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The freetext matching algorithm: a computer program to extract diagnoses and causes of death from unstructured text in electronic health records

Anoop D Shah, Carlos Martinez, Harry Hemingway
2012 BMC Medical Informatics and Decision Making  
We present a platform that combines an approach to semantic extraction of medical information from clinical free-text documents with the processing of structured information from HIS records.  ...  The information extraction process uses a fine-grained linguistic analysis, and maps preprocessed terms to the concepts of domain-specific ontologies.  ...  CDR clients are data-source adapters for storage of structured data or raw clinical texts, enrichment algorithms that produce semantically enriched facts.  ... 
doi:10.1186/1472-6947-12-88 pmid:22870911 pmcid:PMC3483188 fatcat:qvffnbot5jdormq6dgoyephymq

Patient and Graph Embeddings for Predictive Diagnosis of Drug Iatrogenesis [chapter]

Lina F. Soualmia, Vincent Lafon, Stéfan J. Darmoni
2021 Studies in Health Technology and Informatics  
In the context of the IA.TROMED project we intend to develop and evaluate original algorithmic methods that will rely on semantic enrichment of embeddings by combining new deep learning algorithms, such  ...  a layer that will play the role of a queryable and searchable knowledge base that will supply the IA.TROMED's clinical, predictive, and iatrogenic diagnosis support module.  ...  Automatic analysis is performed on heterogeneous data sources, based on a layer of learnt/semantically enriched models (documents, graphs, patients embeddings).  ... 
doi:10.3233/shti210205 pmid:34042611 fatcat:u4vjos5nbnc4bkweuy3yuohflm

Automatic Data Transfer from OMOP-CDM to REDCap: A Semantically-Enriched Framework [chapter]

Emanuele Girani, Matteo Gabetta, Anna Alloni, Morena Stuppia, Lucia Sacchi, Nicola Barbarini
2021 Studies in Health Technology and Informatics  
The aim of this work is proposing a semantically-enriched framework to support automatic data transfer from OMOP CDM to REDCap eCRF.  ...  Thus, the systematic reuse of Real World Data (mainly EHR data) to automatically fill in eCRF may represent a turning point in clinical trials [1] .  ... 
doi:10.3233/shti210805 pmid:34795074 fatcat:zc76vatr3ffbteur5tj3bz4cqm

Evidence-Based Clinical Guidelines in SemanticCT [chapter]

Qing Hu, Zhisheng Huang, Frank van Harmelen, Annette ten Teije, Jinguang Gu
2014 Communications in Computer and Information Science  
That lightweight formalisation of clinical guidelines have been integrated with SemanticCT, a semantically-enabled system for clinical trials.  ...  We have developed several tools to generate semantic data from textual guidelines. We show how they are useful in SemanticCT for the applications of the Semantic Web technology in medical domains.  ...  In this paper, we will report how this approach of the semantics enriched formalization is integrated with SemanticCT, a semantically-enabled system for clinical trials [7] .  ... 
doi:10.1007/978-3-662-45495-4_18 fatcat:nky7a7xidndavgudendoiqnyai

Extracting Clinical Relations in Electronic Health Records Using Enriched Parse Trees

Jisung Kim, Yoonsuck Choe, Klaus Mueller
2015 Procedia Computer Science  
We study six different parse tree structures enriched with various semantic features for determining entity relations in clinical notes using a tree kernel-based relation extraction system.  ...  Our study demonstrates that parse tree enhancements with semantic features are effective for clinical relation extraction.  ...  To the best of our knowledge, no prior work exists in using parse tree enrichment methods for clinical text.  ... 
doi:10.1016/j.procs.2015.07.304 fatcat:vtsjahclvjcp3lyh4ihi5pqesa

Semantic enrichment of longitudinal clinical study data using the CDISC standards and the semantic statistics vocabularies

