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:'''Venue''': [http://hiltongardeninn3.hilton.com/en/hotels/florida/hilton-garden-inn-orlando-airport-ORLAHGI/index.html Hilton Garden Inn Orlando Airport], 7300 Augusta National Drive, Orlando, Florida 32822
:'''Venue''': [http://hiltongardeninn3.hilton.com/en/hotels/florida/hilton-garden-inn-orlando-airport-ORLAHGI/index.html 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
:'''Date''': February 11-12, 2013.  




'''Draft schedule'''
This is the second meeting of the new [[Announcing Clinical and Translational Science Ontology Affinity Group | IKFC Clinical and Translational Science Ontology Affinity Group]] which 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 and existing uses of common ontologies to support sharing and discovery of data and resources, researcher networking, and particularly to support the evaluation of research.


[[Monday, February 11, 2013]]
== Schedule Monday, February 11, 2013 ==


9:00-9:30 Participant introductions: What are your interests? What do you hope to gain out of participating in the ontology interest group?
9:00-9:30 Participant introductions: What are your interests? What do you hope to gain out of participating in the ontology interest group?  


9:30 '''Barry Smith: Limning the CTSA Ontology Landscape'''
9:30 '''Barry Smith: Limning the CTSA Ontology Landscape''' [https://buffalo.box.com/s/egf99ljbvvv2kvpiwy67r2aouik5npop Slides]


10:00 '''Existing initiatives to support consortium-wide data standardization and integration'''
10:00 '''Existing initiatives to support consortium-wide data standardization and integration'''
:CTSAconnect/eagle-i/VIVO/ISF Integrated Semantic Framework (Carlo Torniai)
:Carlo Torniai: CTSAconnect/eagle-i/VIVO/ISF Integrated Semantic Framework ontology efforts to support linking expertise across CTSAs [http://www.carlotorniai.net/docs/torniai_presentation_final.pptx Slides]
:Impact assessment (Kristi Holmes)
:Maria Grando: Permission Ontology for informed consent and HIPAA compliance [http://ontology.buffalo.edu/ctsa/Orlando-Feb-2013/Grando-CTSA-Ontology.pptx Slides]
:Permissions and consent (jihad’s group)
:Ontology-based resource and information tracking to support evaluation of translational research (Dagobert Soergel)


11:15 '''Coffee'''
11:15 '''Coffee'''


11:30 '''Practical applications of ontology to support translational research  
11:30 '''Existing initiatives to support consortium-wide data standardization and integration (Part 2)'''
Brief updates from:
:Dagobert Soergel: Ontology-based resource and information tracking to support evaluation of translational research [https://buffalo.box.com/s/0318gouk4ywq5lxfir0n9sok3lk13uqt Slides]
:Warren Kibbe: Using Disease Ontology for mining medical records
:Layne Johnson: Discussion of CTSA Research Networking Affinity Group purpose, survey of networking platform, data results [https://buffalo.box.com/s/ljbevivzc1a1yo0b83adzu4biwjgq3w1 Survey Slides] [https://buffalo.box.com/s/jvcbdexc5oyq0wkoopzga9p3ltdneh8l Ontology Slides]
:Yongqun He: OGMS, IDO and VO
:Warren Kibbe: Using Disease Ontology for mining medical records [http://ontology.buffalo.edu/ctsa/Orlando-Feb-2013/Kibbe-Disease-Ontology.pptx Slides]
:Rob Wynden: The HOM Health Ontology Mapper / Federated i2b2
:(TBC) Shahim Essaid: Mining Pathology Reports for Better Specimen Query


12:15 '''Lunch'''
12:15 '''Lunch'''


