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Bevan Koopman, Guido Zuccon, Anthony Nguyen, Anton Bergheim, Narelle Grayson
OBJECTIVE: Death certificates are an invaluable source of cancer mortality statistics. However, this value can only be realised if accurate, quantitative data can be extracted from certificates-an aim hampered by both the volume and variable quality of certificates written in natural language. This paper proposes an automatic classification system for identifying all cancer related causes of death from death certificates. METHODS: Detailed features, including terms, n-grams and SNOMED CT concepts were extracted from a collection of 447,336 death certificates...
May 10, 2018: Artificial Intelligence in Medicine
Ghulam Mujtaba, Liyana Shuib, Ram Gopal Raj, Retnagowri Rajandram, Khairunisa Shaikh, Mohammed Ali Al-Garadi
Text categorization has been used extensively in recent years to classify plain-text clinical reports. This study employs text categorization techniques for the classification of open narrative forensic autopsy reports. One of the key steps in text classification is document representation. In document representation, a clinical report is transformed into a format that is suitable for classification. The traditional document representation technique for text categorization is the bag-of-words (BoW) technique...
May 5, 2018: Journal of Biomedical Informatics
Farid Khorrami, Maryam Ahmadi, Abbas Sheikhtaheri
BACKGROUND: One of the most important features studied for adoption of terminologies is content coverage. The content coverage of SNOMED CT as a large scale terminology system has been evaluated in different domains by various methods. OBJECTIVES: This study provided an overview of studies evaluating SNOMED CT content coverage. METHODS: This systematic literature review covered Scopus, Embase, PubMed and Web of Science. It included studies in English language with accessible full-text from the beginning of 2002 to November 2017...
2018: Studies in Health Technology and Informatics
Kenneth C Wang
Standard clinical terms, codes, and ontologies promote clarity and interoperability. Within radiology, there is a variety of relevant content resources, tools and technologies. These provide the basis for fundamental imaging workflows such as reporting and billing, and also facilitate a range of applications in quality improvement and research. This article reviews the key characteristics of lexicons, coding systems, and ontologies. A number of standards are described, including International Classification of Diseases-10-Clinical Modification (ICD-10-CM), Current Procedural Terminology (CPT), Systematized Nomenclature of Medicine-Clinical Terms (SNOMED CT), Logical Observation Identifiers Names and Codes (LOINC), and RadLex...
May 3, 2018: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
Jean Marie Rodrigues, Stefan Schulz, Bassim Mizen, Béatrice Trombert, Alan Rector
An important SNOMED CT use case is to support semantic interoperability between electronic health records and aggregation terminologies such as ICD. From the ongoing alignment exercise between SNOMED CT and the new version of ICD, now in its pre-final form, we studied whether the ambiguity of clinical language as displayed by SNOMED CT synonyms hampers the quality of SNOMED CT axioms following the SNOMED CT "concept model". We measure the rate of synonyms in the semantic misalignment between classes from the chapter on circulatory diseases of the ICD-11 beta version and SNOMED CT concepts with the same description names...
2018: Studies in Health Technology and Informatics
Hugo J Th van Mens, Nicolette F de Keizer, Remko Nienhuis, Ronald Cornet
Patient access to electronic health records (EHRs) is associated with improved efficiency, self-management, and patient engagement. However, the EHR contains medical language that can be difficult to comprehend by patients. In Dutch hospitals, the Diagnosethesaurus (DT) is used as an interface terminology to register diagnoses, but it does not contain patient-friendly terms. Fortunately, the DT is partly mapped to SNOMED CT and there is a proportionately small set of patient-friendly terms available in the Dutch SNOMED CT release...
2018: Studies in Health Technology and Informatics
Heike Dewenter, Sylvia Thun
As the reference terminology SNOMED CT is gaining in significance and seems without alternative in interoperable Electronic Health Records, the holder of its intellectual property, the non-for-profit organization SNOMED International has achieved a quasi-monopoly status as a provider. We examine the current dealing with corporate transparency regarding SNOMED CT licensing together with policy recommendations derived from the research project ASSESS CT, in the context of collaboration with Standardization Organizations...