Hugo Leroux, Laurent Lefort
2015 Journal of Biomedical Semantics  
Methods: We propose a Linked Clinical Data Cube (LCDC), which combines the strength of the RDF Data Cube and DDI-RDF vocabulary to enrich clinical data based on the CDISC standards.  ...  This paper explores the integration of clinical study data exchange standards and semantic statistic vocabularies to deliver clinical data as linked data in a format that is easier to enrich with links  ...  Mr Simon McBride for reviewing the paper and to Mr Simon Gibson and Mr Louis Delachat for their assistance in the project.  ... 
doi:10.1186/s13326-015-0012-6 pmid:25973166 pmcid:PMC4429421 fatcat:6x5e2y3luzbmvafdz7nfuzdbay

Improving the FAIRness of Health Studies in Germany: The German Central Health Study Hub COVID-19 [chapter]

Johannes Darms, Jörg Henke, Xioaming Hu, Carsten Oliver Schmidt, Martin Golebiewski, Juliane Fluck, NFDI4Health Task Force COVID-19
2021 Studies in Health Technology and Informatics  
It combines metadata and other information of epidemiologic, public health and clinical studies into a single data repository for FAIR data access.  ...  Study metadata and survey instruments are decomposed into individual data items and semantically enriched to ease the findability.  ...  We gratefully acknowledge the financial support of the German Research Foundation (DFG) -Project Number 451265285, and from the Klaus Tschira Foundation (KTS).  ... 
doi:10.3233/shti210818 pmid:34795085 fatcat:6vygu5g2evd2piogc2tkeznrhi

Integrated Data Management for Clinical Studies: Automatic Transformation of Data Models with Semantic Annotations for Principal Investigators, Data Managers and Statisticians

Martin Dugas, Susanne Dugas-Breit, Chris Mavergames
2014 PLoS ONE  
Citation: Dugas M, Dugas-Breit S (2014) Integrated Data Management for Clinical Studies: Automatic Transformation of Data Models with Semantic Annotations for Principal Investigators, Data Managers and  ...  Case report forms (CRFs) specify the data model of study subjects, evolve over time and consist of hundreds to thousands of data items per study.  ...  As a third step, the transformation from office into EDC format was tested for a larger set of forms from clinical trials.  ... 
doi:10.1371/journal.pone.0090492 pmid:24587378 pmcid:PMC3938746 fatcat:nux2yeui2bcipexzaym6rik4v4

ACGT newsletter (Farewell article)

Jessica Michel Assoumou, Manolis Tsiknakis
2010 ecancermedicalscience  
Its high level objective has been the development of methods and systems for improved medical knowledge discovery and understanding through integration of biomedical information (e.g. using modeling, visualization  ...  During the course of the four and a half years of its life, the project has defined a detailed architectural blueprint and has developed, tested and validated a range of technologies, such as: • new, domain-specific  ...  Master Ontology on Cancer and use standard clinical and genomic ontologies and metadata for the semantic integration of heterogeneous databases; • an ontology based Trial Builder for helping to easily  ... 
doi:10.3332/ecancer.2010.ed8 pmid:24966883 pmcid:PMC4024806 fatcat:mxh2yxsytjhvxh4prraxlm3wp4

Text-mining approach to evaluate terms for ontology development

Lam C. Tsoi, Ravi Patel, Wenle Zhao, W. Jim Zheng
2009 Journal of Biomedical Informatics  
We have developed a computational method based on a hypergeometric enrichment test to evaluate the relevance of such terms to the intended domain.  ...  While each participant may contribute to construct a list of terms for ontology development, no objective methods have been developed to evaluate how relevant each of these terms is to the intended domain  ...  Acknowledgments The work was inspired by the Ontology of Clinical Investigation project and benefited from many discussions with the group. We also thank Dr.  ... 
doi:10.1016/j.jbi.2009.03.009 pmid:19318137 pmcid:PMC3153945 fatcat:lb7xtcwtrzbldnv2tvzcx2e3ua

Building a Library of Eligibility Criteria to Support Design of Clinical Trials [chapter]

