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.

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.

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.

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.

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.

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.

Peer-reviewed Conference Publications

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.

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.

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.

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.

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.

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.

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.

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).

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.

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

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

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

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).

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.
Data Interoperability through Federated Semantic Metadata Registries.
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