Christoph Beger

About Christoph Beger:
No description specified

LHA ID: 7VV43Q20EY-1

Location:  Germany

Expertise: data integration, ruby, r, java, perl

Tools: Not specified

ORCID: https://orcid.org/0000-0002-1166-0368

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1p and 19q co-deletion acceptable change limit adenocarcinoma (in situ) adolescents adults advance care planning advance directives age aggressive non-hodgkin's lymphoma aging alzheimer's disease amyloid anaemia ankle-brachial index anthropometry antidepressant medication apache uima arachidonic acid arousal array-based comparative genomic hybri... associative memory asthma astrocytoma atrophy automatic data processing b-cell lymphoma bdnf behavioral variant frontotemporal dem... bioconductor bioinformatics biomarker biomathematical model Biomedical Ontologies biomedical ontology bipolar blood disturbances blood transcriptome blood-oxygenation-level dependent body height body mass index boolean implications brain brain arousal regulation brain connectivity brain tumor brain-derived neurotrophic factor brainstem brca1 brca2 breast cancer cancer cancer genetics cancer heterogeneity cancer syndromes cardiorespiratory fitness carotid artery plaque causal inference cdisc odm chemotherapy childhood obesity children cholinergic system cis-eQTL classification clinical genetics clinical research informatics clinical trials cognition cognitive abilities cognitive complaints cognitive control cognitive functioning cognitive neuropsychiatry cognitive reserve cognitive restrain cohort studies colloids colorectal cancer colorectal neoplasm community-acquired pneumonia severity connectivity consciousness construct validity coronary artery disease cryptococcus neoformans crystalloids ctakes darbepoetin data sharing data visualization daytime sleepiness deep-brain stimulation demands dementia depression development dhea-s diabetes mellitus diagnostic criteria differentiation diffuse large B-cell lymphoma disinhibition dlbcl dna methylation dna methylation biomarkers Domain-specific Language dorsolateral prefrontal cortex dried whole blood drug allergy early detection early intervention eating behaviour eating disorders ecg edta-plasma education eeg eeg synchrony eicosanoids eigenvector centrality elderly electronic health records eligibility determination eloreta emotional eating environmental data epidemiology epigenetics epo epworth sleepiness scale eQTL errors eSNP estradiol estrogens evaluation event-related fmri excel executive functions exercise testing expression quantitative trait locus fair false discovery rate family-wise error fdg fdg-pet fhir filgrastim fmri frequency frontotemporal lobar degeneration functional connectivity functional enrichment functional magnetic resonance imaging fungal allergy g-csf gene expression gene expression analysis gene expression profiles gene regulation gene regulatory networks gene signatures gene targeting general population genetic counselling genetic screening genetics genomic imbalances genomic range geriatrics GFO glia glioblastoma glioma global workspace globus pallidus glycosylated hemoglobin grading gray matter density grey matter atrophy gwas hashimoto's thyroiditis hboc head motion health information interoperability Health Level Seven healthy adults hereditary hereditary cancer hormonal transition periods hydrocortisone hyperarousal hypothyroidism idh1 idh1 mutation igh illumina ht-12 v4 expression beadchips imaging puls sequence immune editing immune suppression immunohistochemistry incidence incident dementia independent component analysis infections inflammation inflammatory cells information retrieval information storage Information Storage and Retrieval information storage and retrival insomnia insulin integrative bioinformatics inter-assay precision intima-media thickness intracranial ependymoma isocitrate dehydrogenase knowledge bases language late life late life depression leucopenia leukocyte subsets life style lipolysis liquid biopsy long-term survival longitudinal cohort study lps lymphoma lynch syndrome machine learning macrophages magnetic resonance imaging magnetization-prepared rapid gradient... major depression maldi manchester scoring system mania maximum oxygen uptake mci medial prefrontal cortex medical informatics melanoma memory complaints mendelian randomisation menstrual cycle mental demands meta-analysis metabolites metabolomics metadata metadata repository methylcap-seq mgmt microlesion effect mild cognitive impairment minor depression mismatch repair module molecular oncology molecular subtypes montreal neurological institute mood mood disorder morbidity mortality motivation motor cortex motor part of unified parkinson's dis... mQTL mri multicolor flow cytometry multivariate analysis mutation prevalences myc ncc neuroimaging neuron-specific enolase neurons neuropsychiatric disorders neuropsychiatry neuropsychology neurotransmitters nf-kb nicotinamide nlp non-coding RNA noncoronary atherosclerosis nonlinear lagged coherence normative data normative values novelty nse obesity occupation old people old-age oldest-old age oligodendroglioma ontology organogenesis outcomes ovarian cancer overall survival p53 parkinson's disease pathway activity pathway enrichment pathway signal flow pattern classification pbmc pct peak oxygen uptake pedunculopontine nucleus pegfilgrastim perception peripheral blood peripheral blood monocyte pet pharmacotherapy Phenotype phenotype calculation phenotype classification phenotype definition phenotype ontology phenotype reasoning phenotyping phq-15 pipeline plasticity polygenetic regulation polypharmacy population-based study power of attorney preclinical alzheimer's disease prevalence prevention primary care progesterone prognosis prognostic factors prognostic impact progression risk progression-free survival pseudotime psychological factors quantitative methylation-specific pcr questionnaire r-chop radiofrequence coil recruitment reference intervals repeated measures analysis of variance response resting-state fmri restingstate restrained eating risk criteria risk factors risk prediction models rituximab rs-fmri s100b schizophrenia screening secular trends Selection Criteria self organizing maps self-regulation septic shock sequencing seroreactivity serum serum marker severe sepsis single-cell transcriptomics sleep disturbance sleep quality small-vessel disease smoking snp social isolation social network socio-economic status sodium selenite som somatic mutations somatic symptoms spss stability standard deviation stem cells stem-cell differentiation step test subgenual prefrontal cortex subjective cognition subjective cognitive decline subjective cognitive impairment subjective memory complaints submission subthalamic nucleus support vector machine survey synthea testosterone text mining three-factor eating questionnaire thyroidperoxidase antibodies time trends tissue engineering tissue-specific top-level ontology tp53 mutation trans-cluster trans-eQTL transcriptome and methylome transcriptomics translocation tumor progression tumor suppressor gene tumour heterogeneity uncontrolled eating user acceptance uterine cervical neoplasms validation vascular cognitive impairment vbm vigall vigall 2.1 vigilance vo2max vo2peak voice range profile voxel size voxel-based morphometry vsaq questionnaire Web Archive web portal white matter disease white matter hyperintensities work work environment workflow ymca-step test

