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- PhenoMan Evaluation with 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 can be found in our public GitHub repository: Onto-Med/phenoman-evaluation.
Health Atlas ID: 82UY638KN5-7
Projects: LHA - Leipzig Health Atlas, Onto-Med Research Group, SMITH - Smart Medical Information Technology for Healthcare
Study type: Not specified
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Created: 29th Jun 2020 at 14:53
Last updated: 29th Jun 2020 at 15:31
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Programme: MII - Medical Informatics Initiative
Public web page: https://www.smith.care/
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The Leipzig Health Atlas (LHA) is an alliance of medical ontologists, medical systems biologists and clinical trials groups to design and implement a multi-functional and quality-assured atlas. It provides models, data and metadata on specific use cases from medical research fields in which our team has scientific and clinical expertise.
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The Onto-Med Research Group conducts basic research in formal ontology, designs formal tools for constructing and managing ontologies and develops top level ontologies as well as domain and core ontologies for medicine, bio-medicine and biology, but also for other fields. The Onto-Med group uses an interdisciplinary approach, combining methods from logic, computer science, philosophy and cognitive linguistics. The Onto-Med group considers Formal Ontology as an evolving science which is concerned
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Programme: This Project is not associated with a Programme
Public web page: http://www.onto-med.de
Start date: 1st Jan 2002
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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
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
This data file contains FHIR bundles of observation resources, which were used for the evaluation of the PhenoMan.
Originally the observation data were generated with Synthea(TM) and truncated to reduce overall size and import times into a HAPI FHIR JPA Server.
Please import the patient resources prior to the observations.
This data file contains 8,026,380 observations.
Creators: Alexandr Uciteli, Christoph Beger
Submitter: Christoph Beger
Data file type: Clinical Data
Human Diseases: obesity, bronchial disease, asthma, hypertension
Investigations: Ontology-based Phenotyping
Studies: PhenoMan Evaluation with Synthetic FHIR Data
Resources: PhenoMan Evaluation - Synthetic FHIR Data
This data file contains FHIR bundles of patient resources, which were used for the evaluation of the PhenoMan.
Originally the patient data were generated with Synthea(TM) and truncated to reduce overall size and import times into a HAPI FHIR JPA Server.
This data file contains 66,018 patients.
Creators: Alexandr Uciteli, Christoph Beger
Submitter: Christoph Beger
Data file type: Clinical Data
Human Diseases: obesity, bronchial disease, asthma, hypertension
Investigations: Ontology-based Phenotyping
Studies: PhenoMan Evaluation with Synthetic FHIR Data
Resources: PhenoMan Evaluation - Synthetic FHIR Data
This data file contains FHIR bundles of allergy intolerance resources, which were used for the evaluation of the PhenoMan.
Originally the allergy intolerance data were generated with Synthea(TM) and truncated to reduce overall size and import times into a HAPI FHIR JPA Server.
Please import the patient resources prior to the allergy intolerances.
This data file contains 563 allergy intolerances.
Creators: Alexandr Uciteli, Christoph Beger
Submitter: Christoph Beger
Data file type: Clinical Data
Human Diseases: obesity, bronchial disease, asthma, hypertension
Investigations: Ontology-based Phenotyping
Studies: PhenoMan Evaluation with Synthetic FHIR Data
Resources: PhenoMan Evaluation - Synthetic FHIR Data
This data file contains FHIR bundles of condition resources, which were used for the evaluation of the PhenoMan.
Originally the condition data were generated with Synthea(TM) and truncated to reduce overall size and import times into a HAPI FHIR JPA Server.
Please import the patient resources prior to the conditions.
This data file contains 139,763 conditions.
Creators: Alexandr Uciteli, Christoph Beger
Submitter: Christoph Beger
Data file type: Clinical Data
Human Diseases: obesity, bronchial disease, asthma, hypertension
Investigations: Ontology-based Phenotyping
Studies: PhenoMan Evaluation with Synthetic FHIR Data
Resources: PhenoMan Evaluation - Synthetic FHIR Data