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- 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: This Project is not associated with a Programme
Health Atlas ID: 7VV367KHEC-9
Funding codes:- 031L0026
Public web page: https://www.health-atlas.de
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 Apr 2016
Project end date: 28th Feb 2021
Related items
- Institutions (4)
- Investigations (1)
- Studies (3)
- Resources (3)
- Publications (16)
- Data files (8+2)
- Models (3)
- Documents (4)
- Presentations (1)
- People (12)
- Events (2)
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 (Expand)
Authors: Henry Loeffler-Wirth, Jasmin Reikowski, Siras Hakobyan, Jonas Wagner, Hans Binder
Date Published: 1st Dec 2020
Publication Type: Journal article
DOI: 10.1186/s12859-020-03806-w
Citation: BMC Bioinformatics 21(1),465
Abstract (Expand)
Authors: Alexandr Uciteli, Christoph Beger, Toralf Kirsten, Frank A. Meineke, Heinrich Herre
Date Published: 20th Dec 2019
Publication Type: InProceedings
Citation: CEUR Workshop Proceedings. 2019 Sep;2570. issn: 1613-0073.
Abstract (Expand)
Authors: F. A. Meineke, Sebastian Stäubert, Matthias Löbe, C. Beger, René Hänsel, A. Uciteli, H. Binder, T. Kirsten, M. Scholz, H. Herre, C. Engel, Markus Löffler
Date Published: 19th Sep 2019
Publication Type: Misc
Citation:
Abstract (Expand)
Authors: N. C. Bilz, E. Willscher, H. Binder, J. Bohnke, M. L. Stanifer, D. Hubner, S. Boulant, U. G. Liebert, C. Claus
Date Published: 10th Aug 2019
Publication Type: Not specified
PubMed ID: 31405163
Citation: Cells. 2019 Aug 10;8(8). pii: cells8080870. doi: 10.3390/cells8080870.
Abstract (Expand)
Authors: M. Nikoghosyan, S. Hakobyan, A. Hovhannisyan, H. Loeffler-Wirth, H. Binder, A. Arakelyan
Date Published: 21st May 2019
Publication Type: Not specified
PubMed ID: 31105750
Citation: Front Genet. 2019 Apr 26;10:394. doi: 10.3389/fgene.2019.00394. eCollection 2019.
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...
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...
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...
The PanCancer Browser is a web application for the interactive comparison of molecular landscapes of different cancers provided by the oposSOM analysis pipeline. It complements the single data set-centered browsing tool oposSOM-Browser.
Creator: Henry Löffler-Wirth
Submitter: Henry Löffler-Wirth
Model type: Self-Organizing Map
Model format: R package
Environment: Shiny
Organism: Not specified
Human Disease: Not specified
Investigations: No Investigations
Studies: No Studies
Resources: No Resources
oposSOM is a comprehensive, machine learning based open-source data analysis software combining functionalities such as diversity analyses, biomarker selection, function mining, and visualization. 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
...
Creator: Henry Löffler-Wirth
Submitter: René Hänsel
Model type: Self-Organizing Map
Model format: R package
Environment: Shiny
Organism: Not specified
Human Disease: Not specified
Investigations: No Investigations
Studies: No Studies
Resources: No Resources
Core Ontology of Phenotypes. Contribute to Onto-Med/COP development by creating an account on GitHub.
Creators: Heinrich Herre, Alexandr Uciteli, Christoph Beger
Submitter: Christoph Beger
Model type: Not specified
Model format: Not specified
Environment: Not specified
Organism: Not specified
Human Disease: Not specified
Investigations: No Investigations
Studies: No Studies
Resources: No Resources
The publication of research results is part of good scientific practice and is increasingly ex-pected and demanded. The FAIR data principles of data sharing are an important guideline - even if medical data sharing makes it necessary to define access restrictions.
Creators: René Hänsel, Frank A. Meineke, Christoph Beger
Submitter: Christoph Beger
Investigations: No Investigations
Studies: No Studies
Resources: No Resources
The Leipzig Health Atlas (LHA) offers a platform for presentation and exchange of publications, (bio-) medical data, models and software tools
from the field of health research. The LHA is based on the FAIR Data Principles (Findable, Accessible, Interoperable, Reusable). Currently,
more than 18 research consortia contribute data from the domains lymphoma, glioma, sepsis, hereditary colorectal and breast cancer, and
others. Target groups are clinicians, epidemiologists, molecular geneticists, human
...
Creators: René Hänsel, Frank A. Meineke, Christoph Beger
Submitter: Christoph Beger
Investigations: No Investigations
Studies: No Studies
Resources: No Resources
The need to manage research data is recognised by the research community - sponsors, legislators, publishers expect and encourage good scientific practice, which not only includes archiving, but also the availability of research data and results in line with FAIR principles.
The publication gives a brief overview of the Leipzig Health Atlas (LHA), which is a project for the presentation and exchange of a wide range of publications, (bio) medical data (e.g. clinical, epidemiological, molecular),
...
Creators: René Hänsel, Matthias Löbe, Sebastian Stäubert, Christoph Beger
Submitter: Christoph Beger
Investigations: No Investigations
Studies: No Studies
Resources: No Resources
The need to manage research data is recognised by the research community - sponsors, legislators, publishers expect and encourage good scientific practice, which not only includes archiving, but also the availability of research data and results in line with FAIR principles.
The publication gives a brief overview of the Leipzig Health Atlas (LHA), which is a project for the presentation and exchange of a wide range of publications, (bio) medical data (e.g. clinical, epidemiological, molecular),
...
Creators: René Hänsel, Matthias Löbe, Sebastian Stäubert, Christoph Beger
Submitter: Christoph Beger
Investigations: No Investigations
Studies: No Studies
Resources: No Resources
Presentation on JOWO/ODLS 2019 in Graz
Creators: Alexandr Uciteli, Christoph Beger
Submitter: Christoph Beger
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, 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, ProstataCA, 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

Roles: Technician
Expertise: Data Management, Data analysis, Python, Html
Projects: LHA - Leipzig Health Atlas
Institutions: Institute for Medical Informatics, Statistics and Epidemiology
Projects: LIFE - Leipzig Research Center for Civilization Diseases, LHA - Leipzig Health Atlas
Institutions: Interdisciplinary Center for Bioinformatics, Faculty of Applied Computer and Biological Sciences, University of Applied Sciences Mittweida

Roles: Project Coordinator
Expertise: Record Linkage, Ontology Matching, Schema Matching, FAIR Data, data integration, data sharing
Start Date: 30th Jan 2020
End Date: 30th Jan 2020
Event Website: https://conference.uni-leipzig.de/researchfestival/
Country: Germany
City: Leipzig
The conference will focus on current contributions to research data management in Saxony. On the basis of practical reports and a poster session, it will be shown what research data management can achieve and what advantages it can offer. An advanced training course on data management planning will help to explore the possibilities and challenges of the FDM for oneself and for research projects. Finally, important aspects and questions will be discussed with each other and with experts at several
...
Start Date: 19th Sep 2019
End Date: 19th Sep 2019
Event Website: https://saxfdm.de/termin/erste-saechsische-tagung-zum-forschungsdatenmanagement/
Country: Germany
City: Dresden