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

• MIRACUM (10/2018-now)
• BBMRI-ERIC CS-IT and ADOPT BBMRI-ERIC (10/2015-09/2018)
• German Biobank Node (GBN) (05/2015-04/2017)
• OnkoWiki (04/2015-03/2017)
• Integrated Data Repository Toolkit 1 and 2 (IDRT) (02/2012-2014)
• Electronic Health Records for Clinical Research (EHR4CR) (03/2011-02/2016)

Publications (as of 2019-10-24)

The list below contains publications of any type: full papers, conference papers, talks, posters and theses.

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 (Oct. 2019). 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. O. 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 (Sept. 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: Stud Health Technol Inform 267 (Sept. 2019), pp. 247–253. doi: 10.3233/SHTI190834
• 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 ofMeasurement Biases in Quantitative Epigenetic Data. In: 103. Jahrestagung der Deutschen Gesellschaft für Pathologie. Frankfurt am Main, June 2019, e77–e77 (Poster)

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: Stud Health Technol Inform 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: Stud Health Technol Inform 253 (2018), pp. 3–7. doi: 10.3233/978-1-61499-896-9-3

2017

• R. Proynova, S. Mate, N. Eklund, K. Silander, H. Müller, D. van Enckevort, M. Lablans, P. Holub, M. Hummel, F. Ückert, and BBMRI-ERIC CS-IT Team. Dateninteroperabilität in einer verteilten Plattform für Biomaterialanfragen. In: Nationales Biobanken-Symposium 2017. Berlin, Dec. 2017 (Poster)
• 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: Stud Health Technol Inform 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: Stud Health Technol Inform 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: Stud Health Technol Inform 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: Stud Health Technol Inform 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: Stud Health Technol Inform 243 (2017), pp. 75–79. doi: 10.3233/978-1-61499-808-2-75
• K. Bott, C. Schüttler, S. Mate, D. Kadioglu, N. Eklund, K. Silander, H.-U. Prokosch, and BBMRI-ERIC CS-IT working group. The Harmonisation Toolset Prototype of BBMRI-ERIC’s CS-IT. In: Global Biobank Week. Stockholm, Sept. 2017 (Poster)
• 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? In: Global Biobank Week. Stockholm, Sept. 2017 (Poster)

2016

• D. Alexandre, S. Mate, H.-U. Prokosch, and F. Ückert. Designüberlegungen für BBMRI-ERIC CS-ITs dezentrale Architektur. In: 5. Nationale Biobanken-Symposiums vom 7. – 8. Dezember 2016 in Berlin. Dec. 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: Stud Health Technol Inform 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. German. In: Bundesgesundheitsblatt – Gesundheitsforschung – Gesundheitsschutz 59.3 (Mar. 2016), pp. 373–378. doi: 10.1007/s00103-015-2299-y

2015

• C. R. Bauer, T. Ganslandt, B Baum, J Christoph, I Engel, M. Löbe, S. Mate, S Staubert, 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 Inf Med 55.2 (2016), pp. 125–135. doi: 10.3414/ME15-01-0082
• C. R. Bauer, T. Ganslandt, B. Baum, J. Christoph, I. Engel, M. Löbe, S. Mate, H.-U. Prokosch, U Sax, S. Stäubert, and A. Winter. The Integrated Data Repository Toolkit (IDRT): Accelerating Translational Research Infrastructures. In: Journal of Clinical Bioinformatics 5.Suppl 1 (May 2015), S6. doi: 10.1186/2043-9113-5-S1-S6
• 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 (2015), e0116656. doi: 10.1371/journal.pone.0116656

2014

• S. Mate. Semantische Interoperabilität im Projekt EHR4CR. In: 56. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik. Göttingen, 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. Duesseldorf, May 2014, pp. 1–12

