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TIM: A Semantic Web Application for the Specification of Metadata Items in Clinical Research

Matthias Löbe, Magnus Knuth, Roland Mücke
2009 Workshop on Semantic Web Applications and Tools for Life Sciences  
This paper presents a Semantic-Web-based application for specifying metadata items in clinical research and life sciences.  ...  We developed an ontology for item modeling and an application for managing a repository of items based on W3C standards.  ...  Application We present a tool called Trial Item Manager (TIM). It is based on Semantic Web technology and can be used to create CRFs and to manage clinical trial items.  ... 
dblp:conf/swat4ls/LobeKM09 fatcat:tqjmdnatcjgephlobdmkn7kg5u

Minimal Information for Neural Electromagnetic Ontologies (MINEMO): A standards-compliant method for analysis and integration of event-related potentials (ERP) data

Gwen Frishkoff, Jason Sydes, Kurt Mueller, Robert Frank, Tim Curran, John Connolly, Kerry Kilborn, Dennis Molfese, Charles Perfetti, Allen Malony
2011 Standards in Genomic Sciences  
Checklist terms are explicated in NEMO, a formal ontology that is designed to support ERP data sharing and integration. MINEMO is also linked to an ERP database and web application (the NEMO portal).  ...  Together these spatial, temporal, and functional metadata provide a complete description of ERP data and the context in which these data were acquired.  ...  To this end, we created a web application (the NEMO portal), database and services that enable NEMO users to record their experiment metadata online through a simple web interface at the same time that  ... 
doi:10.4056/sigs.2025347 pmid:22180824 pmcid:PMC3235514 fatcat:4c5q62ouwveynjldh3ztqo2pli

Semantically enabling a genome-wide association study database

Tim Beck, Robert C Free, Gudmundur A Thorisson, Anthony J Brookes
2012 Journal of Biomedical Semantics  
The Semantic Web provides standards for the possibility of further integration of GWAS data and the ability to contribute to the web of Linked Data.  ...  Conclusions: We present a methodology for applying phenotype annotations to a comprehensive genome-wide association dataset and for ensuring compatibility with the Semantic Web.  ...  Acknowledgements We thank the curation team of Robert Hastings, Sirisha Gollapudi and Raheleh Rahbari for providing the high-quality phenotype annotations within GWAS Central.  ... 
doi:10.1186/2041-1480-3-9 pmid:23244533 pmcid:PMC3579732 fatcat:nepqhbjc5rblpd3ckwriiaw7ge

Interoperability and FAIRness through a novel combination of Web technologies

Mark D. Wilkinson, Ruben Verborgh, Luiz Olavo Bonino da Silva Santos, Tim Clark, Morris A. Swertz, Fleur D.L. Kelpin, Alasdair J.G. Gray, Erik A. Schultes, Erik M. van Mulligen, Paolo Ciccarese, Arnold Kuzniar, Anand Gavai (+4 others)
2017 PeerJ Computer Science  
The lack of uniformity in data models from one repository to another, and in the richness and availability of metadata descriptions, makes integration and analysis of these data a manual, time-consuming  ...  Data in the life sciences are extremely diverse and are stored in a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG for pathway data or UniProt for protein  ...  ACKNOWLEDGEMENTS In January 2014 the Lorentz Center hosted the 'Jointly Designing a Data FAIRport' workshop.  ... 
doi:10.7717/peerj-cs.110 fatcat:lvtxp7pex5dkzmbdfswepyn2h4

Produce and Consume Linked Data with Drupal! [chapter]

Stéphane Corlosquet, Renaud Delbru, Tim Clark, Axel Polleres, Stefan Decker
2009 Lecture Notes in Computer Science  
Particularly, large amounts of RDF data can now be accessed over the Web as Linked Data and built into Web applications [11] .  ...  We believe RDF is a good candidate for improving interoperability between sites because RSS can only carry a flat list of news item, while RDF can express any structured data and -by RDFS and OWL -even  ...  In combination, all four modules offer new possibilities to create networked Web applications and pushing further population of the Web of Data by significantly lowering entry barriers for a large user  ... 
doi:10.1007/978-3-642-04930-9_48 fatcat:vwydto3d6newlaswb73poqytda

