A. Anil Sinaci

I am a computer scientist and full-stack software developer with 15+ years of experience ranging from ordinary desktop, web and mobile applications to cutting-edge research projects. I am a senior researcher and principal solutions architect at SRDC Corp. I work as a part-time instructor at the Department of Computer Engineering, Middle East Technical University

I hold a PhD in computer science/engineering since 2014. I actively worked for many large-scale, international R&D projects at different stages such as creating ideas/innovation, compiling the project proposals and leading scientific and technical developments. I authored many papers published in peer-reviewed journals and conferences.

I am an Apache committer and a member of the Project Management Committee (PMC) of the (retired) Apache Stanbol project. I contribute to standardization activities. In the past, I worked as a member of the technical and planning committees of IHE Quality, Research and Public Health Domain (QRPH). I am the leading editor of the ISO/IEC data element exchange (DEX) standard.

My research areas

Data Management

Relational, graph and document databases. Indexing, query planning/optimization and query processing. Distributed data processing and sharding. ETL architectures and domain-specific data transformation. Semantic indexing and semantic search mechanisms on content management systems.

Interoperability

Service Oriented Architectures (SOA). Domain-specific interoperability solutions, interoperability standards, conformance and interoperability testing. Metadata registries, Common Data Elements, syntactic and semantic mappings. Findable, Accessible, Interoperable, Reusable (FAIR) principles.

Semantic Web & Linked Data

Named entity recognition, knowledge representation and entity linking. Semantic modeling, semantic interoperability and graph query processing. Semantic data management and triple-stores. Inference engines (reasoners) and recommendation systems.

Machine Learning

Descriptive and prescriptive statistics. Statistical inference, artificial neural networks. Federated machine learning. Distributed data mining. Privacy-preserving machine learning. Artificial intelligence in healthcare and clinical research.

Big Data Analytics & Business Intelligence

Big data technology stack. Customized big data infrastructures. Distributed big data processing. Data cleaning, transformation and information/meaning extraction. Predictive and prescriptive analytic solutions with data visualization for informed decisions.

eHealth Infrastructures

Clinical decision support systems. Automated clinical guidelines. Health data interoperability. Secondary use of healthcare data, clinical research informatics & biomedical informatics. Practical applications of artificial intelligence in health.

Education

A lifelong learner
2009 - 2014
Middle East Technical University, Ankara, Turkey

Ph.D. in Computer Engineering

The title of my PhD dissertation is Data Interoperability Through Federated Semantic Metadata Registries. During my PhD studies, I designed and implemented a novel interoperability architecture based on the concept of Common Data Elements while utilizing the semantic web technologies and Linked Data principles. My studies led to the development of a new profile, named Data Element Exchange, under Integrating the Healthcare Enterprise and later a new ISO/IEC standard.

2007 - 2009
Middle East Technical University, Ankara, Turkey

MSc. in Computer Engineering

The title of my MSc thesis is A Conformance and Interoperability Test Suite For Turkey's National Health Information System and An Interactive Test Control and Monitoring Environment. The first version of Turkey's National Health Information System (NHIS) was based on HL7 standards. Clients such as the hospital information systems continuously submitted medical data through this system to the central web services. During my masters studies, I built a testing environment so that the clients can test themselves in terms of conformance and interoperability with respect to the standards used in various layers of the web service communication.

2003 - 2007
Middle East Technical University, Ankara, Turkey

BSc. in Computer Engineering

During my undergraduate education, in addition to the core/must courses of the department on Data Structures, Algorithms, Programming Language Concepts, Operating Systems etc., I took several technical elective courses such as Artificial Intelligence, Language Processors, Database Management Systems and Introduction to Bioinformatics. I will always remember the programming assignments, group projects and long and sleepless nights at the laboratories.

1996 - 2003
Icel Anatolian High School, Mersin, Turkey

High School - Science Diploma

From age 11 to 18, more than 7 years at the beautiful campus of my high school by the sea side. Lots of memories, I grew up there...

