Mathias Brochhausen,
CO PROF
Department:
MD-HOBI-BIOMED INFORMATICS
Business Phone:
(352) 627-9467
Business Email:
mbrochhausen@ufl.edu
Teaching Profile
Courses Taught
2019-2021
GMS6805 Information Modeling in Biomedicine
2020
GMS7887 Health Outcomes & Policy PhD Research Seminar
Publications
2022
A Checklist for Reproducible Computational Analysis in Clinical Metabolomics Research.
Metabolites.
12(1)
[DOI] 10.3390/metabo12010087.
[PMID] 35050209.
2022
Assessing the Need for Semantic Data Integration for Surgical Biobanks-A Knowledge Representation Perspective.
Journal of personalized medicine.
12(5)
[DOI] 10.3390/jpm12050757.
[PMID] 35629179.
2022
Integration of Biobanking Architecture with Genomics Data: Genomics Integrated Biobanking Ontology (GIBO).
Studies in health technology and informatics.
295:302-303
[DOI] 10.3233/SHTI220722.
[PMID] 35773868.
2021
Autonomous Systems and Artificial Intelligence – Hype or Prerequisite for P5 Medicine?
Studies in health technology and informatics.
285:3-14
[DOI] 10.3233/SHTI210567.
[PMID] 34734847.
2021
Data Properties or Analytical Methodologies: Too Much Attention to the Former Ignores Concerns About the Latter.
The American journal of bioethics : AJOB.
21(12):70-72
[DOI] 10.1080/15265161.2021.1991037.
[PMID] 34806969.
2021
Standardization of assay representation in the Ontology for Biomedical Investigations.
Database : the journal of biological databases and curation.
2021
[DOI] 10.1093/database/baab040.
[PMID] 34244718.
2021
Understanding the Gap Between Information Models and Realism-Based Ontologies Using the Generic Component Model.
Studies in health technology and informatics.
285:159-164
[DOI] 10.3233/SHTI210590.
[PMID] 34734868.
2020
A Minimal Information Model for Potential Drug-Drug Interactions.
Frontiers in pharmacology.
11
[DOI] 10.3389/fphar.2020.608068.
[PMID] 33762928.
2020
ACS COT participates in study to develop comparative data on trauma care organization.
Bulletin of the American College of Surgeons.
105(4):43-48
[PMID] 34531607.
2020
Automatically classifying the evidence type of drug-drug interaction research papers as a step toward computer supported evidence curation.
AMIA … Annual Symposium proceedings. AMIA Symposium.
2020:554-563
[PMID] 33936429.
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
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.
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.
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.
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.
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.
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.
2018
The Role of Axiomatically-Rich Ontologies in Transforming Medical Data to Knowledge.
Studies in health technology and informatics.
249:38-49
[PMID] 29866954.
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.
2016
Adding evidence type representation to DIDEO.
CEUR workshop proceedings.
1747
[PMID] 33139971.
2016
Easy Extraction of Terms and Definitions with OWL2TL.
CEUR workshop proceedings.
1747
[PMID] 28035214.
2016
OBIB-a novel ontology for biobanking.
Journal of biomedical semantics.
7
[DOI] 10.1186/s13326-016-0068-y.
[PMID] 27148435.
2016
OOSTT: a Resource for Analyzing the Organizational Structures of Trauma Centers and Trauma Systems.
CEUR workshop proceedings.
1747
[PMID] 28217041.
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
The Ontology for Biomedical Investigations.
PloS one.
11(4)
[DOI] 10.1371/journal.pone.0154556.
[PMID] 27128319.
2016
The ontology of medically related social entities: recent developments.
Journal of biomedical semantics.
7
[DOI] 10.1186/s13326-016-0087-8.
[PMID] 27406187.
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.
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.
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.
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
CollaborationViz: interactive visual exploration of biomedical research collaboration networks.
PloS one.
9(11)
[DOI] 10.1371/journal.pone.0111928.
[PMID] 25405477.
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.
2014
Towards a foundational representation of potential drug-drug interaction knowledge.
CEUR workshop proceedings.
1309:16-31
[PMID] 33139970.
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.
2013
Towards a Consistent and Scientifically Accurate Drug Ontology.
CEUR workshop proceedings.
1060:68-73
[PMID] 27867326.
2012
A system-theoretical, architecture-based approach to ontology management.
Studies in health technology and informatics.
180:1087-9
[PMID] 22874362.
2011
ACGT: advancing clinico-genomic trials on cancer – four years of experience.
Studies in health technology and informatics.
169:734-8
[PMID] 21893844.
2011
Architectural approach for providing relations in biomedical terminologies and ontologies.
Studies in health technology and informatics.
169:739-43
[PMID] 21893845.
2011
Discussion of “biomedical ontologies: toward scientific debate”.
Methods of information in medicine.
50(3):217-36
[PMID] 21566855.
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.
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.
2010
User-specific perspectives on ontologies.
Studies in health technology and informatics.
156:114-21
[PMID] 20543346.
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.
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.
2006
The derives_from relation in biomedical ontologies.
Studies in health technology and informatics.
124:769-74
[PMID] 17108607.
Grants
Dec 2019
– Mar 2021
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
– Feb 2021
CAFE: Comparative Assessment Framework for Environments of Trauma Care
Role: Principal Investigator
Funding: NATL INST OF HLTH NIGMS
Contact Details
Phones:
- Business:
- (352) 627-9467
Emails:
- Business:
- mbrochhausen@ufl.edu
Addresses:
- Business Mailing:
-
PO Box 100177
GAINESVILLE FL 32610