13:00 '''Breakouts to discuss ontology-based support for some or all of the following (For more details see [https://ctsacentral.org/consortium/best-practices here]'''
1:00 '''Existing initiatives to support consortium-wide data standardization and integration (Part 3)'''
:Research Networking
:Yongqun He: OGMS the Ontology of General Medical Science, IDO the Infectious Disease Ontology, and VO the Vaccine Ontology [http://ontology.buffalo.edu/ctsa/Orlando-Feb-2013/He-CTSA-Ontology.ppt Slides]
:Evaluation metrics
:Matthias Brochhausen: Enabling semantic integration of biobank administrative data using OMIABIS [https://buffalo.box.com/s/475ld73cpougp4baar8dpe5flyprmfh8]
:Community engagement
:Comparative effectiveness research
:Regulatory knowledge, such as research subject advocacy
:Researcher training
:Research profiling


Each group discusses:
2:00 '''Jon Corson-Rikert: VIVO as an example of both sustainability and cross-CTSA integration efforts''' [https://buffalo.box.com/s/fyxktf8xs20z3cjn1fdouocqhlblomzl Slides]
1. What has been done thus far?
2. What are the different roles that a CTSA can or should play in these contexts?
3. Why is are they difficult
4. How would/could ontologies help?


2:30-3:30 Report back and review in large group
As an example of sustainability and cross-CTSA ontology based efforts, Jon will discuss how VIVO is a part of an open source incubator project with DuraSpace to create an updated and expanded search across additional sites and drawing on VIVO-compatible RDF data from additional software platforms.  The VIVO search effort will also provide opportunities for integrating and searching data expressed in the more comprehensive Integrated Semantic Framework under development through the CTSAconnect project, demonstrating how ontology-based data alignment can enable new functionalities across the CTSAs and for other local, regional, or discipline-based consortia.


3:30-5 Small group work on identifying ontologies and ontology gaps in the areas identified in the breakouts. Documentation of these observations.
2:15 '''Breakouts'''
13:00 Existing initiatives to support consortium-wide data integration
The ISF Integrated Semantic Framework
Other IKCF initiatives


Tuesday, February 12, 2013
:1. to discuss sustainability of cross-CTSA ontology based efforts (William Hogan)
9:00-10:30 Breakouts (see above for topics list, will break into two)
:: What sustainability efforts exist to promote cross-CTSA integration?
Each group discusses the following:
:: How have ontologies helped or been involved in such efforts?
1. What has been done thus far?
:: What roles can or should a CTSA play in these contexts?
2. What are the different roles that a CTSA can or should play in these contexts?
:2. to discuss issues of computability (Pathak Jyotishman) [https://buffalo.box.com/s/mbc57icagystci4va9a69f00bpporwdf Slides]
3. Why is are they difficult
:: Relational databases or triple stores or both?  
4. How would/could ontologies help?
:3. to discuss consents and permissions (Maria Grando)
2:45 '''Coffee'''


10:30-12 Review in large group
4:00 '''Report back and review in large group: Identify action items for the ontology interest group to address use of ontologies in cross-CTSA activities and their sustainability'''


12-1 lunch
5:00 '''Close'''


1-2 Ontology driven tools for CTSAs
== Schedule Tuesday, February 12, 2013 ==


2pm-3pm Identifying goals and key partnerships for the ontology group
9:00 '''Kristi Holmes: Impact assessment and evaluation [http://ontology.buffalo.edu/ctsa/Orlando-Feb-2013/Holmes-CTSA-Ontology.pptx Slides]'''


3-4 Discuss outreach plan
Kristi will discuss efforts at identifying outputs and indicators for research impact; see [https://becker.wustl.edu/impact-assessment] for examples. The idea is to stimulate discussion in the breakout groups surrounding how ontologies can be used to support research impact and evaluation.


