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Sinaci A.A.,SRDC Software Research and Development and Consultancy Ltd. | Laleci Erturkmen G.B.,SRDC Software Research and Development and Consultancy Ltd. | Gonul S.,SRDC Software Research and Development and Consultancy Ltd. | Gonul S.,Middle East Technical University | And 7 more authors.
BioMed Research International | Year: 2015

Postmarketing drug surveillance is a crucial aspect of the clinical research activities in pharmacovigilance and pharmacoepidemiology. Successful utilization of available Electronic Health Record (EHR) data can complement and strengthen postmarketing safety studies. In terms of the secondary use of EHRs, access and analysis of patient data across different domains are a critical factor; we address this data interoperability problem between EHR systems and clinical research systems in this paper. We demonstrate that this problem can be solved in an upper level with the use of common data elements in a standardized fashion so that clinical researchers can work with different EHR systems independently of the underlying information model. Postmarketing Safety Study Tool lets the clinical researchers extract data from different EHR systems by designing data collection set schemas through common data elements. The tool interacts with a semantic metadata registry through IHE data element exchange profile. Postmarketing Safety Study Tool and its supporting components have been implemented and deployed on the central data warehouse of the Lombardy region, Italy, which contains anonymized records of about 16 million patients with over 10-year longitudinal data on average. Clinical researchers in Roche validate the tool with real life use cases. © 2015 A. Anil Sinaci et al. Source


Sinaci A.A.,Middle East Technical University | Sinaci A.A.,SRDC Software Research and Development and Consultancy Ltd. | Laleci Erturkmen G.B.,SRDC Software Research and Development and Consultancy Ltd.
Journal of Biomedical Informatics | Year: 2013

In order to enable secondary use of Electronic Health Records (EHRs) by bridging the interoperability gap between clinical care and research domains, in this paper, a unified methodology and the supporting framework is introduced which brings together the power of metadata registries (MDR) and semantic web technologies. We introduce a federated semantic metadata registry framework by extending the ISO/IEC 11179 standard, and enable integration of data element registries through Linked Open Data (LOD) principles where each Common Data Element (CDE) can be uniquely referenced, queried and processed to enable the syntactic and semantic interoperability. Each CDE and their components are maintained as LOD resources enabling semantic links with other CDEs, terminology systems and with implementation dependent content models; hence facilitating semantic search, much effective reuse and semantic interoperability across different application domains. There are several important efforts addressing the semantic interoperability in healthcare domain such as IHE DEX profile proposal, CDISC SHARE and CDISC2RDF. Our architecture complements these by providing a framework to interlink existing data element registries and repositories for multiplying their potential for semantic interoperability to a greater extent. Open source implementation of the federated semantic MDR framework presented in this paper is the core of the semantic interoperability layer of the SALUS project which enables the execution of the post marketing safety analysis studies on top of existing EHR systems. © 2013 Elsevier Inc. Source


Yuksel M.,SRDC Software Research and Development and Consultancy Ltd. | Gonul S.,SRDC Software Research and Development and Consultancy Ltd. | Gonul S.,Middle East Technical University | Laleci Erturkmen G.B.,SRDC Software Research and Development and Consultancy Ltd. | And 7 more authors.
BioMed Research International | Year: 2016

Depending mostly on voluntarily sent spontaneous reports, pharmacovigilance studies are hampered by low quantity and quality of patient data. Our objective is to improve postmarket safety studies by enabling safety analysts to seamlessly access a wide range of EHR sources for collecting deidentified medical data sets of selected patient populations and tracing the reported incidents back to original EHRs. We have developed an ontological framework where EHR sources and target clinical research systems can continue using their own local data models, interfaces, and terminology systems, while structural interoperability and Semantic Interoperability are handled through rule-based reasoning on formal representations of different models and terminology systems maintained in the SALUS Semantic Resource Set. SALUS Common Information Model at the core of this set acts as the common mediator. We demonstrate the capabilities of our framework through one of the SALUS safety analysis tools, namely, the Case Series Characterization Tool, which have been deployed on top of regional EHR Data Warehouse of the Lombardy Region containing about 1 billion records from 16 million patients and validated by several pharmacovigilance researchers with real-life cases. The results confirm significant improvements in signal detection and evaluation compared to traditional methods with the missing background information. © 2016 Mustafa Yuksel et al. Source


Gigante F.,Aidima Instituto Tecnologico del Mueble | Crespi P.,Aidima Instituto Tecnologico del Mueble | Sinaci A.A.,SRDC Software Research and Development and Consultancy Ltd. | Basar R.V.,SRDC Software Research and Development and Consultancy Ltd.
CEUR Workshop Proceedings | Year: 2013

One of the most important objectives of the Business Innovation and Virtual Enterprise Environment (BIVEE) project is the management and fostering of innovation and production improvement in small and medium enterprises (SMEs). This short paper presents a brief description of the key factors and the methodology followed during the analysis of the current situation of the companies selected as end-users for the BIVEE project. While BIVEE focuses on two spaces (innovation and production spaces), this short paper presents details on the production space. In this space, the furniture cluster of AIDIMA (Technology Institute of Furniture, Wood and Packaging) plays mainly the role of end-user. Due to the nature of the selected companies, the conclusions are also valid for a large number of companies from the furniture industry in Spain. Our objective is to analyse and detect problems on the current processes of the companies inside a Virtual Enterprise Environment. Source


Basar R.V.,SRDC Software Research and Development and Consultancy Ltd. | Sinaci A.A.,SRDC Software Research and Development and Consultancy Ltd. | Smith F.,National Research Council Italy | Taglino F.,National Research Council Italy
CEUR Workshop Proceedings | Year: 2013

Considering innovation as the result of only spontaneous activities is a simplistic vision, because working out inspiration and reaching up to innovation need awareness and knowledge about the application domain and its problems. In this paper, we address the issue of knowledge representation, access and sharing in an enterprise context, by proposing an ontology-based framework (DocOnto) for the semantic description of documents involved in innovation activities. The framework, which is built within the BIVEE European project, is characterized by a customizable approach inspired by the UBL/CCTS, which allows each enterprise to refine the DocOnto at best for its needs. Then UBL-like structures are semantically lifted and used for describing concrete documents. Such a semantic representation enables reasoning services like querying and retrieving of documents, understanding similarities among documents, assessing their status and quality, monitoring innovation activities. The framework is supported by the technological integration of the iSurf eDoCreator, for modelling UBL-like documents structures, and the Production and Innovation Knowledge Repository (PIKR), the semantic knowledge hub of the BIVEE platform. Source

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