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- Christoph Beger

Onto-Med Research Group (Institute for Medical Informatics, Statistics and Epidemiology) ; LHA - Leipzig Health Atlas (Institute for Medical Informatics, Statistics and Epidemiology)
COVID-19 Leipzig (Institute for Medical Informatics, Statistics and Epidemiology) ; SMITH - Smart Medical Information Technology for Healthcare (Institute for Medical Informatics, Statistics and Epidemiology)
Related items
- Projects (4)
- Institutions (1)
- Investigations (3)
- Studies (2)
- Resources (5)
- Publications (220)
- Data files (27+3)
- Models (5)
- Documents (18)
- Presentations (1)
- Events (4)
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
Public web page: https://www.health-atlas.de
Start date: 1st Apr 2016
End date: 28th Feb 2021
Organisms: Homo sapiens
This project serves as a container for all COVID-19 related assets, developed at the University of Leipzig and its partners.
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Human Diseases: COVID-19
Programme: MII - Medical Informatics Initiative
Public web page: https://www.smith.care/
Start date: 1st Jan 2018
Organisms: Homo sapiens
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
Organisms: Not specified
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
Severe sepsis and septic shock have a high mortality. Research has concentrated on adjunctive sepsis therapies; the role of supportive measures is comparatively unclear. In Europe the use of colloids is widespread, but there is no evidence on the role of either crystalloid or colloid volume therapy in sepsis. Recently, a higher incidence of kidney failure in sepsis was reported after administration of colloids.
Snapshots: No snapshots
Studies: VISEP
Resources: VISEP metadata, VISEP trial data
Snapshots: No snapshots
Studies: HYPRESS
Resources: HYPRESS Trial Data, HYPRESS Trial Metadata
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
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Investigation: Ontology-based Phenotyping
Resources: PhenoMan Evaluation - Synthetic FHIR Data
Baseline Data and Endpoints for HYPRESS
Investigation: HYPRESS
Resources: HYPRESS Trial Data, HYPRESS Trial Metadata
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
Demographics, reference pathology diagnosis, Outcome (Event-free survival, Progression-free survival, Overall survival)
Submitter: Christoph Beger
Resource type: Result Dataset of Clinical Study
Technology type: Technology Type
Snapshots: No snapshots
Investigation: MegaCHOEP
Study: MegaCHOEP
Organisms: No organisms
Human Diseases: B-cell lymphoma, non-Hodgkin lymphoma
SOPs: No SOPs
Data files: MegaCHOEP Trial Result Metadata (Excel), MegaCHOEP Trial Result Metadata (ODM)
Adjunctive hydrocortisone (HC) therapy is suggested by the Surviving Sepsis Campaign in refractory septic shock only. The case for septic patients without shock remains controversial. We investigated the efficacy of HC in patients with severe sepsis without shock
Restricted Trial Data
Submitter: Christoph Beger
Resource type: Result Dataset of Clinical Study
Technology type: Technology Type
Snapshots: No snapshots
Investigation: HYPRESS
Study: HYPRESS
Organisms: No organisms
Human Diseases: disease by infectious agent
SOPs: No SOPs
Data files: HYPRESS Trial Data (Excel), HYPRESS Trial Data (SPSS), Hypress Trial Data (ODM)
Submitter: Christoph Beger
Resource type: Result Dataset of Clinical Study
Technology type: Technology Type
Snapshots: No snapshots
Investigation: HYPRESS
Study: HYPRESS
Organisms: No organisms
Human Diseases: disease by infectious agent
SOPs: No SOPs
Data files: HYPRESS Trial Metadata (Excel), HYPRESS Trial Metadata (ODM)
Demographics, reference pathology diagnosis, Outcome (Event-free survival, Progression-free survival, Overall survival)
Submitter: Christoph Beger
Resource type: Result Dataset of Clinical Study
Technology type: Technology Type
Snapshots: No snapshots
Investigation: MInT
Study: MInT
Organisms: No organisms
Human Diseases: non-Hodgkin lymphoma, B-cell lymphoma
SOPs: No SOPs
Data files: MabThera International Trial Metadata, MabThera International Trial Metadata (ODM)
Abstract
Authors: Udo Hahn, Michel Oleynik
Date Published: 21st Aug 2020
Publication Type: Journal article
Citation: Yearb Med Inform 29(01):208-220
Abstract
Authors: Miriam Kesselmeier, Norbert Benda, André Scherag
Date Published: 14th Aug 2020
Publication Type: Journal article
DOI: 10.1371/journal.pone.0237441
Citation: PLoS ONE 15(8):e0237441
Abstract
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
Citation: Proceedings of the 43rd International ACM SIGIR Conference on Research and Development in Information Retrieval,pp.459-468,ACM
Abstract (Expand)
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
Citation:
Abstract (Expand)
Authors: M. Lobe, F. Matthies, S. Staubert, F. A. Meineke, A. Winter
Date Published: 16th Jun 2020
Publication Type: Journal article
PubMed ID: 32570413
Citation: Stud Health Technol Inform. 2020 Jun 16;270:392-396. doi: 10.3233/SHTI200189.