4-5 Action Items, documentation, summary
9:15 '''Breakouts to discuss ontology-based efforts to support impact assessment and evaluation '''
:[https://buffalo.box.com/s/1asfwy29bv76t6leecbt55dwc7vmmhqo Conlon Breakout Slides]
:[https://buffalo.box.com/s/wf4k95dhli6euy0pc8ds9rpozr5559x6 Johnson Breakout Slides]
:[https://buffalo.box.com/s/djhgm1czjuvrp0d8wjrbiz0mg9wdx6wj Brochhausen Breakout Slides]


Use of Ontologies to Support Evaluation of Translational Research
Each group discusses:
Dagobert Soergel: Ontology-based resource and information tracking to support evaluation of translational research
:1. What efforts exist to measure scientific impact?
13:00 Future planning. Mission of the CTS Ontology Affinity Group
:2. What efforts exist to aid in the evaluation of CTSA activities and outcomes?
Identifying gaps in the CTS ontology Landscape
:3. How have ontologies helped, or how could they help, in such efforts?
:4. What roles can or should a CTSA and the ontology interest group play in these contexts?


Principal Focus
10:00 '''Report back and review in large group'''
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 and existing uses of the common ontologies to support 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, resource sharing, .researcher networking, and biomedical informatics.


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.
10:45 '''Coffee'''


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.
11:00 '''Discuss Regulatory knowledge and use of ontologies for aiding in its dissemination and consistency across CTSAs. see [https://ctsacentral.org/best_practices/research-subject-advocacy-best-practices] for examples'''


Subgoals
12:00 '''Lunch'''
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.


1:00 '''Identifying goals and key partnerships for the CTSOAG''' [https://buffalo.box.com/s/n3nxt9dqyj0ib048dwzjbp92mfa0c1v9 Slides]


9:00 '''Introduction'''
2:00 '''Coffee'''
:Barry Smith: Limning the CTS ontology landscape
:Melissa Haendel: The eagle-i ontology


10:45 '''Coffee'''
2:15 '''Outreach plan, documentation, summary, action items'''
:Possible deliverables:
::A list of ontology-related efforts across the CTSA Consortium compiled from the knowledge of participants
::A draft list of requirements for an ontology-based system to support CTSA research and evaluation
::A draft list of the major families of data which will be collected through the activities of a CTSA institution


11:00 '''Practical applications of ontology to support translational research'''
3:00 '''Birds of a Feather Discussion'''  
Brief updates from:
[https://buffalo.box.com/s/dqitt6drxrhtvviwb0map9pknmm4mrkm Slides]


:Warren Kibbe: Using Disease Ontology for mining medical records
:Research Networking
:Evaluation (including evaluation metrics)
:Community engagement
:Comparative effectiveness research
:Researcher training
(for more details see [https://ctsacentral.org/consortium/best-practices here]
 
4:30 '''Close'''


:Rob Wynden: The HOM Health Ontology Mapper
== Participants ==


12:00 '''Lunch'''
:Sivaram Arabandi (Smart Content Team, Elsevier)
:Mathias Brochhausen (Arkansas CTSA)
:Jennifer L. Bufford (Arkansas CTSA)
:Michael Conlon (University of Florida CTSA / VIVO)
:Jon Corson-Rikert (Cornell / VIVO)
:James Demery (Evaluation Lead, University of Florida CTSA)
:Davera Gabriel (University of California, Davis CTSC)
:Solomon T. Garner (RCMI Translational Research Network, Jackson State University)
:Maria Grando (UCSD)
:Yongqun He (Ann Arbor, Michigan CTSA)
:William Hogan (Arkansas CTSA)
:Kristi L. Holmes (Washington University ICTS)
:Pathak Jyotishman (Mayo Clinic)
: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)
:Richard Rauscher (Penn State University)
:Katherine G. Reilly (Medical University of South Carolina)
:Nicholas Rejack (VIV0/CTSA, University of Florida)
:Barry Smith (Buffalo)
:Dagobert Soergel (Buffalo)
:Carlo Torniai (Oregon / CTSAconnect)
:Patricia Whetzel (NCBO / Stanford)


13:00 '''Existing initiatives to support consortium-wide data integration
'''Organizers''': William Hogan,  Barry Smith and Melissa Haendel
:The ISF Integrated Semantic Framework
:Other IKCF initiatives