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Onto-Med Research Group

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 ...

Programme: This Project is not associated with a Programme

Public web page: http://www.onto-med.de

Start date: 1st Jan 2002

SMITH - Smart Medical Information Technology for Healthcare
No description specified

Programme: MII - Medical Informatics Initiative

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

Start date: 1st Jan 2018

COVID-19 Leipzig

This project serves as a container for all COVID-19 related assets, developed at the University of Leipzig and its partners.

Programme: Epidemiology

Public web page: Not specified

Start date: 20th May 2020

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

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

Start date: 1st Apr 2016

End date: 28th Feb 2021

LIFE - Leipzig Research Center for Civilization Diseases: inactive since

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: Epidemiology

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

Start date: 1st Jan 2009

LIFE Child

LIFE Child wants to find out how environmental factors and lifestyles can affect the health of children and adolescents. The aim of the study is to examine civilization diseases such as allergies, obesity, diabetes, cardiovascular diseases in more detail. Furthermore, the study also focuses on healthy mental and physical development from the infant to the young adult. The team of the LIFE Child study around Prof. Dr. med. Wieland Kiess would like to examine and question about 5,000 subjects aged ...

Programme: This Project is not associated with a Programme

Public web page: http://www.life-child.de/

Start date: 1st Jan 2009

Ontology-based Phenotyping
SMITH - Smart Medical Information Technology for Healthcare, LHA - Leipzig Health Atlas, Onto-Med Research Group
No description specified

Submitter: Alexandr Uciteli

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

Efficacy of Volume Substitution and Insulin Therapy in Severe Sepsis (VISEP Trial)
SepNet - German Competence Network Sepsis

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.

