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Past Projects

OPMQoL: an ontology for pain and related disability, mental health and quality of life.

   
(July 2011 - July 2014)
Supported by the National Institute of Dental and Craniofacial Research (NIH) grant 1 R01 DE021917-01A1
(Press release, video)

The goal of this project was to obtain better insight into the complexity of pain disorders, specifically concerning the assessment of different pain types as well as pain-related disablement and its association with mental health and quality of life. The short-term was to integrate five existing datasets that broadly encompass the major types of pain (orofacial pains, temporomandibular disorder pain, headache) recognized to occur in the oral and associated regions and incorporating a broad array of measures consistent with a biopsychosocial perspective regarding pain.
The datasets cover the same domain, but are distinct in various respects:
(1) some variables are identical across datasets, others involving, for instance, somatization, depression and anxiety, are different because measured with distinct instruments;
(2) the data exhibit different levels of granularity;
(3) because of their distinct origins (US, UK, Sweden, Israel, and Germany), the datasets incorporate cultural influences related to pain report that have an impact on the comparability of the data sets, despite the use of common instruments.
Referent Tracking was used to describe the datasets in a uniform and formal way, thereby using principles general enough to include other datasets in the same domain once they become available.

Related literature

  • Smith B, Ceusters W, Goldberg LJ, Ohrbach R. Towards an Ontology of Pain. In: Mitsu Okada (ed.), Proceedings of the Conference on Logic and Ontology, Tokyo: Keio University Press, February 2011:23-32. (paper)
  • Hastings J, Ceusters W, Smith B, Mulligan K. Dispositions and processes in the Emotion Ontology. International Conference on Biomedical Ontology, Buffalo NY, July 28-30, 2011:71-78. (paper)
  • Nixdorf D, Drangsholt M, Ettlin D, Gaul C, de Leeuw R, Svensson P, Zakrzewska J, DeLaat A, Ceusters W. Classifying orofacial pains: a new proposal of taxonomy based on ontology. Journal of Oral Rehabilitation 2012;39(3):161-169. (PMC3383028, paper, final draft)
  • Ceusters W. SNOMED CT's RF2: is the Future Bright? Medical Informatics Europe Conference, MIE 2011, Oslo, Norway, August 28-31, 2011. Studies in Health Technology and Informatics 2011;169:829-833. (PMC3379709, paper, response to reviewers, slides)
  • Hastings J, Ceusters W, Smith B, Mulligan K. The Emotion Ontology: enabling interdisciplinary research in the affective sciences. In: Beigl M, Christiansen H, Roth-Berghofer TR, Kofod-Petersen A, Coventry KR, Schmidtke HR (Eds.) Modeling and Using Context; Proceedings of CONTEXT 2011, Karlsruhe, Germany, September 26-30, 2011, Lecture Notes in Artificial Intelligence 6967;119-123. (slides)
  • Hastings J, le Novère N, Ceusters W, Mulligan K, Smith B. Wanting what we don't want to want; representing addiction in interoperable bio-ontologies. International Conference on Biomedical Ontology (ICBO2012), Graz, Austria, July 22-25, 2012. (paper, response to reviewers)
