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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>
Line 13: Line 14:
<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
</font>
== '''Registration''' ==
<font size="+1">Registration is now open.
There is a $80 registration fee to support venue expenses and conference meals.
* Please register [https://sctrweb2.musc.edu/CTS_Ontology_Registration.html here].
* Hotel [https://bookings.ihotelier.com/bookings.jsp?groupID=1419298&hotelID=76320 group rate booking]. (Group rate available until 8/24.)
* Charleston Harbor Cruise and Dinner (optional) [[#More Information]] below.


</font>
</font>
Line 39: Line 27:
'''Day 1 (afternoon) and Day 2''' will focus on applications in translational research.
'''Day 1 (afternoon) and Day 2''' will focus on applications in translational research.


== '''Sponsors''' ==
== '''Our Sponsors''' ==


Coming soon...
[[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]]


== Draft Agenda ==
<font size="+1" style="color: blue">'''Evening before the Conference: Wed 9/23/15 '''</font>


5:00pm - 6:00pm
[[File:Ncor-logo.jpg|link=http://ncor.buffalo.edu/|NCOR]]    &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp;
* '''Evening reception in Lobby Bar'''
[[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]]
 
== Agenda ==
[http://ncor.buffalo.edu/2015/CTSO/CTS_Ontology_booklet.pdf Conference Brochure]
 
'''Evening before the Conference: Wed 9/23/15 '''
 
6:00pm - 7:00pm
* '''Evening reception '''
   
   
<font size="+1" style="color: blue">'''Day 1: Thu 9/24/15'''</font>
<font size="+1" style="color: blue">'''Day 1: Thu 9/24/15'''</font>
Line 53: Line 50:
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 (Background info [http://www.interfaceware.com/blog/taking-fhir/ FHIR],  [http://hl7-fhir.github.io/rdf.html FHIR-rdf])
** 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: [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]


9:45-10:00 '''Break'''
9:45-10:00 '''Break'''
Line 60: Line 58:
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]
** Suzette Stoutenburg (MITRE) Applying Semantic Technology for Enhanced Electronic Health Record (EHR) Visualization
** 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'''
Line 68: Line 66:
1:00-2:30
1:00-2:30
* '''Ontology practices'''
* '''Ontology practices'''
** Bill Hogan and Amanda Hicks (Florida): Continuity of Care Document & RDF/OWL
** Bill Hogan and Amanda Hicks (Florida): Continuity of Care Document & RDF/OWL [http://ncor.buffalo.edu/2015/CTSO/Hogan.pptx Slides]
** James Overton (Knocean): Pathology Imaging Ontology
** Ludger Jansen (Universität Rostock): Good Ontology Design: Philosophical and Empirical Perspectives [http://ncor.buffalo.edu/2015/CTSO/Jansen.pdf Slides]
** Ludger Jansen (Universität Rostock): Good Ontology Design: Philosophical and Empirical Perspectives


2:30-2:45 '''Break'''
2:30-2:45 '''Break'''
Line 76: Line 73:
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]
** Helen Moore, Ping Guan (NIH/NCI): [http://biospecimens.cancer.gov/newsevents/news/07172015.asp CDR, an NCI-developed vocabulary and database for biobanking]
** 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]
** Helena Ellis (Duke): [http://biobank.duke.edu/biobanking-informatics/labvantage-biobanking-information-management-system Biobank terminology in practice]
** 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.'''
7:00-9:00 '''Dinner (separate registration - Optional.) [[#More Information]] below.'''
Line 86: Line 83:
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'''
Line 101: Line 99:
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]
** Geoff Low (Medidata Solutions) From PDF to RDF - Representing the CDISC Foundational Standards
** Geoff Low (Medidata Solutions): From PDF to RDF - Representing the CDISC Foundational Standards [http://ncor.buffalo.edu/2015/CTSO/Low.pptx Slides]
** Sriram Sridhar (BAH) Enhancing Scientific and Clinical Data Management Using Semantic Technologies
** Sriram Sridhar and Santosh Srinivasaiah (BAH) Enhancing Scientific and Clinical Data Management Using Semantic Technologies [http://ncor.buffalo.edu/2015/CTSO/Sridhar.pdf Slides]
** Wrap-up session.
** Closing remarks


== Participant list ==
== Participant list ==
Abend, Aaron (AARDA, Inc)
Abend, Aaron (AARDA Inc)


Arabani, Sivaram (OntoPro)
Arabandi, Sivaram (OntoPro)


Booth, David (FHIR)
Awaysheh, Abdullah  (Virginia Tech)


Boyles, Rebecca (NIE Health Sciences Inst.)
Bona, Jonathan  (University at Buffalo)


Brochhausen, Mathias (Univ of Arkansas (Med Sci))
Booth, David  (FHIR)


Carson, Matthew (Northwestern University)
Boyles, Rebecca  (NIE Health Sciences Inst.)


Diehl, Alexander (Univ at Buffalo)
Brochhausen, Mathias  (University of Arkansas (Med Sci))
 
Carson, Matthew  (Northwestern University)
 
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)
 
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)


Eichmann, David (Univ at Iowa)
Low, Geoffrey  (Medidata Solutions UK)


Ellis, Hellena (Duke University)
Manion, Frank J.  (University of Michigan)


Esposito, John (TriNetX)
Marshall, Elizabeth  (MUSC)


Facelli, Julio (University of Utah)
Masci, Anna Maria  (Duke University)


Farinelli, Fernanda (Univ at Buffalo)
Meeks, Eric  (University of California-SF)


Gibson, Bryan (University of Utah)
Mockus, Susan  (Jackson Lab Farmington CT)


Harris, Marcy (Univ of Michigan)
Moore, Helen  (National Cancer Institutes)


Hicks, Amanda (Univ of Florida)
Natale, Darren  (Georgetown University)


Hogan, William (Univ of Florida)
Obeid, Jihad  (MUSC)


Holmgren, Stephanie (NIH)
Richesson, Rachel  (Duke University)


Jansen, Ludger (Univ of Rostock)
Rodman, Daniel  (University at Buffalo)


Lin, Yu (Univ of Michigan Ann Arb)
Schick, Lisa  (Samvit Solutions)


Low, Geoffrey (Medidata Solutions, UK)
Seppälä, Selja  (University at Buffalo)


Manion, Frank (Univ of Michigan)
Smith, Barry  (University at Buffalo)


Meeks, Eric (Univ of California-SF)
Soergel, Dagobert  (University at Buffalo)


Mockus, Susan (Jackson Lab,Farmington CT)
Sridhar, Sriram  (BAH)


Natale, Darren (Georgetown)
Srinivasaiah, Santosh  (BAH)


Richesson, Rachel (Duke University)
Steele, Robert  (MUSC)


Seppala, Selja (University at Buffalo)
Stoeckert, Christian  (University of Pennsylvania)


Smith, Barry (Univ at Buffalo)
Stoutenburg, Suzette  (MITRE Corporation)


Soergel, Dagobert (University at Buffalo)
Stratman, Jennifer  (Duke University )


Stoeckert, Christian (Univ of Pennsylvania)
Welch, Brandon (MUSC)


Stoutenburg, Suzette (MITRE Corporation)
Xu, Julia  (NYU)


Xu, Julia (NYU)
Zheng, Jie  (University of Pennsylvania)


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


== Organizing Committee ==
== Organizing Committee ==
Line 185: Line 233:
[[File:CharlestonBluesBBQ2015.jpg|link=|right|Charleston Harbor cruise]]
[[File:CharlestonBluesBBQ2015.jpg|link=|right|Charleston Harbor cruise]]


The Charleston Harbor cruise starts at 7pm on Thursday 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.
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]
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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