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


* Please register [https://sctrweb2.musc.edu/CTS_Ontology_Registration.html here]
'''Day 1 (afternoon) and Day 2''' will focus on applications in translational research.


* Hotel [https://bookings.ihotelier.com/bookings.jsp?groupID=1419298&hotelID=76320 group rate booking]
== '''Our Sponsors''' ==


</font>
[[File:TriNetX.png|link=http://trinetx.com/|TriNetX]]    &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp;
[[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]]


== '''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.  
[[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]]


'''Day 1 (afternoon) and Day 2''' will focus on applications in translational research.
== Agenda ==
[http://ncor.buffalo.edu/2015/CTSO/CTS_Ontology_booklet.pdf Conference Brochure]


== Draft Agenda ==
'''Evening before the Conference: Wed 9/23/15 '''
'''Evening before the Conference: Wed 9/23/15 '''
5:00pm - 6:00pm
 
* Evening reception in Lobby Bar
6:00pm - 7:00pm
* '''Evening reception '''
   
   
'''Day 1: Thu 9/24/15'''
<font size="+1" style="color: blue">'''Day 1: Thu 9/24/15'''</font>


8:00-9:45
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
9:45-10:00 '''Break'''


10:00-12:00
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]
** Jonathan P. Bona (Buffalo) Toward replacing EHR structured data with explicit representations
** Jonathan P. Bona (Buffalo): Toward replacing EHR structured data with explicit representations [http://ncor.buffalo.edu/2015/CTSO/bona.pdf Slides]
** Bill Hogan and Amanda Hicks (Florida): Continuity of Care Document & RDF/OWL
** 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
12:00-1:00 '''Lunch'''


1:00-2:30
1:00-2:30
* '''Ontology practices'''
* '''Ontology practices'''
** James Overton (Knocean): Pathology Imaging Ontology
** 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
** 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
2:30-2:45 '''Break'''


2:45-4:15
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]


'''Day 2: Fri 9/25/2015'''
7:00-9:00 '''Dinner (separate registration - Optional.) [[#More Information]] below.'''
 
<font size="+1" style="color: blue">'''Day 2: Fri 9/25/2015'''</font>


8:00-9:45
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


945-10 Break
9:45-10:00 '''Break'''


10:00-12:00
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]


12:00-1:00 Lunch
12:00-1:00 '''Lunch'''


1:00-3:00
1:00-3:00
* '''Clinical and Translational Science Relevant projects'''
* '''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
** 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]
** Interoperability between OBO foundry and other ontologies and (e.g. SNOMED, LOINC, NCI Thesaurus, ICD-9/10, RxNorm)
** Geoff Low (Medidata Solutions): From PDF to RDF - Representing the CDISC Foundational Standards [http://ncor.buffalo.edu/2015/CTSO/Low.pptx Slides]
** Geoff Low (Medidata Solutions) From PDF to RDF - Representing the CDISC Foundational Standards
** 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


== Participant list ==
== Participant list ==
Abend, Aaron (AARDA, Inc)
Abend, Aaron (AARDA Inc)
 
Arabandi, Sivaram  (OntoPro)
 
Awaysheh, Abdullah  (Virginia Tech)


Arabani, Sivaram (OntoPro)
Bona, Jonathan  (University at Buffalo)


Booth, David (FHIR)
Booth, David (FHIR)


Boyles, Rebecca (NIE Health Sciences Inst.)
Boyles, Rebecca (NIE Health Sciences Inst.)


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


Carson, Matthew (Northwestern University)
Carson, Matthew (Northwestern University)


Diehl, Alexander (Univ at Buffalo)
Daniels, Mark  (MUSC)
 
Diehl, Alexander (University at Buffalo)


Dolan, Mary (The Jackson Laboratory)
Dolan, Mary (The Jackson Laboratory)


Duncan, Bill (Regenstrief Institute)
Duncan, Bill (Regenstrief Institute)


Eichmann, David (Univ at Iowa)
Eichmann, David (Univ at Iowa)


Ellis, Hellena (Duke University)
Elkin, Peter  (University at Buffalo)


Esposito, John (TriNetX)
Ellis, Helena  (Duke University)


Facelli, Julio (University of Utah)
Esposito, John  (TriNetX)


Farinelli, Fernanda (Univ at Buffalo)
Facelli, Julio  (University of Utah)


Gibson, Bryan (University of Utah)
Farinelli, Fernanda  (Univ at Buffalo)


Harris, Marcy (Univ of Michigan)
Farkas, Csilla  (University of SC)


Hicks, Amanda (Univ of Florida)
Frey, Lewis (MUSC)


Hogan, William (Univ of Florida)
Gibson, Bryan  (University of Utah)


Holmgren, Stephanie (NIH)
Guan, Ping  (Nat. Cancer Institutes)


Jansen, Ludger (Univ of Rostock)
Habrat, Melissa  (MUSC)


Lin, Yu (Univ of Michigan Ann Arb)
Hammond, William E.  (Duke University)


Low, Geoffrey (Medidata Solutions, UK)
Hanna, Joshua  (University of Florida)


Manion, Frank (Univ of Michigan)
Harris, Marcy  (University of Michigan)


Meeks, Eric (Univ of California-SF)
Hicks, Amanda  (University of Florida)


Mockus, Susan (Jackson Lab,Farmington CT)
Hogan, William  (University of Florida)


Seppala, Selja (University at Buffalo)
Holmgren, Stephanie  (NIH)


Smith, Barry (Univ at Buffalo)
Jansen, Ludger  (Univ of Rostock)


Soergel, Dagobert (University at Buffalo)
Kamerick, Michael  (TrinetX Inc)


Stoeckert, Christian (Univ of Pennsylvania)
Landis-Lewis, Zach  (Univ of Michigan)


Stoutenburg, Suzette (MITRE Corporation)
Larsen, Rick  (HSSC)


Xu, Julia (NYU)
Lin, Asiyah Yu  (University of Michigan Ann Arb)


Zheng, Jie (Univ of Pennsylvania)
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 ==
== Organizing Committee ==
Line 166: 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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