Publications
I do research
Peer-reviewed Journal Publications
From Raw Data to FAIR Data: The FAIRification Workflow for Health Research
Sinaci AA, Núñez-Benjumea FJ, Gencturk M, Jauer ML, Deserno T, Chronaki C, Cangioli G, Cavero-Barca C, Rodríguez-Pérez JM, Pérez-Pérez MM, Laleci Erturkmen GB, Hernández-Pérez T, Méndez-Rodríguez E, Parra-Calderón CL.
From Raw Data to FAIR Data: The FAIRification Workflow for Health Research.
Methods Inf Med. 2020 Jun;59(S 01):e21-e32. doi: 10.1055/s-0040-1713684. Epub 2020 Jul 3. PMID: 32620019.
Total number of citations: 79
A federated semantic metadata registry framework for enabling interoperability across clinical research and care domains
Sinaci AA, Erturkmen GB.
A federated semantic metadata registry framework for enabling interoperability across clinical research and care domains.
Journal of biomedical informatics. 2013 Oct 1;46(5):784-94.
Total number of citations: 78
A semantic backend for content management systems
Laleci GB, Aluc G, Dogac A, Sinaci AA, Kilic O, Tuncer F.
A semantic backend for content management systems.
Knowledge-based systems. 2010 Dec 1;23(8):832-43.
Total number of citations: 44
A Semantic Transformation Methodology for the Secondary Use of Observational Healthcare Data in Postmarketing Safety Studies
Pacaci A, Gonul S, Sinaci AA, Yuksel M, Laleci Erturkmen GB.
A semantic transformation methodology for the secondary use of observational healthcare data in postmarketing safety studies.
Frontiers in pharmacology. 2018 Apr 30;9:435.
Total number of citations: 23
An Interoperability Platform Enabling Reuse of Electronic Health Records for Signal Verification Studies
Yuksel M, Gonul S, Laleci Erturkmen GB, Sinaci AA, Invernizzi P, Facchinetti S, Migliavacca A, Bergvall T, Depraetere K, De Roo J.
An interoperability platform enabling reuse of electronic health records for signal verification studies.
BioMed research international. 2016 Oct;2016.
Total number of citations: 13
Applying the FAIR4Health Solution to Identify Multimorbidity Patterns and Their Association with Mortality through a Frequent Pattern Growth Association Algorithm
Carmona-Pírez J, Poblador-Plou B, Poncel-Falcó A, Rochat J, Alvarez-Romero C, Martínez-García A, Angioletti C, Almada M, Gencturk M, Sinaci AA, Ternero-Vega JE, Gaudet-Blavignac C, Lovis C, Liperoti R, Costa E, Parra-Calderón CL, Moreno-Juste A, Gimeno-Miguel A, Prados-Torres A.
Applying the FAIR4Health Solution to Identify Multimorbidity Patterns and Their Association with Mortality through a Frequent Pattern Growth Association Algorithm.
International Journal of Environmental Research and Public Health. 2022; 19(4):2040. https://doi.org/10.3390/ijerph19042040
Total number of citations: 10
BOFRF: A Novel Boosting-Based Federated Random Forest Algorithm on Horizontally Partitioned Data
Gencturk M, Sinaci AA, Cicekli NK
BOFRF: A Novel Boosting-Based Federated Random Forest Algorithm on Horizontally Partitioned Data.
IEEE Access. vol. 10, pp. 89835-89851, 2022. https://doi.org/10.1109/ACCESS.2022.3202008
Total number of citations: 9
Postmarketing Safety Study Tool: A Web Based, Dynamic, and Interoperable System for Postmarketing Drug Surveillance Studies
Sinaci AA, Laleci Erturkmen GB, Gonul S, Yuksel M, Invernizzi P, Thakrar B, Pacaci A, Cinar HA, Cicekli NK.
Postmarketing safety study tool: a web based, dynamic, and interoperable system for postmarketing drug surveillance studies.
BioMed research international. 2015 Jan 1;2015.
