View source for Ontology for Precision Medicine: From Genomes to Public Health

<span style="font-size:150%">Seventh Clinical and Translational Science Ontology Workshop</span>

== '''Announcement''' ==

'''The Clinical and Translational Science Ontology Group (CTSOG)''' invites you to join us on February 20-21, 2019 in Orlando, Florida 

The hotel block is available: use this [https://www.marriott.com/event-reservations/reservation-link.mi?id=1543505145775&key=GRP&app=resvlink link] to reserve your hotel room.

''We are happy to announce as keynote speaker:''

* '''Janna Hastings (Babraham Institute, Cambridge, UK)'''  speaking on ''Can ontologies help overcome the impasse in mental health research?''

[[File:JannaHastings_OntologyPrecisionHealthWorkshop.png]]

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== '''Organizers''' == 

[https://hobi.med.ufl.edu/about/faculty-directory-2/hogan-bill/ William Hogan] (University of Florida, Gainesville, FL), hoganwr@ufl.edu 

[http://ontology.buffalo.edu/smith Barry Smith] (University at Buffalo, Buffalo, NY), phismith@buffalo.edu

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== '''Background''' ==

From genomes to public health, newer and larger datasets are increasingly available to inform precision approaches to the treatment and prevention of disease and disorders. Managing these datasets--especially their integration--for everything from managing the opioid epidemic to the learning health system to translational science--requires more and better ontologies.  This workshop will briefly survey the state-of-the-art in ontology at the nexus of these trends, identify needs and opportunities for future work and collaborations, and develop one or more white papers charting the course for the future, including a set of recommendations for key stakeholders.

If you are interested in presenting cutting edge work in this area, please email a brief presentation proposal to Barry Smith (phismith@buffalo.edu) and Bill Hogan (hoganwr@ufl.edu).  We are primarily interested in ontology, but also are interested to hear from experts in the CTSA network working in a diverse range of areas, from precision medicine, to the opioid epidemic, to precision public health.

For earlier meetings in the CTS Ontology Workshop series see [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group here].

Persons interested in attending or in presenting at the meeting should write to [mailto:hoganwr@ufl.edu].

== '''Sponsors''' == 

[http://ncor.us National Center for Ontological Research]

[https://hobi.med.ufl.edu/biomedical-informatics/ University of Florida Division of Biomedical Informatics]

[https://www.ctsi.ufl.edu/ University of Florida Clinical and Translational Science Institute]

== '''Date'''  ==

February 20 (Wednesday) - 21 (Thursday), 2019

== '''Venue'''==

Venue: <b>Meyer-Clementine (main lobby area behind Zest Restaurant)</b>, Sheraton Lake Buena Vista Resort

12205 S Apopka Vineland Rd, Orlando, FL 32836

A block of rooms is available: use this [https://www.marriott.com/event-reservations/reservation-link.mi?id=1543505145775&key=GRP&app=resvlink link] to reserve your hotel room.

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=='''Schedule Day 1: February 20'''==

<b>Wednesday Morning</b>

8:00am: Registration and Breakfast

8:45am: Session: An Agenda for Ontology in Pursuit of the Precision Health

* William Hogan: [https://buffalo.box.com/s/s36qhxqlbu51eytf0ys7zub0gblkhy6k Introduction to the Meeting, and a Proposed Agenda for Ontology for Precision Health]
* Peter Elkin: [https://buffalo.box.com/s/vy4ztzfop51awsrrhkuoudbma72cxr1q How Ontology can be used to Direct Treatment for the Opioid Epidemic]
* Michael Sinclair: [https://buffalo.box.com/s/9cp2dk4vqr7nxkk3nuyn1z3htds7d91h Cross Products for Clinical Information Retrieval from the Human Disease Ontology]

10:00-10:30am: Break

10:30-12:15pm: The Role of Ontology in Addressing the Opioid Crisis

* Mathias Brochhausen: [https://buffalo.box.com/s/9cp2dk4vqr7nxkk3nuyn1z3htds7d91h Making Opioid Use Data Discoverable]
* William Hogan: [https://buffalo.box.com/s/a4eu07nmgzz56dcuw10hpxou6k9etcr9 Drug Ontology for Opioid Research]
* Stuart Nelson: [https://buffalo.box.com/s/ld0o12zxgspj11kgywzlvgt267doimkz A Feasibility Study of a Therapeutic Intent Ontology]

Therapeutic intent can be thought of as the reason for commencing a therapy, not just a disease being treated, but the context in which the therapy is appropriate.  We are investigating if it is possible to represent the therapeutic intent as seen in drug indications in the Structured Product Label approved by the FDA in a formal, computable manner, using standard controlled vocabularies and an upper level application ontology.

12:15: Lunch
 
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<b>Wednesday Afternoon </b>

1:00pm: Session: Applications of Ontology in Precision Medicine and Precision Public Health

* Jiang Bian: [https://buffalo.box.com/s/ufjqwy26g7xt4n6uesdmihrm7jhjwq9q An Ontology-Driven Data Integration Framework for Analysis of Cancer Risk Factor Data]

Barriers to linking, integrating, and efficiently exploiting health information across different sites and domains slow down healthcare research and the development of precision health programs.  The effort required to connect different sources is substantial due at least in part to the lack of clear definitions (i.e. data semantics) of variables, measures, and constructs, but it can be eased by semantic interoperability via an ontology-driven data infrastructure.  In this talk, we will discuss our initial attempts to build a semantic data integration framework through ontology-driven data access framework and its use cases.

* Chris Stoeckert: [https://buffalo.box.com/s/secs9u2hoozag1b97590g0by8mozomv8 Penn TURBO for Patient Profiles and Precision Medicine]
* Oliver He: [https://buffalo.box.com/s/rkfi4iyv79e4cuomx8u9ddu9luwdl5yq Developing and Using Ontologies for Precision Medicine in Kidney Disease]
* Matt Diller: [https://buffalo.box.com/s/iaeigy7zrot0jqkpho7syge7crx2zcb3 An Ontological Analysis of Symbiotic Interactions]

3:00pm: Break

3:30pm:  Session

* Jonathan Bona: [https://buffalo.box.com/s/hafd3bg82p4mxl5vy5tj4ga604awdd5d Ontology-Based Representations in the Platform for Imaging in Precision Medicine (PRISM)]

The Cancer Imaging Archive (TCIA) hosts over 11 million de-identified medical images in DICOM format related to cancer for research reuse. Many TCIA collections also include diverse sets of non-image data in a variety of formats, which are difficult to interpret, integrate, and use. The PRISM (Platform for Imaging in Precision Medicine) initiative seeks to sustain and expand TCIA’s capabilities to meet the rapidly evolving requirements of cancer Precision Medicine research. This presentation highlights our work to make these TCIA non-image data more accessible and usable by transforming them into integrated semantic representations using Open Biomedical Ontologies. 

* Amanda Hicks: [https://buffalo.box.com/s/pefq5ymrxioe8rn8duyb1yxh97pxex44 More Than Ontology Reuse: Developing a Hypertension Ontology For Precision Medicine]
* Hansi Zhang: [https://buffalo.box.com/s/dyqjykc0wq8s63tmfzsgdn1c6z00s70c Computable Eligibility Criteria through Ontology-Driven Data Access]

The increasing adoption of electronic health record (EHR) systems and proliferation of clinical data offer unprecedented opportunities for cohort identification to accelerate patient recruitment. However, the effort required to translate trial eligibility criteria to the correct cohort identification queries for clinical investigators is substantial, at least in part due to the lack of clear definitions in both the free-text eligibility criteria and the data models used to structure the available data elements in target patient databases. We propose to adopt an ontology-driven data access approach that generates formal representations of the connections between the entities in eligibility criteria and the available data elements to (1) narrow the semantic gap between researchers’ cohort identification needs and the underlying database nuances, and (2) render the eligibility criteria computable.
 
4:15pm: '''Keynote address'''

''Janna Hastings: [https://buffalo.box.com/s/fsfpqsxsw5471qw3ca0n3mqybc26frh9 Can Ontologies Help Overcome the Impasse in Mental Health Research?]''

Mental health conditions, including addiction, are among the most widespread causes of disability across the developed world, yet progress towards much-needed new treatments has stalled in recent years. Mental health research is hindered by a plethora of competing and often contradictory theoretical paradigms and frameworks, dividing available resources. There is no systematic overview of what is already known, and for each new result, it is difficult to predict whether and to what extent it may be applicable outside of its own (often narrowly defined) scope. The field urgently needs new approaches, which many organisations and funding agencies are calling for. I will argue that only after truly comprehensive theory and data synthesis is possible, will we be able to start to address the challenges in mental health research, and that ontologies are essential for this to happen. I will present recent work in the Mental Functioning Ontology to provide a truly integrative framework across sociocultural and biomedical perspectives on mental health. Finally, I will argue that even beyond the domain of mental health, a new focus on mental functioning in all medical conditions is a much needed ingredient for putting the "person" into "personalized medicine".

6:30pm: Dinner

=='''Schedule Day 2: February 21'''==

<b>Thursday Morning </b>

8:00am: Registration and Breakfast

8:20am: Session: Cognitive Ontologies applied to the Representation of the Diagnostic Process

* Barry Smith: [https://buffalo.box.com/s/ajxg38z3plbt9mu5uine2iskmbnir45r What is a Mental Function?]
* David Limbaugh: [https://buffalo.box.com/s/yz5hbri1iir0rlku8lro53qqjrwd8d12 The Cognitive Process Ontology and Its Application to Medical Diagnosis]

9:30-9:45am: Break

9:45am: Panel Discussion: The Role of Ontology in Contributing to Solving the Opioid Crisis

12:15pm:  Lunch

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<b>Thursday - Afternoon</b>

1:00pm: Working session: Setting the agenda for ontology in precision health and next steps

4:00pm: ''Close''

=='''Rationale'''==

== '''Goals'''==

== '''Participants will include''' ==

Rehab Alhasani (Montreal, Canada)

Farzaneh Ashrafi (SNOMED, London, UK)

Jiang Bian (Gainesville, FL)

Matthias Brochhausen (Little Rock, Arkansas)

David Buckeridge (Montreal, Canada)

Mike Cisnero-Franco (Montreal, Canada)

Michael Conlon (Gainesville, FL)

Lindsay Cowell (Dallas, TX)

Matthew Diller (Gainesville, FL)

Peter Elkin (Buffalo, NY)

Janna Hastings (Cambridge, UK)

Oliver He (Ann Arbor, MI)

Amanda Hicks (Gainesville, FL)

William Hogan (Gainesville, FL)

Hyeoneui Kim (Durham, NC)

David Limbaugh (Buffalo, NY)

Alex Loiacono (Gainesville, FL)

Matthew McConnell (Gainesville, FL)

Tona Mendoza (Gainesville, FL)

Mark Miller (Philadelphia, PA)

Stuart J. Nelson (Albuquerque, NM)

Jihad Obeid (Charleston, SC)

Anna Okhmatovskaia (Montreal, Canada)

Michael Sinclair (Baltimore, MD)

Barry Smith (Buffalo, NY)

Suzanne Santamaria (SNOMED, London, UK)

Chris Stoeckert (U Penn, PA)

Sonya White (Gainesville, FL)

Hansi Zhang (Gainesville, FL)