SMITH - Smart Medical Information Technology for Healthcare

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: MII - Medical Informatics Initiative

LHA ID: 81CN2DP7WT-9

Funding codes:
  • 01ZZ1803A

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

Human Diseases: No Human Disease specified

Leipzig Health Atlas PALs: Markus Löffler

Project Coordinators: No Project coordinators for this Project

Project start date: 1st Jan 2018

Project Hierarchy

Related items

PhenoMan Evaluation with Synthetic FHIR Data
SMITH - Smart Medical Information Technology for Healthcare, LHA - Leipzig Health Atlas, Onto-Med Research Group

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 ...

Submitter: Christoph Beger

Investigation: Ontology-based Phenotyping

Resources: PhenoMan Evaluation - Synthetic FHIR Data

Study type: Not specified

Ontological Modelling of Basic Eligibility Criteria
SMITH - Smart Medical Information Technology for Healthcare, LHA - Leipzig Health Atlas, Onto-Med Research Group
No description specified

Submitter: Alexandr Uciteli

Investigation: Ontology-based Phenotyping

Resources: Basic Eligibility Criteria of an Example Blood Pressure Study

Study type: Not specified

Ontological Modelling of Type 2 Diabetes Mellitus (T2DM) Phenotype
SMITH - Smart Medical Information Technology for Healthcare, LHA - Leipzig Health Atlas, Onto-Med Research Group
No description specified

Submitter: Alexandr Uciteli

Investigation: Ontology-based Phenotyping

Resources: Ontological Modelling of T2DM Phenotype using Phenotype Manager (PhenoMan)

Study type: Not specified

PhenoMan Evaluation - Synthetic FHIR Data
LHA - Leipzig Health Atlas, Onto-Med Research Group, SMITH - Smart Medical Information Technology for Healthcare

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

Investigation: Ontology-based Phenotyping

Study: PhenoMan Evaluation with Synthetic FHIR Data

Basic Eligibility Criteria of an Example Blood Pressure Study
LHA - Leipzig Health Atlas, Onto-Med Research Group, SMITH - Smart Medical Information Technology for Healthcare
No description specified

Submitter: Alexandr Uciteli

Biological problem addressed: Model Analysis Type

Investigation: Ontology-based Phenotyping

Study: Ontological Modelling of Basic Eligibility Crit...

Ontological Modelling of T2DM Phenotype using Phenotype Manager (PhenoMan)
LHA - Leipzig Health Atlas, Onto-Med Research Group, SMITH - Smart Medical Information Technology for Healthcare

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

Investigation: Ontology-based Phenotyping

Study: Ontological Modelling of Type 2 Diabetes Mellit...

Ontological Modelling and Execution of Phenotypic Queries in the Leipzig Health Atlas.
LHA - Leipzig Health Atlas, Onto-Med Research Group, SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

Sharing data is of great importance for research in medical sciences. It is the basis for reproducibility and reuse of already generated outcomes in new projects and in new contexts. FAIR data principles … are the basics for sharing data. The Leipzig Health Atlas (LHA) platform follows these principles and provides data, describing metadata, and models that have been implemented in novel software tools and are available as demonstrators. LHA reuses and extends three different major components that have been previously developed by other projects. The SEEK management platform is the foundation providing a repository for archiving, presenting and secure sharing a wide range of publication results, such as published reports, (bio)medical data as well as interactive models and tools. The LHA Data Portal manages study metadata and data allowing to search for data of interest. Finally, PhenoMan is an ontological framework for phenotype modelling. This paper describes the interrelation of these three components. In particular, we use the PhenoMan to, firstly, model and represent phenotypes within the LHA platform. Then, secondly, the ontological phenotype representation can be used to generate search queries that are executed by the LHA Data Portal. The PhenoMan generates the queries in a novel domain specific query language (SDQL), which is specific for data management systems based on CDISC ODM standard, such as the LHA Data Portal. Our approach was successfully applied to represent phenotypes in the Leipzig Health Atlas with the possibility to execute corresponding queries within the LHA Data Portal.

