Dr. Sebastian Mate

Dr. Sebastian Mate

Medizinische Fakultät (Med)
Medizinisches Zentrum für Informations- und Kommunikationstechnik (Medizinisches IK-Zentrum, MIK) im Klinikum

Raum: Raum A 04 132
Krankenhausstraße 12
91054 Erlangen

 

About me

I’m a computer scientist working and researching in the medical informatics domain. I’m especially interested in technologies that make medical routine care data accessible for clinical research, e.g. data warehousing, integrating and querying heterogeneous medical data, ontologies, and the Semantic Web.

Also see my ResearchGate profile at: https://www.researchgate.net/profile/Sebastian_Mate

Projects

Publications

2021

  • L. A. Kapsner, J. M. Mang, S. Mate, S. A. Seuchter, A. Vengadeswaran, F. Bathelt, N. Deppenwiese, D. Kadioglu, D. Kraska, and H.-U. Prokosch. Linking a Consortium-Wide Data Quality Assessment Tool with the MIRACUM Metadata Repository. In: Applied Clinical Informatics 12.04 (2021), pp. 826–835. doi: 10.1055/s-0041-1733847
  • S. Mate, S. A. Seuchter, K. Ehrenberg, N. Deppenwiese, J. Zierk, H.-U. Prokosch, D. Kraska, and L. A. Kapsner. A Multi-User Terminology Mapping Toolbox. In: Studies in Health Technology and Informatics 278 (2021), pp. 217–223. issn: 09269630, 18798365. doi: 10.3233/SHTI210072
  • L. A. Kapsner, M. G. Zavgorodnij, S. P. Majorova, A. Hotz-Wagenblatt, O. V. Kolychev, I. N. Lebedev, J. D. Hoheisel, A. Hartmann, A. Bauer, S. Mate, H.-U. Prokosch, F. Haller, and E. A. Moskalev. BiasCorrector: Fast and Accurate Correction of All Types of Experimental Biases in Quantitative DNA Methylation Data Derived by Different Technologies. In: International Journal of Cancer (May 2021). doi: 10. 1002/ijc.33681
  • J. Gründner, C. Gulden, M. Kampf, S. Mate, H.-U. Prokosch, and J. Zierk. A Framework for Criteria-Based Selection and Processing of Fast Healthcare Interoperability Resources (FHIR) Data for Statistical Analysis: Design and Implementation Study. In: JMIR Medical Informatics 9.4 (Apr. 2021), e25645. doi: 10.2196/25645
  • C. Maier, L. A. Kapsner, S. Mate, H.-U. Prokosch, and S. Kraus. Patient Cohort Identification on Time Series Data Using the OMOP Common Data Model. In: Applied Clinical Informatics 12.01 (Jan. 2021), pp. 057–064. doi: 10.1055/s-0040-1721481
  • L. A. Kapsner, M. O. Kampf, S. A. Seuchter, J. Grendner, C. Gulden, S. Mate, J. M. Mang, C. Schüttler, N. Deppenwiese, L. Krause, D. Zöller, J. Balig, T. Fuchs, P. Fischer, C. Haverkamp, M. Holderried, G. Mayer, H. Stenzhorn, A. Stolnicu, M. Storck, H. Storf, J. Zohner, O. Kohlbacher, A. Strzelczyk, J. Schüttler, T. Acker, M. Boeker, U. X. Kaisers, H. A. Kestler, and H.-U. Prokosch. Reduced Rate of Inpatient Hospital Admissions in 18 German University Hospitals During the COVID-19 Lockdown. In: Frontiers in Public Health 8 (Jan. 2021). doi: 10.3389/fpubh.2020.594117

2020

  • S. Kraus, D. Toddenroth, M. Staudigel, W. Rödle, P. Unberath, L. Griebel, H.-U. Prokosch, and S. Mate. Mapping the Entire Record – An Alternative Approach to Data Access from Medical Logic Modules. In: Applied Clinical Informatics 11.02 (Mar. 2020), pp. 342–349. doi: 10. 1055/s-0040-1709708
  • N. Eklund, N. H. Andrianarisoa, E. van Enckevort, G. Anton, A. Debucquoy, H. Müller, L. Zaharenko, C. Engels, L. Ebert, M. Neumann, J. Geeraert, V. T’Joen, H. Demski, É. Caboux, R. Proynova, B. Parodi, S. Mate, E. van Iperen, R. Merino-Martinez, P. R. Quinlan, P. Holub, and K. Silander. Extending the Minimum Information about Biobank Data Sharing Terminology to Describe Samples, Sample Donors, and Events. In: Biopreservation and Biobanking 18.3 (June 2020), pp. 155–164. doi: 10.1089/bio.2019.0129

