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.

A scalable and transparent data pipeline for AI-enabled health data ecosystems

Namli T, Sinaci AA, Gonul, S, Herguido CR, Garcia-Canadilla P, Muñoz AM, Esteve AV and Laleci Ertürkmen GB
A scalable and transparent data pipeline for AI-enabled health data ecosystems
Frontiers in Medicine, 11, 1393123. DOI: 10.3389/fmed.2024.1393123.

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.
Poster session. XIth Congress of Medical Informatics, Ankara, 2018.

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