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<font size="+3">Ontology in Practice</font>
<font size="+3">Ontology in Practice</font>  


<font size="+2">The Fourth Clinical and Translational Science Ontology Workshop</font>


<font size="+2">The Fourth Clinical and Translational Science Ontology Workshop</font>
For the 2023 meeting please see [[CTS Ontology Workshop 2023]].


<font size="+2">September 23 - 25, Charleston, SC</font>
<font size="+2">September 23 - 25, Charleston, SC</font>


[[File:Chs02.jpg|link=|right|Charleston]]


== '''Venue''' ==
== '''Venue''' ==
<font size="+1">[http://www.francismarionhotel.com/ The Francis Marion Hotel]    '''•'''    [https://goo.gl/maps/zVpKx 387 King Street, Charleston, SC 29403]  
<font size="+1">[http://www.francismarionhotel.com/ The Francis Marion Hotel]    '''•'''    [https://goo.gl/maps/zVpKx 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.
Starts: Wed 9/23/15 at 6pm with an optional reception. The workshop begins at 8am Thu 9/24/15.


Ends:  Fri 9/25/2015 3pm
Ends:  Fri 9/25/2015 3pm
Line 18: Line 20:
</font>
</font>


== '''Registration''' ==
== '''Goals''' ==
<font size="+1">Registration is now open.
'''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.'''
 
There is a $80 registration fee to support venue expenses and conference meals.


* Please register [https://sctrweb2.musc.edu/CTS_Ontology_Registration.html here]
'''Day 1 (before noon)''' will focus on how ontologies are being used in EHR interoperability.  


* Hotel [https://bookings.ihotelier.com/bookings.jsp?groupID=1419298&hotelID=76320 group rate booking]
'''Day 1 (afternoon) and Day 2''' will focus on applications in translational research.


</font>
== '''Our Sponsors''' ==


== '''Goals''' ==
[[File:TriNetX.png|link=http://trinetx.com/|TriNetX]]    &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp;
'''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.'''
[[File:HSSC.jpg|link=http://www.healthsciencessc.org/|HSSC]]    &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp;
[[File:SCTR.png|link=http://academicdepartments.musc.edu/sctr|SCTR]]


'''Day 1 (before 3pm)''' 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.
[[File:Ncor-logo.jpg|link=http://ncor.buffalo.edu/|NCOR]]    &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp;
[[File:PROlogo.png|link=http://pir.georgetown.edu/pro/|Protein Ontology Consortium]]    &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp;
[[File:ub_dbmi.png|link=http://www.smbs.buffalo.edu/biomedicalinformatics/|DBMI]]


== '''Themes''' ==
== Agenda ==
# '''FHIR and Ontology'''
[http://ncor.buffalo.edu/2015/CTSO/CTS_Ontology_booklet.pdf Conference Brochure]
# '''Making ontologies work in real world use cases
# '''Modifying or adopting existing ontologies
# '''Practical benefits -- and disbenefits -- of using ontologies'''
# '''Mapping terminologies to ontologies; Automated classification/annotation/NLP'''


== Sub-themes ==
'''Evening before the Conference: Wed 9/23/15 '''
* 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 ==
6:00pm - 7:00pm
'''Day 0'''
* '''Evening reception '''
* Evening reception
   
   
'''Day 1'''
<font size="+1" style="color: blue">'''Day 1: Thu 9/24/15'''</font>


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 [https://goo.gl/RNfUai Slides]
** Barry Smith (Buffalo): Ontology for FHIR
** Barry Smith (Buffalo): FHIR and Ontology [http://ncor.buffalo.edu/2015/CTSO/Smith.pptx Slides] [https://www.youtube.com/watch?v=LV_DZvhGoJQ Video]
::Background on [http://www.interfaceware.com/blog/taking-fhir/ FHIR]
::Background: [http://www.interfaceware.com/blog/taking-fhir/ FHIR]; [http://hl7-fhir.github.io/rdf.html FHIR-rdf]; [http://yosemiteproject.org/2015/webinars/fhir-rdf/ The Yosemite Project]
::[http://hl7-fhir.github.io/rdf.html FHIR.rdf]
 