2019

  • S. Mate, T. Bürkle, L. A. Kapsner, D. Toddenroth, M. O. Kampf, M. Sedlmayr, I. Castellanos, H.-U. Prokosch, and S. Kraus. A Method for the Graphical Modeling of Relative Temporal Constraints. In: Journal of Biomedical Informatics 100 (Dec. 2019), p. 103314. doi: 10.1016/j.jbi.2019.103314
  • J. Gründner, T. Schwachhofer, P. Sippl, N. Wolf, M. Erpenbeck, C. Gulden, L. A. Kapsner, J. Zierk, S. Mate, M. Stürzl, R. Croner, H.-U. Prokosch, and D. Toddenroth. KETOS: Clinical Decision Support and Machine Learning as a Service – A Training and Deployment Platform Based on Docker, OMOP-CDM, and FHIR Web Services. In: PLOS ONE 14.10 (Oct. 2019), e0223010. doi: 10.1371/journal.pone.0223010.s005
  • S. Mate, M. Kampf, W. Rödle, S. Kraus, R. Proynova, K. Silander, L. Ebert, M. Lablans, C. Schüttler, C. Knell, N. Eklund, M. Hummel, P. Holub, and H.-U. Prokosch. Pan-European Data Harmonization for Biobanks in ADOPT BBMRI-ERIC. In: Applied Clinical Informatics 10.04 (Aug. 2019), pp. 679–692. doi: 10.1055/s-0039-1695793
  • L. A. Kapsner, M. O. Kampf, S. A. Seuchter, G. Kamdje-Wabo, T. Gradinger, T. Ganslandt, S. Mate, J. Gründner, D. Kraska, and H.-U. Prokosch. Moving Towards an EHR Data Quality Framework: The MIRACUM Approach. In: Studies in Health Technology and Informatics 267 (Sept. 2019), pp. 247–253. doi: 10.3233/SHTI190834

2018

  • D. Kadioglu, B. Breil, C. Knell, M. Lablans, S. Mate, D. Schlue, H. Serve, H. Storf, F. Ückert, T. O. F. Wagner, P. Weingardt, and H.-U. Prokosch. Samply.MDR – A Metadata Repository and Its Application in Various Research Networks. In: Studies in Health Technology and Informatics 253 (2018), pp. 50–54. doi: 10.3233/978-1-61499-896-9-50
  • C. Gulden, S. Mate, H.-U. Prokosch, and S. Kraus. Investigating the Capabilities of FHIR Search for Clinical Trial Phenotyping. In: Studies in Health Technology and Informatics 253 (2018), pp. 3–7. issn: 0926-9630. doi: 10.3233/978-1-61499-896-9-3

2017

  • D. Schlue, S. Mate, J. Haier, D. Kadioglu, H.-U. Prokosch, and B. Breil. From a Content Delivery Portal to a Knowledge Management System for Standardized Cancer Documentation. In: Studies in Health Technology and Informatics 243 (2017), pp. 180–184. doi: 10.3233/978-1-61499-808- 2-180
  • S. Mate, D. Kadioglu, R. W. Majeed, M. R. Stöhr, M. Folz, P. Vormstein, H. Storf, D. P. Brucker, D. Keune, N. Zerbe, M. Hummel, K. Senghas, H.-U. Prokosch, and M. Lablans. Proof-of-Concept Integration of Heterogeneous Biobank IT Infrastructures into a Hybrid Biobanking Network. In: Studies in Health Technology and Informatics 243 (2017), pp. 100–104. doi: 10.3233/978-1-61499-808-2-100
  • S. Mate, P. Vormstein, D. Kadioglu, R. W. Majeed, M. Lablans, H.-U. Prokosch, and H. Storf. On-the-Fly Query Translation between i2b2 and Samply in the German Biobank Node (GBN) Prototypes. In: Studies in Health Technology and Informatics 243 (2017), pp. 42–46. doi: 10.3233/978-1-61499-808-2-42
  • S. Mate, I. Castellanos, T. Ganslandt, H.-U. Prokosch, and S. Kraus. Standards-Based Procedural Phenotyping: The Arden Syntax on i2b2. In: Studies in Health Technology and Informatics 243 (2017), pp. 37–41. doi: 10.3233/978-1-61499-808-2-37
  • R. Proynova, D. Alexandre, M. Lablans, D. van Enckevort, S. Mate, N. Eklund, K. Silander, M. Hummel, P. Holub, and F. Ückert. A Decentralized IT Architecture for Locating and Negotiating Access to Biobank Samples. In: Studies in Health Technology and Informatics 243 (2017), pp. 75–79. doi: 10.3233/978-1-61499-808-2-75