Submitter: Christoph Beger

Studies: VISEP

Resources: VISEP metadata, VISEP trial data

HYPRESS
SepNet - German Competence Network Sepsis
No description specified

Submitter: Christoph Beger

Studies: HYPRESS

Resources: HYPRESS Trial Data, HYPRESS Trial Metadata

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

HYPRESS
SepNet - German Competence Network Sepsis

Baseline Data and Endpoints for HYPRESS

Submitter: Christoph Beger

Investigation: HYPRESS

Resources: HYPRESS Trial Data, HYPRESS Trial Metadata

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

MegaCHOEP Trial Metadata
GLA - German Lymphoma Alliance

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

Investigation: MegaCHOEP

Study: MegaCHOEP

HYPRESS Trial Data
SepNet - German Competence Network Sepsis

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

Investigation: HYPRESS

Study: HYPRESS

HYPRESS Trial Metadata
SepNet - German Competence Network Sepsis
No description specified

Submitter: Christoph Beger

Resource type: Result Dataset of Clinical Study

Technology type: Technology Type

Investigation: HYPRESS

Study: HYPRESS

MInt Trial Result Metadata
GLA - German Lymphoma Alliance

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

Investigation: MInT

Study: MInT

1 hidden item
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

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

Towards GFO 2.0: Architecture, Modules and Applications
Onto-Med Research Group

Abstract

Not specified

Authors: Patryk Burek, Frank Loebe, Heinrich Herre

Date Published: 22nd Oct 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

Expression Data from Malignant Lymphoma
MMML-MYC-SYS

We performed gene-expression profiling using Affymetrix U133A GeneChips with RNA from 220 mature aggressive B-cell lymphomas, including a core group of 8 Burkitt's lymphomas that met all World Health Organization (WHO) criteria. A molecular signature for Burkitt's lymphoma was generated, and chromosomal abnormalities were detected with interphase fluorescence in situ hybridization and array-based comparative genomic hybridization.

Creator: Michael Hummel

Submitter: Christoph Beger

Data file type: Genomic Data

Human Diseases: B-cell lymphoma

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Expression data from cerebral tumors of WHO grade II and III (Expression Data)
GGN - German Glioma Network

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

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Methylation data from cerebral tumors of WHO grade II and III (Betas)
GGN - German Glioma Network

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

MDR Survey Metadata RedCap
Evaluation Metadata Repository
No description specified

Creator: Matthias Löbe

Submitter: Christoph Beger

Data file type: Not specified

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Massive Transcriptional Perturbation in Subgroups of Diffuse Large B-cell Lymphomas
MMML-MYC-SYS

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 ...

Creator: Maciej Rosolowski

Submitter: Christoph Beger

Data file type: Transcriptomic Data

Human Diseases: diffuse large B-cell lymphoma

External Link
Single cell expression data of melanoma
Leipzig Melanoma Studies

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

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Methylation data from cerebral tumors of WHO grade II and III (Level 1)
GGN - German Glioma Network

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

PhenoMan Evaluation - Observation FHIR Resources
Onto-Med Research Group

This data file contains FHIR bundles of observation resources, which were used for the evaluation of the PhenoMan. Originally the observation data were generated with Synthea(TM) and truncated to reduce overall size and import times into a HAPI FHIR JPA Server. Please import the patient resources prior to the observations.

This data file contains 8,026,380 observations.

Creators: Alexandr Uciteli, Christoph Beger

Submitter: Christoph Beger

Data file type: Clinical Data

Human Diseases: obesity, bronchial disease, asthma, hypertension

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PhenoMan Evaluation - Patient FHIR Resources
Onto-Med Research Group

This data file contains FHIR bundles of patient resources, which were used for the evaluation of the PhenoMan. Originally the patient data were generated with Synthea(TM) and truncated to reduce overall size and import times into a HAPI FHIR JPA Server.

This data file contains 66,018 patients.

Creators: Alexandr Uciteli, Christoph Beger

Submitter: Christoph Beger

Data file type: Clinical Data

Human Diseases: obesity, bronchial disease, asthma, hypertension

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PhenoMan Evaluation - AllergyIntolerance FHIR Resources
Onto-Med Research Group

This data file contains FHIR bundles of allergy intolerance resources, which were used for the evaluation of the PhenoMan. Originally the allergy intolerance data were generated with Synthea(TM) and truncated to reduce overall size and import times into a HAPI FHIR JPA Server. Please import the patient resources prior to the allergy intolerances.