9:45-10:00 '''Break'''


1pm-3pm
10:00-12:00
* '''EHR and ontology'''
* '''EHR and ontology'''
** Peter Elkin (Buffalo): Ontologies driving EHRs
** Peter Elkin (Buffalo): Ontologies driving EHRs [http://ncor.buffalo.edu/2015/CTSO/Elkin.pptx Slides]
** Bill Hogan and Amanda Hicks (Florida): Continuity of Care Document & RDF/OWL
** Jonathan P. Bona (Buffalo): Toward replacing EHR structured data with explicit representations [http://ncor.buffalo.edu/2015/CTSO/bona.pdf Slides]
** James Overton (Knocean): Pathology Imaging Ontology
** Suzette Stoutenburg (MITRE): Applying Semantic Technology for Enhanced Electronic Health Record (EHR) Visualization [http://ncor.buffalo.edu/2015/CTSO/Stoutenburg.pptx Slides]
 
12:00-1:00 '''Lunch'''
 
1:00-2:30
* '''Ontology practices'''
** Bill Hogan and Amanda Hicks (Florida): Continuity of Care Document & RDF/OWL [http://ncor.buffalo.edu/2015/CTSO/Hogan.pptx Slides]
** Ludger Jansen (Universität Rostock): Good Ontology Design: Philosophical and Empirical Perspectives [http://ncor.buffalo.edu/2015/CTSO/Jansen.pdf Slides]
 
2:30-2:45 '''Break'''


3:15-4:15
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  
** Helen Moore, Ping Guan (NIH/NCI): [http://biospecimens.cancer.gov/newsevents/news/07172015.asp CDR, an NCI-developed vocabulary and database for biobanking] [http://ncor.buffalo.edu/2015/CTSO/Moore.ppt Slides]
** Helena Ellis (Duke): [http://biobank.duke.edu/biobanking-informatics/labvantage-biobanking-information-management-system Biobank terminology in practice]
** Helena Ellis (Duke): [http://biobank.duke.edu/biobanking-informatics/labvantage-biobanking-information-management-system Biobank terminology in practice] [http://ncor.buffalo.edu/2015/CTSO/Ellis.pdf Slides]
** Chris Stoeckert, Jie Zheng (Penn): and Mathias Brochhausen (Arkansas): The [http://www.ontobee.org/browser/index.php?o=OBIB OBIB] Ontology for Biobanking [http://ncor.buffalo.edu/2015/CTSO/Stoeckert.pptx Slides]
 
7:00-9:00 '''Dinner (separate registration - Optional.) [[#More Information]] below.'''


'''Day 2'''
<font size="+1" style="color: blue">'''Day 2: Fri 9/25/2015'''</font>


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 [http://ncor.buffalo.edu/2015/CTSO/Diehl.pptx Slides]
** Alan Ruttenberg (Buffalo): Using Semantic Web tools to analyse ontology-structured dental records
** Aaron Abend ([http://www.aarda.org/ AARDA, Inc]): Developing an Ontology for Autoimmune Disease: A key step to a unified view of [https://en.wikipedia.org/wiki/Autoimmune_disease autoimmune disease] [http://ncor.buffalo.edu/2015/CTSO/Abend.pptx Slides]
** Csilla Farkas (University of SC): Medical Data Protection:  Semantics-Aware Security Policies
 
9:45-10:00 '''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] [http://ncor.buffalo.edu/2015/CTSO/Manion.ppt Slides]
** Asiyah Yu Lin (Michigan/FDA) [https://code.google.com/p/ico-ontology/ Informed Consent Ontology with focus on Vaccine Informed Consent Ontology]  
** Asiyah Yu Lin (Michigan/FDA): [https://github.com/VICO-ontology/ Informed Consent Ontology with focus on Vaccine Informed Consent Ontology (VICO)] [http://ncor.buffalo.edu/2015/CTSO/Lin.pptx Slides]
** Mathias Brochhausen (Arkansas) Documents and Document Acts
** Mathias Brochhausen (Arkansas) Documents and Document Acts [http://ncor.buffalo.edu/2015/CTSO/Brochhausen.pptx Slides]


