Jonas Wagner

About Jonas Wagner:
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LHA ID: 805RQ6G0V7-7

Location:  Germany

ORCID: Not specified

Joined: 9th Dec 2019

Expertise: Not specified

Tools: Not specified

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Related items

LHA - Leipzig Health Atlas

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.

Programme: i:DSem - Integrative Datensemantik in der Systemmedizin

Public web page: https://www.health-atlas.de

Start date: 1st Apr 2016

End date: 28th Feb 2021

NFDI4Health - TA3 Services

TA3 focusses on the services, service enabling tools, and software that NFDI4Health will provide to the user community. Services and tools that will be developed or advanced during the project will be published as open source software.

Programme: NFDI - German National Research Data Infrastructure

Public web page: https://www.nfdi4health.de/en/about-us/task-areas/ta3-services.html

NFDI4Health: inactive since

NFDI4Health - the National Research Data Infrastructure for Personal Health Data - deals with data generated in clinical trials, epidemiological and public health studies. The collection and analysis of these data on health and disease status and important factors influencing it are an essential component for the development of new therapies, comprehensive care approaches and preventive measures in a modern health care system. Although these data already meet high content quality standards, they ...

Programme: NFDI - German National Research Data Infrastructure

Public web page: https://www.nfdi4health.de/en

LIFE - Leipzig Research Center for Civilization Diseases

Goal of the Leipzig Research Center for Civilization Diseases (LIFE) is the investigation of civilization diseases like depression, diabetes, allergies or cardiovascular diseases. For this purpose we collect as much data as possible regarding health and living conditions of the population in Leipzig and provide these data for scientists of the University of Leipzig and other research institutions.

Programme: LIFE Management Cluster

Public web page: http://life.uni-leipzig.de/

Start date: 1st Jan 2009

The Leipzig Health Atlas-An Open Platform to Present, Archive, and Share Biomedical Data, Analyses, and Models Online.
LHA - Leipzig Health Atlas

Abstract (Expand)

BACKGROUND: Clinical trials, epidemiological studies, clinical registries, and other prospective research projects, together with patient care services, are main sources of data in the medical research … domain. They serve often as a basis for secondary research in evidence-based medicine, prediction models for disease, and its progression. This data are often neither sufficiently described nor accessible. Related models are often not accessible as a functional program tool for interested users from the health care and biomedical domains. OBJECTIVE: The interdisciplinary project Leipzig Health Atlas (LHA) was developed to close this gap. LHA is an online platform that serves as a sustainable archive providing medical data, metadata, models, and novel phenotypes from clinical trials, epidemiological studies, and other medical research projects. METHODS: Data, models, and phenotypes are described by semantically rich metadata. The platform prefers to share data and models presented in original publications but is also open for nonpublished data. LHA provides and associates unique permanent identifiers for each dataset and model. Hence, the platform can be used to share prepared, quality-assured datasets and models while they are referenced in publications. All managed data, models, and phenotypes in LHA follow the FAIR principles, with public availability or restricted access for specific user groups. RESULTS: The LHA platform is in productive mode (https://www.health-atlas.de/). It is already used by a variety of clinical trial and research groups and is becoming increasingly popular also in the biomedical community. LHA is an integral part of the forthcoming initiative building a national research data infrastructure for health in Germany.

Authors: T. Kirsten, F. A. Meineke, H. Loeffler-Wirth, C. Beger, A. Uciteli, S. Staubert, M. Lobe, R. Hansel, F. G. Rauscher, J. Schuster, T. Peschel, H. Herre, J. Wagner, S. Zachariae, C. Engel, M. Scholz, E. Rahm, H. Binder, M. Loeffler

Date Published: 3rd Aug 2022

Publication Type: Journal article

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 execution of phenotypic queries in the Leipzig Health Atlas
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: Alexandr Uciteli, Christoph Beger, Jonas Wagner, Alexander Kiel, Frank A Meineke, Sebastian Stäubert, Matthias Löbe, René Hänsel, Judith Schuster, Toralf Kirsten, Heinrich Herre