  • Hastings J, Ceusters W, Jensen M, Mulligan K, Smith B. Representing mental functioning: Ontologies for mental health and disease. Workshop Towards an Ontology of Mental Functioning, International Conference on Biomedical Ontology, Graz, Austria, July 22, 2012. (paper)
  • Hastings J, Ceusters W, Mulligan K, Smith B. Annotating affective neuroscience data with the Emotion Ontology. Workshop Towards an Ontology of Mental Functioning, International Conference on Biomedical Ontology, Graz, Austria, July 22, 2012. (paper)
  • Ceusters W. An Information Artifact Ontology Perspective on Data Collections and Associated Representational Artifacts. Medical Informatics Europe Conference (MIE 2012), Pisa, Italy, August 26-29, 2012,Stud Health Technol Inform 2012;180:68-72. (Pubmed, final draft, response to 'reviewers')
  • Doing-Harris K, Meystre SM, Samore M, Ceusters W. Applying Ontological Realism to Medically Unexplained Syndromes. 14th World Congress on Medical and Health Informatics (MEDINFO 2013), accepted for publication.
  • Ceusters W, Hsu CY, Smith B. Clinical Data Wrangling using Ontological Realism and Referent Tracking. International Conference on Biomedical Ontologies, ICBO 2014, Houston, Texas, Oct 6-9, 2014. (paper, response to reviewers, slides)
  • Ceusters W. Pain Assessment Terminology in the NCBO BioPortal: Evaluation and Recommendations. International Conference on Biomedical Ontologies, ICBO 2014, Houston, Texas, Oct 6-9, 2014. (paper, response to reviewers, slides, supplementary data - raw, supplementary data - analysis)
  • Ceusters W. An alternative terminology for pain assessment. In Workshop on Definitions in Ontology, International Conference on Biomedical Ontologies, ICBO 2014, Houston, Texas, Oct 7, 2014. (paper, slides)
  • Schiffman E, Ohrbach R, Truelove E, Look J, Anderson G, Goulet J-P, List T, Svensson P, Gonzalez Y, Lobbezoo F, Michelotti A, Brooks S.L, Ceusters W, Drangsholt M, Ettlin D, Gaul C, Goldberg L, Haythornthwaite J, Hollender L, Jensen R, John M.T, deLaat A, deLeeuw R, Maixner W, van der Meulen M, Murray G.M, Nixdorf D.R, Palla S, Petersson A, Pionchon P, Smith B, Visscher C.M, Zakrzewska J, Dworkin SF. Diagnostic Criteria for Temporomandibular Disorders (DC/TMD) for Clinical and Research Applications: Recommendations of the International RDC/TMD Consortium Network and Orofacial Pain Special Interest Group. Journal of Orofacial Pain and Headache 2014;28(1):6-27. (PMID:24482784)
  • Ceusters W, Michelotti A, Raphael KG, Durham J, Ohrbach R. Perspectives on Next Steps in Classification of Orofacial Pain – Part 1: Role of Ontology. Journal of Oral Rehabilitation 2015;42(12):926-41 (paper, prefinal draft).
  • Durham J, Raphael KG, Benoliel R, Ceusters W, Michelotti A, Ohrbach R. Perspectives on Next Steps in Classification of Orofacial Pain – Part 2: Role of psychosocial factors. Journal of Oral Rehabilitation 2015;42(12):942-55 (paper).
  • Ceusters W, Cibele Nasri-Heir C, Alnaas D, Cairns BE, Michelotti A, Ohrbach R. Perspectives on Next Steps in Classification of Orofacial Pain - Part 3: Biomarkers of Chronic Orofacial Pain - From Research to Clinic. Journal of Oral Rehabilitation 2015;42(12):56-66 (paper).
  • Ceusters W, Bona J. Pain in SNOMED CT: is there an anesthetic? In Zaibert, Leo (ed.) The Theory and Practice of Ontology. Palgrave MacMillan, 2016:157-185. (annotated proof)

