CTS Ontology Workshop 2015: Difference between revisions

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'''The goal of this meeting is to examine the benefits of and barriers to the use of ontologies and semantic web infrastructure in support of real-world applications in clinical care and translational research.'''
'''The goal of this meeting is to examine the benefits of and barriers to the use of ontologies and semantic web infrastructure in support of real-world applications in clinical care and translational research.'''


'''Day 1 (before 3pm)''' will focus on how ontologies are being used in EHR interoperability.  
'''Day 1 (before noon)''' will focus on how ontologies are being used in EHR interoperability.  


'''Day 1 (after 3pm) and Day 2''' will focus on applications in translational research.
'''Day 1 (afternoon) and Day 2''' will focus on applications in translational research.


== '''Themes''' ==
== '''Themes''' ==
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'''Day 1'''
'''Day 1'''


8am-noon
8:00-9:45
* '''Fast Healthcare Interoperability Resources''' [http://wiki.hl7.org/index.php?title=FHIR_Ontology_Requirements (FHIR)]  
* '''Fast Healthcare Interoperability Resources''' [http://wiki.hl7.org/index.php?title=FHIR_Ontology_Requirements (FHIR)]  
** David Booth (FHIR): An introduction to FHIR
** David Booth (FHIR): An introduction to FHIR
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::[http://hl7-fhir.github.io/rdf.html FHIR.rdf]
::[http://hl7-fhir.github.io/rdf.html FHIR.rdf]


1pm-3pm
9:45-10:00 Break
 
10:00-12:00
* '''EHR and ontology'''
* '''EHR and ontology'''
** Peter Elkin (Buffalo): Ontologies driving EHRs
** Peter Elkin (Buffalo): Ontologies driving EHRs
** Bill Hogan and Amanda Hicks (Florida): Continuity of Care Document & RDF/OWL
** Bill Hogan and Amanda Hicks (Florida): Continuity of Care Document & RDF/OWL
12:00-1:00 Lunch
1:00-2:30
* '''Ontology practices'''
** James Overton (Knocean): Pathology Imaging Ontology
** James Overton (Knocean): Pathology Imaging Ontology
** Ludger Jansen (Universität Rostock): Good Ontology Design: Philosophical and Empirical Perspectives


3:15-4:15
2:30-2:45 Break
 
2:45-4:15
* '''Ontology and biobanking'''
* '''Ontology and biobanking'''
** Chris Stoeckert, Jie Zheng (Penn) and Mathias Brochhausen (Arkansas): The [http://www.ontobee.org/browser/index.php?o=OBIB OBIB] Ontology for Biobanking  
** Chris Stoeckert, Jie Zheng (Penn) and Mathias Brochhausen (Arkansas): The [http://www.ontobee.org/browser/index.php?o=OBIB OBIB] Ontology for Biobanking  
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'''Day 2'''
'''Day 2'''


8am-noon
8:00-9:45
* '''Practical examples of ontology use'''
* '''Practical examples of ontology use'''
** Alexander Diehl (Buffalo): Using an applied neurology ontology framework for analysis of MS patient data
** Alexander Diehl (Buffalo): Using an applied neurology ontology framework for analysis of MS patient data
** Alan Ruttenberg (Buffalo): Using Semantic Web tools to analyse ontology-structured dental records
** Alan Ruttenberg (Buffalo): Using Semantic Web tools to analyse ontology-structured dental records
945-10 Break
10:00-12:00
* '''Consents & medical practice documents'''
* '''Consents & medical practice documents'''
** Frank J. Manion and Marcelline R. Harris  (Michigan) [https://code.google.com/p/ico-ontology/ Informed Consent Ontology]  
** Frank J. Manion and Marcelline R. Harris  (Michigan) [https://code.google.com/p/ico-ontology/ Informed Consent Ontology]  
Line 88: Line 102:
** Mathias Brochhausen (Arkansas) Documents and Document Acts
** Mathias Brochhausen (Arkansas) Documents and Document Acts


1pm to 3pm
12:00-1:00 Lunch
 
1:00-3:00
* '''Wrapup session addressing issues of specific relevance to the Clinical and Translational Science Consortium'''
* '''Wrapup session addressing issues of specific relevance to the Clinical and Translational Science Consortium'''
** VIVO/eagle-i/ VIVO-ISF/ and LOD: role in CTS project evaluation
** VIVO/eagle-i/ VIVO-ISF/ and LOD: role in CTS project evaluation

Revision as of 21:39, 31 July 2015


Ontology in Practice


The Fourth Clinical and Translational Science Ontology Workshop

September 23 - 25, Charleston, SC


Venue

The Francis Marion Hotel • 387 King Street, Charleston, SC 29403

Starts: Wed 9/23/15 at 5pm with an optional reception. The workshop begins at 8am Thu 9/24/15.

