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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
Licong Cui, Olivier Bodenreider, Jay Shi, Guo-Qiang Zhang
OBJECTIVE: We introduce a structural-lexical approach for auditing SNOMED CT using a combination of non-lattice subgraphs of the underlying hierarchical relations and enriched lexical attributes of fully specified concept names. Our goal is to develop a scalable and effective approach that automatically identifies missing hierarchical IS-A relations. METHODS: Our approach involves 3 stages. In stage 1, all non-lattice subgraphs of SNOMED CT's IS-A hierarchical relations are extracted...
December 20, 2017: Journal of Biomedical Informatics
R A M M Kieft, E M Vreeke, E M de Groot, P A Volkert, A L Francke, D M J Delnoij
BACKGROUND: Since the emergence of electronic health records, nursing information is increasingly being recorded and stored digitally. Several studies have shown that a wide range of nursing information is not interoperable and cannot be re-used in different health contexts. Difficulties arise when nurses share information with others involved in the delivery of nursing care. The aim of this study is to develop a nursing subset of patient problems that are prevalent in nursing practice, based on the SNOMED CT terminology to assist in the exchange and comparability of nursing information...
December 4, 2017: BMC Medical Informatics and Decision Making
Xavier Sanz, Laura Pareja, Ariadna Rius, Pepi Rodenas, Núria Abdón, Jordi Gálvez, Laura Esteban, Josep Maria Escribà, Josep Maria Borràs, Josepa Ribes
SNOMED CT terminology is not backed by standard norms of encoding among pathologists. The vast number of concepts ordered in hierarchies and axes, together with the lack of rules of use, complicates the functionality of SNOMED CT for coding, extracting, and analyzing the data. Defining subgroups of SNOMED CT by discipline could increase its functionality. The challenge lies in how to choose the concepts to be included in a subset from a total of over 300,000. Besides, SNOMED CT does not cover daily need, as the clinical reality is dynamic and changing...
February 2018: Journal of Biomedical Informatics
Majid Rastegar-Mojarad, Sunghwan Sohn, Liwei Wang, Feichen Shen, Troy C Bleeker, William A Cliby, Hongfang Liu
Clinical registries are designed to collect information relating to a particular condition for research or quality improvement. Intuitively, informatics in the area of data management and extraction plays a central role in clinical registries. Due to various reasons such as lack of informatics awareness or expertise, there may be little informatics involvement in designing clinical registries. In this paper, we studied a clinical registry from two critical perspectives, data quality and interoperability, where informatics can play a role...
December 2017: International Journal of Medical Informatics
Chin Lin, Chia-Jung Hsu, Yu-Sheng Lou, Shih-Jen Yeh, Chia-Cheng Lee, Sui-Lung Su, Hsiang-Cheng Chen
BACKGROUND: Automated disease code classification using free-text medical information is important for public health surveillance. However, traditional natural language processing (NLP) pipelines are limited, so we propose a method combining word embedding with a convolutional neural network (CNN). OBJECTIVE: Our objective was to compare the performance of traditional pipelines (NLP plus supervised machine learning models) with that of word embedding combined with a CNN in conducting a classification task identifying International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) diagnosis codes in discharge notes...
November 6, 2017: Journal of Medical Internet Research
Dorinda Mullen, Sarah Mullins, Aoife Doyle, Rachel K Crowley, Stephen Skehan, Enda W McDermott, Ruth S Prichard, David Gibbons
OBJECTIVE: Thyroid nodules are common within the general population. Cytological analysis of fine needle aspirates (FNAs) of these lesions allows for identification of those that require further surgery. A numerical classification system is in place to streamline reporting. The 3a category is used for lesions that are neither benign nor malignant but show atypia of undetermined significance. We reviewed our use and clinical outcomes of Thy3a over a 4-year period. METHODS: All thyroid FNAs performed at this institute from January 2012 to December 2015 were identified from our laboratory information system using SNOMED codes...
September 2017: European Thyroid Journal
Lawrence W C Chan, S C Cesar Wong, Choo Chiap Chiau, Tak-Ming Chan, Liang Tao, Jinghan Feng, Keith W H Chiu
Electronic Health Record (EHR) system enables clinical decision support. In this study, a set of 112 abdominal computed tomography imaging examination reports, consisting of 59 cases of hepatocellular carcinoma (HCC) or liver metastases (so-called HCC group for simplicity) and 53 cases with no abnormality detected (NAD group), were collected from four hospitals in Hong Kong. We extracted terms related to liver cancer from the reports and mapped them to ontological features using Systematized Nomenclature of Medicine (SNOMED) Clinical Terms (CT)...