2013

• M. Hackmann, M. Oberländer, J. Ingenerf, J. Christoph, S. Mate, H.-U. Prokosch, and J. Habermann. IT-Solution for Feasible Data Protected Multicentric Clinical Biobanking. In: ESBB Conference. Verona, Oct. 2013 (Poster)
• 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. In: Europe Biobank Week. Vienna, Sept. 2013 (Poster)
• T. Ganslandt, S. Mate, and H.-U. Prokosch. Forschungsinfrastruktur, ETL und Data Warehouse. In: GMDS 2013. July 2013. doi: 10.3205/13gmds282
• 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, pp. 1–25
• 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, pp. 1–18. url: http://www.tmf-ev.de/News/articleType/ArticleView/articleId/1274.aspx
• 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 ColoNet consortium. The „North German Tumor Bank of Colorectal Cancer“: Status Report After the First 2 Years of Support by the German Cancer Aid Foundation. In: Langenbeck’s archives of surgery 398.2 (Feb. 2013), pp. 251–258. doi: 10.1007/s00423-012-1043-4

2012

• T. Ganslandt, U Sax, M. Löbe, J. Drepper, C Bauer, B Baum, J Christoph, S. Mate, M Quade, S Staubert, and H.-U. Prokosch. Integrated Data Repository Toolkit: Werkzeuge zur Nachnutzung medizinischer Daten für die Forschung. In: INFORMATIK 2012. Ed. by U. Goltz, M. Magnor, H.-J. Appelrath, H. K. Matthies, W.-T. Balke, and L. Wolf. Bonn: Gesellschaft für Informatik e.V., 2012, pp. 1252–1259. url: http://dl.gi.de/handle/20.500.12116/17760
• M. Hackmann, J. Habermann, M. Oberländer, H.-U. Prokosch, S. Mate, J. Christoph, H. Handels, and J. Ingenerf. Datenschutzkonforme IT-Lösung für multizentrische klinische Biobanking-Projekte. In: MDS 2012. 57. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e.V. (GMDS). Braunschweig, 16.-20.09.2012. Düsseldorf: German Medical Science GMS Publishing House; 2012. Sept. 2012. doi: 10.3205/12gmds027
• 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: Stud Health Technol Inform 180 (2012), pp. 559–563. doi: 10.3233/978-1-61499-101-4-559
• D. Toddenroth, S. Mate, H.-U. Prokosch, and T. Ganslandt. Using Federated Queries for On-The-Fly Retrospective Observational Studies. In: 24th International Conference of the European Federation for Medical Informatics (MIE2012), Short Communications. Ed. by J Mantas. 2012. url: http://person.hst.aau.dk/ska/mie2012/CD/Interface_MIE2012/MIE_2012_Content/MIE_2012_Content/SCO/287_CD_SC_Oral_ID_427.pdf
• 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, pp. 1–25

2011

• 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: Mainz//2011. 56. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (gmds), 6. Jahrestagung der Deutschen Gesellschaft für Epidemiologie (DGEpi). Mainz, 26.-29.09.2011. Düsseldorf: German Medical Science GMS Publishing House; 2011. Sept. 2011. doi: 10.3205/11gmds480
• 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: Stud Health Technol Inform 169 (2011), pp. 892–896. url: https://www.ncbi.nlm.nih.gov/pubmed/21893875
• 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: Stud Health Technol Inform 169 (2011), pp. 502–506. doi: 10.3233/978-1-60750-806-9-502
• 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. In: 1st Annual i2b2 AUG Conference, Harvard Medical School. Boston, June 2011, pp. 1–1. doi: 10.13140/RG.2.2.35879.09122 (Poster)
• 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
• S. Mate. Ein Semantic-Web-Ansatz zum Mapping klinischer Metadaten am Beispiel eines Bioproben-/Projektvermittlungs-Portals für das DPKK auf der Basis von i2b2. Diplomarbeit. Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Jan. 2011

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

2009

• S. Mate, A. Becker, H.-U. Prokosch, and T. Ganslandt. Evaluation der Einsetzbarkeit von i2b2 im deutschen Umfeld. German. In: Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie. 54. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (gmds). Essen, 07.-10.09.2009. Sept. 2009. doi: 10.3205/09gmds337
• S. Mate. Evaluation von i2b2 am Universitätsklinikum Erlangen. Studienarbeit. Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 2009