Predicting 30-days Readmission Risk for COPD Patients Care through a Federated Machine Learning Architecture on FAIR Data: Development and Validation Study
Alvarez-Romero C, Martínez-García A, Ternero-Vega JE, Diaz-Jimenez P, Jimenez-De-Juan C, Nieto-Martin MD, Roman-Villaran E, Kovacevic T, Bokan D, Hromis S, Djekic Malbasa J, Beslac S, Zaric B, Gencturk M, Sinaci AA, Ollero-Baturone M, Parra-Calderón CL.
Predicting 30-Day Readmission Risk for Patients With Chronic Obstructive Pulmonary Disease Through a Federated Machine Learning Architecture on Findable, Accessible, Interoperable, and Reusable (FAIR) Data: Development and Validation Study.
JMIR Medical Informatics. 2022;10(6):e35307. http://dx.doi.org/10.2196/35307
A Data Transformation Methodology to Create Findable, Accessible, Interoperable, and Reusable Health Data: Software Design, Development, and Evaluation Study
Sinaci AA, Gencturk M, Teoman H, Laleci Erturkmen G, Alvarez-Romero C, Martinez-Garcia A, Poblador-Plou B, Carmona-Pírez J, Löbe M, Parra-Calderon C
A Data Transformation Methodology to Create Findable, Accessible, Interoperable, and Reusable Health Data: Software Design, Development, and Evaluation Study
J Med Internet Res 2023;25:e42822. https://doi.org/10.2196/42822
Privacy-preserving federated machine learning on FAIR health data: A real-world application
Sinaci AA, Gencturk M, Alvarez-Romero C, Laleci Erturkmen G, Martinez-Garcia A, Escalona-Cuaresma M, Parra-Calderon C
Privacy-preserving federated machine learning on FAIR health data: A real-world application
Comput Struct Biotechnol J. 2024;24:136-145. doi: 10.1016/j.csbj.2024.02.014.
A Nationwide Chronic Disease Management Solution via Clinical Decision Support Services: Software Development and Real-Life Implementation Report
Ulgu M, Laleci Erturkmen G, Yuksel M, Namli T, Postacı Ş, Gencturk M, Kabak Y, Sinaci AA, Gonul S, Dogac A, Özkan Altunay Z, Ekinci B, Aydin S, Birinci S
A Nationwide Chronic Disease Management Solution via Clinical Decision Support Services: Software Development and Real-Life Implementation Report
JMIR Med Inform 2024;12:e49986 DOI: 10.2196/49986.
Peer-reviewed Conference Publications
A Framework for Evaluating and Utilizing Medical Terminology Mappings
Hussain S, Sun H, Sinaci AA, Erturkmen GB, Mead C, Gray AJ, McGuinness DL, Prud'Hommeaux E, Daniel C, Forsberg K.
A framework for evaluating and utilizing medical terminology mappings.
Stud Health Technol Inform. 2014;205:594-8. PMID: 25160255.
Total number of citations: 12
Optimization of just-in-time adaptive interventions using reinforcement learning
Gonul S, Namli T, Baskaya M, Sinaci AA, Cosar A, Toroslu IH.
Optimization of just-in-time adaptive interventions using reinforcement learning.
International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems 2018 Jun 25 (pp. 334-341). Springer, Cham.
Total number of citations: 10
Testing the Conformance and Interoperability of NHIS to Turkey’s HL7 Profile
Namli T, Aluc G, Sinaci AA, Kose I, Akpinar N, Gurel M, Arslan Y, Ozer H, Yurt N, Kirici S, Sabur E.
Testing the Conformance and Interoperability of NHIS to Turkey’s HL7 Profile.
9th International HL7 Interoperability Conference [Internet]. Crete, Greece 2008 Oct (pp. 63-8).
Total number of citations: 10
Standard-based EHR-enabled applications for clinical research and patient safety: CDISC -- IHE QRPH -- EHR4CR & SALUS collaboration
Daniel C, Erturkmen GB, Sinaci AA, Delaney BC, Curcin V, Bain L.