Krystyna Milian, Anca Bucur, Frank van Harmelen
2012 Lecture Notes in Computer Science  
The paper presents the first steps, a method for automatic comparison of criteria content and the library of structured and ordered eligibility criteria that can be browsed with the fine-grained queries  ...  The completion of clinical trial depends on sufficient participant enrollment, which is often difficult due to the restrictiveness of eligibility criteria, and effort required to verify patient eligibility  ...  Another rich source of clinical trial data is provided by the LinkedCT project, which publishes data as RDF, according to the principles of Linked Data, enriched with the links to other sources.  ... 
doi:10.1007/978-3-642-33876-2_29 fatcat:k7syaqnfkregpcx5vzpppjvn5a

Molecularly and clinically related drugs and diseases are enriched in phenotypically similar drug-disease pairs

Ingo Vogt, Jeanette Prinz, Mónica Campillos
2014 Genome Medicine  
We assessed and visualized the enrichment over random of clinical and molecular relationships among drug-disease pairs that share phenotypes using lift plots.  ...  Methods: We present here the first analysis of phenotypically related drug-disease pairs.  ...  Acknowledgements The authors gratefully acknowledge Michael Kuhn for providing the STITCH data and Lucia Himmelein and Bernd Streppel for their valuable assistance in compiling phenotypic data.  ... 
doi:10.1186/s13073-014-0052-z pmid:25276232 pmcid:PMC4165361 fatcat:3j3xn2zig5hqrkkowsaz7ojvkq

CDEGenerator: an online platform to learn from existing data models to build model registries

Julian Varghese, Michael Fujarski, Stefan Hegselmann, Philipp Neuhaus, Martin Dugas
2018 Clinical Epidemiology  
Results: The analysis and item-tailoring module provides multilingual comparisons of semantically complex eligibility criteria of clinical trials.  ...  A novel Internet-based method for rapid comparison of published data models was implemented to enable reuse, customization, and harmonization of item catalogs for the early planning and development phase  ...  Acknowledgment This project is funded by the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG grant DU 352/11-1). Disclosure The authors report no conflicts of interest in this work.  ... 
doi:10.2147/clep.s170075 pmid:30127646 pmcid:PMC6089100 fatcat:7xrv52x5jjhtpintzgtyvjhfji

SNOMED CT normal form and HL7 RIM binding to normalize clinical data from cancer trials

Antonio Rico-Diez, Santiago Aso, David Perez-Rey, Raul Alonso-Calvo, Anca Bucur, Brecht Claerhout, Victor Maojo
2013 13th IEEE International Conference on BioInformatics and BioEngineering  
Results suggest that the level of semantic interoperability required to manage patient data in modern clinical trials on breast cancer can be achieved with the proposed methodology.  ...  In this field, the EU funded INTEGRATE project aims to develop the basic knowledge to allow data sharing of data from post-genomic clinical trials on breast cancer.  ...  METHODS In the process of managing data from breast cancer clinical trials, data from different and heterogeneous sources have to be integrated.  ... 
doi:10.1109/bibe.2013.6701688 dblp:conf/bibe/Rico-DiezAPABCM13 fatcat:e3ku47ko65f4fk7i2bu5vfcg2a

iSMART: Ontology-based Semantic query of CDA documents

Shengping Liu, Yuan Ni, Jing Mei, Hanyu Li, Guotong Xie, Gang Hu, Haifeng Liu, Xueqiao Hou, Yue Pan
2009 AMIA Annual Symposium Proceedings  
In this paper, we present iSMART (interactive Semantic MedicAl Record reTrieval), a prototype system designed for ontology-based semantic query of CDA documents.  ...  The Health Level 7 Clinical Document Architecture (CDA) is widely accepted as the format for electronic clinical document.  ...  Acknowledgement We thank GuangDong Hospital of Traditional Chinese Medicine for their great supports.  ... 
pmid:20351883 pmcid:PMC2815425 fatcat:eghhst7zf5fbngsltzbaww5gii
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