2017: Journal of Healthcare Engineering
Taqdir Ali, Sungyoung Lee
Use of heterogeneous data models in hospital information systems (HIS), obstructs the integration of clinical decision support system (CDSS) with clinical workflows. The diverse concepts diminish the interoperability level among the CDSS knowledge bases and data models of HIS. Standard terminology utilization in knowledge acquisition and its reconciliation with HIS data models are the candidate solution to overcome the interoperability barrier. We propose a reconciliation model to map concepts of diverse domain clinical models (DCM) with the standard terminology...
July 2017: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Walter S Campbell, Daniel Karlsson, Daniel J Vreeman, Audrey J Lazenby, Geoffrey A Talmon, James R Campbell
Background: The College of American Pathologists (CAP) introduced the first cancer synoptic reporting protocols in 1998. However, the objective of a fully computable and machine-readable cancer synoptic report remains elusive due to insufficient definitional content in Systematized Nomenclature of Medicine - Clinical Terms (SNOMED CT) and Logical Observation Identifiers Names and Codes (LOINC). To address this terminology gap, investigators at the University of Nebraska Medical Center (UNMC) are developing, authoring, and testing a SNOMED CT observable ontology to represent the data elements identified by the synoptic worksheets of CAP...
September 13, 2017: Journal of the American Medical Informatics Association: JAMIA
Lingyun Luo, Ling Tong, Xiaoxi Zhou, Jose L V Mejino, Chunping Ouyang, Yongbin Liu
Organizing the descendants of a concept under a particular semantic relationship may be rather arbitrarily carried out during the manual creation processes of large biomedical terminologies, resulting in imbalances in relationship granularity. This work aims to propose scalable models towards systematically evaluating the granularity balance of semantic relationships. We first utilize "parallel concepts set (PCS)" and two features (the length and the strength) of the paths between PCSs to design the general evaluation models, based on which we propose eight concrete evaluation models generated by two specific types of PCSs: single concept set and symmetric concepts set...
October 4, 2017: Journal of Biomedical Informatics
Keith Danahey, Brittany A Borden, Brian Furner, Patrick Yukman, Sheena Hussain, Donald Saner, Samuel L Volchenboum, Mark J Ratain, Peter H O'Donnell
BACKGROUND: A barrier to the use of genomic information during prescribing is the limited number of software solutions that combine a user-friendly interface with complex medical data. We built and designed an online, secure, electronic custom interface termed the Genomic Prescribing System (GPS). METHODS: Actionable pharmacogenomic (PGx) information was reviewed, collected, and stored in the back-end of GPS to enable creation of customized drug- and variant-specific clinical decision support (CDS) summaries...
September 26, 2017: Journal of Biomedical Informatics
Amit Garg, Jonathan Lavian, Andrew Strunk
BACKGROUND: There are limited data evaluating the utilization of dermatologists for the care of patients with hidradenitis suppurativa. OBJECTIVE: To determine the utilization of the dermatology ambulatory encounter among hidradenitis suppurativa patients, and to evaluate whether utilization varies by insurance status. METHODS: This was a retrospective cohort analysis in an adult population sample of 42,030 hidradenitis suppurativa patients with either private or public health insurance who were identified by a validated scheme using SNOMED-CT terminology...
September 28, 2017: Dermatology: International Journal for Clinical and Investigative Dermatology
Sarah Collins, Stephanie Klinkenberg-Ramirez, Kira Tsivkin, Perry L Mar, Dina Iskhakova, Hari Nandigam, Lipika Samal, Roberto A Rocha
OBJECTIVE: Develop a prototype of an interprofessional terminology and information model infrastructure that can enable care planning applications to facilitate patient-centered care, learn care plan linkages and associations, provide decision support, and enable automated, prospective analytics. DESIGN: The study steps included a 3 step approach: 1) Process model and clinical scenario development, and 2) Requirements analysis, and 3) Development and validation of information and terminology models...
September 19, 2017: Journal of Biomedical Informatics
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