Standard-based integration profiles for clinical research and patient safety.
AMIA Jt Summits Transl Sci Proc. 2013;2013:47-49. Published 2013 Mar 18.
Total number of citations: 9
End User Evaluation of the FAIR4Health Data Curation Tool
Gencturk M, Teoman A, Alvarez-Romero C, Martinez-Garcia A, Parra-Calderon CL, Poblador-Plou B, Löbe M, Sinaci AA.
End User Evaluation of the FAIR4Health Data Curation Tool.
Studies in health technology and informatics. 2021 May 27;281:8-12.
Total number of citations: 6
Standard-based integration profiles for clinical research and patient safety
Daniel C, Erturkmen GB, Sinaci AA, Delaney BC, Curcin V, Bain L.
Standard-based integration profiles for clinical research and patient safety.
AMIA Summits on Translational Science Proceedings. 2013;2013:47.
Total number of citations: 4
A Document Centric Approach for User Requirements in BIVEE
Sinaci AA, Piersantelli M, Cristalli C, Gigante F, Erturkmen GB, Basar RV.
A Document Centric Approach for User Requirements in BIVEE.
CAiSE Conference, Workshop on New Generation Enterprise and Business Innovation Systems, June, 2012, Gdansk, Poland.
Total number of citations: 5
FAIR4Health FAIRification Tools
Alvarez-Romero C, Martinez-Garcia A, Gencturk M, Sinaci AA, Parra-Calderon CL.
FAIR4Health FAIRification Tools.
Studies in health technology and informatics. 2021 May 27;281:8-12.
Transforming Health Data into Timeseries for Predictive Analytics
Sinaci AA, Namli T, Postaci S, Gencturk M, Erturkmen GB.
End User Evaluation of the FAIR4Health Data Curation Tool.
Studies in health technology and informatics. 2021 May 27;281:8-12.
The Health Data Ingestion Stack
Erturkmen GB, Sinaci AA, Namli T.
The Health Data Ingestion Stack.
Informatics for Health 2017, April, 2017, Manchester, UK
keyCRF: Using Semantic Metadata Registries to Populate an eCRF with EHR Data
Erturkmen GB, Bain L, Sinaci AA.
keyCRF: Using Semantic Metadata Registries to Populate an eCRF with EHR Data.
International Semantic Web Conference (Industry Track) 2014.
Adverse Drug Event Notification on a Semantic Interoperability Framework
Krahn T, Eichelberg M, Müller F, Gönül S, Laleci Erturkmen GB, Sinaci AA, Appelrath HJ.
Adverse drug event notification on a semantic interoperability framework.
Stud Health Technol Inform. 2014;205:111-5. PMID: 25160156.
Patient History Navigation with the Use of Common Data Elements
Sinaci AA, Erturkmen GB, Gönül S, Cinar HA, Kaya A.
Patient History Navigation with the Use of Common Data Elements.
SWAT4LS 2013.
Demonstration of the SALUS Semantic Interoperability Framework for Case Series Characterization Studies
Yuksel M, Gönül S, Erturkmen GB, Sinaci AA, Depraetere K, De Roo J, Bergvall T.
Demonstration of the SALUS Semantic Interoperability Framework for Case Series Characterization Studies.
SWAT4LS 2013.
Analysis of the Information Resources for the Furniture Industry in BIVEE
Gigante F, Crespí P, Sinaci AA, Basar RV.
Analysis of the Information Resources for the Furniture Industry in BIVEE.
NGEBIS Short Papers 2013 (pp. 1-6).
Semantic UBL-like documents for innovation
Basar RV, Sinaci AA, Smith F, Taglino F.
Semantic UBL-like documents for innovation.
NGEBIS Short Papers 2013 (pp. 39-44).
Semantic-sensitive extraction of EHR data to support adverse drug event reporting
Declerck G, Hussain S, Parès Y, Daniel C, Jaulent MC, Yuksel M, Sinaci AA, Erturkmen GB.
Semantic-sensitive Extraction of EHR data to Support Adverse Drug Event Reporting.
