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Guangming Xing, Guo-Qiang Zhang, Licong Cui
BACKGROUND: Redundant hierarchical relations refer to such patterns as two paths from one concept to another, one with length one (direct) and the other with length greater than one (indirect). Each redundant relation represents a possibly unintended defect that needs to be corrected in the ontology quality assurance process. Detecting and eliminating redundant relations would help improve the results of all methods relying on the relevant ontological systems as knowledge source, such as the computation of semantic distance between concepts and for ontology matching and alignment...
2016: BioData Mining
María Del Mar Roldán-García, María Jesús García-Godoy, José F Aldana-Montes
BACKGROUND: Systematized Nomenclature of Medicine - Clinical Terms (SNOMED CT) has been designed as standard clinical terminology for annotating Electronic Health Records (EHRs). EHRs textual information is used to classify patients' diseases into an International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) category (usually by an expert). Improving the accuracy of classification is the main purpose of using ontologies and OWL representations at the core of classification systems...
October 13, 2016: Journal of Biomedical Semantics
J T Helgstrand, N Klemann, M A Røder, B G Toft, K Brasso, B Vainer, P Iversen
BACKGROUND: Systematized Nomenclature of Medicine (SNOMED) codes are computer-processable medical terms used to describe histopathological evaluations. SNOMED codes are not readily usable for analysis. We invented an algorithm that converts prostate SNOMED codes into an analyzable format. We present the methodology and early results from a new national Danish prostate database containing clinical data from all males who had evaluation of prostate tissue from 1995 to 2011. MATERIALS AND METHODS: SNOMED codes were retrieved from the Danish Pathology Register...
2016: Clinical Epidemiology
Elizabeth Craig, Neal Kerr, Gabrielle McDonald
AIM: In New Zealand, there is a paucity of information on children with chronic conditions and disabilities (CCD). One reason is that many are managed in hospital outpatients where diagnostic coding of health-care events does not occur. This study explores the feasibility of coding paediatric outpatient data to provide health planners with information on children with CCD. METHODS: Thirty-seven clinicians from six District Health Boards (DHBs) trialled coding over 12 weeks...
October 7, 2016: Journal of Paediatrics and Child Health
Hadyl Asfari, Julien Souvignet, Agnès Lillo-Le Louët, Béatrice Trombert, Marie-Christine Jaulent, Cédric Bousquet
AIM: To propose an alternative approach for building custom groupings of terms that complements the usual approach based on both hierarchical method (selection of reference groupings in medical dictionary for regulatory activities [MedDRA]) and/or textual method (string search), for case reports extraction from a pharmacovigilance database in response to a safety problem. Here we take cardiac valve fibrosis as an example. METHODS: The list of terms obtained by an automated approach, based on querying ontology of adverse drug reactions (OntoADR), a knowledge base defining MedDRA terms through relationships with systematized nomenclature of medicine-clinical terms (SNOMED CT) concepts, was compared with the reference list consisting of 53 preferred terms obtained by hierarchical and textual method...
July 21, 2016: Thérapie
Begoña Martínez-Salvador, Mar Marcos, Alejandro Mañas, José Alberto Maldonado, Monserrat Robles
Clinical decision-support systems (CDSSs) should be able to interact with the electronic health record (EHR) to obtain the patient data they require. A recent solution for the interoperability of CDSSs and EHR systems consists in the use of a mediated schema which provides a unified view of their two schemas. The use of such a mediated schema requires the definition of a mapping between this schema and the EHR one. In this paper we investigate the use of the SNOMED CT Expression Constraint Language to characterize these mappings...
2016: Studies in Health Technology and Informatics
V M Giménez-Solano, J A Maldonado, S Salas-García, D Boscá, M Robles
The need to achieve high levels of semantic interoperability in the health domain is regarded as a crucial issue. Nowadays, one of the weaknesses when working in this direction is the lack of a coordinated use of information and terminological models to define the meaning and content of clinical data. IHTSDO is aware of this problem and has recently developed the SNOMED CT Expression Constraint Language to specify subsets of concepts. In this paper, we describe an implementation of an execution engine of this language...