16:00 '''Close'''
'''Sponsor''': [https://www.uamshealth.com/?id=11050&sid=1 Translational Research Institute of the University of Arkansas for Medical Sciences]


[[Tuesday, February 12, 2013]]
Co-Sponsored by [http://bioontologies.org National Center for Biomedical Ontology]


9:00 '''Use of Ontologies to Support Evaluation of Translational Research'''
'''Further information''': Please write to [mailto:phismith@buffalo.edu Barry Smith]
:Dagobert Soergel: Ontology-based resource and information tracking to support evaluation of translational research


10:45 '''Coffee'''
== Background ==


12:00 '''Lunch'''
*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 and existing uses of the common ontologies to support 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, resource sharing, .researcher networking, and biomedical informatics.


13:00 '''Future planning. Mission of the CTS Ontology Affinity Group'''
*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.
:Identifying gaps in the CTS ontology Landscape


*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.


'''Principal Focus'''
'''Some subgoals of this meeting'''
*Subgoals of the meeting include some or all of:
: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.
: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
:3. This meeting will serve as the second meeting of the new [http://ncorwiki.buffalo.edu/index.php/Announcing_Clinical_and_Translational_Science_Ontology_Affinity_Group 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.


The [[Announcing Clinical and Translational Science Ontology Affinity Group | 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.
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.
Line 160: Line 174:
: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.
: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 [[Announcing Clinical and Translational Science Ontology Affinity Group | 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)
[[Third CTS Ontology Workshop]]
: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''': [https://www.uamshealth.com/?id=11050&sid=1 Translational Research Institute of the University of Arkansas for Medical Sciences]
 
'''Further information''': Please write to [mailto:phismith@buffalo.edu Barry Smith]

Latest revision as of 21:11, 17 November 2023

Venue: Hilton Garden Inn Orlando Airport, 7300 Augusta National Drive, Orlando, Florida 32822
Date: February 11-12, 2013.


This is the second meeting of the new IKFC Clinical and Translational Science Ontology Affinity Group which 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 and existing uses of common ontologies to support sharing and discovery of data and resources, researcher networking, and particularly to support the evaluation of research.

Schedule Monday, February 11, 2013

9:00-9:30 Participant introductions: What are your interests? What do you hope to gain out of participating in the ontology interest group?

9:30 Barry Smith: Limning the CTSA Ontology Landscape Slides

10:00 Existing initiatives to support consortium-wide data standardization and integration

Carlo Torniai: CTSAconnect/eagle-i/VIVO/ISF Integrated Semantic Framework ontology efforts to support linking expertise across CTSAs Slides
Maria Grando: Permission Ontology for informed consent and HIPAA compliance Slides

11:15 Coffee

11:30 Existing initiatives to support consortium-wide data standardization and integration (Part 2)

Dagobert Soergel: Ontology-based resource and information tracking to support evaluation of translational research Slides
Layne Johnson: Discussion of CTSA Research Networking Affinity Group purpose, survey of networking platform, data results Survey Slides Ontology Slides
Warren Kibbe: Using Disease Ontology for mining medical records Slides

12:15 Lunch

1:00 Existing initiatives to support consortium-wide data standardization and integration (Part 3)

Yongqun He: OGMS the Ontology of General Medical Science, IDO the Infectious Disease Ontology, and VO the Vaccine Ontology Slides
Matthias Brochhausen: Enabling semantic integration of biobank administrative data using OMIABIS [1]

2:00 Jon Corson-Rikert: VIVO as an example of both sustainability and cross-CTSA integration efforts Slides

As an example of sustainability and cross-CTSA ontology based efforts, Jon will discuss how VIVO is a part of an open source incubator project with DuraSpace to create an updated and expanded search across additional sites and drawing on VIVO-compatible RDF data from additional software platforms. The VIVO search effort will also provide opportunities for integrating and searching data expressed in the more comprehensive Integrated Semantic Framework under development through the CTSAconnect project, demonstrating how ontology-based data alignment can enable new functionalities across the CTSAs and for other local, regional, or discipline-based consortia.