Ends: Fri 9/25/2015 3pm

Registration

Registration is now open.

There is a $80 registration fee to support venue expenses and conference meals.

  • Please register here

Goals

The goal of this meeting is to examine the benefits of and barriers to the use of ontologies and semantic web infrastructure in support of real-world applications in clinical care and translational research.

Day 1 (before noon) will focus on how ontologies are being used in EHR interoperability.

Day 1 (afternoon) and Day 2 will focus on applications in translational research.

Themes

  1. FHIR and Ontology
  2. Making ontologies work in real world use cases
  3. Modifying or adopting existing ontologies
  4. Practical benefits -- and disbenefits -- of using ontologies
  5. Mapping terminologies to ontologies; Automated classification/annotation/NLP

Sub-themes

  • Using ontologies for electronic data capture.
  • Ontologies for biobanking and informed consents.
  • Automated annotation, automated classification, clinical (or other) notes NLP, are some ontologies are better for NLP than others?
  • In the medical space: ontology and HL7 Fast Healthcare Interoperability Resources (FHIR); Ontology and LOINC.
  • Work on merging LOINC, SNOMED-CT and RxNorm; Leveraging Basic Formal Ontology (BFO).
  • Ontology portals: connecting ontologies, using ontologies in non-redundant comprehensive manner, separating the wheat from the chaff, promoting ontology reuse.
  • Bridging research resources and expertise using ontologies.
  • Licensing issues in adoption of ontologies or terminologies.

Draft Agenda

Day 0

  • Evening reception

Day 1

8:00-9:45

  • Fast Healthcare Interoperability Resources (FHIR)
    • David Booth (FHIR): An introduction to FHIR
    • Barry Smith (Buffalo): Ontology for FHIR
Background on FHIR
FHIR.rdf

9:45-10:00 Break

10:00-12:00

  • EHR and ontology
    • Peter Elkin (Buffalo): Ontologies driving EHRs
    • Bill Hogan and Amanda Hicks (Florida): Continuity of Care Document & RDF/OWL

12:00-1:00 Lunch

1:00-2:30

  • Ontology practices
    • James Overton (Knocean): Pathology Imaging Ontology
    • Ludger Jansen (Universität Rostock): Good Ontology Design: Philosophical and Empirical Perspectives

2:30-2:45 Break

2:45-4:15

  • Ontology and biobanking

Day 2

8:00-9:45

  • Practical examples of ontology use
    • Alexander Diehl (Buffalo): Using an applied neurology ontology framework for analysis of MS patient data
    • Alan Ruttenberg (Buffalo): Using Semantic Web tools to analyse ontology-structured dental records

945-10 Break

10:00-12:00

12:00-1:00 Lunch

1:00-3:00

  • Wrapup session addressing issues of specific relevance to the Clinical and Translational Science Consortium
    • VIVO/eagle-i/ VIVO-ISF/ and LOD: role in CTS project evaluation
    • Interoperability between OBO foundry and other ontologies and (e.g. SNOMED, LOINC, NCI Thesaurus, ICD-9/10, RxNorm)
    • CDISC to RDF for clinical trials

Participants will include

Sivaram Arabandi (OntoPro)

David Booth (FHIR)

Mathias Brochhausen (University of Arkansas for Medical Sciences)

Alex Diehl (University at Buffalo)

David Eichmann (University at Iowa)

Peter Elkin (University at Buffalo)

Helena Ellis (Duke University)

Fernanda Farinelli (University at Buffalo)

Amanda Hicks (University of Florida)

William Hogan (University of Florida)

Ludger Jansen (University of Rostock)

Jihad Obeid (Medical University of South Carolina)

James Overton (Knocean)

Alan Ruttenberg (University at Buffalo)

Barry Smith (University at Buffalo)

Dagobert Sorgel (University at Buffalo)

Chris Stoeckert (University of Pennsylvania)

Asiyah Yu Lin (University of Michigan, Ann Arbor)

Jie Zheng (University of Pennsylvania)

Organizing Committee

Barry Smith (University at Buffalo)

William Hogan (University of Florida)

Jihad Obeid (Medical University of South Carolina) (Chair)

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