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SMITH

Overview
Motivation:

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.

Description:
No description specified

Programme: This Project is not associated with a Programme

LHA-ID: 81CN2DP7WT-9

Funding codes:
  • 01ZZ1803A

Public web page: https://www.smith.care/

Organisms: No Organisms specified

Human Diseases: No Human Disease specified

Leipzig Health Atlas PALs: Markus Löffler

Project start date: 1st Jan 2018

Related items

PhenoMan Evaluation with Synthetic FHIR Data
Leipzig Health Atlas, Onto-Med Research Group, SMITH

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
...

Person responsible: Christoph Beger

Snapshots: No snapshots

Study type: Not specified

Ontological Modelling of Basic Eligibility Criteria
Leipzig Health Atlas, Onto-Med Research Group, SMITH
No description specified

Person responsible: Alexandr Uciteli

Snapshots: No snapshots

Study type: Not specified

Ontological Modelling of Type 2 Diabetes Mellitus (T2DM) Phenotype
Leipzig Health Atlas, Onto-Med Research Group, SMITH
No description specified

Person responsible: Alexandr Uciteli

Snapshots: No snapshots

Study type: Not specified

PhenoMan Evaluation - Synthetic FHIR Data
Leipzig Health Atlas, Onto-Med Research Group, SMITH

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

Assay type: Result Dataset of Clinical Study

Technology type: Technology Type

Snapshots: No snapshots

Basic Eligibility Criteria of an Example Blood Pressure Study
Leipzig Health Atlas, Onto-Med Research Group, SMITH
No description specified

Submitter: Alexandr Uciteli

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Ontological Modelling of T2DM Phenotype using Phenotype Manager (PhenoMan)
Leipzig Health Atlas, Onto-Med Research Group, SMITH

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

T2DM Ontology
Leipzig Health Atlas, Onto-Med Research Group, SMITH

T2DM Phenotype Algorithm Specification Ontology (PASO) developed using PhenoMan

Creator: Alexandr Uciteli

Submitter: Alexandr Uciteli

Data file type: Not specified

Download
Eligibility Criteria Ontology for an Example Blood Pressure Study
Onto-Med Research Group, SMITH
No description specified

Creator: Alexandr Uciteli

Submitter: Alexandr Uciteli

Data file type: Not specified

Download
T2DM Case 5 Reasoner Report
Leipzig Health Atlas, Onto-Med Research Group, SMITH

Example Reasoner Report generated by PhenoMan

Creator: Alexandr Uciteli

Submitter: Alexandr Uciteli

Data file type: Not specified

Download
T2DM Case 4 Reasoner Report
Leipzig Health Atlas, Onto-Med Research Group, SMITH

Example Reasoner Report generated by PhenoMan

Creator: Alexandr Uciteli

Submitter: Alexandr Uciteli

Data file type: Not specified

Download
T2DM Case 3 Reasoner Report
Leipzig Health Atlas, Onto-Med Research Group, SMITH

Example Reasoner Report generated by PhenoMan

Creator: Alexandr Uciteli

Submitter: Alexandr Uciteli

Data file type: Not specified

Download
Ontological Modelling and Reasoning of Phenotypes
Leipzig Health Atlas, Onto-Med Research Group, SMITH

Abstract (Expand)

The successful determination and analysis of phenotypes plays a key role in the diagnostic process, the evaluation of risk factors and the recruitment of participants for clinical and epidemiological … studies. The development of computable phenotype algorithms to solve these tasks is a challenging problem, caused by various reasons. Firstly, the term ‘phenotype’ has no generally agreed definition and its meaning depends on context. Secondly, the phenotypes are most commonly specified as non-computable descriptive documents. Recent attempts have shown that ontologies are a suitable way to handle phenotypes and that they can support clinical research and decision making. The SMITH Consortium is dedicated to rapidly establish an integrative medical informatics framework to provide physicians with the best available data and knowledge and enable innovative use of healthcare data for research and treatment optimization. In the context of a methodological use case “phenotype pipeline” (PheP), a technology to automatically generate phenotype classifications and annotations based on electronic health records (EHR) is developed. A large series of phenotype algorithms will be implemented. This implies that for each algorithm a classification scheme and its input variables have to be defined. Furthermore, a phenotype engine is required to evaluate and execute developed algorithms. In this article we present a Core Ontology of Phenotypes (COP) and a software Phenotype Manager (PhenoMan), which implements a novel ontology-based method to model and calculate phenotypes. Our solution includes an enhanced iterative reasoning process combining classification tasks with mathematical calculations at runtime. The ontology as well as the reasoning method were successfully evaluated based on different phenotypes (including SOFA score, socioeconomic status, body surface area and WHO BMI classification) and several data sets.

Authors: Alexandr Uciteli, Christoph Beger, Toralf Kirsten, Frank A. Meineke, Heinrich Herre

Date Published: 20th Dec 2019

Publication Type: Proceedings

Joint Ontology Workshops (JOWO) 2019

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.

Start Date: 23rd Sep 2019

End Date: 25th Sep 2019

Event Website: https://www.iaoa.org/jowo/2019/

Country:  Austria

City: Graz

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The Leipzig Health Atlas 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.

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