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Running Projects

ProWATCH – MUS component    
(July 2011 - ...)

We are assisting Kristina Doing-Harris in developing a realism-based ontology for the MUS (Medically Unexplained Syndromes) component of the ProWATCH project. This component is a joint project between the University of Utah and the Salt Lake City Veterans Health Administration and is being run by Stéphan Meystre, MD, PhD (at the University of Utah) and Matthew Samore, MD (at the VA). The project focuses on providing VA clinical research with methods and instruments for syndrome surveillance, on improving detection and mitigation of health problems in deployed veterans, and more specifically on the detection of medically unexplained syndromes (MUS) and emergent infectious diseases.

Much of the information contained in electronic medical records like the VA CPRS is recorded in unstructured narrative text format. Some information such as diagnoses, test, or treatments, is mostly based on a fairly stable collection of terms used by healthcare providers, partly represented in standard vocabularies shared by healthcare organizations. Clinical information reported by patients such as symptoms is often described in general English language and varies significantly more than the terminology used by healthcare providers.

Developing tools to effectively use information extracted from VA clinical documents depends on expertise in information extraction, ontology development, symptom identification, predictive modeling, and interactive information visualization. Thus, execution of the work entailed by this project depends on the capacity to work across a range of clinical areas, and to engage a scientific team that brings together experts from a variety of disciplines including epidemiology, infectious disease, mental health, computer science, biomedical informatics, and statistics.

Related literature

  • 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.
  • Doing-Harris K, Meystre SM, Samore M, Ceusters W. Domain and Application Ontologies for Medically Unexplained Syndromes. In American Medical Informatics Association 2012 Annual Symposium Proceedings, Chicago IL, November 3-7, 2012;1606.

SMART-Amy: a smart guide towards the diagnosis of systemic amyloidosis    
(April 2013 - ...)

We are assisting Paola Russo in developing a realism-based ontology for the reality covered by diagnostic guidelines for systemic amyloidoses according to Ontological Realism and the OBO Foundry principles.

Systemic amyloidoses are a family of rare diseases that can cause multi-organ failure and be life-threatening. It is acknowledged and emphasized by public health strategies that the first priority to respond to rare diseases consists in improving their visibility and recognition, favoring an early diagnosis and, if possible, an early treatment. Due to the complexity and variety of rare diseases, they are usually managed and treated in a few referral centers that have the knowledge needed to assess diagnosis and treatment as well as the necessary tools (e.g. biomarkers, diagnostic techniques) to do so. The current practice to redirect patients to a few referral centers is indeed a way to guarantee the best quality of care, but in absence of effective public strategies promoting the recognition of patients affected by rare diseases on large scale, many patients remain deprived of this solution. This problem is even more dramatic whenever the disease is life threatening. In those cases, the diagnostic delay may lead to an early death despite of treatment initiation. The solution proposed by the SMART-Amy project is: 1) to develop a framework according to which it is possible to formally assess the degree to which a consensus diagnostic algorithm for systemic amyloidoses is emerging, integrating for instance the International Society of Amyloidosis (ISA) guidelines and best practices applied by referral centers, 2) to build a corresponding realism-based ontology to be used in 3) a clinical decision support system (CDSS) to make more reliably a diagnosis of systemic amyloidosis.

As an ancillary branch of the project core, BMI is implementing the AmyGuide interactive tool for smartphones and tablets in order to provide, both online and offline, patient-oriented information, combining information about the disease with hints to promote health behaviors and self-care, and to manage the demand for health services. It is built on top of the Gquest application for Android operating systems, a platform conceived for computerizing and administering questionnaires.

Related literature

  • Brochhausen M, Burgun-Parenthoine A, Ceusters W, Hasman A, Leong TY, Musen M, Oliveira J, Peleg M, Rector A, Schulz S. Discussion of “Biomedical Ontologies: Toward Scientific Debate”, Methods of Information in Medicine, 2011;50(3):217-36. (paper commented on, long version of my comments, published comments)
  • Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, the OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Shah N, Whetzel PL, Lewis S. The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration. Nature Biotechnology 2007;25:1251-1255. (full paper)
  • Smith B, Ceusters W. Ontological Realism as a Methodology for Coordinated Evolution of Scientific Ontologies. Applied Ontology, 2010;5(3-4):139-188. (Published version, final draft)
  • Ceusters W, Smith B. Referent Tracking for Treatment Optimisation in Schizophrenic Patients. Journal of Web Semantics 4(3) 2006:229-36; Special issue on semantic web for the life sciences. (Long draft, published paper)

Referent Tracking enabled web sites    
(Sept 2008 - ...)

Did you ever think about the fact that when you are viewing a web page, you are not looking at a concrete file which is on some medium on the remote web server, but to an exact copy of that file which has been sent to your computer? In many cases, there is not even a concrete file on the server, but what you see through your browser has been assembled out of several components using, for instance, php. Logically, when you view the page at different times, assuming the browser refreshed its contents, you get each time a different copy, and so do other viewers. Moreover, in between two access events, the page on the remote server might have been changed.
RT-enabled websites keep track of these copies, of their distribution, and of the evolution of the web pages that they contain over time. From Oct 2, 2008, the RTU RT-enabled web site until June 2017, the RTU website was RT-enabled. Each distributed page, at the time of a request, was branded with an Instance Unique Identifier (IUI) which is of course different from the IUI of the remote file. The IUI was printed on the right side of the menu bar.
In addition, a checksum was generated over the IUI taken together the content of the page in a way which protects authors against claims that certain information was there, when it actually was not. At the same, it is a guarantee for viewers that the authors cannot deny that specific information was there. The checksum was shown on the bottom of the page.
In the background, an RT-database kept track of all the IUIs, including revisions and new versions of pages, as well as of when and to which IP address the copies were sent.
The RT-enabled website technology is available for licensing but needs migrating from PHP 5.2 to later versions.

Making existing EHR systems RT compatible    (Dec 2006 - )

By advocating the use of instance unique identifiers to refer to the entities comprising the subject matter of patient health records, Referent Tracking promises many benefits to those who use health record data to improve patient care. One challenge ahead lies in furthering the adoption of the paradigm by developers of existing EHR applications. To meet this challenge, we have begun the process of integrating RT into commercial EHR applications A part of this process is an analysis of the extent to which the data collected by an EHR application needs to be reformulated to make it compatible with the requirements of RT, namely that the particulars assigned an IUI (for Instance Unique Identifier) are instances of the kinds included in Basic Formal Ontology (BFO).

  • An initial exploratory analysis was carried out for Praxis which allowed us to identify the obstacles and the directions that future research in relation to this system should take. (Dec 2006 - July 2007)
  • A more in depth analysis was performed on MedtuityEMR which led to the formulation of a research proposal. (Dec 2006)
  • For Sigmund Software LLC, we explored how their Target Behavior Tracking system which is currently used within individual organizations can benefit from referent tracking to develop a cross-institutional knowledgebase linked to other behavioral assessment tools. (March 2007)


Past projects