2016: Studies in Health Technology and Informatics
Rainer Thiel, Strahil Birov, Klaus Piesche, Anne Randorff Højen, Kirstine Rosenbeck Gøeg, Heike Dewenter, Reza Fathollah Nejad, Sylvia Thun, Pim Volkert, Vesna Kronstein Kufrin, Veli Stroetmann
As part of its investigations, the EU-funded ASSESS CT project developed an Economic Assessment Model for assessing SNOMED CT's and other terminologies' socio-economic impact in a systematic approach. Methodology and key elements of the model are presented: cost and benefit indicators for assessing deployment, and a cost-benefit analysis tool to collect, estimate, and evaluate data.
2016: Studies in Health Technology and Informatics
Anne Randorff Højen, Dorthe Brønnum, Kirstine Rosenbeck Gøeg, Pia Britt Elberg
This paper presents an analysis of the extent to which SNOMED CT is suitable for representing data within the domain of head and neck cancer. In this analysis we assess whether the concept model of SNOMED CT comply with the documentation needed within this clinical domain. Attributes from the follow-up template of the clinical quality registry for Danish Head and Neck Cancer, and their respective value sets were mapped to SNOMED CT using existing mapping guidelines. Results show that post-coordination is important to represent specific types of value sets, such as absence of findings and severities...
2016: Studies in Health Technology and Informatics
Marzouk Mamou, Alan Rector, Stefan Schulz, James Campbell, Harold Solbrig, Jean-Marie Rodrigues
It is investigated whether the content of the Joint Linearization for Mortality and Morbidity Statistics of the 11th ICD revision can be semantically represented by formalisms acting on the clinical terminology SNOMED CT, viz. the IHTSDO Compositional Grammar (CG) and the Expression Constraint Language (ECL). Whereas CG provides a composition syntax for building coordinated SNOMED CT expressions, ECL provides a powerful query mechanism. Both formalisms can be leveraged to guarantee inter-operation between an ontology-based terminology like SNOMED CT and a statistical classification like ICD, characterized by single hierarchies and exhaustive, mutually exclusive classes...
2016: Studies in Health Technology and Informatics
Manuel Quesada-Martínez, Jesualdo Tomás Fernández-Breis, Daniel Karlsson
The number of biomedical ontologies has increased significantly in recent years. Many of such ontologies are the result of efforts of communities of domain experts and ontology engineers. The development and application of quality assurance (QA) methods should help these communities to develop useful ontologies for both humans and machines. According to previous studies, biomedical ontologies are rich in natural language content, but most of them are not so rich in axiomatic terms. Here, we are interested in studying the relation between content in natural language and content in axiomatic form...
2016: Studies in Health Technology and Informatics
Syed Sibte Raza Abidi, Abhinav Kumar Singh, Sean Christie
In this paper we present a framework for the semi-automatic extraction of medical entities from referral letters and use them to transcribe a case report form. Our framework offers the functionality to: (a) extract the medical entity from the unstructured referral letters, (b) classify them according to their semantic type, and (c) transcribe a case report form based on the extracted information from the referral letter. We take a semantic text analytics approach where SNOMED-CT ontology is used to both classify referral concepts and to establish semantic similarities between referral concepts and CRF elements...
2016: Studies in Health Technology and Informatics
Dorthe Brønnum, Anne Randorff Højen, Kirstine Rosenbeck Gøeg, Pia Britt Elberg
INTRODUCTION: Collecting clinical data once for the use in both electronic health record (EHR) and registries requires semantic interoperability. This paper presents the results of a systematic semantic analysis of similarities and differences in clinical documentation across regional EHR and a national oncology registry to assess options for an integration of recording templates. METHODS: A comparison of current clinical information in EHR and the national registry was carried out, using SNOMED CT as frame of reference to find exact-, similar- and non-match...
2016: Studies in Health Technology and Informatics
Yihan Deng, Jan Gaebel, Kerstin Denecke
Events such as clinical interventions, adverse drug events are one of the basic semantic units in the clinical workflow and are the foundation of the pathway representation. Current research has mainly concentrated on event recognition through concept mapping using from medical ontologies (UMLS, SNOMED CT) and gene relation detection in the biological context. However, the analysis of the patient status and the interaction between the patient status and a context event is still at the primary stage. In order to realize an efficient personalized treatment design and pathway planning, the correlation between a patient status and different types of clinical events should be analyzed...
