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SemanticCT: A Semantically-Enabled System for Clinical Trials [chapter]

Zhisheng Huang, Annette ten Teije, Frank van Harmelen
2013 Lecture Notes in Computer Science  
In this paper, we propose an approach of semantically enabled systems for clinical trials.  ...  We have implemented the proposed approach in a system called Se-manticCT. SemanticCT is built on the top of LarKC (Large Knowledge Collider), a platform for scalable semantic data processing.  ...  In [2] the authors present a method, entirely based on standard semantic web technologies and tool, that allows the automatic recruitment of a patient to the available clinical trials.  ... 
doi:10.1007/978-3-319-03916-9_2 fatcat:fqlcfon6crckjcok6g3qkxfwvy

Rule-Based Formalization of Eligibility Criteria for Clinical Trials [chapter]

Zhisheng Huang, Annette ten Teije, Frank van Harmelen
2013 Lecture Notes in Computer Science  
We have implemented the proposed rule-based formalization in SemanticCT, a semantically-enabled system for clinical trials, showing the feasibility of using our rule-based formalization of eligibility  ...  In this paper, we propose a rule-based formalization of eligibility criteria for clinical trials. The rule-based formalization is implemented by using the logic programming language Prolog.  ...  In our approach we first do the modeling of the eligibility criteria based on the three different levels of knowledge in a rule-based approach and then we do the matching against the patient data automatically  ... 
doi:10.1007/978-3-642-38326-7_7 fatcat:ispiytltjbcypowztqoam4qapy

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  
In this paper, we present a semantic approach of evidence-based clinical guidelines.  ...  That lightweight formalisation of clinical guidelines have been integrated with SemanticCT, a semantically-enabled system for clinical trials.  ...  In this paper, we have introduced the semantic approach of evidence-based clinical guidelines in which evidence-based clinical guidelines are represented as the Semantic Web standards such as RDF/RDFS/  ... 
doi:10.1007/978-3-662-45495-4_18 fatcat:nky7a7xidndavgudendoiqnyai

Analysis of the Suitability of Existing Medical Ontologies for Building a Scalable Semantic Interoperability Solution Supporting Multi-site Collaboration in Oncology

Ahmed Ibrahim, Anca Bucur, Andre Dekker, M. Scott Marshall, David Perez-Rey, Raul Alonso-Calvo, Holger Stenzhorn, Sheng Yu, Cyril Krykwinski, Anouar Laarif, Keyur Mehta
2014 2014 IEEE International Conference on Bioinformatics and Bioengineering  
criteria, of the clinical trial data (e.g., Clinical Report Forms), and of the corresponding patient record data that would enable the automatic identification of eligible patients.  ...  An important objective of this work is to create a semantic link between clinical research and care environments to enable applications such as streamlining the execution of multi-centric clinical trials  ...  In [7] the authors present a method that uses the Web Ontology Language (OWL) and the Semantic Web Rule Language (SWRL) for automatic recruitment of a patient to available clinical trials.  ... 
doi:10.1109/bibe.2014.12 dblp:conf/bibe/IbrahimBDMPASYK14 fatcat:npctwn5x5rfj3mdavk3ktzs2bm

An interactive retrieval system for clinical trial studies with context-dependent protocol elements

Junseok Park, Seongkuk Park, Kwangmin Kim, Woochang Hwang, Sunyong Yoo, Gwan-Su Yi, Doheon Lee
2020 PLoS ONE  
Based on the database, we developed a web application called the clinical trial protocol database system (CLIPS; available at  ...  In this study, we present a database system with a context-dependent and protocol-element-selection function for successfully designing a clinical trial protocol.  ...  Acknowledgments We would like to thank David Sharpe for his cooperation in using ChemSpider APIs and Seyol Yoon for helping us select phenotypic TUIs from UMLS.  ... 
doi:10.1371/journal.pone.0238290 pmid:32946464 pmcid:PMC7500653 fatcat:cswx67mqv5gitd5lucne4uvgvy

DebugIT: Ontology-mediated Layered Data Integration for Real-time Antibiotics Resistance Surveillance

Daniel Schober, Rémy Choquet, Kristof Depraetere, Frank Enders, Philipp Daumke, Marie-Christine Jaulent, Douglas Teodoro, Emilie Pasche, Christian Lovis, Martin Boeker
2014 Workshop on Semantic Web Applications and Tools for Life Sciences  
We present an ontology-based integration approach serving an EU project in making antibiotics resistance data semantically and geographically interoperable.  ...  The data semantics is formalized by multiple layers of terminology-bound description logic ontologies.  ...  Conflict of Interest We declare that there are no conflicts of interest. 10 References  ... 
dblp:conf/swat4ls/SchoberCDEDJTPLB14 fatcat:5lcrnf6kcbeaxptf2fuhkshb5m

LinkedCT: A Linked Data Space for Clinical Trials [article]

Oktie Hassanzadeh, Anastasios Kementsietsidis, Lipyeow Lim, Renee J. Miller, Min Wang
2009 arXiv   pre-print
Our approach for semantic link discovery involves using state-of-the-art approximate string matching techniques combined with ontology-based semantic matching of the records, all performed in a declarative  ...  The Linked Clinical Trials (LinkedCT) project aims at publishing the first open semantic web data source for clinical trials data.  ...  Creating a single web data source of clinical trials data that is highly interlinked with existing medical data sources and that can be queried with semantically rich and complex queries, is a challenging  ... 
arXiv:0908.0567v1 fatcat:i5if25dtvbfwbnrecypdg2ny7y

Exploiting Ontology Based Search and EHR Interoperability to Facilitate Clinical Trial Design [chapter]