Authors: A. Uciteli, C. Beger, J. Wagner, A. Kiel, F. A. Meineke, S. Staubert, M. Lobe, R. Hansel, J. Schuster, T. Kirsten, H. Herre

Date Published: 24th May 2021

Publication Type: Journal article

Ontological modelling and FHIR Search based representation of basic eligibility criteria
LHA - Leipzig Health Atlas, Onto-Med Research Group, SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

Planning clinical studies to check medical hypotheses requires the specification of eligibility criteria in order to identify potential study participants. Electronically available patient data allows … to support the recruitment of patients for studies. The Smart Medical Information Technology for Healthcare (SMITH) consortium aims to establish data integration centres to enable the innovative use of available healthcare data for research and treatment optimization. The data from the electronic health record of patients in the participating hospitals is integrated into a Health Data Storage based on the Fast Healthcare Interoperability Resources standard (FHIR), developed by HL7. In SMITH, FHIR Search is used to query the integrated data. An investigation has shown the advantages and disadvantages of using FHIR Search for specifying eligibility criteria. This paper presents an approach for modelling eligibility criteria as well as for generating and executing FHIR Search queries. Our solution is based on the Phenotype Manager, a general ontological phenotyping framework to model and calculate phenotypes using the Core Ontology of Phenotypes.

Authors: A. Uciteli, C. Beger, J. Wagner, T. Kirsten, F. A. Meineke, S. Staubert, M. Lobe, H. Herre

Date Published: 26th Apr 2021

Publication Type: Journal article

Integration of allergy documentation into an interoperable archiving and communication platform to improve patient care and clinical research at the Jena University Hospital
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

As part of the digitalization strategy for medical documentation, we introduced a vendor-neutral archive (VNA) at the Jena University Hospital. The VNA provides data based on interoperable formats for … all clinical systems and for communication with other actors as well as for secondary data use. HL7 FHIR is used as a standard for structuring individual data. Using the example of allergy documentation, the paper describes objectives, work status, and experiences from several sub-projects currently being pursued in Jena to establish FHIR. Challenges in information modelling, semantic annotation, connection of clinical sub-systems and integration of FHIR resources in archiving structures and processes are discussed and the necessary cooperation for profiling technical standards is indicated.

Authors: Henner M. Kruse, Alexander Helhorn, Lo An Phan-Vogtmann, Julia Palm, Eric Thomas, Andreas Iffland, Andrew Heidel, Susanne Müller, Kutaiba Saleh, Karsten Krohn, Martin Specht, Michael Hartmann, Katrin Farker, Cord Spreckelsen, Andreas Henkel, Andre Scherag, Danny Ammon

Date Published: 26th Apr 2021

Publication Type: Journal article

Ontological representation, classification and data-driven computing of phenotypes.
LHA - Leipzig Health Atlas, Onto-Med Research Group, SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

BACKGROUND: 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 optimisation. 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. RESULTS: In this article, we present a Core Ontology of Phenotypes (COP) and the software Phenotype Manager (PhenoMan), which implements a novel ontology-based method to model, classify and compute phenotypes from already available data. 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 with selected phenotypes including SOFA score, socio-economic status, body surface area and WHO BMI classification based on available medical data. CONCLUSIONS: We developed a novel ontology-based method to model phenotypes of living beings with the aim of automated phenotype reasoning based on available data. This new approach can be used in clinical context, e.g., for supporting the diagnostic process, evaluating risk factors, and recruiting appropriate participants for clinical and epidemiological studies.

Authors: A. Uciteli, C. Beger, T. Kirsten, F. A. Meineke, H. Herre

Date Published: 21st Dec 2020

Publication Type: Journal article

Medical Information Extraction in the Age of Deep Learning
SMITH - Smart Medical Information Technology for Healthcare

Abstract

Not specified

Authors: Udo Hahn, Michel Oleynik

Date Published: 21st Aug 2020

Publication Type: Journal article

Effect size estimates from umbrella designs: Handling patients with a positive test result for multiple biomarkers using random or pragmatic subtrial allocation
SMITH - Smart Medical Information Technology for Healthcare

Abstract

Not specified

Authors: Miriam Kesselmeier, Norbert Benda, André Scherag

Date Published: 14th Aug 2020

Publication Type: Journal article

What Makes a Top-Performing Precision Medicine Search Engine?
SMITH - Smart Medical Information Technology for Healthcare

Abstract

Not specified

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

GGPONC: A Corpus of German Medical Text with Rich Metadata Based on Clinical Practice Guidelines
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

The lack of publicly available text corpora is a major obstacle for progress in clinical natural language processing, for non-English speaking countries in particular. In this work, we present GGPONC … (German Guideline Program in Oncology NLP Corpus), a freely distributable German language corpus based on clinical practice guidelines in the field of oncology. The corpus is one of the largest corpora of German medical text to date. It does not contain any patient-related data and can therefore be used without data protection restrictions. Moreover, it is the first corpus for the German language covering diverse conditions in a large medical subfield. In addition to the textual sources, we provide a large variety of metadata, such as literature references and evidence levels. By applying and evaluating existing medical information extraction pipelines for German text, we are able to draw comparisons for the use of medical language to other medical text corpora.