Presentations

  • Foundations for an Ontology for pain-related disablement, mental health and quality of life (OPMQoL). Meeting on Pain and Neurological Disease Ontologies, SUNY at Buffalo, Jan 20, 2012. (slides)
  • Pain and Mental Health: a Case-Study in Information Driven Research.. Lecture as part of the Core Curriculum in Clinical And Translational Research Seminar Series (info), Buffalo, NY, February 22, 2012. (slides)
  • Assessment instruments and biomedical reality: examples in the pain domain. Ontology Dissemination Workshop, University at Buffalo, June, 13, 2012, Buffalo, NY. (slides)
  • Ontology: innovative approach to orofacial pain classification. IADR Satellite Symposium on Orofacial Pain Assessment: Classification, Biobehavior, QST, and Biomarkers, March 19, 2013, Seattle, WA. (abstract, slides)
  • A common framework for representing data and what they are about. Ontology seminar, April 1, 2013, Dept. of Philosophy, University at Buffalo, Buffalo, NY. (abstract, slides, recording)
  • Ontology, TMD and beyond; Principles for Taxonomy Development. ACTTION-APS Pain Taxonomy Meeting, Westin Annapolis, Annapolis, MD, July-18-19, 2014. (slides)
  • Data Dictionaries for Pain and Chronic Conditions Ontology. Investigators Meeting on Chronic Overlapping Pain Conditions, NIH Main Campus Bldg. 31, Bethesda, MD, September 16-17th, 2014. (slides)

Tutorials

  • Realism-Based Ontology for Integrating Individually Compiled Biomedical Data Repositories. 3-Hour tutorial as part of the Medical Informatics Europe Conference (MIE 2012), Pisa, Italy, August 26-29, 2012. (Tutorial outline, slides)
  • Biomedical Ontology and Referent Tracking: Introduction to Basic Principles. IADR Satellite Workshop on Orofacial Pain, March 20, 2013, Seattle, WA. (slides)


Final report:) Ceusters W. An Ontology for Pain and related disability, Mental health and Quality of Life (OPMQoL). Final Report for grant R01DE021917 from the National Institute of Dental and Craniofacial Research, NIH), September 27, 2014, 141p.



ARGOS: Transatlantic Observatory for Meeting Global Health Policy Challenges through ICT-Enabled Solutions

   
(Jan 2010 - June 2011)
Supported by the European Union grant SI2.548981

The overall goal of the ARGOS eHealth Pilot Project is to contribute to establishing a “Transatlantic Observatory for Meeting Global Health Policy Challenges through ICT-Enabled Solutions” in order to develop and promote “Common Methods for Responding to Global eHealth Challenges in the EU and the US”.

Our contribution is to evaluate the role of ontology in semantic interoperability and the modelling and simulation of human physiology and diseases with a focus on the Virtual Physiological Human (VPH) and the use of such solutions to support the diagnosis and treatment of rare diseases.


Related literature:
  • Ceusters W, Smith B. Semantic Interoperability in Healthcare - State of the Art in the US - a Position Paper, March 2010. (position paper, slides)
  • Kalra D, Musen M, Smith B, Ceusters W, De Moor G. ARGOS Policy Brief on Semantic Interoperability. In De Moor G. (ed.) Transatlantic Cooperation Surrounding Health Related Information and Communication Technology. Studies in Health Technology and Informatics 2011;170:1-15. (paper, final draft)

Realism-based versioning for biomedical ontologies

   
(Apr 2009 - Apr 2011)
Supported by the National Library of Medicine grant 1R21LM009824-01A1

The vision behind this project is one in which biomedical ontologies do not just reflect the state of the art in biomedical science in terms of what entities exist in reality and of how they are related, but that they also keep track of whether the changes introduced in successive versions of ontologies reflect (1) changes in the underlying reality, (2) in the views of ontology authors - or in associated scientific theories, or (3) are corrections of editorial mistakes. To make this vision come true, especially in the context of ontologies that will work in complex domains such as biomedicine, we must have objective measures for ontology quality.
Our hypothesis is that when this vision is endorsed by the authors of biomedical ontologies and when the ontology authoring environments support the application of this view by means of appropriate software, it would become possible to develop an objective measure for the quality of an ontology as it evolves over time. We test this hypothesis by applying realism-based ontology versioning to the Systematized Nomenclature of Medicine (SNOMED). We do this on the basis of the following specific aims:

  1. analyze SNOMED-CT's existing history mechanism to find out whether the principles of realism-based ontology versioning are able to cope with all requirements put forward by SNOMED-CT. Adjust when needed.
  2. develop a prototype of a realism-based ontology versioning software component that can serve as plug in for ontology authoring systems such as Protégé, ODE or SWOOP.
  3. use the prototype to restructure SNOMED-CT's history information in line with the principles of realism-based ontology versioning.
  4. to compute the quality improvement of SNOMED-CT over time in order to demonstrate the usefulness of the approach and foster its acceptance in other ontologies
Related literature:
  • Ceusters W, Smith B. A Realism-Based Approach to the Evolution of Biomedical Ontologies. Proceedings of AMIA 2006, Washington DC, 2006;:121-125. (draft paper, slides)
  • Ceusters W, Spackman KA, Smith B. Would SNOMED CT benefit from Realism-Based Ontology Evolution? In Teich JM, Suermondt J, Hripcsak C. (eds.), American Medical Informatics Association 2007 Annual Symposium Proceedings, Biomedical and Health Informatics: From Foundations to Applications to Policy, Chicago IL, 2007;:105-109. (abstract, draft)
  • Ceusters W. Applying Evolutionary Terminology Auditing to the Gene Ontology. Journal of Biomedical Informatics 2009;42:518–529. (Official version, accepted draft, reviewers comments and responses)
  • Ceusters W, Smith B. A Unified Framework for Biomedical Terminologies and Ontologies. Proceedings of the 13th World Congress on Medical and Health Informatics (Medinfo 2010), Cape Town, South Africa, 12-15 September 2010. Studies in Health Technology and Informatcis 2010;160:1050-1054. (PMID: 20841844) (Final draft, Reviewers' comments and responses, slides)
  • Ceusters W. Applying Evolutionary Terminology Auditing to SNOMED CT. In American Medical Informatics Association 2010 Annual Symposium (AMIA 2010) Proceedings, Washington DC, November 13-17, 2010:96-100. (paper, slides, response to reviewers)
  • Ceusters W. SNOMED CT's RF2: is the Future Bright? Medical Informatics Europe Conference, MIE 2011, Oslo, Norway, August 28-31, 2011. Studies in Health Technology and Informatics 2011;169:829-833. (paper, response to reviewers, slides)
  • Ceusters W. SNOMED CT Revisions and Coded Data Repositories: When to Upgrade? In American Medical Informatics Association 2011 Annual Symposium Proceedings, Washington DC, October 22-26, 2011:197-206 (final draft, response to reviewers, slides).
final report: Ceusters W. Realism-based versioning for biomedical ontologies; final report on grant 1R21LM009824-01A1 from the National Library of Medicine, June 21, 2011, 93p.

Teaching slides.


ISTARE: Intelligent Spatio-Temporal Activity Reasoning Engine

   
(July 2010 - July 2012)
Supported by Army Research Lab and DARPA grant W911NF-10-2-0062

The goal of ISTARE is to develop video-analysis software able to capture articulated motion in a threelayer hierarchical dynamical graphical model: (i) development of spatial-temporal atoms for basic features such as points, lines, and regions, (ii) semi-supervisedly examine spatial and temporal coherence inherent in appearance, structure and motion of these lowlevel atoms to induce parts at the mid-level over which joint probabilistic and statistical mechanics models are learned; and (iii) generalizations of these (reusable) mid-level parts into full objects and activities at the high-level by means of a realism-based ontology.

The ontology will describe types of real-world phenomena relevant for video surveillance including aspects of human motion, with more specific parts focused on the “verbs” that have been recognized to be important for surveillance. These aspects will include two layers: one involving how humans interact with objects and other humans in various scenarios and one how motions of body parts contribute to human body motion (e.g. the specific ways arms and legs move when a person is walking).