2018: Studies in Health Technology and Informatics
Christophe Gaudet-Blavignac, Vasiliki Foufi, Eric Wehrli, Christian Lovis
Medical data is multimodal. In particular, it is composed of both structured data and narrative data (free text). Narrative data is a type of unstructured data that, although containing valuable semantic and conceptual information, is rarely reused. In order to assure interoperability of medical data, automatic annotation of free text with SNOMED CT concepts via Natural Language Processing (NLP) tools is proposed. This task is performed using a hybrid multilingual syntactic parser. A preliminary evaluation of the annotation shows encouraging results and confirms that semantic enrichment of patient-related narratives can be accomplished by hybrid NLP systems, heavily based on syntax and lexicosemantic resources...
2018: Studies in Health Technology and Informatics
Mark R Stöhr, Raphael W Majeed, Andreas Günther
The German Center for Lung Research (DZL) is a research network with the aim of researching respiratory diseases. The participating study sites' register data differs in terms of software and coding system as well as data field coverage. To perform meaningful consortium-wide queries through one single interface, a uniform conceptual structure is required covering the DZL common data elements. No single existing terminology includes all our concepts. Potential candidates such as LOINC and SNOMED only cover specific subject areas or are not granular enough for our needs...
2018: Studies in Health Technology and Informatics
Kirstine Rosenbeck Gøeg, Mark Hummeluhr
Information exchange at the level of semantic interoperability requires that information models and clinical terminologies work well together. In HL7 FHIR resources, terminology binding to standard terminologies such as SNOMED CT are suggested, and even though most are suggestions rather than rules, they still must reflect the clinical domain accurately. In this study, we suggest a method for empirically evaluating whether a terminology binding represents the value sets used in practice. We evaluated the terminology binding associated with the MedicationRequest...
2018: Studies in Health Technology and Informatics
Moumita Bhattacharya, Claudine Jurkovitz, Hagit Shatkay
Patients associated with multiple co-occurring health conditions often face aggravated complications and less favorable outcomes. Co-occurring conditions are especially prevalent among individuals suffering from kidney disease, an increasingly widespread condition affecting 13% of the general population in the US. This study aims to identify and characterize patterns of co-occurring medical conditions in patients employing a probabilistic framework. Specifically, we apply topic modeling in a non-traditional way to find associations across SNOMED-CT codes assigned and recorded in the EHRs of >13,000 patients diagnosed with kidney disease...
April 12, 2018: Journal of Biomedical Informatics
Huanying Gu, Zhe He, Duo Wei, Gai Elhanan, Yan Chen
BACKGROUND: The UMLS assigns semantic types to all its integrated concepts. The semantic types are widely used in various natural language processing tasks in the biomedical domain, such as named entity recognition, semantic disambiguation, and semantic annotation. Due to the size of the UMLS, erroneous semantic type assignments are hard to detect. It is imperative to devise automated techniques to identify errors and inconsistencies in semantic type assignments. OBJECTIVES: Designing a methodology to perform programmatic checks to detect semantic type assignment errors for UMLS concepts with one or more SNOMED CT terms and evaluating concepts in a selected set of SNOMED CT hierarchies to verify our hypothesis that UMLS semantic type assignment errors may exist in concepts residing in semantically inconsistent groups...
February 2018: Methods of Information in Medicine
Zachary M Grinspan, Niu Tian, Elissa G Yozawitz, Patricia E McGoldrick, Steven M Wolf, Tiffani L McDonough, Aaron Nelson, Baria Hafeez, Stephen B Johnson, Dale C Hesdorffer
Identifying individuals with rare epilepsy syndromes in electronic data sources is difficult, in part because of missing codes in the International Classification of Diseases (ICD) system. Our objectives were the following: (1) to describe the representation of rare epilepsies in other medical vocabularies, to identify gaps; and (2) to compile synonyms and associated terms for rare epilepsies, to facilitate text and natural language processing tools for cohort identification and population-based surveillance...
March 2018: Epilepsia Open
Guo-Qiang Zhang, Guangming Xing, Licong Cui
One of the basic challenges in developing structural methods for systematic audition on the quality of biomedical ontologies is the computational cost usually involved in exhaustive sub-graph analysis. We introduce ANT-LCA, a new algorithm for computing all non-trivial lowest common ancestors (LCA) of each pair of concepts in the hierarchical graph induced by an ontology. The computation of LCA is a fundamental step for non-lattice approach for ontology quality assurance. Distinct from existing approaches, ANT-LCA only computes LCAs for non-trivial pairs, those having at least one common ancestor...