1pm to 3pm
12:00-1:00 '''Lunch'''
* '''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 ==
1:00-3:00
Sivaram Arabandi (OntoPro)
* '''Clinical and Translational Science Relevant projects'''
** Dave Eichmann (University of Iowa): The Pragmatics of Ontology and Heterogeneous Data Sources: the Ins and Outs of [http://research.icts.uiowa.edu/polyglot/ CTSAsearch] [http://ncor.buffalo.edu/2015/CTSO/Eichmann.pptx Slides]
** Geoff Low (Medidata Solutions): From PDF to RDF - Representing the CDISC Foundational Standards [http://ncor.buffalo.edu/2015/CTSO/Low.pptx Slides]
** Sriram Sridhar and Santosh Srinivasaiah (BAH) Enhancing Scientific and Clinical Data Management Using Semantic Technologies [http://ncor.buffalo.edu/2015/CTSO/Sridhar.pdf Slides]
** Closing remarks


David Booth (FHIR)
== Participant list ==
Abend, Aaron  (AARDA Inc)


Mathias Brochhausen (University of Arkansas for Medical Sciences)
Arabandi, Sivaram  (OntoPro)


Alex Diehl (University at Buffalo)
Awaysheh, Abdullah  (Virginia Tech)


David Eichmann (University at Iowa)
Bona, Jonathan  (University at Buffalo)


Peter Elkin (University at Buffalo)
Booth, David  (FHIR)


Helena Ellis (Duke University)
Boyles, Rebecca  (NIE Health Sciences Inst.)


Fernanda Farinelli (University at Buffalo)
Brochhausen, Mathias  (University of Arkansas (Med Sci))


Amanda Hicks (University of Florida)
Carson, Matthew  (Northwestern University)


William Hogan (University of Florida)
Daniels, Mark  (MUSC)
 
Diehl, Alexander  (University at Buffalo)
 
Dolan, Mary (The Jackson Laboratory)
 
Duncan, Bill  (Regenstrief Institute)
 
Eichmann, David  (Univ at Iowa)
 
Elkin, Peter  (University at Buffalo)
 
Ellis, Helena  (Duke University)
 
Esposito, John  (TriNetX)
 
Facelli, Julio  (University of Utah)
 
Farinelli, Fernanda  (Univ at Buffalo)
 
Farkas, Csilla  (University of SC)
 
Frey, Lewis (MUSC)
 
Gibson, Bryan  (University of Utah)
 
Guan, Ping  (Nat. Cancer Institutes)
 
Habrat, Melissa  (MUSC)
 
Hammond, William E.  (Duke University)
 
Hanna, Joshua  (University of Florida)
 
Harris, Marcy  (University of Michigan)
 
Hicks, Amanda  (University of Florida)
 
Hogan, William  (University of Florida)
 
Holmgren, Stephanie  (NIH)
 
Jansen, Ludger  (Univ of Rostock)
 
Kamerick, Michael  (TrinetX Inc)
 
Landis-Lewis, Zach  (Univ of Michigan)
 
Larsen, Rick  (HSSC)
 
Lin, Asiyah Yu  (University of Michigan Ann Arb)
 
Low, Geoffrey  (Medidata Solutions UK)
 
Manion, Frank J.  (University of Michigan)
 
Marshall, Elizabeth  (MUSC)
 
Masci, Anna Maria  (Duke University)
 
Meeks, Eric  (University of California-SF)
 
Mockus, Susan  (Jackson Lab Farmington CT)
 
Moore, Helen  (National Cancer Institutes)
 
Natale, Darren  (Georgetown University)
 
Obeid, Jihad  (MUSC)
 
Richesson, Rachel  (Duke University)
 
Rodman, Daniel  (University at Buffalo)
 
Schick, Lisa  (Samvit Solutions)
 
Seppälä, Selja  (University at Buffalo)
 
Smith, Barry  (University at Buffalo)
 
Soergel, Dagobert  (University at Buffalo)
 
Sridhar, Sriram  (BAH)


Ludger Jansen (University of Rostock)
Srinivasaiah, Santosh  (BAH)


Jihad Obeid (Medical University of South Carolina)
Steele, Robert  (MUSC)


James Overton (Knocean)
Stoeckert, Christian  (University of Pennsylvania)


Alan Ruttenberg (University at Buffalo)
Stoutenburg, Suzette  (MITRE Corporation)


Barry Smith (University at Buffalo)
Stratman, Jennifer  (Duke University )


Dagobert Sorgel (University at Buffalo)
Welch, Brandon (MUSC)


Chris Stoeckert (University of Pennsylvania)
Xu, Julia  (NYU)


Asiyah Yu Lin (University of Michigan, Ann Arbor)
Zheng, Jie  (University of Pennsylvania)


Jie Zheng (University of Pennsylvania)
Zhu, Vivienne (MUSC)


== Organizing Committee ==
== Organizing Committee ==
Line 139: Line 229:


Jihad Obeid (Medical University of South Carolina) (Chair)
Jihad Obeid (Medical University of South Carolina) (Chair)
== More Information ==
[[File:CharlestonBluesBBQ2015.jpg|link=|right|Charleston Harbor cruise]]
The Charleston Blues & BBQ Harbor Cruise starts at 7pm on Thursday 9/24 night and includes dinner. This trip is optional and requires a separate registration directly with '''Charleston Harbor Tours'''. To get the '''group rate of $38.95''' please call '''843-722-1112''' and use the Group Rate for '''"MUSC Biomedical Informatics"'''. Note that registration online at their site will NOT give you the group rate.
More info at [http://www.charlestonharbortours.com/main/specialevent/27#.VddjUJeYAXY Harbor Cruise and Thursday Night Dinner]

Latest revision as of 15:05, 18 November 2022


Ontology in Practice

The Fourth Clinical and Translational Science Ontology Workshop

For the 2023 meeting please see CTS Ontology Workshop 2023.

September 23 - 25, Charleston, SC

Charleston

Venue

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

Starts: Wed 9/23/15 at 6pm with an optional reception. The workshop begins at 8am Thu 9/24/15.

Ends: Fri 9/25/2015 3pm

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.

Our Sponsors

TriNetX            HSSC            SCTR


NCOR            Protein Ontology Consortium            DBMI

Agenda

Conference Brochure

Evening before the Conference: Wed 9/23/15

6:00pm - 7:00pm

  • Evening reception

Day 1: Thu 9/24/15

8:00-9:45

  • Fast Healthcare Interoperability Resources (FHIR)
    • David Booth (FHIR): An introduction to FHIR Slides
    • Barry Smith (Buffalo): FHIR and Ontology Slides Video
Background: FHIR; FHIR-rdf; The Yosemite Project

9:45-10:00 Break

10:00-12:00

  • EHR and ontology
    • Peter Elkin (Buffalo): Ontologies driving EHRs Slides
    • Jonathan P. Bona (Buffalo): Toward replacing EHR structured data with explicit representations Slides
    • Suzette Stoutenburg (MITRE): Applying Semantic Technology for Enhanced Electronic Health Record (EHR) Visualization Slides

12:00-1:00 Lunch

1:00-2:30

  • Ontology practices
    • Bill Hogan and Amanda Hicks (Florida): Continuity of Care Document & RDF/OWL Slides
    • Ludger Jansen (Universität Rostock): Good Ontology Design: Philosophical and Empirical Perspectives Slides

2:30-2:45 Break

2:45-4:15

7:00-9:00 Dinner (separate registration - Optional.) #More Information below.

