups involved
- Deliverables: Outline of a plan and ways to realize the plan, including a list of participants
1. To identify existing efforts in tracking and evaluation of research activities that can be facilitated by the use of ontologies, especially within the framework of the CTSA consortium, and to share the lessons learned from such experiments. One central example under this heading is the Integrated Semantic Framework (ISF), which is being developed in the context of the CTSAconnect project (http://www.ctsaconnect.org), which has as one central component an ontology for Agents, Resources, and Grants (ARG) and which draws on the eagle-i and VIVO ontologies and on the tagging taxonomy from the CTSA ShareCenter.
2. To explore strategies to create an evaluation and tracking system for an organization like a CTSA based on, or working with, a university-wide system for faculty reporting and to identify potential collaborators working on or interested in the implementation of different aspects of such a strategy. The sorts of data which might be imported into an ontology-based tracking and evaluation system would include:
- university-wide reporting data
- national data for example pertaining to grants, patents
- social networking data for example pertaining to existing collaborations, including mentoring
- clinical study data for example available through IRBnet
- Electronic Health Record data pertaining to clinicians and clinician expertise
- Deliverables: A list of such efforts compiled from the knowledge of participants. A draft list of requirements for such a system. This includes objectives 2 and 4 (which may be the same), a draft list of such data resulting from a brainstorming at the meeting.
3. To identify the major families of data which will be collected in support of clinical research activities and to consider strategies whereby these data might be collected in such a way that they automatically generate data relevant to evaluation, tracking and discovery.
- Deliverable: A list of such efforts
4. This meeting will serve as the second meeting of the new CTSOAG , and will provide opportunities for participants to provide updates on recent activities promoting the use of ontologies for the sharing of data across the CTSA consortium.
Participants will include:
- Sivaram Arabandi (Smart Content Team, Elsevier)
- Mathias Brochhausen (Arkansas CTSA)
- Jennifer L. Bufford (Arkansas CTSA)
- Michael Conlon (University of Florida CTSA / VIVO)
- James Demery (University of Florida CTSA)
- Davera Gabriel (University of California, Davis CTSC)
- Katherine G. Reilly (Medical University of South Carolina)
- Yongqun He (Ann Arbor, Michigan CTSA)
- William Hogan (Arkansas CTSA)
- Warren Kibbe (Northwestern CTSA)
- Layne Johnson (University of Minnesota)
- Fabian Neuhaus (National Institute of Standards and Technology)
- Clara M. Pelfrey (Evaluation Director, Case Western Reserve CTSC)
- Katherine G. Reilly (Medical University of South Carolina)
- Nicholas Rejack (University of Florida)
- Barry Smith (Buffalo)
- Dagobert Soergel (Buffalo)
- Carlo Torniai (Oregon / CTSAconnect)
- Patricia Whetzel (NCBO / Stanford)
- Rob Wynden (HOM / UCSF)
Organizers: William Hogan and Barry Smith
Sponsor: Translational Research Institute of the University of Arkansas for Medical Sciences
Further information: Please write to Barry Smith