Based on the assumption that molecular mechanisms involved in cancerogenesis are characterized by groups of coordinately expressed genes, we developed and validated a novel method for analyzing transcriptional data called Correlated Gene Set Analysis (CGSA). Using 50 extracted gene sets we identified three different profiles of tumors in a cohort of 364 Diffuse large B-cell (DLBCL) and related mature aggressive B-cell lymphomas other than Burkitt lymphoma. The first profile had high level of
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Creator: Maciej Rosolowski
Submitter: Christoph Beger
Data file type: Transcriptomic Data
Human Diseases: diffuse large B-cell lymphoma
Investigations: No Investigations
Studies: No Studies
Resources: No Resources
307 single cells cultured from three biopsies of three different patients with a BRAF/NRAS wild type, BRAF mutant/NRAS wild type and BRAF wild type/NRAS mutant melanoma metastasis, respectively
Creators: Hans Binder, Henry Löffler-Wirth, Manfred Kunz
Submitter: Christoph Beger
Data file type: Genomic Data
Human Diseases: melanoma
Investigations: No Investigations
Studies: No Studies
Resources: No Resources
Molecular profiling of cerebral gliomas distinguishes biologically distinct tumor groups and provides prognostically relevant information beyond histological classification and IDH1/2 mutation status. We performed Methylation profiling of primary tumor samples from 122 patients with cerebral gliomas with WHO grade II and grade III tumors.
Creators: Hans Binder, Markus Kreuz, Henry Löffler-Wirth
Submitter: Christoph Beger
Data file type: Methylation Data
Human Diseases: brain glioma
Investigations: No Investigations
Studies: No Studies
Resources: No Resources
Molecular profiling of cerebral gliomas distinguishes biologically distinct tumor groups and provides prognostically relevant information beyond histological classification and IDH1/2 mutation status. We performed Methylation profiling of primary tumor samples from 122 patients with cerebral gliomas with WHO grade II and grade III tumors.
Creators: Hans Binder, Henry Löffler-Wirth, Markus Kreuz
Submitter: Christoph Beger
Data file type: Methylation Data
Human Diseases: brain glioma
Investigations: No Investigations
Studies: No Studies
Resources: No Resources
Molecular profiling of cerebral gliomas distinguishes biologically distinct tumor groups and provides prognostically relevant information beyond histological classification and IDH1/2 mutation status. We performed microarray-based genome- and transcriptome-wide molecular profiling of primary tumor samples from 137 patients with cerebral gliomas, 61 WHO grade II and 76 WHO grade III tumors.
Creators: Henry Löffler-Wirth, Markus Kreuz
Submitter: Christoph Beger
Data file type: Genomic Data
Human Diseases: brain glioma
Investigations: No Investigations
Studies: No Studies
Resources: No Resources
Motivation:
By using the NLP4CR tool, medical facts (e.g. diagnoses, laboratory values) can be extracted from German medical full texts.
