4A Clinical and Translational Ontology Services
4A.1 Overview
How can we master the ever-increasing flood of biomedical information in a world in which each biological and medical discipline and each hospital system, clinic, government agency and research group uses its own guidelines for terminology and categorization? The discipline which seeks answers to this question is called ‘ontology’. OOntologists in the BTC are seek prtoviding a service to Buffalo clinical scientists develop robust category systems for to allow collection, the description and management of data in ways which will be of benefit to their research, to the dissemination of the results of their work, and to the satisfaction of NIH mandates governing reuse, information, and knowledge of all kinds, through the application of methods derived not only from computer, management and information science, from logic, philosophy and linguistics, but also, and most importantly, from the scientists who are collecting data and formulating and testing hypotheses with their aid. Ontologists in Buffalo are seeking to establish consistent structured representations of given domains of reality that are accessible to both human beings and computers, working specifically to support bioscience and translational research and clinical care in a maximally effective way.
UB is a leading center of research and training in biomedical ontology. It, and is, with Stanford and the Mayo Clinic, one of the three constituent US institutions of the NIH Roadmap U54 National Center for Biomedical Ontology (NCBO) recently renewed by the NHGRI, and a partner of the NCATS-funded CTSAconnect initiative, which is using ontologies to promote integration and discovery of research activities, resources, and clinical expertise across the CTSA Consortium..
The BTC’s Clinical and Translational Ontology Services This Key Function will contribute to the realization of multiple strategic goals of the National CTSA Consortium through the creation and testing of ontology resources designed to improve human health by transforming the environment in which clinical data is collected, shared, and analyzed, translated, and used to provide quality health care.
4A.2 Specific Aims
Aim 1: To develop ontology services for clinical scientists (1) within the framework of three interrelated pilot experiments designed to test our methods, (2) on an ad hoc basis through consulting with specific clinical communities, both inside and outside the BTC.
The three pilot experiments will be in the areas of
Electronic Health Record interoperability
neurological diseaseespecially Alzheimer's, MS, and Stroke
cancer pathology including cancer surgical pathology, and cancer flow cytometry.
Aim 2: To create an ontology-based Clinical and Translational Data Exchange which will leverage the work performed under Aim 1 to establish an evolving repository of integrated, de-identified Web-based patient data and biological knowledge available for use by members of the National CTSA Consortium and other external institutions and individuals.
Aim 3: To create, test, and implement an innovative Resource Discovery, Tracking, and Evaluation System building on the ontology-based resource discovery technology of eagle-i, VIVO and CTSAconnect, and contribute this system to the CTSA consortium.
Aim 4: To create a cross-disciplinary on-line Advanced Graduate Certificate Program in Biomedical Ontology directed towards trainee scientists both in Buffalo and in the National CTSA Consortium.
4A.3 Background
Two Buffalo-developed The work described below grows out of a multi-year collaboration between UB ontologists and the Gene Ontology (GO) Consortium(1). Of all the attempts to use ontology-based technology to advance the goals of clinical and translational science, the Gene Ontology is by far the most successful. This success turns, we believe, on the fact that the GO is created and maintained by biologists and is in consequence widely used in the description of many different sorts of biological data. Where terms from the GO are used to describe given bodies of data, these data become linked, in a growing network, to other bodies of data tagged or annotated with the same ontology terms (2). This brings immediate benefits to search, data mining, and aggregation, and integration; increasingly it is allowing also intelligent querying and algorithmic reasoning (3) and also new kinds of distributed research within the framework of the Semantic Web (4, 5). Its utility to clinical research draws on the multiple ways in which GO annotation information can be applied statistically to elucidate how gene products functionally interact to drive both normal biological phenomena and associated pathologies. (6)
Through their work with the developers of the GO, UB researchers can claim to have brought about a transformation in logical sophistication of bio-ontology research and to have created and disseminated techniques for evidence-based ontology development, application, and evaluation which have been adopted by public and private research groups and organizations throughout the world.