Experience

15 years of experience
2011 - Current
SRDC Software Research Development and Consultancy Corporation, Ankara, Turkey

Principle Solutions Architect, Senior Researcher

2016 - 2020
Department of Computer Engineering, Middle East Technical University, Ankara, Turkey

Instructor

Course instructor for Ceng230 and Ceng229

2009 - 2011
Department of Computer Engineering, Middle East Technical University, Ankara, Turkey

Teaching Assistant

During the 2 years (4 semesters) at the Department of Computer Engineering, I worked as a teaching assistant; lectured the laboratory sessions and recitations, and prepared and evaluated many programming assignments. Here is the list of the courses that I worked for:

2010 - 2011
Cengsoft, Ankara, Turkey

R&D Consultant

Maecenas tempus faucibus rutrum. Duis eu aliquam urna. Proin vitae nulla tristique, ornare felis id, congue libero. Nam volutpat euismod quam.

2009 - 2010
AGMLab Information Technologies, Ankara, Turkey

R&D Consultant

I worked as an academic R&D consultant to support AGMLab's international research project called SEMbySEM. I contributed to the semantic modeling of large system services and their dynamic integration to support interoperability of services on the fly.

2007 - 2009
Software Research Development Center, Middle East Technical University, Ankara, Turkey

Software Engineer, Researcher

Maecenas tempus faucibus rutrum. Duis eu aliquam urna. Proin vitae nulla tristique, ornare felis id, congue libero. Nam volutpat euismod quam.

2006 - 2007
Software Research Development Center, Middle East Technical University, Ankara, Turkey

Part-time Software Developer

After successfully completing my summer practice at SRDC, I was offered a part-time job. I worked as a software developer to support the ongoing R&D projects which were mainly on service oriented architectures, peer-to-peer communication and databases.

Skills

My technical skills & Domain knowledge

Programming Paradigms & Methodologies

Object-oriented & Imperative Programming

100%

Functional Programming

95%

Architectural & Software Design Patterns

95%

Distributed & Concurrent Computing

90%

Test-driven Development

85%

Event-driven Programming

85%

Programming Languages

Java

98%

Scala

95%

Python

95%

C & C++

95%

JavaScript & TypeScript & ActionScript

95%

C#

85%

Data Management

SQL - MySQL, PostgreSQL, H2, JPA/Hibernate

98%

NoSQL systems, MongoDB, Redis, Cassandra

95%

Apache Spark - Batch & Stream Processing

90%

XML, XSD Schema, Schematron, XPath, XSLT, WSDL, JSON

95%

ISO/IEC 11179 - Metadata Management

98%

Apache Lucene, Apache Solr

90%

Web Development

Model-View-Controller (MVC)

98%

RESTful Architectures, SOAP Web Services, WS-Security, JAX-WS

98%

MEAN Stack

95%

Angular

85%

VueJS

85%

Authentication & Authorization - OpenID Connect

95%

Semantic Technologies

Knowledge Representation & Management Systems

98%

Inference Engines (Reasoners)

90%

Triple Stores - Jena TDB, Virtuoso

90%

RDF, RDFS, OWL, SPARQL

95%

Apache Jena

95%

Apache Stanbol

100%

System Administration & DevOps

Linux Command Line

98%

Docker

95%

Git, GitHub, GitLab, GitlabCI

95%

Maven

95%

Network, DNS, Mail Server Configuration

95%

AWS

85%

Healthcare Data Management (eHealth)

HL7 FHIR

90%

HL7 RIM, CDA, CCD

90%

IHE Profiles: XDS, QED, CM & DEX

90%

Common Data Element Models: HITSP/C154, HITSP/C32, S&I CEDD

85%

Clinical Research Informatics (eHealth)

Common Data Models: OMOP/OHDSI CDM, i2b2

95%

ICH Individual Case Safety Reports (E2B)

90%

BRIDG Model

85%

CDISC SDTM, CDASH

85%

eBusiness

OASIS Universal Business Language (UBL)

90%

UN/CEFACT Core Components Technical Specification (CCTS)

85%

UN/CEFACT Core Component Library (CCL)

85%

Global Standards 1 (GS1) XML

80%

Portfolio

My Works
FAIR4Health

FAIR4Health

Artificial Intelligence, eHealth, FAIR, Machine Learning

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

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