Day 2: Fri 9/25/2015

8:00-9:45

  • Practical examples of ontology use
    • Alexander Diehl (Buffalo): Using an applied neurology ontology framework for analysis of MS patient data Slides
    • Aaron Abend (AARDA, Inc): Developing an Ontology for Autoimmune Disease: A key step to a unified view of autoimmune disease Slides
    • Csilla Farkas (University of SC): Medical Data Protection: Semantics-Aware Security Policies

9:45-10:00 Break

10:00-12:00

12:00-1:00 Lunch

1:00-3:00

  • Clinical and Translational Science Relevant projects
    • Dave Eichmann (University of Iowa): The Pragmatics of Ontology and Heterogeneous Data Sources: the Ins and Outs of CTSAsearch Slides
    • Geoff Low (Medidata Solutions): From PDF to RDF - Representing the CDISC Foundational Standards Slides
    • Sriram Sridhar and Santosh Srinivasaiah (BAH) Enhancing Scientific and Clinical Data Management Using Semantic Technologies Slides
    • Closing remarks

Participant list

Abend, Aaron (AARDA Inc)

Arabandi, Sivaram (OntoPro)

Awaysheh, Abdullah (Virginia Tech)

Bona, Jonathan (University at Buffalo)

Booth, David (FHIR)

Boyles, Rebecca (NIE Health Sciences Inst.)

Brochhausen, Mathias (University of Arkansas (Med Sci))

Carson, Matthew (Northwestern University)

Daniels, Mark (MUSC)

Diehl, Alexander (University at Buffalo)

Dolan, Mary (The Jackson Laboratory)

Duncan, Bill (Regenstrief Institute)

Eichmann, David (Univ at Iowa)

Elkin, Peter (University at Buffalo)

Ellis, Helena (Duke University)

Esposito, John (TriNetX)

Facelli, Julio (University of Utah)

Farinelli, Fernanda (Univ at Buffalo)

Farkas, Csilla (University of SC)

Frey, Lewis (MUSC)

Gibson, Bryan (University of Utah)

Guan, Ping (Nat. Cancer Institutes)

Habrat, Melissa (MUSC)

Hammond, William E. (Duke University)

Hanna, Joshua (University of Florida)

Harris, Marcy (University of Michigan)

Hicks, Amanda (University of Florida)

Hogan, William (University of Florida)

Holmgren, Stephanie (NIH)

Jansen, Ludger (Univ of Rostock)

Kamerick, Michael (TrinetX Inc)

Landis-Lewis, Zach (Univ of Michigan)

Larsen, Rick (HSSC)

Lin, Asiyah Yu (University of Michigan Ann Arb)

Low, Geoffrey (Medidata Solutions UK)

Manion, Frank J. (University of Michigan)

Marshall, Elizabeth (MUSC)

Masci, Anna Maria (Duke University)

Meeks, Eric (University of California-SF)

Mockus, Susan (Jackson Lab Farmington CT)

Moore, Helen (National Cancer Institutes)

Natale, Darren (Georgetown University)

Obeid, Jihad (MUSC)

Richesson, Rachel (Duke University)

Rodman, Daniel (University at Buffalo)

Schick, Lisa (Samvit Solutions)

Seppälä, Selja (University at Buffalo)

Smith, Barry (University at Buffalo)

Soergel, Dagobert (University at Buffalo)

Sridhar, Sriram (BAH)

Srinivasaiah, Santosh (BAH)

Steele, Robert (MUSC)

Stoeckert, Christian (University of Pennsylvania)

Stoutenburg, Suzette (MITRE Corporation)

Stratman, Jennifer (Duke University )

Welch, Brandon (MUSC)

Xu, Julia (NYU)

Zheng, Jie (University of Pennsylvania)

Zhu, Vivienne (MUSC)

Organizing Committee

Barry Smith (University at Buffalo)

William Hogan (University of Florida)

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

More Information

Charleston Harbor cruise

The Charleston Blues & BBQ Harbor Cruise starts at 7pm on Thursday 9/24 night and includes dinner. This trip is optional and requires a separate registration directly with Charleston Harbor Tours. To get the group rate of $38.95 please call 843-722-1112 and use the Group Rate for "MUSC Biomedical Informatics". Note that registration online at their site will NOT give you the group rate.

More info at Harbor Cruise and Thursday Night Dinner

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