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

Problems in FAIRifying Medical Datasets.
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

Despite their young age, the FAIR principles are recognised as important guidelines for research data management. Their generic design, however, leaves much room for interpretation in domain-specific … application. Based on practical experience in the operation of a data repository, this article addresses problems in FAIR provisioning of medical data for research purposes in the use case of the Leipzig Health Atlas project and shows necessary future developments.

Authors: M. Lobe, F. Matthies, S. Staubert, F. A. Meineke, A. Winter

Date Published: 16th Jun 2020

Publication Type: Journal article

An Evolutionary Approach to the Annotation of Discharge Summaries.
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

We here describe the evolution of annotation guidelines for major clinical named entities, namely Diagnosis, Findings and Symptoms, on a corpus of approximately 1,000 German discharge letters. Due to … their intrinsic opaqueness and complexity, clinical annotation tasks require continuous guideline tuning, beginning from the initial definition of crucial entities and the subsequent iterative evolution of guidelines based on empirical evidence. We describe rationales for adaptation, with focus on several metrical criteria and task-centered clinical constraints.

Authors: C. Lohr, L. Modersohn, J. Hellrich, T. Kolditz, U. Hahn

Date Published: 16th Jun 2020

Publication Type: Journal article

T2DM Ontology
LHA - Leipzig Health Atlas, Onto-Med Research Group, SMITH - Smart Medical Information Technology for Healthcare

T2DM Phenotype Algorithm Specification Ontology (PASO) developed using PhenoMan

Creator: Alexandr Uciteli

Submitter: Alexandr Uciteli

Data file type: Not specified

Download
T2DM Tabular Representation
LHA - Leipzig Health Atlas, Onto-Med Research Group, SMITH - Smart Medical Information Technology for Healthcare

The tabular representation of the T2DM phenotype algorithm generated by PhenoMan using the T2DM ontology

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 - Smart Medical Information Technology for Healthcare
No description specified

Creator: Alexandr Uciteli

Submitter: Alexandr Uciteli

Data file type: Not specified

Download
T2DM Case 5 Reasoner Report
LHA - Leipzig Health Atlas, Onto-Med Research Group, SMITH - Smart Medical Information Technology for Healthcare

Example Reasoner Report generated by PhenoMan

Creator: Alexandr Uciteli

Submitter: Alexandr Uciteli

Data file type: Not specified

Download
T2DM Case 4 Reasoner Report
LHA - Leipzig Health Atlas, Onto-Med Research Group, SMITH - Smart Medical Information Technology for Healthcare

Example Reasoner Report generated by PhenoMan

Creator: Alexandr Uciteli

Submitter: Alexandr Uciteli

Data file type: Not specified

Download
T2DM Case 3 Reasoner Report
LHA - Leipzig Health Atlas, Onto-Med Research Group, SMITH - Smart Medical Information Technology for Healthcare

Example Reasoner Report generated by PhenoMan

Creator: Alexandr Uciteli

Submitter: Alexandr Uciteli

Data file type: Not specified

Download
T2DM Case 2 Reasoner Report
LHA - Leipzig Health Atlas, Onto-Med Research Group, SMITH - Smart Medical Information Technology for Healthcare

Example Reasoner Report generated by PhenoMan

Creator: Alexandr Uciteli

Submitter: Alexandr Uciteli

Data file type: Not specified

Download
T2DM Case 1 Reasoner Report
LHA - Leipzig Health Atlas, Onto-Med Research Group, SMITH - Smart Medical Information Technology for Healthcare

Example Reasoner Report generated by PhenoMan

Creator: Alexandr Uciteli

Submitter: Alexandr Uciteli

Data file type: Not specified

Download
T2DM Graphical Representation
LHA - Leipzig Health Atlas, Onto-Med Research Group, SMITH - Smart Medical Information Technology for Healthcare

The decision tree was generated by PhenoMan in GraphML format and was processed using an automatic layout of the yEd Graph Editor. Nonetheless, it is also possible to generate the complete tree as image in PNG format.