Our collaboration with the GO led to the creation of the ontology resources – the Basic Formal Ontology and the Relation Ontology (7), (8) – along with the associated methodology for ontology-driven data analysis, are, now providing a common integrating architecture for being used by more than 100 biomedical ontology projects throughout the world, including major initiatives such as the harmonization of SNOMED CT and ICD 10/11 (11-13), openEHR, the Open Biomedical Ontologies Foundary, and the Neuroscience Information Framework (NIF) Standard. We lead the dissemination efforts of the NCBO Where, on the hitherto dominant approach, multiple ontologies for each domain were created in ad hoc ways by multiple groups of researchers, the increasing acceptance of this common architecture enables scientists to create ontologies in a coordinated fashion in such a way that the data annotated in their terms is automatically linked together (9). Our collaboration with the GO led also to the creation of the OBO (Open Biomedical Ontologies) Foundry (10), which is seeking to create an evolving set of semantically interoperable ontologies, with the GO at its core, to support information-driven research across the entire domain of the life sciences.
UB ontologists have played an important role also in scientific research pertaining to health IT, for example through our influence on terminology initiatives such as SNOMED CT (11-13) and the National Cancer Institute Thesaurus (14). We have made contributions to diagnostic decision support (15), to the scientific study of the Electronic Health Record and of health information exchange and standardization (16-22), and to research in medical natural language understanding (23, 24) (see Hogan letter of support). Buffalo ontologists are involved in a range of funded ontology projects, currently including the Cell Ontology (funded as part of the Gene Ontology Consortium by NHGRI) (25, 26), the Protein Ontology (funded by NIGMS) (27), the Infectious Disease Ontology (funded by NIAID) (28), the Plant Ontology (funded by the NSF) and the Biometrics Ontology (funded by the Department of Defense).
4A.4 Key Personnel and Staffing
Werner Ceusters, MD, has degrees in medicine, neuropsychiatry, informatics, and knowledge engineering. Currently he is Professor of Psychiatry and Director of UB’s Ontology Research Group. He joined UB in 2006 after having served as Chief Technology Officer and VP for Research of L&C Inc., a company providing ontology-based Natural Language Understanding services to companies such as Eclipsys, First DataBank, Merck and WebMD that was acquired in 2010 by Nuance (owner of the Dragon Naturally Speaking software and world leader in natural language understanding for health information technology). Ceusters has received some is PI of an NLM grant applying Referent Tracking to the evaluation of the SNOMED CT clinical terminology.
· Responsibilities. (30% effort). As Co-Director of the Key Function, Dr. Ceusters will manage the day to day operations with Dr. Smith. Dr. Ceusters will Chair the Executive Committee for this Key Function, lead the Electronic Health Record Semantic Interoperability Project (Aim 1, Pilot 1), collaborate with BTC investigators on multiple ontology development and implementation efforts, and participate in ontology education in Aim 4.
Barry Smith, PhD, Distinguished Professor of Philosophy and Professor in the Departments of Neurology and Computer Science and Engineering in UB, is a prominent contributor to both theoretical and applied research in the field of biomedical ontology, who has received over $10M in funding for his ontology work. He is Director of the National Center for Ontological Research, a principal scientist of the National Center for Biomedical Ontology, and a Coordinating Editor of the OBO Foundry initiative. He is also a scientific advisor/consultant to ontology projects in the Cleveland Clinic, Johns Hopkins University School of Medicine, Mount Sinai School of Medicine, University of California at San Francisco, the German Federal Ministry of Health, the US Army, and the US Joint Forces Command. He is, with Melissa Haendel of the Oregon Health Sciences University, leader of the Expertise Ontology Working Group of the NCRR-funded eagle-I and VIVO resource discovery initiatives. (See Haendel letter of support and Aim 3 below)
· Responsibilities. (30% effort). As Co Director of the Key Function, Dr. Smith will manage the day to day operations with Dr. Ceusters. He will serve as Co-Director of the Resource Discovery, Tracking, and Evaluation System (RDTE) (Aim 3) and Director of the Advanced Certificate Program in Biomedical Ontology (Aim 4). He will collaborate with BTC investigators on biomedical ontology development and implementation efforts
Alexander Diehl, PhD, has been recruited to the UB Department of Neurology after serving as Research Scientist for the Mouse Genome Informatics resource of the Jackson Lab. He is an active developer of the Gene and Cell Ontologies, currently directing a project to revise and restructure the Cell Ontology with a major focus on hematopoietic and nervous system cell types. He is also a member of the Infectious Disease Ontology and Vaccine Ontology development teams, and of the International Neuroinformatics Coordinating Facility Program on Ontologies of Neural Structures Representation and Deployment Task Force.Formerly he worked for Decode Genetics in Iceland on target validation in MS, Stroke, and Peripheral Artery Disease.
· Responsibilities. (40% effort) Dr. Diehl will serve as Director of Ontology Services, providing guidance and support to BTC clinical scientists using ontologies in their work. He leads the Neurological Disease Data Project (Aim 1, Pilot 2) and will teach in the Advanced Certificate Program in Biomedical Ontology (Aim 4).
Albert Goldfain, PhD. From 2002 to 2008 Goldfain worked as software engineer for themedical device manufacture Welch Allyn Inc. where he is first inventor on a patent specifying a language for medical device information exchange. Since 2008 he has worked for Blue Highway, Inc., a subsidiary of Welch Allyn devoted to innovative projects in informatics and medical device technology. He also serves under Smith’s direction as postdoctoral researcher on an NIAID-funded grant on the development of an Infectious Disease Ontology to support research on Staph. aureus biology and treatment.
· Responsibilities. (10% effort) Dr. Goldfain will lead the Vital Signs Ontology initiative as part of Aim 1, Pilot 1. His salary costs will be met by Blue Highway, Inc. (See letter).
Alan Ruttenberg, MSc, was employed from 1998 as a computational biologist by Millennium Pharmaceuticals, working as project lead on the award-winning PARIS system, which addresses a key problem in drug discovery – that of identifying the cellular pathways that are active or perturbed in microarray experiments, where thousands of genes may be differentially expressed (29-31). Since 2007 he has directed the Neurocommons Project, which supports computationally aided discovery in the domain of neurological diseases through collaborations with Yale’s Senselab (32), the Cure Huntington’s Disease Initiative Foundation, the Alzheimer Research Forum (Alzforum) (33) and the NIH Roadmap Neuroscience Information Framework (55). Ruttenberg serves on the Oversight Committee of the Digital Brain Atlasing Task Force of the International Neuroinformatics Coordinating Facility and is a lead in its Program on Ontologies of Neural Structures (34). He is also a Chair of the World Wide Web Consortium Web Ontology Language Working Group (35).
· Responsibilities. (30% effort) Ruttenberg will serve as Director of the Clinical and Translational Data Exchange (Aim 2) and lead the Surgical Pathology Ontology Project (Aim 1, Pilot 3). He will also collaborate with BTC investigators on ontology development and in ontology education under Aim 4.
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· Carmelo Gaudioso, MD, MBA, PhD in Medical Informatics, he currently is Assistant Professor of Oncology, Director of Medical Informatics, and Director of the Clinical Data Network at Roswell Park Cancer Institute and has over 25 years of experience in the health care field with both clinical and management positions. In these roles he works in close collaboration with the VP of Information Technology, the Director of Clinical Informatics, and the Director of Bioinformatics to provide seamless leadership and infrastructures for the development of an informatics program and data management required to support translational research clinical informatics efforts at RPCI. He is currently working with Dr, Steve Edge, Chair of the Breast Cancer Program at Roswell Park Cancer Institute, and Dr. Judy Smith, medical Director at Roswell park Cancer Institute, to design and develop care plans designed to meet meaning use requirements. He chairs the Inforamtics Governance Committee at Roswell Park Cancer Institute and serves on a Clinical Informatics, IT Governance, and Continuous Medical Education Committees. His research is focused multidisciplinary knowledge management and decision support systems, including ontology driven systems, patient centered healthcare and the use patient-physician portals to support patient-physicians partnership across the continuum of care.
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· Responsibilities. (20% effort) He will work with Alan Ruttenberg on the Surgical Pathology Ontology Project (Aim 1, Pilot 3) and Dr. Ceusters in the Electronic Health Record Semantic Interoperability Project (Aim 1, Pilot 1),
Staff Clinical scientists/informaticians involved in the realization of the three pilots under Aim 1.
Gunther Kohn, CIO of UB’s School of Dental Medicine, will manage extensions to the Picasso system and applications of the system to test our EHR interoperability strategy in Aim 1, Pilot 1 (20 (?% effort).
Kinga Szigeti, MD, Assistant Professor, Department of Neurology will devote 40?% of effort to management and research of the Alzheimers.
Jose Luis Tapia, DDS, MS, is Assistant Professor, Oral Diagnostic Sciences. He will create and apply the ontology content for the Breast Cancer Pilot (Aim 1, Pilot 3) (?40% effort).