Using the Micropublications Ontology and the Open Annotation Data Model to Represent Evidence within a Drug-Drug Interaction Knowledge Base

Jodi Schneider, Paolo Ciccarese, Tim Clark, Richard D. Boyce
2014 International Semantic Web Conference  
In this paper, we describe the context and goals of our work, propose competency questions for a dynamic PDDI evidence base, outline our new knowledge representation model for PDDIs, and discuss the challenges  ...  Semantic web technologies can support the rapid and transparent validation of scientific claims by interconnecting the assumptions and evidence used to support or challenge assertions.  ...  The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement n o 246016, and a grant from the National Library of  ... 
dblp:conf/semweb/SchneiderCCB14 fatcat:h2iclcjpnrarllosrv5p4mcrxe

The SWAN biomedical discourse ontology

Paolo Ciccarese, Elizabeth Wu, Gwen Wong, Marco Ocana, June Kinoshita, Alan Ruttenberg, Tim Clark
2008 Journal of Biomedical Informatics  
The SWAN ontology has been developed in the context of building a series of applications for biomedical researchers, as well as in extensive discussions and collaborations with the larger bio-ontologies  ...  SWAN (Semantic Web Applications in Neuromedicine) is an interdisciplinary project to develop a practical, common, semantically structured, framework for biomedical discourse initially applied, but not  ...  Acknowledgements We are grateful to the Ellison Medical Foundation, the Alzheimer Association, Eli Lilly and Company, and to an anonymous foundation, for their generous support of the SWAN project.  ... 
doi:10.1016/j.jbi.2008.04.010 pmid:18583197 pmcid:PMC4536833 fatcat:mtq6hvo565g65dtwuvdifo7e5y

Semantic Annotation: The Mainstay of Semantic Web

Thabet Slimani
2013 International Journal of Computer Applications Technology and Research  
However, semantic annotation of the web documents is the successful way to make the Semantic Web vision a reality.  ...  Given that semantic Web realization is based on the critical mass of metadata accessibility and the representation of data with formal knowledge, it needs to generate metadata that is specific, easy to  ...  However, the requirement of massive metadata for the web content allows various Semantic Web applications to appear and gain broad approval.  ... 
doi:10.7753/ijcatr0206.1025 fatcat:ef366mdcdzbc3j3c5pheiubtou

PAV ontology: provenance, authoring and versioning

Paolo Ciccarese, Stian Soiland-Reyes, Khalid Belhajjame, Alasdair JG Gray, Carole Goble, Tim Clark
2013 Journal of Biomedical Semantics  
We present the Provenance, Authoring and Versioning ontology (PAV): a lightweight ontology for capturing just enough descriptions essential for tracking the provenance, authoring and versioning of web  ...  Provenance is a critical ingredient for establishing trust of published scientific content.  ...  We thank the Journal of Biomedical Semantics reviewers, who provided valuable feedback which led to further improvements of the ontology and this paper.  ... 
doi:10.1186/2041-1480-4-37 pmid:24267948 pmcid:PMC4177195 fatcat:qslnq733evhktl5fviicm24jce

Analysis of professional competencies for the clinical research data management profession: implications for training and professional certification

Meredith N Zozus, Angel Lazarov, Leigh R Smith, Tim E Breen, Susan L Krikorian, Patrick S Zbyszewski, Shelly K Knoll, Debra A Jendrasek, Derek C Perrin, Demetris N Zambas, Tremaine B Williams, Carl F Pieper
2017 JAMIA Journal of the American Medical Informatics Association  
The increases in the types of data managed and variety of research settings in which data are managed indicate a need for formal education in principles and methods that can be applied to different research  ...  Conclusion: The results document the scope of the profession and will serve as a foundation for the next revision of the Certified Clinical Data Manager TM exam.  ...  For clinical research data management, we defined 3 important application contexts: the type of study for which the data will be managed, the research setting in which the data will be managed, and the  ... 
doi:10.1093/jamia/ocw179 pmid:28339721 pmcid:PMC6080682 fatcat:d7xnsni53bf4xhyrss2fk5ktui

