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Improving EHR semantic interoperability: future vision and challenges

Catalina Martínez-Costa, Dipak Kalra, Stefan Schulz
2014 Studies in Health Technology and Informatics  
links the data items to clinical ontologies via user-friendly content patterns.  ...  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  ...  Query patterns based on the ontology content patterns used for the semantic mapping should guide queries.  ... 
pmid:25160254 fatcat:vugqostaarfxbf5f2unbncut4u

Best Paper Selection

2020 IMIA Yearbook of Medical Informatics  
Ontology patterns for the representation of quality changes of cells in time.  ...  UK phenomics platform for developing and validating electronic health record phenotypes: CALIBER.  ...  Validation evidence was established on cross-EHR source concordance, clinical note review, etiology, prognosis, genetic associations, and external population.  ... 
doi:10.1055/s-0040-1702011 fatcat:f4e6koub2zaarkob5ek5zg77fy

Ontology Patterns for Clinical Information Modelling

Catalina Martínez-Costa, Daniel Karlsson, Stefan Schulz
2014 International Semantic Web Conference  
Motivated by our experiences of representing clinical information using OWL DL, which often resulted in highly complex expressions, we propose the use of ontology content patterns to facilitate this task  ...  data, and to guide the creation of clinical models and detect semantic inconsistencies across them.  ...  a great variety of clinical information, we propose the use of semantic patterns as proxy to the semantic representation of clinical information encoded by EHR structured clinical models and ontology-based  ... 
dblp:conf/semweb/Martinez-CostaKS14 fatcat:g3yrujhsw5gwhnnlhpwqnfc5sq

Transformation of standardized clinical models based on OWL technologies: from CEM to OpenEHR archetypes

M. d. C. Legaz-Garcia, M. Menarguez-Tortosa, J. T. Fernandez-Breis, C. G. Chute, C. Tao
2015 JAMIA Journal of the American Medical Informatics Association  
International initiatives pursue the use of semantically interoperable clinical models, and ontologies have frequently been used in semantic interoperability efforts.  ...  Methods Our transformation method exploits the fact that the information models of the most relevant EHR specifications are available in the Web Ontology Language (OWL).  ...  We use structural ontology patterns, which permit the expression of the source clinical model content according to the target information model.  ... 
doi:10.1093/jamia/ocu027 pmid:25670753 pmcid:PMC5566199 fatcat:2to2ilqr7jg6dmbdmiihexo37a

Semantic enrichment of clinical models towards semantic interoperability. The heart failure summary use case

C. Martinez-Costa, R. Cornet, D. Karlsson, S. Schulz, D. Kalra
2015 JAMIA Journal of the American Medical Informatics Association  
These requirements are supported by semantic patterns. Other potential uses of this approach, such as clinical models validation, require further investigation.  ...  Results Using a set of finite top-level patterns to derive semantic patterns, we demonstrate that those patterns, or compositions thereof, can be used to represent information from clinical models.  ...  ACKNOWLEDGEMENTS We thank John Gutai of Accenture for his collaboration in developing the data entry applications used.  ... 
doi:10.1093/jamia/ocu013 pmid:25670758 fatcat:736wvvjvqnc5hljfhdituqrwyq

High-throughput Phenotyping with Temporal Sequences [article]

Hossein Estiri, Thomas H. McCoy, Kavishwar B. Wagholikar, Alyssa P. Goodson, Katie Murphy, Shawn N. Murphy
2019 bioRxiv   pre-print
Using expert labeled clinical data from a congestive heart failure (CHF) cohort, we applied a four-phase framework to mine new data representations from temporal sequences of EHR observations, reduce dimensionality  ...  Our results demonstrated that data representations obtained from sequencing EHR observations can present novel insight about the progression of disease that is difficult to discern when clinical observation  ...  As a result, meaningfully changing clinical care by identifying and validating novel temporal patterns between diseases has seen limited success.  ... 
doi:10.1101/590307 fatcat:sqtbxfzudnhbjiycbku3zrmt3e