This data file contains 563 allergy intolerances.

Creators: Alexandr Uciteli, Christoph Beger

Submitter: Christoph Beger

Data file type: Clinical Data

Human Diseases: obesity, bronchial disease, asthma, hypertension

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3 hidden items
General Formal Ontology (GFO)
Onto-Med Research Group

The General Formal Ontology is a top-level ontology for conceptual modeling. It includes elaborations of categories like objects, processes, time and space, properties, relations, roles, functions, facts, and situations.

Creator: Heinrich Herre

Submitter: Christoph Beger

External Link
NLP for Clinical Research Tool
NLP4CR - Natural Language Processing for Clinical Research

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

Interactive Pathway Activity Analysis Platform
GGN - German Glioma Network

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 ...

Creators: Hans Binder, Siras Hakobyan

Submitter: Christoph Beger

External Link
HT12ProcessoR: Preprocessing ILLUMINA HT12v4 data intended for project up to thousands of samples
Genetical Statistics and Systems Biology

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

External Link
Core Ontology of Phenotypes
Onto-Med Research Group, LHA - Leipzig Health Atlas

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

External Link
Simple Ontology Loader in Drupal (SOLID)
Onto-Med Research Group

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 ...

Creator: Christoph Beger

Submitter: Christoph Beger

External Link
Bulletin COVID-19 Leipzig 2021-07-12
COVID-19 Leipzig

Summary of the current COVID-19 pandemic development in Leipzig and Saxony. This work was done as part of the NFDI4Health Task Force COVID-19 (nfdi4health.de). We gratefully acknowledge the financial support of the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project Number 451265285.

Creators: Torsten Thalheim, Markus Scholz, Markus Löffler, Holger Kirsten, Peter Ahnert, Karolin Bucksch, Anne Dietrich, Dirk Hasenclever, Matthias Horn, Yuri Kheifetz, Tyll Krüger, Sibylle Schirm

Submitter: Christoph Beger

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Bulletin COVID-19 Leipzig 2021-04-22
COVID-19 Leipzig, Genetical Statistics and Systems Biology

Summary of the current COVID-19 pandemic development in Leipzig and Saxony. This work was done as part of the NFDI4Health Task Force COVID-19 (nfdi4health.de). We gratefully acknowledge the financial support of the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project Number 451265285.

Creators: Torsten Thalheim, Holger Kirsten, Markus Scholz, Markus Löffler, Peter Ahnert, Anne Dietrich, Dirk Hasenclever, Matthias Horn, Yuri Kheifetz, Tyll Krüger, Sibylle Schirm

Submitter: Christoph Beger

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Bulletin COVID-19 Leipzig 2021-05-31
COVID-19 Leipzig

Summary of the current COVID-19 pandemic development in Leipzig and Saxony. This work was done as part of the NFDI4Health Task Force COVID-19 (nfdi4health.de). We gratefully acknowledge the financial support of the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project Number 451265285.

Creators: Holger Kirsten, Markus Scholz, Markus Löffler, Peter Ahnert, Karolin Bucksch, Anne Dietrich, Dirk Hasenclever, Matthias Horn, Yuri Kheifetz, Tyll Krüger, Sibylle Schirm

Submitter: Christoph Beger

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Bulletin COVID-19 Leipzig 2021-02-20
Genetical Statistics and Systems Biology, COVID-19 Leipzig

Summary of the current COVID-19 pandemic development in Leipzig and Saxony. This work was done as part of the NFDI4Health Task Force COVID-19 (nfdi4health.de). We gratefully acknowledge the financial support of the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project Number 451265285.

Creators: Holger Kirsten, Markus Löffler, Markus Scholz, Peter Ahnert, Anne Dietrich, Dirk Hasenclever, Matthias Horn, Yuri Kheifetz, Tyll Krüger, Sibylle Schirm

Submitter: Christoph Beger

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Bulletin COVID-19 Leipzig 2021-01-27
COVID-19 Leipzig, Genetical Statistics and Systems Biology

Summary of the current COVID-19 pandemic development in Leipzig and Saxony. This work was done as part of the NFDI4Health Task Force COVID-19 (nfdi4health.de). We gratefully acknowledge the financial support of the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project Number 451265285.