March 13, 2018: Journal of Biomedical Informatics
Cristina Soguero-Ruiz, Inmaculada Mora-Jiménez, Javier Ramos-López, Teresa Quintanilla Fernández, Antonio García-García, Daniel Díez-Mazuela, Arcadi García-Alberola, José Luis Rojo-Álvarez
Many indices have been proposed for cardiovascular risk stratification from electrocardiogram signal processing, still with limited use in clinical practice. We created a system integrating the clinical definition of cardiac risk subdomains from ECGs and the use of diverse signal processing techniques. Three subdomains were defined from the joint analysis of the technical and clinical viewpoints. One subdomain was devoted to demographic and clinical data. The other two subdomains were intended to obtain widely defined risk indices from ECG monitoring: a simple-domain (heart rate turbulence (HRT)), and a complex-domain (heart rate variability (HRV))...
March 1, 2018: International Journal of Environmental Research and Public Health
Jonathan P Bona, Werner Ceusters
The fully specified name of a concept in SNOMED CT is formed by a term to which in the typical case is added a semantic tag. The latter is meant to disambiguate homonymous terms and to indicate in which major subhierarchy of SNOMED CT that concept fits. We have developed a method to determine whether a concept's tag correctly identifies its place in the hierarchy, and applied this method to an analysis of all active concepts in every SNOMED CT release from January 2003 to January 2017. Our results show (1) that there are concepts in almost every release whose semantic tag does not match their placement in the hierarchy, (2) that it is primarily disorder concepts that are involved, and (3) that the number of such mismatches increase since the July 2012 version...
February 17, 2018: Journal of Biomedical Informatics
R A M M Kieft, E M Vreeke, E M de Groot, H I de Graaf-Waar, C H van Gool, N Koster, H Ten Napel, A L Francke, D M J Delnoij
BACKGROUND: Nurses register data in electronic health records, which can use various terminology and coding systems. The net result is that information cannot be exchanged and reused properly, for example when a patient is transferred from one care setting to another. A nursing subset of patient problems was therefore developed in the Netherlands, based on comparable and exchangeable terms that are used throughout the healthcare sector and elsewhere (semantic interoperability). The purpose of the current research is to develop a mapping between the subset of patient problems and three classifications in order to improve the exchangeability of data...
March 2018: International Journal of Medical Informatics
Jay G Ronquillo, Chunhua Weng, William T Lester
BACKGROUND:   Precision medicine involves three major innovations currently taking place in healthcare:  electronic health records, genomics, and big data.  A major challenge for healthcare providers, however, is understanding the readiness for practical application of initiatives like precision medicine. OBJECTIVE:   To better understand the current state and challenges of precision medicine interoperability using a national genetic testing registry as a starting point, placed in the context of established interoperability formats...
November 17, 2017: Journal of Innovation in Health Informatics
John D Osborne, Matthew B Neu, Maria I Danila, Thamar Solorio, Steven J Bethard
BACKGROUND: Traditionally text mention normalization corpora have normalized concepts to single ontology identifiers ("pre-coordinated concepts"). Less frequently, normalization corpora have used concepts with multiple identifiers ("post-coordinated concepts") but the additional identifiers have been restricted to a defined set of relationships to the core concept. This approach limits the ability of the normalization process to express semantic meaning. We generated a freely available corpus using post-coordinated concepts without a defined set of relationships that we term "compositional concepts" to evaluate their use in clinical text...
January 10, 2018: Journal of Biomedical Semantics
José Ferreira Mendes, Ana Margarida Ferreira, Cristina Freitas
INTRODUCTION: We intend to evaluate clinically, topographically and morphologically all surgical specimens sent by the Department of Ophthalmology of Hospital de Braga to the Department of Pathology of the same hospital. MATERIAL AND METHODS: Two hundred and fifty eight surgically obtained specimens, from the Department of Ophthalmology of Hospital de Braga, analyzed in the Department of Pathology, from January 2002 to June 2015, were characterized. Data was arranged according to year, age, sex, topography and morphological diagnosis according to the SNOMED® coding system...
November 29, 2017: Acta Médica Portuguesa
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