A Semantic Transformation Methodology for the Secondary Use of Observational Healthcare Data in Postmarketing Safety Studies

Anil Pacaci, Suat Gonul, A. Anil Sinaci, Mustafa Yuksel, Gokce B. Laleci Erturkmen
2018 Frontiers in Pharmacology  
Use of common data models (CDM) is the predominant approach in order to enable large scale systematic analyses on disparate data models and vocabularies.  ...  Rigorous because the mappings would be based on computer readable semantics which are amenable to validation through logic-based inference methods.  ...  healthcare concepts (e.g., drugs and conditions) in order to enable the secondary use of EHR data for clinical research activities.  ... 
doi:10.3389/fphar.2018.00435 pmid:29760661 pmcid:PMC5937227 fatcat:4rlk2rjckfchbjc64uz7fgxk7u

Medical Concept Embedding with Multiple Ontological Representations

Lihong Song, Chin Wang Cheong, Kejing Yin, William K. Cheung, Benjamin C. M. Fung, Jonathan Poon
2019 Proceedings of the Twenty-Eighth International Joint Conference on Artificial Intelligence  
Medical concepts even under the same ontological category may not follow similar occurrence patterns in the EHR data, leading to contradicting objectives for the representation learning.  ...  In this paper, we propose a deep learning model called MMORE which alleviates this conflicting objective issue by allowing multiple representations to be inferred for each ontological category via an attention  ...  ., 2016a] or in the clinical narratives [Choi et al., 2016c] . Some others make use of the sequential information in the EHR data.  ... 
doi:10.24963/ijcai.2019/641 dblp:conf/ijcai/SongCYCFP19 fatcat:ysqx3oiq4bfmrpl4xt4n5qgd3e

Combining Semantic Web Technologies with Evolving Fuzzy Classifier eClass for EHR-Based Phenotyping: A Feasibility Study [chapter]

M. Arguello, S. Lekkas, J. Des, M.J. Fernandez-Prieto, L. Mikhailov
2014 Research and Development in Intelligent Systems XXXI  
A current bottleneck in using EHRs data for obtaining computable phenotypes is to transform the raw EHR data into clinically relevant features.  ...  from 1956 clinical statements from EHRs.  ...  Nowadays, validation of EHR-based phenotypes remains an important aspect of their use.  ... 
doi:10.1007/978-3-319-12069-0_15 dblp:conf/sgai/CasteleiroLDPM14 fatcat:qvhxa4s4lfc3lij6obv42h7wii

Design and Use of Semantic Resources: Findings from the Section on Knowledge Representation and Management of the 2020 International Medical Informatics Association Yearbook

Ferdinand Dhombres, Jean Charlet, Section Editors for the IMIA Yearbook Section on Knowledge Representation and Management
2020 IMIA Yearbook of Medical Informatics  
Besides new ontologies and sound methodological guidance to rethink knowledge bases design, we observed large scale applications, promising results for phenotypes characterization, semantic-aware machine  ...  Validation evidence was established on cross-EHR source concordance, clinical note review, etiology, prognosis, genetic associations, and external population.  ...  They analyze the performance of each pattern with respect to standard criteria used in software engineering and data modeling, i.e., simplicity, scalability, extensibility, and adequacy.  ... 
doi:10.1055/s-0040-1702010 pmid:32823311 fatcat:rpbzawie7nf3hl5jzc6ttfycte

Developing a Semantic Web-based Framework for Executing the Clinical Quality Language Using FHIR

