Mathias Brochhausen

Mathias Brochhausen,

CO PROF

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

Publications

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.
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.
View on: PubMed
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.
View on: PubMed
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.
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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.
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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.
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2016
Adding evidence type representation to DIDEO.
CEUR workshop proceedings. 1747 [PMID] 33139971.
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2016
Easy Extraction of Terms and Definitions with OWL2TL.
CEUR workshop proceedings. 1747 [PMID] 28035214.
View on: PubMed
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.
View on: PubMed
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.
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.
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.
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2014
Towards a foundational representation of potential drug-drug interaction knowledge.
CEUR workshop proceedings. 1309:16-31 [PMID] 33139970.
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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.
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2013
Towards a Consistent and Scientifically Accurate Drug Ontology.
CEUR workshop proceedings. 1060:68-73 [PMID] 27867326.
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2012
A system-theoretical, architecture-based approach to ontology management.
Studies in health technology and informatics. 180:1087-9 [PMID] 22874362.
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2011
ACGT: advancing clinico-genomic trials on cancer – four years of experience.
Studies in health technology and informatics. 169:734-8 [PMID] 21893844.
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2011
Architectural approach for providing relations in biomedical terminologies and ontologies.
Studies in health technology and informatics. 169:739-43 [PMID] 21893845.
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2011
Discussion of “biomedical ontologies: toward scientific debate”.
Methods of information in medicine. 50(3):217-36 [PMID] 21566855.
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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.
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2010
User-specific perspectives on ontologies.
Studies in health technology and informatics. 156:114-21 [PMID] 20543346.
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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.
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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 – 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

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: