Running Projects
Exploring eyeGENE from a Bioinformatics Perspective
(June 2008 - )
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:
- 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.
- Review the unique features of eyeGENE and identify opportunities for future enhancements of value both for eyeGENE and for the medical informatics community.
- Offer recommendations on future steps for synchronizing eyeGENE data with applicable medical information standards.
- Present innovative ideas for extending the capabilities of eyeGENE and the richness and availability of anonymized data to the research community.
Ontology for Risks Against Patient Safety (RAPS)
(April 2008 - November 2009)
We will develop 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. This component will consist of two parts. One part is an ontology describing the portions of reality salient to the domain of RAPS occurring in hospitals. This ontology will itself consist of two different parts. One part is the “RAPS domain ontology” which will be developed following the principles of unqualified realism and therefore will be lined up with Basic Formal Ontology. This ontology will 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 the OBO Relation Ontology that has been developed under the same realist assumptions.
- it will contain defined classes to represent characteristics of groups of particulars that do not correspond with universals,
- it will eliminate detail which is irrelevant for the purposes of the application.
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:
- 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;
- 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;
- 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.
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 are exploring 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
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.
List of projects
- Exploring eyeGENE from a Bioinformatics Perspective
- Ontology for Risks Against Patient Safety
- UB Task Force for ontology-based IT support for large scale field studies in Psychiatry
- Making existing EHR systems RT compatible
- Oral Diagnostic Consultation Tracking