Guoqian Jiang, Eric Prud'hommeaux, Harold Solbrig
2017 Workshop on Semantic Web Applications and Tools for Life Sciences  
FHIR adopts RDF as its third representation/interchange format in addition to XML and JSON, and uses the Shape Expressions (ShEx) schema to standardize and validate the FHIR RDF graphs.  ...  of any specific data model (e.g., Quality Data Model, HL7 Fast Healthcare Interoperability Resources -FHIR).  ...  FHIR metadata vocabulary and an open-source Ontology-based Data Access (OBDA) system Ontop 11, 14 , in which an OHDSI virtual machine 12 is used to provide sample clinical research data for the testing  ... 
dblp:conf/swat4ls/JiangPS17 fatcat:abilfss67rf5nazskl3icyk27q

Experiments to Create Ontology-based Disease Models for Diabetic Retinopathy from Different Biomedical Resources

Mercedes Argüello Casteleiro, Catalina Martínez-Costa, Jose Julio Des Diz, Maria Jesus Fernandez Prieto, Chris Wroe, Diego Maseda-Fernandez, George Demetriou, Goran Nenadic, John A. Keane, Stefan Schulz, Robert Stevens
2017 Workshop on Semantic Web Applications and Tools for Life Sciences  
Secondly, we use content ontology design patterns with Bio-TopLite2 and SNOMED CT that act as templates to semantically represent clinical content in OWL. We report on the effectiveness of the method.  ...  records; 2) the clinical practice guideline for DR by the American Academy of Ophthalmology; 3) the BMJ Best Practice for DR; and 4) neural language models from Deep Learning (CBOW and Skip-gram) using  ...  Arguably, the best resources to obtain disease models for DR are the CPG for DR by the AAO [2] and the BMJ Best Practice for DR [3] .  ... 
dblp:conf/swat4ls/CasteleiroMDPWM17 fatcat:hrvg6bup7vh25cowtj56uqdsua

OWL-based reasoning methods for validating archetypes

Marcos Menárguez-Tortosa, Jesualdo Tomás Fernández-Breis
2013 Journal of Biomedical Informatics  
The validation method consists of reasoning on those ontologies to find modeling errors in archetypes: incorrect restrictions over the reference model, non-conformant archetype specializations and inconsistent  ...  Some modern Electronic Healthcare Record (EHR) architectures and standards are based on the dual model-based architecture, which defines two conceptual levels: reference model and archetype model.  ...  This material includes SNOMED Clinical Terms (SNOMED-CT) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO). All rights reserved.  ... 
doi:10.1016/j.jbi.2012.11.009 pmid:23246613 fatcat:iagesbyienhofmqsrmiflle4eu

Semantically Inspired Electronic Healthcare Records [chapter]

Kamran Farooq, Amir Hussain, Stephen Leslie, Chris Eckl, Calum MacRae, Warner Slack
2012 Lecture Notes in Computer Science  
The Patient Semantic Profile specifically developed for generating EHRs has been validated using a sample of real patients' data acquired from the Raigmore Hospital's RACPC (Rapid Access Chest Pain Clinic  ...  Using ontologies is a cost effective and pragmatic solution to implementing a shift from simple patient interviewing systems to more intelligent systems in the primary and secondary care.  ...  We modelled clinical data of RACPC patients using Patient Semantic profile ontology.  ... 
doi:10.1007/978-3-642-31561-9_5 fatcat:d6oomvk52zbffdcjeaf36bpl24

Discovering and Comparing Relational Knowledge, the Example of Pharmacogenomics

Pierre Monnin
2018 International Conference Knowledge Engineering and Knowledge Management  
or clinical counterpart.  ...  Additionally, Electronic Health Records of hospitals can be mined to discover such knowledge units that can then be compared with the state of the art, in order to confirm or temper relationships lacking validation  ...  Similarly, Beyan and Decker [4] proposed to use RDF to model temporal relations in EHRs. Indeed, the flexible schema of RDF graphs seems suited to the sparsity and heterogeneousness of EHRs data.  ... 
dblp:conf/ekaw/Monnin18 fatcat:vtgfjv3c2fffhb6t37dmxqblje
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