2016

  • M. Löbe, T. Ganslandt, L. Lotzmann, S. Mate, J. Christoph, B. Baum, M. Sariyar, J. Wu, and S. Stäubert. Simplified Deployment of Health Informatics Applications by Providing Docker Images. In: Studies in Health Technology and Informatics 228 (2016), pp. 643–647. doi: 10.3233/ 978-1-61499-678-1-643
  • M. Lablans, D. Kadioglu, S. Mate, I. Leb, H.-U. Prokosch, and F. Ückert. Strategien zur Vernetzung von Biobanken. Klassifizierung verschiedener Ansätze zur Probensuche und Ausblick auf die Zukunft in der BBMRI-ERIC. In: Bundesgesundheitsblatt – Gesundheitsforschung – Gesundheitsschutz 59.3 (Mar. 2016), pp. 373–378. doi: 10.1007/s00103-015-2299-y
  • C. R. Bauer, T. Ganslandt, B Baum, J Christoph, I Engel, M. Löbe, S. Mate, S Stäubert, J. Drepper, H.-U. Prokosch, A Winter, and U Sax. Integrated Data Repository Toolkit (IDRT). A Suite of Programs to Facilitate Health Analytics on Heterogeneous Medical Data. In: Methods of Information in Medicine 55.2 (2 2016), pp. 125–135. issn: 2511-705X. doi: 10.3414/ME15- 01-0082

2015

  • S. Mate, F. Köpcke, D. Toddenroth, M. Martin, H.-U. Prokosch, T. Bürkle, and T. Ganslandt. Ontology-Based Data Integration between Clinical and Research Systems. In: PLOS ONE 10.1 (Jan. 2015), e0116656. doi: 10.1371/journal.pone.0116656

2013

  • M. Oberländer, M. Linnebacher, A. König, V. Bogoevska, C. Brodersen, R. Kaatz, M. Krohn, M. Hackmann, J. Ingenerf, J. Christoph, S. Mate, H.-U. Prokosch, E. F. Yekebas, C. Thorns, J. Büning, F. Prall, R. Uhlig, U. J. Roblick, J. R. Izbicki, E. Klar, H.-P. Bruch, B. Vollmar, J. K. Habermann, and das ColoNet-Konsortium. The “North German Tumor Bank of Colorectal Cancer”: Status Report After the First 2 Years of Support by the German Cancer Aid Foundation. In: Langenbecks Archives of Surgery 398.2 (Feb. 2013), pp. 251–258. doi: 10.1007/s00423- 012-1043-4

2012

  • H.-U. Prokosch, S. Mate, J. Christoph, A. Beck, F. Köpcke, S. Stephan, M. W. Beckmann, T. T. Rau, A. Hartmann, B. Wullich, B. Breil, K.-U. Eckardt, S. Titze, J. K. Habermann, J. Ingenerf, M. Hackmann, M. Ries, T. Bürkle, and T. Ganslandt. Designing and Implementing a Biobanking IT Framework for Multiple Research Scenarios. In: Studies in Health Technology and Informatics 180 (2012), pp. 559–563. doi: 10.3233/978-1-61499-101-4-559