Anastasios Tagaris, Vassiliki Andronikou, Efthymios Chondrogiannis, George Tsatsaronis, Michael Schroeder, Theodora Varvarigou, Dionysios-Dimitrios Koutsouris
2014 Annals of Information Systems  
They focus on single interventions, whereas the clinical practice environment comprises various features that affect the efficacy, feasibility, duration and costs of a clinical trial.  ...  and disease knowledge databases, clinical care and clinical research information systems, and guiding the users automatically though the whole pipeline of the clinical trial protocol design.  ...  Such an approach, would primarily serve the purpose of aiding the Principal Investigator (PI) to formulate precisely and unambiguously the main research hypothesis based on which, the clinical trial will  ... 
doi:10.1007/978-3-319-06844-2_3 fatcat:2wzn2qrapjhv3pchtpx5dn73gq

An interactive retrieval system for clinical trial studies with context-dependent protocol elements [article]

JunSeok Park, Kwangmin Kim, Seongkuk Park, Woochang Hwang, Sunyong Yoo, Gwansu Yi, Doheon Lee
2019 bioRxiv   pre-print
Moreover, we developed a web application called the clinical trial protocol database system (CLIPS; available at, which enables an interactive search based on protocol elements  ...  A clinical trial protocol defines the procedural methods that should be performed during a clinical trial. Every clinical trial starts with the design of its protocol.  ...  Acknowledgment We would like to thank David Sharpe for his cooperation in using ChemSpider APIs and Seyol Yoon for helping us select phenotypic TUIs from UMLS.  ... 
doi:10.1101/814996 fatcat:p4ze7qezkbf2pn7bbar3xti3wq

Active Semantic Electronic Medical Record [chapter]

A. Sheth, S. Agrawal, J. Lathem, N. Oldham, H. Wingate, P. Yadav, K. Gallagher
2006 Lecture Notes in Computer Science  
This showcases an application of Semantic Web in health care, especially small clinics.  ...  Active Semantic Electronic Medical Record (ASEMR) application discussed here uses Semantic Web technologies to reduce medical errors, improve physician efficiency with accurate completion of patient charts  ...  Kashyap et al present a semantics-based approach to automate structured clinical documentation based on a description logics (DL) system for ontology management in [5] .  ... 
doi:10.1007/11926078_66 fatcat:ngh66c5tafdjzbr5qjidgeauee

A federated semantic metadata registry framework for enabling interoperability across clinical research and care domains

A. Anil Sinaci, Gokce B. Laleci Erturkmen
2013 Journal of Biomedical Informatics  
framework is introduced which brings together the power of metadata registries (MDR) and semantic web technologies.  ...  marketing safety analysis studies on top of existing EHR systems.  ...  The Roche Global Data Standards Repository (GDSR) [23] MDR has been implemented based on semantic web technologies as a triple store.  ... 
doi:10.1016/j.jbi.2013.05.009 pmid:23751263 fatcat:gssi4yalivexvnw7qgn7n2zxju

Dynamic categorization of clinical research eligibility criteria by hierarchical clustering

Zhihui Luo, Meliha Yetisgen-Yildiz, Chunhua Weng
2011 Journal of Biomedical Informatics  
Objective: To semi-automatically induce semantic categories of eligibility criteria from text and to automatically classify eligibility criteria based on their semantic similarity.  ...  Design: The UMLS semantic types and a set of previously developed semantic preference rules were utilized to create an unambiguous semantic feature representation to induce eligibility criteria categories  ...  Its contents are solely the responsibility of the authors and do not necessarily represent the official view of NIH.  ... 
doi:10.1016/j.jbi.2011.06.001 pmid:21689783 pmcid:PMC3183114 fatcat:gtpyli2fa5gktgph6yoqcdlfni

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.  ...  This strategy of combining automatic and supervised fact generation promises to be a reasonable approach to improving the semantic exploitation of data.  ... 
doi:10.1186/1472-6947-12-88 pmid:22870911 pmcid:PMC3483188 fatcat:qvffnbot5jdormq6dgoyephymq

The p-medicine portal-a collaboration platform for research in personalised medicine

Fatima Schera, Gabriele Weiler, Elias Neri, Stephan Kiefer, Norbert Graf
2014 ecancermedicalscience  
In this document, we describe the community-based structure of the p-medicine portal and provide information about the p-medicine security framework implemented in the portal.  ...  to improve personalised treatments of patients.  ...  The authors would like to thank all the developers of p-medicine tools and services integrated into the portal who provided us with the possibility of completing this paper.  ... 
doi:10.3332/ecancer.2014.398 pmid:24567755 pmcid:PMC3919481 fatcat:4rz4qjn5tfej5niq2zf2pl5igq

Computable Eligibility Criteria through Ontology-driven Data Access: A Case Study of Hepatitis C Virus Trials

Hansi Zhang, Zhe He, Xing He, Yi Guo, David R Nelson, François Modave, Yonghui Wu, William Hogan, Mattia Prosperi, Jiang Bian
2018 AMIA Annual Symposium Proceedings  
We implemented our approach based on an analysis of the eligibility criteria from 77 Hepatitis C trials.  ...  We built a prototype system that helps researchers write computable eligibility criteria and execute them against clinical data in real-time to find potential trial cohorts.  ...  The HCV clinical trial Computable Eligibility Criteria Cohort Identification (HCV-CECCI) web application We created a prototype web-based application, HCV-CECCI, to facilitate the construction of CEC and  ... 
pmid:30815206 pmcid:PMC6371316 fatcat:36q2bjp6x5axnesaoxfmneebtu
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