Description:
The NLP4CR tool is a prototype that demonstrates the applicability of Apache UIMA and cTakes to medical full texts in German language.
Creators: Sebastian Stäubert, Matthias Löbe, Colleen Goldberg
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 platform is intended for visualization of expression- and mutation-driven changes in biological pathway activities in cancer datasets available in ICGC. The impact of somatic mutations on protein-protein interactions were calculated using Mechismo. Overall activity of biological pathway was evaluated using Pathway Signal Flow algorithm. The application provides interactive heatmaps for pathway output sink node activities and pathway images with mapped affected interactions and output node
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Creators: Hans Binder, Siras Hakobyan
Submitter: Christoph Beger
Model type: Self-Organizing Map
Model format: R package
Environment: Shiny
Organism: Homo sapiens
Human Disease: cancer
Investigations: No Investigations
Studies: No Studies
Resources: No Resources
Preprocessing Illumina HT12v4 gene expression data including quality filtering, data transformation and normalisation and batch-effect removal as well as visualisation
Creators: Markus Scholz, Holger Kirsten
Submitter: Christoph Beger
Model type: Not specified
Model format: R package
Environment: Not specified
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
This is a Drupal 8 Module to import nodes and taxonomies into Drupal, using the available API. The module is capable of importing a JSON or OWL file. Idea is to enable users to upload a file containing all information about nodes and their relations. The module will then import all contained information with the Drupal 8 API. Nodes can be specified as "articles" or any other custom node type. The node classification becomes one (or multiple) hierachical vocabulary. Supported import formats are
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Creator: 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
Summary of the current COVID-19 pandemic development in Leipzig and Saxony.
Creators: Markus Löffler, Markus Scholz, Peter Ahnert, Anne Dietrich, Dirk Hasenclever, Matthias Horn, Yuri Kheifetz, Holger Kirsten, Tyll Krüger, Sibylle Schirm
Submitter: Christoph Beger
Investigations: No Investigations
Studies: No Studies
Resources: No Resources
Summary of the current COVID-19 pandemic development in Leipzig and Saxony.
Creators: Markus Löffler, Markus Scholz, Peter Ahnert, Dirk Hasenclever, Matthias Horn, Yuri Kheifetz, Holger Kirsten, Sibylle Schirm
Submitter: Christoph Beger
Investigations: No Investigations
Studies: No Studies
Resources: No Resources
Summary of the current COVID-19 pandemic development in Leipzig and Saxony.
Creators: Markus Löffler, Markus Scholz, Peter Ahnert, Dirk Hasenclever, Matthias Horn, Yuri Kheifetz, Holger Kirsten, Sibylle Schirm
Submitter: Christoph Beger
Investigations: No Investigations
Studies: No Studies
Resources: No Resources
Summary of the current COVID-19 pandemic development in Leipzig and Saxony.
Creators: Markus Scholz, Markus Löffler, Peter Ahnert, Matthias Horn, Yuri Kheifetz, Holger Kirsten, Kolja Nenoff, Sibylle Schirm
Submitter: Christoph Beger
Investigations: No Investigations
Studies: No Studies
Resources: No Resources
Summary of the current COVID-19 pandemic development in Leipzig and Saxony.
Creators: Markus Löffler, Markus Scholz, Peter Ahnert, Matthias Horn, Yuri Kheifetz, Holger Kirsten, Kolja Nenoff, Sibylle Schirm
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
Start Date: 30th Jan 2020
End Date: 30th Jan 2020
Event Website: https://conference.uni-leipzig.de/researchfestival/
Country: Germany
City: Leipzig
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.
Country: Austria
City: Graz
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
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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
Start Date: 6th Mar 2019
End Date: 8th Mar 2019
Event Website: https://www.gfhev.de/de/kongress/index.htm
Country: Germany
City: Weimar