SWAT4LS 2012.
Jena based Implementation of a ISO 11179 Metadata Registry
Sinaci AA.
Jena based Implementation of a ISO 11179 Metadata Registry.
ApacheCon, Sinsheim, Germany, 2012.
Semantic Content Management and Integration with JCR/CMIS Compliant Content Repositories
Gonul S, Sinaci AA.
Semantic Content Management and Integration with JCR/CMIS Compliant Content Repositories.
I-Semantics Conference, September, 2012, Graz, Austria
Semantic Content Management with Apache Stanbol
Sinaci AA, Gonul S.
Semantic Content Management with Apache Stanbol.
ESWC Conference, May, 2012, Heraklion, Crete, Greece
Building the Semantic Interoperability Architecture Enabling Sustainable Proactive Post Market Safety Studies
Erturkmen GB, Dogac A, Yuksel M, Hussain S, Declerck G, Daniel C, Sun H, Depraetere K, Colaert D, Devlies J, Krahn T, Thakrar B, Freriks G, Bergvall T, Sinaci AA.
Building the Semantic Interoperability Architecture Enabling Sustainable Proactive Post Market Safety Studies.
SIMI Workshop (Semantic Interoperability in Medical Informatics), in ESCW 2012: Extended Semantic Web Conference, May, 2012, Heraklion, Crete, Greece.
A semantically Enriched Persistence Mechanism for Interactive Knowledge Stack
Dogac A., Laleci G. B., Aluc G., Sinaci AA., Behrendt W., Delacretaz B., Pittet J. M.
A semantically Enriched Persistence Mechanism for Interactive Knowledge Stack.
eChallenges Conference, October, 2009, Istanbul, Turkey
Testing the Interoperability and Conformance of UBL/NES based Applications
Namli T, Dogac A, Sinaci AA, Aluc G.
Testing the Interoperability and Conformance of UBL/NES based Applications.
eChallenges Conference, October, 2009, Istanbul, Turkey
Book Chapters
Innovation and Production Improvement in Virtual Enterprises: The User Perspective
Pacaci A, Sinaci AA, Dogac A.
Innovation and Production Improvement in Virtual Enterprises: The User Perspective.
Enterprise Innovation: From Creativity to Engineering. 2015 Aug 20:233-56.
A Day of Networked Production Improvement
Valencia FG, Pacaci A, Sinaci AA.
A Day of Networked Production Improvement.
Enterprise Innovation 2015 Aug 7.
Standards & Profiles
Information technology — Concepts and usage of metadata — Part 23: Data element exchange (DEX) for a subset of ISO/IEC 11179-3
Erturkmen GB, Sinaci AA.
Information technology — Concepts and usage of metadata — Part 23: Data element exchange (DEX) for a subset of ISO/IEC 11179-3.
ISO/IEC TR 19583-23:2020
Data Element Exchange (DEX) Interoperability Profile
Bain L, Erturkmen GB, Daniel C, Sinaci AA.
Data Element Exchange (DEX) Interoperability Profile.
Technical report, IHE Quality, Research and Public Health Domain (QRPH) Technical Framework, September, 2013
Dissertations
Data Interoperability through Federated Semantic Metadata Registries
Sinaci AA.
Data Interoperability through Federated Semantic Metadata Registries.
PhD Dissertation, Middle East Technical University, Turkey, July 2014.
A Conformance and Interoperability Test Suite for Turkey’s NHIS and An Interactive Test Control and Monitoring Environment
Sinaci AA.
A Conformance and Interoperability Test Suite for Turkey’s NHIS and An Interactive Test Control and Monitoring Environment.
MSc. Dissertation, Middle East Technical University, Turkey, June 2009.
Others
User scenarios to promote the use of FAIR data on health research
Almada M, Dias I, Portela D, Midão L, Sinaci AA, Núñez-Benjumea FJ, Parra-Calderón CL, Costa E.
User scenarios to promote the use of FAIR data on health research.
Open Science Fair, September, 2019, Porto, Portugal