Date Published: 1st May 2021

Publication Type: InCollection

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

oposSOM-Browser: an interactive tool to explore omics data landscapes in health science
LHA - Leipzig Health Atlas, oBIG - omics Bioinformatics for Health

Abstract (Expand)

Background: oposSOM is a comprehensive, machine learning based open-source data analysis software combining functionalities such as diversity analyses, biomarker selection, function mining, and … visualization. Results: These functionalities are now available as interactive web-browser application for a broader user audience interested in extracting detailed information from high-throughput omics data sets pre-processed by oposSOM. It enables interactive browsing of single-gene and gene set profiles, of molecular 'portrait landscapes', of associated phenotype diversity, and signalling pathway activation patterns. Conclusion: The oposSOM-Browser makes available interactive data browsing for five transcriptome data sets of cancer (melanomas, B-cell lymphomas, gliomas) and of peripheral blood (sepsis and healthy individuals) at www.izbi.uni-leipzig.de/opossom-browser .

Authors: Henry Loeffler-Wirth, Jasmin Reikowski, Siras Hakobyan, Jonas Wagner, Hans Binder

Date Published: 1st Dec 2020

Publication Type: Journal article

Metabolite Investigator v0.1.2 (Docker Image)
Genetical Statistics and Systems Biology

#UPDATE

This archive has been replaced by the GitLab docker registry. Follow the Link under Data Portal (https://gitlab.com/imise-genstat/metabolite-investigator-archive/container_registry/1612096) to find all previous versions of the app (starting from 0.1.6). The images can be downloaded and run using a working docker environment using the following commands:

Using the initial release version 0.1.6 as an example

docker pull registry.gitlab.com/imise-genstat/metabolite-investigator-archive:0.1.6 ...

Creators: Markus Scholz, Jonas Wagner, Carl Beuchel, Holger Kirsten

Submitter: Carl Beuchel

Data file type: Other OMICs Data

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LIFE Management Cluster
No description specified

Projects: LIFE Heart, LIFE - Leipzig Research Center for Civilization Diseases, LIFE HNC - Head and Neck Cancer Group, SepNet - German Competence Network Sepsis, GC-HNPCC - German Consortium for Hereditary Non-Polyposis Colorectal Cancer, LIFE Child, GC-HBOC - German Consortium for Hereditary Breast and Ovarian Cancer, LIFE Adult

Web page: https://www.uniklinikum-leipzig.de/einrichtungen/life

i:DSem - Integrative Datensemantik in der Systemmedizin

Within the framework of the funding measure "i:DSem - Integrative Data Semantics in Systems Medicine", the Federal Ministry of Education and Research supports research projects that take up this approach. Interdisciplinary research projects are to create the basis so that in the future, for example, the attending physician will have application-oriented computer programmes at his or her disposal that will enable him or her to access all clinically relevant data. This should significantly support ...

Projects: LHA - Leipzig Health Atlas

Web page: https://www.gesundheitsforschung-bmbf.de/de/i-dsem-integrative-datensemantik-in-der-systemmedizin-3367.php

NFDI - German National Research Data Infrastructure

In the German National Research Data Infrastructure (NFDI), valuable data from science and research are systematically accessed, networked and made usable in a sustainable and qualitative manner for the entire German science system. Up to now, they have mostly been available on a decentralised, project-related or temporary basis. The NFDI aims to create a permanent digital repository of knowledge as an indispensable prerequisite for new research questions, findings and innovations. Relevant data ...

Projects: NFDI4Health, Task Force COVID-19 Leipzig, NFDI4Health - TA3 Services, Clinical Trials Leipzig

Web page: https://www.nfdi.de/?lang=en

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Health Atlas - Local Data Hub/Leipzig

The Health Atlas - Local Data Hub/Leipzig 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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