Creators: Holger Kirsten, Markus Löffler, Markus Scholz, Peter Ahnert, Dirk Hasenclever, Matthias Horn, Yuri Kheifetz, Sibylle Schirm

Submitter: Christoph Beger

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Bulletin COVID-19 Leipzig 2021-01-10
COVID-19 Leipzig, Genetical Statistics and Systems Biology

Summary of the current COVID-19 pandemic development in Leipzig and Saxony. This work was done as part of the NFDI4Health Task Force COVID-19 (nfdi4health.de). We gratefully acknowledge the financial support of the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project Number 451265285.

Creators: Holger Kirsten, Markus Löffler, Markus Scholz, Peter Ahnert, Dirk Hasenclever, Matthias Horn, Yuri Kheifetz, Sibylle Schirm

Submitter: Christoph Beger

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Bulletin COVID-19 Leipzig 2020-12-11
COVID-19 Leipzig, Genetical Statistics and Systems Biology

Summary of the current COVID-19 pandemic development in Leipzig and Saxony. This work was done as part of the NFDI4Health Task Force COVID-19 (nfdi4health.de). We gratefully acknowledge the financial support of the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project Number 451265285.

Creators: Holger Kirsten, Markus Scholz, Markus Löffler, Peter Ahnert, Matthias Horn, Yuri Kheifetz, Kolja Nenoff, Sibylle Schirm

Submitter: Christoph Beger

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Bulletin COVID-19 Leipzig 2020-12-30
COVID-19 Leipzig, Genetical Statistics and Systems Biology

Summary of the current COVID-19 pandemic development in Leipzig and Saxony. This work was done as part of the NFDI4Health Task Force COVID-19 (nfdi4health.de). We gratefully acknowledge the financial support of the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project Number 451265285.

Creators: Holger Kirsten, Markus Löffler, Markus Scholz, Peter Ahnert, Matthias Horn, Yuri Kheifetz, Kolja Nenoff, Sibylle Schirm

Submitter: Christoph Beger

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Bulletin COVID-19 Leipzig 2020-11-15
COVID-19 Leipzig, Genetical Statistics and Systems Biology

Summary of the current COVID-19 pandemic development in Leipzig and Saxony. This work was done as part of the NFDI4Health Task Force COVID-19 (nfdi4health.de). We gratefully acknowledge the financial support of the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project Number 451265285.

Creators: Holger Kirsten, Markus Scholz, Markus Löffler, Peter Ahnert, Matthias Horn, Yuri Kheifetz, Kolja Nenoff, Sibylle Schirm

Submitter: Christoph Beger

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Bulletin COVID-19 Leipzig 2020-04-07
COVID-19 Leipzig, Genetical Statistics and Systems Biology

Summary of the current COVID-19 pandemic development in Leipzig and Saxony. This work was done as part of the NFDI4Health Task Force COVID-19 (nfdi4health.de). We gratefully acknowledge the financial support of the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project Number 451265285.

Creators: Holger Kirsten, Markus Scholz, Markus Löffler, Peter Ahnert, Matthias Horn, Yuri Kheifetz, Sibylle Schirm

Submitter: Christoph Beger

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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

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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

Epidemiology
No description specified

Projects: LIFE - Leipzig Research Center for Civilization Diseases, LIFE Heart, SepNet - German Competence Network Sepsis, GC-HNPCC - German Consortium for Hereditary Non-Polyposis Colorectal Cancer, COVID-19 Leipzig, LIFE Adult, GC-HBOC - German Consortium for Hereditary Breast and Ovarian Cancer

Web page: Not specified

16th Leipzig Research Festival for Life Sciences
No description specified

Start Date: 30th Jan 2020

End Date: 30th Jan 2020

Event Website: https://conference.uni-leipzig.de/researchfestival/

Country:  Germany

City: Leipzig

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

„Forschungsdaten in Sachsen: Planen – Organisieren – Nachnutzen“ – 1. sächsische FDM-Tagung

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

30. GfH-Jahrestagung Weimar 2019
No description specified

Start Date: 6th Mar 2019

End Date: 8th Mar 2019

Event Website: https://www.gfhev.de/de/kongress/index.htm

Country:  Germany

City: Weimar

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Health Atlas

The 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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