2011

  • H.-U. Prokosch, M. Ries, A. Beyer, M. Schwenk, C. Seggewies, F. Köpcke, S. Mate, M. Martin, B. Bärthlein, M. W. Beckmann, M. Stürzl, R. Croner, B. Wullich, T. Ganslandt, and T. Bürkle. IT Infrastructure Components to Support Clinical Care and Translational Research Projects in a Comprehensive Cancer Center. In: Studies in Health Technology and Informatics 169 (2011), pp. 892–896. doi: 10.3233/978-1-60750-806-9-892
  • S. Mate, T. Bürkle, F. Köpcke, B. Breil, B. Wullich, M. Dugas, and T. Ganslandt. Populating the i2b2 Database with Heterogeneous EMR Data: A Semantic Network Approach. In: Studies in Health Technology and Informatics 169 (2011), pp. 502–506. doi: 10.3233/978-1-60750-806- 9-502
  • T. Ganslandt, S. Mate, K. Helbing, U. Sax, and H.-U. Prokosch. Unlocking Data for Clinical Research – The German i2b2 Experience. In: Applied Clinical Informatics 2.1 (2011), pp. 116–127. doi: 10.4338/ACI-2010-09- CR-0051

2010

  • T. Ganslandt, H.-U. Prokosch, A. Beyer, M. Schwenk, K. Starke, B. Bärthlein, F. Köpcke, S. Mate, M. Martin, W. Schöch, C. Seggewies, and T. Bürkle. Single-Source-Projekte am Universitätsklinikum Erlangen. In: mdi Forum der Medizin-Dokumentation und Medizin-Informatik 2 (2010), pp. 62–66

Theses

  • S. Mate. Föderierte medizinische Forschungsdatenbanken: Architekturen, Datenintegration und Abfragelogik. Doctoral thesis. Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Oct. 2021. url: https://nbn-resolving.org/urn:nbn:de:bvb:29-opus4-173689
  • S. Mate. Ein Semantic-Web-Ansatz zum Mapping klinischer Metadaten am Beispiel eines Bioproben-/Projektvermittlungs-Portals für das DPKK auf der Basis von i2b2. Diploma thesis. Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Jan. 2011. doi: 10.13140/2.1.5033.1843
  • S. Mate. Evaluation von i2b2 am Universitätsklinikum Erlangen. Studienarbeit. Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Aug. 2009. doi: 10.13140/RG.2.2.24833.89441

Conferences

  • S. Mate. Semantische Interoperabilität im Projekt EHR4CR. In: GMDS 2014: 59. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e.V. (GMDS). Düsseldorf, Sept. 2014
  • S. Mate, C. R. Bauer, B. Baum, I. Engel, M. Lobe, H.-U. Prokosch, M. Quade, U. Sax, S. Stäubert, A. Winter, and T. Ganslandt. i2b2, EHR4CR & IDRT. Components to Accelerate Translational Research. In: Clinical Research Informatics Solution Days. Düsseldorf, May 2014, pp. 1–12
  • S. Mate, C. R. Bauer, B. Baum, I. Engel, M. Lobe, H.-U. Prokosch, M. Quade, U. Sax, S. Stäubert, A. Winter, and T. Ganslandt. The Integrated Data Repository Toolkit. Platform Architecture and Tools to Support the Re-Use of Routine Clinical Data for Research. In: 3rd Annual i2b2 AUG Conference, Harvard Medical School. Boston, June 2013
  • S. Mate. i2b2 Wizard Installation. In: 1st European i2b2 Academic User Group Meeting, Erlangen, Germany, March 25-26, 2013. Mar. 2013. url: https://www.tmf-ev.de/EnglishSite/News/articleType/ArticleView/articleId/1277/A-Toolkit-for-Using-the-i2b2-Platform-.aspx
  • S. Mate, C. R. Bauer, B. Baum, J. Christoph, I. Engel, T. Ganslandt, M. Löbe, D. Plog, H.-U. Prokosch, M. Quade, U. Sax, S. Stäubert, L. Voitel, and A. Winter. IDRT: Platform Architecture and Tools to Support the Re-Use of Routine Clinical Data for Research. In: 1st European i2b2 Academic User Group Meeting, Erlangen, Germany, March 25-26, 2013. Erlangen, Mar. 2013. url: http://www.tmf-ev.de/News/articleType/ArticleView/articleId/1274.aspx
  • S. Mate, T. Ganslandt, and H.-U. Prokosch. i2b2 Wizard and Related Developments at Erlangen University. DPKK & ColoNet. In: 2nd Annual i2b2 AUG Conference, Harvard Medical School. Boston, July 2012. doi: 10.13140/RG.2.2.33886.77121
  • S. Mate, F. Köpcke, B. Wullich, B. Breil, M. Dugas, Bürkle, Thomas, H.-U. Prokosch, and T. Ganslandt. Aufbau einer auf Routinedaten basierenden, standortübergreifenden Forschungsplattform für das Deutsche Prostatakarzinom-Konsortium e.V. In: GMDS 2011: 56. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e.V. (GMDS), 6. Jahrestagung der Deutschen Gesellschaft für Epidemiologie (DGEpi). Mainz, 26.-29.09.2011. Düsseldorf: German Medical Science GMS Publishing House, Sept. 2011. doi: 10.3205/ 11gmds480
  • S. Mate, A. Becker, H.-U. Prokosch, and T. Ganslandt. Evaluation der Einsetzbarkeit von i2b2 im deutschen Umfeld. In: GMDS 2009: 54. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e.V. (GMDS). Düsseldorf: German Medical Science GMS Publishing House, Sept. 2009. doi: 10.3205/09gmds337