2:15 Breakouts

1. to discuss sustainability of cross-CTSA ontology based efforts (William Hogan)
What sustainability efforts exist to promote cross-CTSA integration?
How have ontologies helped or been involved in such efforts?
What roles can or should a CTSA play in these contexts?
2. to discuss issues of computability (Pathak Jyotishman) Slides
Relational databases or triple stores or both?
3. to discuss consents and permissions (Maria Grando)

2:45 Coffee

4:00 Report back and review in large group: Identify action items for the ontology interest group to address use of ontologies in cross-CTSA activities and their sustainability

5:00 Close

Schedule Tuesday, February 12, 2013

9:00 Kristi Holmes: Impact assessment and evaluation Slides

Kristi will discuss efforts at identifying outputs and indicators for research impact; see [2] for examples. The idea is to stimulate discussion in the breakout groups surrounding how ontologies can be used to support research impact and evaluation.

9:15 Breakouts to discuss ontology-based efforts to support impact assessment and evaluation

Conlon Breakout Slides
Johnson Breakout Slides
Brochhausen Breakout Slides

Each group discusses:

1. What efforts exist to measure scientific impact?
2. What efforts exist to aid in the evaluation of CTSA activities and outcomes?
3. How have ontologies helped, or how could they help, in such efforts?
4. What roles can or should a CTSA and the ontology interest group play in these contexts?

10:00 Report back and review in large group

10:45 Coffee

11:00 Discuss Regulatory knowledge and use of ontologies for aiding in its dissemination and consistency across CTSAs. see [3] for examples

12:00 Lunch

1:00 Identifying goals and key partnerships for the CTSOAG Slides

2:00 Coffee

2:15 Outreach plan, documentation, summary, action items

Possible deliverables:
A list of ontology-related efforts across the CTSA Consortium compiled from the knowledge of participants
A draft list of requirements for an ontology-based system to support CTSA research and evaluation
A draft list of the major families of data which will be collected through the activities of a CTSA institution

3:00 Birds of a Feather Discussion Slides

Research Networking
Evaluation (including evaluation metrics)
Community engagement
Comparative effectiveness research
Researcher training

(for more details see here

4:30 Close

Participants

Sivaram Arabandi (Smart Content Team, Elsevier)
Mathias Brochhausen (Arkansas CTSA)
Jennifer L. Bufford (Arkansas CTSA)
Michael Conlon (University of Florida CTSA / VIVO)
Jon Corson-Rikert (Cornell / VIVO)
James Demery (Evaluation Lead, University of Florida CTSA)
Davera Gabriel (University of California, Davis CTSC)
Solomon T. Garner (RCMI Translational Research Network, Jackson State University)
Maria Grando (UCSD)
Yongqun He (Ann Arbor, Michigan CTSA)
William Hogan (Arkansas CTSA)
Kristi L. Holmes (Washington University ICTS)
Pathak Jyotishman (Mayo Clinic)
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)
Richard Rauscher (Penn State University)
Katherine G. Reilly (Medical University of South Carolina)
Nicholas Rejack (VIV0/CTSA, University of Florida)
Barry Smith (Buffalo)
Dagobert Soergel (Buffalo)
Carlo Torniai (Oregon / CTSAconnect)
Patricia Whetzel (NCBO / Stanford)

Organizers: William Hogan, Barry Smith and Melissa Haendel

Sponsor: Translational Research Institute of the University of Arkansas for Medical Sciences

Co-Sponsored by National Center for Biomedical Ontology

Further information: Please write to Barry Smith

Background

  • 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 and existing uses of the common ontologies to support 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, resource sharing, .researcher networking, and biomedical informatics.
  • 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.

Some subgoals of this meeting

  • Subgoals of the meeting include some or all of:
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.
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
3. 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.


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.


Third CTS Ontology Workshop