Mathias Brochhausen

Mathias Brochhausen, Ph.D.

ASO PROF

Department: MD-HOBI-GENERAL
Business Phone: (352) 627-9467
Business Email: mbrochhausen@ufl.edu

Research Profile

My area of specialization is the use of semantic web technologies (especially biomedical ontologies) to assist in the collection, curation and maintenance of biomedical data. My particular focus is on the semantic web as a knowledge representation technology to allow automatic inferences. In addition to that I have an interest in general questions related to medical humanities, such as medical ethics. I also have a keen interest in formal logic and social ontologies. The biomedical areas in which I have worked so far are: oncology, pharmacy and pharmacology (drug-drug interactions), radiology, trauma care, pathology, biobanking.

Publications

2020
Autonomous Systems and Artificial Intelligence in Healthcare Transformation to 5P Medicine – Ethical Challenges.
Studies in health technology and informatics. 270:1089-1093 [DOI] 10.3233/SHTI200330. [PMID] 32570549.
2020
DICOM re-encoding of volumetrically annotated Lung Imaging Database Consortium (LIDC) nodules.
Medical physics. 47(11):5953-5965 [DOI] 10.1002/mp.14445. [PMID] 32772385.
2020
Collecting data on organizational structures of trauma centers: the CAFE web service.
Trauma surgery & acute care open. 5(1) [DOI] 10.1136/tsaco-2020-000473. [PMID] 32789188.
2019
Enhancing Clinical Data and Clinical Research Data with Biomedical Ontologies – Insights from the Knowledge Representation Perspective.
Yearbook of medical informatics. 28(1):140-151 [DOI] 10.1055/s-0039-1677912. [PMID] 31419826.
2019
Enhancing the drug ontology with semantically-rich representations of National Drug Codes and RxNorm unique concept identifiers.
BMC bioinformatics. 20(Suppl 21) [DOI] 10.1186/s12859-019-3192-8. [PMID] 31865907.
2019
Development and Validation of a Controlled Vocabulary: An OWL Representation of Organizational Structures of Trauma Centers and Trauma Systems.
Studies in health technology and informatics. 264:403-407 [DOI] 10.3233/SHTI190252. [PMID] 31437954.
2018
Developing User Personas to Aid in the Design of a User-Centered Natural Product-Drug Interaction Information Resource for Researchers.
AMIA … Annual Symposium proceedings. AMIA Symposium. 2018:279-287 [PMID] 30815066.
View on: PubMed
2018
Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse.
Journal of biomedical semantics. 9(1) [DOI] 10.1186/s13326-018-0183-z. [PMID] 29743102.
2018
Modeling the Personal Health Ecosystem.
Studies in health technology and informatics. 249:3-16 [PMID] 29866950.
View on: PubMed
2018
The Role of Axiomatically-Rich Ontologies in Transforming Medical Data to Knowledge.
Studies in health technology and informatics. 249:38-49 [PMID] 29866954.
View on: PubMed
2017
Formalizing Evidence Type Definitions for Drug-Drug Interaction Studies to Improve Evidence Base Curation.
Studies in health technology and informatics. 245:960-964 [PMID] 29295242.
View on: PubMed
2016
The ontology of medically related social entities: recent developments.
Journal of biomedical semantics. 7 [DOI] 10.1186/s13326-016-0087-8. [PMID] 27406187.
2016
The Ontology for Biomedical Investigations.
PloS one. 11(4) [DOI] 10.1371/journal.pone.0154556. [PMID] 27128319.
2016
The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.
Journal of biomedical semantics. 7 [DOI] 10.1186/s13326-016-0092-y. [PMID] 27538448.
2016
OBIB-a novel ontology for biobanking.
Journal of biomedical semantics. 7 [DOI] 10.1186/s13326-016-0068-y. [PMID] 27148435.
2016
Easy Extraction of Terms and Definitions with OWL2TL.
CEUR workshop proceedings. 1747 [PMID] 28035214.
View on: PubMed
2016
OOSTT: a Resource for Analyzing the Organizational Structures of Trauma Centers and Trauma Systems.
CEUR workshop proceedings. 1747 [PMID] 28217041.
View on: PubMed
2016
Adding evidence type representation to DIDEO.
CEUR workshop proceedings. 1747 [PMID] 33139971.
View on: PubMed
2015
Toward a complete dataset of drug-drug interaction information from publicly available sources.
Journal of biomedical informatics. 55:206-17 [DOI] 10.1016/j.jbi.2015.04.006. [PMID] 25917055.
2015
Biomedical imaging ontologies: A survey and proposal for future work.
Journal of pathology informatics. 6 [DOI] 10.4103/2153-3539.159214. [PMID] 26167381.
2015
Measuring the Usability of Triple Stores for Knowledge Management on Trauma Care Organizations.
CEUR workshop proceedings. 1546:241-242 [PMID] 27013932.
View on: PubMed
2015
Toward a common language for biobanking.
European journal of human genetics : EJHG. 23(1):22-8 [DOI] 10.1038/ejhg.2014.45. [PMID] 24713663.