Related literature

  • Ceusters W, Corso J, Fu Y, Petropoulos M, Krovi V. Introducing Ontological Realism for Semi-Supervised Detection and Annotation of Operationally Significant Activity in Surveillance Videos. Proceedings of the 5th International Conference on Semantic Technologies for Intelligence, Defense, and Security (STIDS 2010), Fairfax, VA, October 27-28, 2010. (accepted paper with responses to reviewers, slides)


UB Task Force for ontology-based IT support for large scale field studies in Psychiatry

   
(Sept 2007 - March 2009) (press release, UB Reporter)

The John R. Oishei Foundation's mission is to enhance the quality of life for Buffalo area residents by supporting education, healthcare, scientific research and the cultural, social, civic and other charitable needs of the community. The Foundation was established in 1940 by John R. Oishei, founder of Trico Products Corporation.
In August 2007, the John R. Oishei Foundation authorized a grant to establish at SUNY at Buffalo (UB) a Taskforce for Ontology-Based IT Support for Large-Scale Studies in Psychiatry. The goal of the taskforce is to create the foundation for making UB the best positioned information technology partner to participate in large, multi-center data collection and analysis efforts that are underway to solve a number of diagnostic problems in the domain of psychiatry. The taskforce, led by Werner Ceusters, MD (PI), will draw on the expertise available in the UB Departments of Psychiatry, Philosophy (Barry Smith, PhD), and Computer Science and Engineering (Stuart C. Shapiro, PhD), including the Center for Cognitive Science. The specific aims addressed by the taskforce are:

  1. to assess the functional and technical requirements to be fulfilled by a data management system able to do justice to both the dimensional and categorical approach in psychiatric diagnosis;
  2. to design an implementation and funding plan for the technical infrastructure to be built in order to support data collection and analyses in large-scale field studies in psychiatry, and;
  3. to initiate the collaborations needed to deliver data collection and analyses services to provide the answers to the questions raised in the DSM-V research agenda.

Publications:

Presentations:

  • Ontology and the Future of Psychiatric Diagnosis. FALL 2006 PUBLIC LECTURES SHOWCASE SERIES on Ontology, Bioinformatics and the Life Sciences. UB North Campus, Baldy Hall 101, Buffalo NY, USA, October 19, 2006. (slides)
  • What is a diagnosis ? . Workshop on Ontology of Diseases. Baltimore, MD, USA, November 7, 2006. (slides)
    (For an application of this work by Saul Lozano: see Dengue Ontology)
  • Advancing Translational Research in Psychiatry through Realism-based Ontology and Referent Tracking. University Grand Rounds, UB, Buffalo - February 13, 2009. (slides)
  • Foundations for a Realist Ontology of Mental Disease. Academic Development Symposium, Department of Psychiatry, UB, August 25, 2010. (slides)
  • Defining Mental Disease. Lecture as part of PHI548 - Biomedical Ontology, Philosophical Aspects of Health and Disease. University at Buffalo, Oct 18, 2010. (slides)

Ontology for Risks Against Patient Safety (RAPS)

   
(April 2008 - November 2009)

We developed in collaboration with RAMIT vzw a component that contains in a machine understandable way all the domain knowledge that is required to be able to prevent, predict, detect or deal appropriately with RAPS in the context of the disease history of a patient. Our work was focused on an ontology describing the portions of reality salient to the domain of RAPS occurring in hospitals. This ontology itself consist of two different parts. One part is the RAPS domain ontology which has been developed following the principles of ontological realism and therefore is lined up with Basic Formal Ontology. This ontology thus consist exclusively of

  • representational units that refer to salient universals in the domain covered, examples being person, drug, allergic reaction, and
  • relationships taken from (or inspired by) the OBO Relation Ontology that has been developed under the same realist assumptions.
The second part of the ontology is the RAPS application ontology that uses the domain ontology as a reference, but differs from it in a few aspects:
  • it contains defined classes to represent characteristics of groups of particulars that do not correspond with universals,
  • it eliminates detail which is irrelevant for the purposes of the application.
Pilot sites of the ReMINE project used the ontology to construct a taxonomy of terms in various languages that are commonly used as linguistic denotations for the universals, particulars, relationships and the more complex portions of reality of which the former three are constituents. Thus, whereas the ontology part describes (some aspects of) what is the case in reality, the terminology part describes (some aspects of) how humans communicate by means of language about reality.