Posters

  • L. A. Kapsner, M Zavgorodnij, S Majorova, A Hartmann, S. Mate, H.-U. Prokosch, F Haller, and E Moskalev. BiasCorrector: An Online Tool for Correction of Measurement Biases in Quantitative Epigenetic Data. Poster. 103. Jahrestagung der Deutschen Gesellschaft für Pathologie. Frankfurt am Main, June 2019
  • K. Silander, N. Eklund, N. H. Andrianarisoa, G. Anton, E. Caboux, A. Debucquoy, H. Demski, D. van Enckevort, J. Geeraer, P. Holub, S. Mate, R. Merino-Martinez, H. Müller, B. Parodi, P. Quinlan, and L. Zaharenko. MIABIS 2.0 Sample/Donor Module: Introducing Sample and Sample Donor Components in the Minimum Information about Biobank Data Sharing (MIABIS). Poster. Europe Biobank Week 2018. Antwerpen, Sept. 2018
  • R. Proynova, S. Mate, N. Eklund, K. Silander, H. Müller, D. van Enckevort, M. Lablans, P. Holub, M. Hummel, and F. Ückert. Dateninteroperabilität in einer verteilten Plattform für Biomaterialanfragen. Poster. Nationales Biobanken-Symposium 2017. Berlin, Dec. 2017
  • N. Eklund, K. Silander, S. Mate, K. Bott, C. Schüttler, A Pourabdollah, R. Proynova, D. van Enckevort, M. A. Swertz, F. Ückert, H.-U. Prokosch, M. Hummel, and P. Holub. How Biobanks Can Benefit From BBMRI-ERIC’s CS-IT Services and What Researchers Will Get Out of Them? Poster. Global Biobank Week 2017. Stockholm, Sept. 2017
  • M. Hackmann, M. Oberländer, J. Ingenerf, H. Handels, J. Christoph, S. Mate, H.-U. Prokosch, and J. Habermann. IT-Solution for Feasible Data Protected Multicentric Clinical Biobanking. Poster. ESBB Conference 2013. Verona, Oct. 2013. url: https://web.archive.org/web/20170830072209/http://www.esbb.org/verona/download/poster_abstracts.pdf
  • N. Eklund, C. Schüttler, S. Mate, J Knuuttila, H.-U. Prokosch, K. Silander, and BBMRI-ERIC CS-IT working group. Survey of Data Harmonization Activities Across BBMRI-ERIC Partner Biobanks. Poster. Europe Biobank Week 2013. Vienna, Sept. 2013
  • S. Mate, T. Bürkle, H.-U. Prokosch, and T. Ganslandt. Populating the i2b2 Database with Data From the Electronic Medical Record: Ontology-Based Form Data Integration for i2b2. Poster. 1st Annual i2b2 AUG Conference, Harvard Medical School. Boston, June 2011. doi: 10. 13140/RG.2.2.35879.09122