Investigating a new tablet-based telerehabilitation app in patients with aphasia: a randomised, controlled, evaluator-blinded, multicentre trial protocol

Arif Sinan Uslu, Stephan M Gerber, Nadine Schmidt, Carina Röthlisberger, Patric Wyss, Tim Vanbellingen, Sandra Schaller, Corina Wyss, Monica Koenig-Bruhin, Thomas Berger, Thomas Nyffeler, René Müri (+2 others)
2020 BMJ Open  
Both groups will train over a period of 4 weeks for 2 hours per day.  ...  Patients in the experimental condition will devote 80% of their training time to teleSLT and the remaining 20% (24 min/day) to teleCT, vice versa for patients in the control condition.  ...  Collections are intended to train a specific language impairment (eg, semantically categorising items). Patients are free to select specific collections from among the assigned ones.  ... 
doi:10.1136/bmjopen-2020-037702 pmid:33177134 fatcat:bujvgnsvnzg33ojxappv5xh7pe

A Survey Of Semantic Integration Approaches In Bioinformatics

Chaimaa Messaoudi, Rachida Fissoune, Hassan Badir
2016 Zenodo  
Semantic integration is an active area of research in several disciplines, such as databases, information-integration, and ontology.  ...  We provide a survey of some approaches and techniques for integrating biological data, we focus on those developed in the ontology community.  ...  Semantic Web Languages Semantic web, proposed by Tim Berners Lee in 2001, is broadly accepted in biological research.  ... 
doi:10.5281/zenodo.1128003 fatcat:hqgxuhfqwrgori2u7ox2c3c2ce

A new wave of innovation in Semantic web tools for drug discovery

Samantha Kanza, Jeremy Graham Frey
2019 Expert Opinion on Drug Discovery  
Researchers in this domain have realized that semantic web technologies are key to dealing with the high levels of data for drug discovery.  ...  The main types of semantic web technologies are explained, outlining how they work and how they can be used in the drug discovery process, with a consideration of how the use of these technologies has  ...  [98] illustrating the added value of using Semantic web technologies for drug discovery.  ... 
doi:10.1080/17460441.2019.1586880 pmid:30884989 fatcat:qsss5sv2jndo3dnlr7medsushy

Using document-based databases for medical information systems in unreliable environments

Oliver Schmitt, Tim A. Majchrzak
2012 International Conference on Information Systems for Crisis Response and Management  
In order to find a more adequate solution in a development project for a patientregistry, we evaluated a document-based database incorporated into the data storage layer of a system.  ...  We found that document-based databases such as CouchDB are well-suited for IS in medical contexts and might be a feasible option for the future implementation of systems in various fields of healthcare  ...  ACKNOWLEDGMENTS The first author of the paper wrote his master thesis in cooperation with the department of medical informatics at the University of Münster, Germany, in the group of Frank Ückert.  ... 
dblp:conf/iscram/SchmittM12 fatcat:izfisatyizgfvfvb2v7dcnjuf4

Auto-CORPus: A Natural Language Processing Tool for Standardizing and Reusing Biomedical Literature

Tim Beck, Tom Shorter, Yan Hu, Zhuoyu Li, Shujian Sun, Casiana M. Popovici, Nicholas A. R. McQuibban, Filip Makraduli, Cheng S. Yeung, Thomas Rowlands, Joram M. Posma
2022 Frontiers in Digital Health  
The BioC specification does not include a data structure for representing publication table data, so we present a JSON format for sharing table content and metadata.  ...  The BioC format is a community-driven simple data structure for sharing text and annotations, however there is limited access to biomedical literature in BioC format and a lack of bioinformatics tools  ...  The BioC specification does not include a data structure for representing publication table data, so we present a JSON format for sharing table content and metadata.  ... 
doi:10.3389/fdgth.2022.788124 pmid:35243479 pmcid:PMC8885717 fatcat:fx5juyzi35cgdm3rlrcvhchike
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