Creator: Alexandr Uciteli

Submitter: Alexandr Uciteli

Data file type: Not specified

Download
Ontological Modelling and Reasoning of Phenotypes
LHA - Leipzig Health Atlas, Onto-Med Research Group, SMITH - Smart Medical Information Technology for Healthcare

Presentation on JOWO/ODLS 2019 in Graz

Creators: Alexandr Uciteli, Christoph Beger

Submitter: Christoph Beger

Download
Danny Ammon

Projects: SMITH - Smart Medical Information Technology for Healthcare, POLAR - Polypharmacy, Drug Interactions, Risks

Institutions: Universitätsklinikum Jena

https://orcid.org/0000-0001-8960-7316
Christoph Beger adminproject_administratorasset_housekeeper

Projects: LHA - Leipzig Health Atlas, Onto-Med Research Group, SMITH - Smart Medical Information Technology for Healthcare, COVID-19 Leipzig, LIFE Child, LIFE - Leipzig Research Center for Civilization Diseases

Institutions: Institute for Medical Informatics, Statistics and Epidemiology (IMISE), Universitätsklinikum Leipzig, AöR

https://orcid.org/0000-0002-1166-0368
Philipp Daumke

Projects: SMITH - Smart Medical Information Technology for Healthcare

Institutions: Averbis GmbH Freiburg

Armin de Greiff

Projects: SMITH - Smart Medical Information Technology for Healthcare

Institutions: Universitätsklinikum Essen

Daniel Diekmann

Projects: SMITH - Smart Medical Information Technology for Healthcare

Institutions: ID Information und Dokumentation im Gesundheitswesen GmbH & Co. KGaA

Claudia Fischer

Projects: SMITH - Smart Medical Information Technology for Healthcare

Institutions: Universitätsklinikum Jena

Jan Erik Gewehr

Projects: SMITH - Smart Medical Information Technology for Healthcare, POLAR - Polypharmacy, Drug Interactions, Risks

Institutions: Universitätsklinikum Hamburg-Eppendorf (UKE)

Udo Hahn

Projects: SMITH - Smart Medical Information Technology for Healthcare

Institutions: Friedrich-Schiller-Universität Jena

René Hänsel adminproject_administratorasset_housekeeperasset_gatekeeperprogramme_administrator

Projects: LHA - Leipzig Health Atlas, LIFE Adult, LIFE - Leipzig Research Center for Civilization Diseases, LIFE HNC - Head and Neck Cancer Group, LIFE Heart, MMML - Molecular mechanisms in malignant lymphoma, GLA - German Lymphoma Alliance, MMML Demonstrators - Molecular Mechanisms in Malignant Lymphomas - Demonstrators of Personalized Medicine, HaematoOpt - Individualized model-based managing of the next-cycle thrombopenia of CHOEP/CHOP treated patients based on platelets dynamics during the previous cycles, e:Med, GC-HBOC - German Consortium for Hereditary Breast and Ovarian Cancer, GC-HNPCC - German Consortium for Hereditary Non-Polyposis Colorectal Cancer, MMML-MYC-SYS, NLP4CR - Natural Language Processing for Clinical Research, Genetical Statistics and Systems Biology, SepNet - German Competence Network Sepsis, LIFE Child, HNPCC-Sys - Genomic and transcriptomic heterogeneity of colorectal tumours arising in Lynch syndrome, GGN - German Glioma Network, CAPSys - Footprints of Sepsis Framed Within Community Acquired Pneumonia in the Blood Transcriptome, CapSys - Systems Medicine of Community Acquired Pneumonia, ProstataCA, HaematoSys - Systems biology of haematopoiesis and haematopoietic neoplasia, SMITH - Smart Medical Information Technology for Healthcare, COVID-19 Leipzig, Management of health information systems, LivSys Transfer - Transfer of the LivSys in vitro system for hepatotoxicity into application, Project Test Demonstrator

Institutions: Institute for Medical Informatics, Statistics and Epidemiology (IMISE)

https://orcid.org/0000-0001-8344-0658
Thomas Klöss

Projects: SMITH - Smart Medical Information Technology for Healthcare

Institutions: Universitätsklinikum Halle (Saale), AöR

MII - Medical Informatics Initiative

The medical informatics initiative was created to close the gap between research and healthcare. All of Germany’s university hospitals have joined forces with research institutions, businesses, health insurers, and patient advocacy groups to create a framework that harnesses research findings to the direct benefit of patients. The German Federal Ministry of Education and Research (BMBF) is investing around 160 million euros in the programme through 2021. The digitisation of medicine is creating ...

Projects: SMITH - Smart Medical Information Technology for Healthcare, POLAR - Polypharmacy, Drug Interactions, Risks

Web page: https://www.medizininformatik-initiative.de/en

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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