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"Clinical ontology"

Andrew McGovern, Michael Feher, Neil Munro, Simon de Lusignan
BACKGROUND: Sodium-glucose co-transporter-2 (SGLT2) inhibitors (gliflozins) are the newest class of medication available to treat type 2 diabetes (T2DM). Recent findings from the first complete cardiovascular safety trial in SGLT2 inhibitors, the Empagliflozin, Cardiovascular Outcomes, and Mortality in type 2 diabetes (EMPA-REG OUTCOMES) trial, demonstrated reduced cardiovascular outcomes in people with high cardiovascular risk. How to apply these findings to clinical practice remains unclear, with questions remaining on who will reap this cardiovascular benefit...
April 2017: Diabetes Therapy: Research, Treatment and Education of Diabetes and related Disorders
Jennifer E Posey, Tamar Harel, Pengfei Liu, Jill A Rosenfeld, Regis A James, Zeynep H Coban Akdemir, Magdalena Walkiewicz, Weimin Bi, Rui Xiao, Yan Ding, Fan Xia, Arthur L Beaudet, Donna M Muzny, Richard A Gibbs, Eric Boerwinkle, Christine M Eng, V Reid Sutton, Chad A Shaw, Sharon E Plon, Yaping Yang, James R Lupski
BACKGROUND: Whole-exome sequencing can provide insight into the relationship between observed clinical phenotypes and underlying genotypes. METHODS: We conducted a retrospective analysis of data from a series of 7374 consecutive unrelated patients who had been referred to a clinical diagnostic laboratory for whole-exome sequencing; our goal was to determine the frequency and clinical characteristics of patients for whom more than one molecular diagnosis was reported...
January 5, 2017: New England Journal of Medicine
Katherine Leavey, Samantha J Benton, David Grynspan, John C Kingdom, Shannon A Bainbridge, Brian J Cox
Preeclampsia (PE) is a complex, hypertensive disorder of pregnancy, demonstrating considerable variability in maternal symptoms and fetal outcomes. Unfortunately, prior research has not accounted for this variability, resulting in a lack of robust biomarkers and effective treatments for PE. Here, we created a large (N=330) clinically relevant human placental microarray data set, consisting of 7 previously published studies and 157 highly annotated new samples from a single BioBank. Applying unsupervised clustering to this combined data set identified 3 clinically significant probable etiologies of PE: "maternal", with healthy placentas and term deliveries; "canonical", exhibiting expected clinical, ontological, and histopathologic features of PE; and "immunologic" with severe fetal growth restriction and evidence of maternal antifetal rejection...
July 2016: Hypertension
Jonathan M Mortensen, Natalie Telis, Jacob J Hughey, Hua Fan-Minogue, Kimberly Van Auken, Michel Dumontier, Mark A Musen
Biomedical ontologies contain errors. Crowdsourcing, defined as taking a job traditionally performed by a designated agent and outsourcing it to an undefined large group of people, provides scalable access to humans. Therefore, the crowd has the potential to overcome the limited accuracy and scalability found in current ontology quality assurance approaches. Crowd-based methods have identified errors in SNOMED CT, a large, clinical ontology, with an accuracy similar to that of experts, suggesting that crowdsourcing is indeed a feasible approach for identifying ontology errors...
April 2016: Journal of Biomedical Informatics
Guo-Qiang Zhang, Olivier Bodenreider
We present a scalable, SPARQL-based computational pipeline for testing the lattice-theoretic properties of partial orders represented as RDF triples. The use case for this work is quality assurance in biomedical ontologies, one desirable property of which is conformance to lattice structures. At the core of our pipeline is the algorithm called NuMi, for detecting the Number of Minimal upper bounds of any pair of elements in a given finite partial order. Our technical contribution is the coding of NuMi completely in SPARQL...
2010: Semantic Web—ISWC: International Semantic Web Conference Proceedings
Catalina Martínez-Costa, Dipak Kalra, Stefan Schulz
We propose a semantic-driven architecture to improve EHR semantic interoperability. This architecture is constituted by five layers: structured heterogeneous data (i), as found in (un-)standardised clinical information models, which are consumed by a semantic mapping layer (ii), which links the data items to clinical ontologies via user-friendly content patterns. A semantic mediator (iii) then translates these content patterns into ontology-based annotations, which populate a virtual homogeneous data store (iv), which serves the application layer (v)...
2014: Studies in Health Technology and Informatics
Gustavo A Uribe, Diego M López, Bernd Blobel
Comprehensive interoperability between eHealth/pHealth systems requires properly represented shared knowledge. Formal ontologies allow specifying the semantics of health knowledge representation in a well-defined and unambiguous manner. The objective of this paper is to formally analyze - from a system-theoretical architectural perspective - existing clinical ontologies. The paper defines important ontology requirements for semantically interoperable pHealth/eHealth systems. Then, based on those requirements, 17 criteria are defined and used for analyzing 129 clinical ontologies...