2016: Studies in Health Technology and Informatics
Anca Bucur, Jasper van Leeuwen, Njin-Zu Chen, Brecht Claerhout, Kristof de Schepper, David Perez-Rey, Sergio Paraiso-Medina, Raul Alonso-Calvo, Keyur Mehta, Cyril Krykwinski
This paper describes a new Cohort Selection application implemented to support streamlining the definition phase of multi-centric clinical research in oncology. Our approach aims at both ease of use and precision in defining the selection filters expressing the characteristics of the desired population. The application leverages our standards-based Semantic Interoperability Solution and a Groovy DSL to provide high expressiveness in the definition of filters and flexibility in their composition into complex selection graphs including splits and merges...
2016: AMIA Summits on Translational Science Proceedings
Asma Ben Abacha, Julio Cesar Dos Reis, Yassine Mrabet, Cédric Pruski, Marcos Da Silveira
BACKGROUND: The increasing number of open-access ontologies and their key role in several applications such as decision-support systems highlight the importance of their validation. Human expertise is crucial for the validation of ontologies from a domain point-of-view. However, the growing number of ontologies and their fast evolution over time make manual validation challenging. METHODS: We propose a novel semi-automatic approach based on the generation of natural language (NL) questions to support the validation of ontologies and their evolution...
2016: Journal of Biomedical Semantics
Susan A Matney, Theresa Tess Settergren, Jane M Carrington, Rachel L Richesson, Amy Sheide, Bonnie L Westra
Disparate data must be represented in a common format to enable comparison across multiple institutions and facilitate big data science. Nursing assessments represent a rich source of information. However, a lack of agreement regarding essential concepts and standardized terminology prevent their use for big data science in the current state. The purpose of this study was to align a minimum set of physiological nursing assessment data elements with national standardized coding systems. Six institutions shared their 100 most common electronic health record nursing assessment data elements...
July 18, 2016: Western Journal of Nursing Research
Luis Marco-Ruiz, Carlos Pedrinaci, J A Maldonado, Luca Panziera, Rong Chen, J Gustav Bellika
BACKGROUND: The high costs involved in the development of Clinical Decision Support Systems (CDSS) make it necessary to share their functionality across different systems and organizations. Service Oriented Architectures (SOA) have been proposed to allow reusing CDSS by encapsulating them in a Web service. However, strong barriers in sharing CDS functionality are still present as a consequence of lack of expressiveness of services' interfaces. Linked Services are the evolution of the Semantic Web Services paradigm to process Linked Data...
August 2016: Journal of Biomedical Informatics
Julien Souvignet, Gunnar Declerck, Hadyl Asfari, Marie-Christine Jaulent, Cédric Bousquet
INTRODUCTION: Efficient searching and coding in databases that use terminological resources requires that they support efficient data retrieval. The Medical Dictionary for Regulatory Activities (MedDRA) is a reference terminology for several countries and organizations to code adverse drug reactions (ADRs) for pharmacovigilance. Ontologies that are available in the medical domain provide several advantages such as reasoning to improve data retrieval. The field of pharmacovigilance does not yet benefit from a fully operational ontology to formally represent the MedDRA terms...
June 28, 2016: Journal of Biomedical Informatics
Julien Souvignet, Hadyl Asfari, Jérémy Lardon, Emilie Del Tedesco, Gunnar Declerck, Cédric Bousquet
OBJECTIVE: To propose a method to build customized sets of MedDRA terms for the description of a medical condition. We illustrate this method with upper gastrointestinal bleedings (UGIB). RESEARCH DESIGN AND METHODS: We created a broad list of MedDRA terms related to UGIB and defined a gold standard with the help of experts. MedDRA terms were formally described in a semantic resource named OntoADR. We report the use of two semantic queries that automatically select candidate terms for UGIB...
September 2016: Expert Opinion on Drug Safety
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