Downloads:
  1. Ceusters W, Capolupo M, Devlies J. D4.2 – RAPS Domain Ontology (M12 Version). Background materials and methodology used to develop the Domain Ontology for Risks against Patient Safety, January 11, 2009, 55p.
  2. Ceusters W, Capolupo M, Devlies J. D4.3 – RAPS Application ontology (Version 1). Background materials and methodology used to develop Application Ontologies for Risks against Patient Safety, January 11, 2009, 53p.
  3. Ceusters W, Capolupo M, De Moor G, Devlies J. Introducing Realist Ontology for the Representation of Adverse Events. In: Eschenbach C, Gruninger M. (eds.) Formal Ontology in Information Systems, IOS Press, Amsterdam, 2008;:237-250.(first submission, reviews, final draft)
  4. Ceusters W, Capolupo M, Smith B, De Moor G. An Evolutionary Approach to the Representation of Adverse Events. In: Medical Informatics Europe 2009, Sarajevo, Bosnia and Herzegovina, August 31, 2009. Studies in health technology and informatics 2009;150:537-541. (NIH Open Access, paper, final draft, slides)
  5. Ceusters W, Capolupo M, De Moor G, Devlies J, Smith B. An Evolutionary Approach to Realism-Based Adverse Event Representations. Methods of Information in Medicine, 2010;49(6) (Epub ahead of print, uncorrected draft accepted for publication, response to reviewers).
  6. He Y, Xiang Z, Sarntivijai S, Toldo S, Ceusters W. AEO: a realism-based biomedical ontology for the representation of adverse events. Workshop on 'Representing adverse events', International Conference on Biomedical Ontology, Buffalo NY, July 26, 2011:309-315. (paper, response to reviewers)


Exploring eyeGENE from a Bioinformatics Perspective

   
(June 2008 - December 2010)

The eyeGENE database, launched in 2006, collects genotype and phenotype information for patients with eye diseases as a tool to further eye research. To make the system maximally useful from a bio-informatics perspective, the RTU has been requested to perform the following activities:

  1. Prepare an updated review of existing and emerging medical information standards of note in the U.S. as applicable to clinical research data and all major standards committees, with clarification as to how the various standards and standards committees overlap and which ones are likely to have or gain broad acceptance.
  2. Review the unique features of eyeGENE and identify opportunities for future enhancements of value both for eyeGENE and for the medical informatics community.
  3. Offer recommendations on future steps for synchronizing eyeGENE data with applicable medical information standards.
  4. Present innovative ideas for extending the capabilities of eyeGENE and the richness and availability of anonymized data to the research community.

Publications

  • Rudnicki R, Ceusters W. Emerging medical information standards as applicable to clinical research data. A study performed in the context of the project 'Exploring eyeGENE, an International Genotype / Phenotype Database, from a Bioinformatics Perspective', July 16, 2008. 104pp
  • Ceusters W. Providing a Realist Perspective on the eyeGENE Database System. In: Smith B. (ed.) Proceedings of the International Conference on Biomedical Ontologies (ICBO), Buffalo, NY, July 23-26, 2009;67-70. (accepted draft, slides).

Oral Diagnostic Consultation Tracking

   (Oct 2005 - March 2007)

The UB School of Dental Medicine started a project involving tracking patients in their dental school clinics for whom a request has been made for a consultation by an oral medicine specialist from the department of oral diagnostic sciences. The school, who is responsible for all patients in its clinics, wants to ensure that these patients are, in fact, seen by an oral medicine consultant. It wants to know why the consultation was requested, what the findings were, what recommendations were made by the consultant and if and how the recommendations were carried through. A form was constructed to be filled out by the consultants when they are called to see a patient. An ontology has been created, referring to the universals of which the entities that are referred to by the data captured by means of this form are instances.