2012: Studies in Health Technology and Informatics
Simon J McBride, Michael J Lawley, Hugo Leroux, Simon Gibson
A large scale, long term clinical study faced significant quality issues with its medications use data which had been collected from participants using paper forms and manually entered into a data capture system. A method was developed that automatically mapped 72.2% of the unique medication names collected for the study to the AMT and SNOMED CT-AU using Ontoserver, a terminology server for clinical ontologies. These initial results are promising and, with further improvements to the algorithms and evaluation, are expected to greatly improve the analysis of medication data gathered from the study...
2012: Studies in Health Technology and Informatics
Sebastian Mate, Thomas Bürkle, Felix Köpcke, Bernhard Breil, Bernd Wullich, Martin Dugas, Hans-Ulrich Prokosch, Thomas Ganslandt
In an ongoing effort to share heterogeneous electronic medical record (EMR) data in an i2b2 instance between the University Hospitals Münster and Erlangen for joint cancer research projects, an ontology based system for the mapping of EMR data to a set of common data elements has been developed. The system translates the mappings into local SQL scripts, which are then used to extract, transform and load the facts data from each EMR into the i2b2 database. By using Semantic Web standards, it is the authors' goal to reuse the laboriously compiled "mapping knowledge" in future projects, such as a comprehensive cancer ontology or even a hospital-wide clinical ontology...
2011: Studies in Health Technology and Informatics
Pinar Wennerberg, Klaus Schulz, Paul Buitelaar
Searching for medical images and patient reports is a significant challenge in a clinical setting. The contents of such documents are often not described in sufficient detail thus making it difficult to utilize the inherent wealth of information contained within them. Semantic image annotation addresses this problem by describing the contents of images and reports using medical ontologies. Medical images and patient reports are then linked to each other through common annotations. Subsequently, search algorithms can more effectively find related sets of documents on the basis of these semantic descriptions...
February 2011: Journal of Biomedical Informatics
Mathias Brochhausen, Laura Slaughter, Holger Stenzhorn, Norbert Graf
Ontologies are more and more used in clinical informatics in different settings and supporting different functionalities. Most experts see the role of ontologies as operating in a black box and being invisible for the end-user. With respect to some of the systems that have recently been developed this is only partly possible. Therefore, we provide a methodology to create an end-user perspective on a clinical ontology. This will foster participation of the clinical expert in both ontology exploitation and ontology maintenance...
2010: Studies in Health Technology and Informatics
Holger Stenzhorn, Stefan Schulz, Martin Boeker, Barry Smith
The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term 'ontology' has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects...
2008: Journal of Universal Computer Science: J. UCS
Heather J Howard, Ourania Horaitis, Richard G H Cotton, Mauno Vihinen, Raymond Dalgleish, Peter Robinson, Anthony J Brookes, Myles Axton, Robert Hoffmann, Sylvie Tuffery-Giraud
The May 2009 Human Variome Project (HVP) Forum "Towards Establishing Standards" was a round table discussion attended by delegates from groups representing international efforts aimed at standardizing several aspects of the HVP: mutation nomenclature, description and annotation, clinical ontology, means to better characterize unclassified variants (UVs), and methods to capture mutations from diagnostic laboratories for broader distribution to the medical genetics research community. Methods for researchers to receive credit for their effort at mutation detection were also discussed...
March 2010: Human Mutation
Mojgan Haghighi, Michihiko Koeda, Takako Takai, Hiroshi Tanaka
We have developed a new educational/clinical ontology named the "Haghighi-Koeda Mood Disorder Ontology", which involves both medical and psychological approaches for mood disorders in order to promote the exchange of information between psychiatrists and psychologists. Data was gathered from more than 5000 articles published in journals and websites specialized in life science. We evaluated and selected articles which were related to 4 main categories of mood disorders. Using Protege 3.4 beta, information related to mood disorders was classified by class/subclass tree in an ontological structure...
March 2009: Journal of Medical and Dental Sciences
Stefan Schulz, Holger Stenzhorn
We present ten principles for clinical ontologies that describe the authors' opinion about what should be understood by the notion of clinical ontologies and what not. In contrast to clinical terminology systems, clinical ontologies are considered to be semantic reference systems and for that--first of all--strive to account for the properties of the domain entities themselves and their proper formal definitions--rather than just linking clinical terms together.
2007: Studies in Health Technology and Informatics
Allyson L Robichaud
In the clinical setting, not enough attention is paid to the role that emotion plays. It is at worst ignored or avoided, isolating those who are suffering, at best treated as something to help another to endure. This is the result, in part, of an impoverished idea that views emotion as mere feelings. However, emotions are not just feelings, they are cognitive. If we look beneath the surface, emotions can provide information about values and beliefs, some of which may be false or unreasonable. When they are motivating decisions that seriously affect the lives of others, there is a moral obligation to ferret them out and correct or deal with them...
February 2003: Bioethics
M A Musen
In computer science, the notion of a domain ontology--a formal specification of the concepts and of the relationships among concepts that characterize an application are a--has received considerable attention. In human-computer interaction, ontologies play a key role in defining the terms with which users and computer systems communicate. Such ontologies either implicitly or explicitly drive all dialogs between the computer and the user. In the construction of health-telematics applications, professionals need to understand how to design and apply domain ontologies to ensure effective communication with end-users...
2000: Studies in Health Technology and Informatics
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