2014
Clinical modeling–a critical analysis.
International journal of medical informatics. 83(1):57-69 [DOI] 10.1016/j.ijmedinf.2013.09.003. [PMID] 24161541.
2014
Drug-drug interaction data source survey and linking.
AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science. 2014 [PMID] 25717393.
View on: PubMed
2014
Towards a foundational representation of potential drug-drug interaction knowledge.
CEUR workshop proceedings. 1309:16-31 [PMID] 33139970.
View on: PubMed
2014
CollaborationViz: interactive visual exploration of biomedical research collaboration networks.
PloS one. 9(11) [DOI] 10.1371/journal.pone.0111928. [PMID] 25405477.
2013
Building a drug ontology based on RxNorm and other sources.
Journal of biomedical semantics. 4(1) [DOI] 10.1186/2041-1480-4-44. [PMID] 24345026.
2013
Developing a semantically rich ontology for the biobank-administration domain.
Journal of biomedical semantics. 4(1) [DOI] 10.1186/2041-1480-4-23. [PMID] 24103726.
2013
The core clinical protocol ontology (C2PO): A realist ontology for representing the recommendations within clinical guidelines.
Studies in health technology and informatics. 192 [PMID] 23920771.
View on: PubMed
2013
Towards a Consistent and Scientifically Accurate Drug Ontology.
CEUR workshop proceedings. 1060:68-73 [PMID] 27867326.
View on: PubMed
2012
A system-theoretical, architecture-based approach to ontology management.
Studies in health technology and informatics. 180:1087-9 [PMID] 22874362.
View on: PubMed
2011
Discussion of “biomedical ontologies: toward scientific debate”.
Methods of information in medicine. 50(3):217-36 [PMID] 21566855.
View on: PubMed
2011
The ACGT Master Ontology and its applications–towards an ontology-driven cancer research and management system.
Journal of biomedical informatics. 44(1):8-25 [DOI] 10.1016/j.jbi.2010.04.008. [PMID] 20438862.
2011
ACGT: advancing clinico-genomic trials on cancer – four years of experience.
Studies in health technology and informatics. 169:734-8 [PMID] 21893844.
View on: PubMed
2011
Architectural approach for providing relations in biomedical terminologies and ontologies.
Studies in health technology and informatics. 169:739-43 [PMID] 21893845.
View on: PubMed
2010
Putting biomedical ontologies to work.
Methods of information in medicine. 49(2):135-40 [DOI] 10.3414/ME9302. [PMID] 20135080.
2010
The ObTiMA system – ontology-based managing of clinical trials.
Studies in health technology and informatics. 160(Pt 2):1090-4 [PMID] 20841852.
View on: PubMed
2010
User-specific perspectives on ontologies.
Studies in health technology and informatics. 156:114-21 [PMID] 20543346.
View on: PubMed
2008
[Virtual tissue. Quaoaring].
Der Pathologe. 29 Suppl 2:123-8 [DOI] 10.1007/s00292-008-1045-8. [PMID] 19039616.
2008
A semantic grid infrastructure enabling integrated access and analysis of multilevel biomedical data in support of postgenomic clinical trials on cancer.
IEEE transactions on information technology in biomedicine : a publication of the IEEE Engineering in Medicine and Biology Society. 12(2):205-17 [DOI] 10.1109/TITB.2007.903519. [PMID] 18348950.
2008
Establishing and harmonizing ontologies in an interdisciplinary health care clinical research environment.
Studies in health technology and informatics. 134:219-33 [PMID] 18376049.
View on: PubMed
2007
Developing a European grid infrastructure for cancer research: vision, architecture and services.
Ecancermedicalscience. 1 [DOI] 10.3332/ecms.2007.56. [PMID] 22275955.
2007
Ontology based data management systems for post-genomic clinical trials within a European Grid Infrastructure for Cancer Research.
Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference. 2007:6435-8 [PMID] 18003495.
View on: PubMed
2006
The derives_from relation in biomedical ontologies.
Studies in health technology and informatics. 124:769-74 [PMID] 17108607.
View on: PubMed

Grants

Dec 2019 ACTIVE
TCIA Sustainment and Scalability: Platforms for Quantitative Imaging Informatics in Precision Medicine
Role: Principal Investigator
Funding: UNIV OF ARKANSAS FOR MEDICAL SCIENCES via NATL INST OF HLTH NCI
Aug 2019 ACTIVE
CAFE: Comparative Assessment Framework for Environments of Trauma Care
Role: Principal Investigator
Funding: NATL INST OF HLTH NIGMS

Education

Ph.D.
2000-2004 · Johannes Gutenberg University, Mainz, Germany
M.A.
1995-2000 · Johannes Gutenberg Univerity, Mainz, Germany

Teaching Profile

Courses Taught
2019-2021
GMS6805 Information Modeling in Biomedicine
2020
GMS7887 Health Outcomes & Policy PhD Research Seminar

Contact Details

Phones:
Business:
(352) 627-9467
Emails: