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Within the concept phase of the Medical Informatics Funding Scheme of the Federal Ministry of Education and Research (BMBF), the university hospitals in Aachen, Jena, Leipzig, Hamburg, Bonn, Essen and Halle are involved and funded. Their aim within the scope of SMITH is the development of an innovative structure for cross-institutional linking and exchange of healthcare and research data between sites and beyond.
Programme: MII - Medical Informatics Initiative
Health Atlas ID: 81CN2DP7WT-9
Funding codes:- 01ZZ1803A
Public web page: https://www.smith.care/
Organisms: Homo sapiens
Human Diseases: No Human Disease specified
Health Atlas PALs: Markus Löffler
Project Coordinators: No Project coordinators for this Project
Project start date: 1st Jan 2018
Related items
- Institutions (20)
- Investigations (1)
- Studies (3)
- Resources (3)
- Publications (31)
- Data files (9)
- Presentations (1)
- People (26)
- Events (1)
Snapshots: No snapshots
Studies: Ontological Modelling of Basic Eligibility Criteria, Ontological Modelling of Type 2 Diabetes Mellitus (T2DM) Phenotype, PhenoMan Evaluation with Synthetic FHIR Data
Resources: Basic Eligibility Criteria of an Example Blood Pressure Study, Ontological Modelling of T2DM Phenotype using Phenotype Manager (PhenoMan), PhenoMan Evaluation - Synthetic FHIR Data
We evaluated if the PhenoMan returns correct/complete result sets and if it is working with real data. To simulate a FHIR health data store with real data we used Synthea(TM) to generate a large data set and imported it into a HAPI FHIR JPA Server. Based on the synthetic data set we developed ten example queries with different structure and complexity with PhenoMan and SQL. We compared the results of the queries in means of execution time and equality of results.
The detailed steps of the evaluation
...
Investigation: Ontology-based Phenotyping
Resources: PhenoMan Evaluation - Synthetic FHIR Data
Investigation: Ontology-based Phenotyping
Resources: Basic Eligibility Criteria of an Example Blood Pressure Study
Investigation: Ontology-based Phenotyping
Resources: Ontological Modelling of T2DM Phenotype using Phenotype Manager (PhenoMan)
This assay bundles all synthetic FHIR data of the PhenoMan evaluation. The data arised from a subset of a Synthea(TM) generated data set.
We truncated some resource types like Encounter and Provider to reduce the size of the data set and to speed up the import in a FHIR health data store.
Submitter: Christoph Beger
Resource type: Result Dataset of Clinical Study
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Ontology-based Phenotyping
Study: PhenoMan Evaluation with Synthetic FHIR Data
Organisms: No organisms
Human Diseases: asthma, bronchial disease, hypertension, obesity
SOPs: No SOPs
Data files: PhenoMan Evaluation - AllergyIntolerance FHIR R..., PhenoMan Evaluation - Condition FHIR Resources, PhenoMan Evaluation - Observation FHIR Resources, PhenoMan Evaluation - Patient FHIR Resources
Submitter: Alexandr Uciteli
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Ontology-based Phenotyping
Study: Ontological Modelling of Basic Eligibility Crit...
Organisms: No organisms
Human Diseases: No human diseases
Models: No Models
SOPs: No SOPs
Data files: Eligibility Criteria Ontology for an Example Bl...
We modelled the algorithm for determining Type 2 Diabetes Mellitus (T2DM) cases presented by PheKB.org using Phenotype Manager (PhenoMan).
Submitter: Alexandr Uciteli
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Ontology-based Phenotyping
Study: Ontological Modelling of Type 2 Diabetes Mellit...
Organisms: No organisms
Human Diseases: diabetes mellitus
Models: No Models
SOPs: No SOPs
Data files: T2DM Case 1 Reasoner Report, T2DM Case 2 Reasoner Report, T2DM Case 3 Reasoner Report, T2DM Case 4 Reasoner Report, T2DM Case 5 Reasoner Report, T2DM Graphical Representation, T2DM Ontology, T2DM Tabular Representation
Abstract
Authors: Udo Hahn, Michel Oleynik
Date Published: 21st Aug 2020
Publication Type: Journal article
Citation: Yearb Med Inform 29(01):208-220
Abstract
Authors: Miriam Kesselmeier, Norbert Benda, André Scherag
Date Published: 14th Aug 2020
Publication Type: Journal article
DOI: 10.1371/journal.pone.0237441
Citation: PLoS ONE 15(8):e0237441
Abstract
Authors: Jimmy Huang, Yi Chang, Xueqi Cheng, Jaap Kamps, Vanessa Murdock, Ji-Rong Wen, Yiqun Liu, Erik Faessler, Michel Oleynik, Udo Hahn
Date Published: 25th Jul 2020
Publication Type: InProceedings
Citation: Proceedings of the 43rd International ACM SIGIR Conference on Research and Development in Information Retrieval,pp.459-468,ACM
Abstract (Expand)
Authors: F. Borchert, C. Lohr, L. Modersohn, T. Langer, M. Follmann, J. P. Sachs, U. Hahn, M. P. Schapranow
Date Published: 13th Jul 2020
Publication Type: Misc
Citation:
Abstract (Expand)
Authors: M. Lobe, F. Matthies, S. Staubert, F. A. Meineke, A. Winter
Date Published: 16th Jun 2020
Publication Type: Journal article
PubMed ID: 32570413
Citation: Stud Health Technol Inform. 2020 Jun 16;270:392-396. doi: 10.3233/SHTI200189.
T2DM Phenotype Algorithm Specification Ontology (PASO) developed using PhenoMan
Investigations: Ontology-based Phenotyping
Studies: Ontological Modelling of Type 2 Diabetes Mellit...
Resources: Ontological Modelling of T2DM Phenotype using P...
The tabular representation of the T2DM phenotype algorithm generated by PhenoMan using the T2DM ontology
Investigations: Ontology-based Phenotyping
Studies: Ontological Modelling of Type 2 Diabetes Mellit...
Resources: Ontological Modelling of T2DM Phenotype using P...
Investigations: Ontology-based Phenotyping
Studies: Ontological Modelling of Basic Eligibility Crit...
Resources: Basic Eligibility Criteria of an Example Blood ...
Example Reasoner Report generated by PhenoMan
Investigations: Ontology-based Phenotyping
Studies: Ontological Modelling of Type 2 Diabetes Mellit...
Resources: Ontological Modelling of T2DM Phenotype using P...
Example Reasoner Report generated by PhenoMan
Investigations: Ontology-based Phenotyping
Studies: Ontological Modelling of Type 2 Diabetes Mellit...
Resources: Ontological Modelling of T2DM Phenotype using P...
Presentation on JOWO/ODLS 2019 in Graz
Creators: Alexandr Uciteli, Christoph Beger
Submitter: Christoph Beger
Projects: SMITH - Smart Medical Information Technology for Healthcare
Institutions: Averbis GmbH Freiburg
Projects: SMITH - Smart Medical Information Technology for Healthcare
Institutions: Universitätsklinikum Essen
The Joint Ontology WOrkshops (JOWO) is a venue of workshops that, together, address a wide spectrum of topics related to ontology research, ranging from Cognitive Science to Knowledge Representation, Natural Language Processing, Artificial Intelligence, Logic, Philosophy, and Linguistics.
Country: Austria
City: Graz