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- Dagmar Waltemath
I am a computer scientist by training with a specialisation on database and information systems. Since December 2018 I am professor of Medical Informatics at the University Medicine in Greifswald, Germany, at the Institute of Community Medicine. My lab focuses on research data management in biomedicine, data integration across health care providers, and provenance of clinical research data items within clinical information systems. Furthermore, I am actively involved in COMBINE standardisation efforts (http://co.mbine.org). My lab will continue to develop methods and tools for model management in computational biology.
SEEK ID: https://fairdomhub.org/people/600
Location:
Germany
Expertise: Data Management, Databases, standards, model management, Information Retrieval, Semantic Enrichment, Provenance, Medical informatics, Data Integration
Tools: Computational Systems Biology, Data Management, Databases, Neo4J, SBML, SED-ML, Ontologies

de.NBI-SysBio (University of Rostock) ; GenoSysFat (University of Rostock) ; Kinetics on the move - Workshop 2016 (University of Rostock) ; Example use cases (University of Rostock) ; COMBINE Multicellular Modelling (University of Rostock) ; GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik" (University of Greifswald) ; COVID-19 related studies and tools in Germany (University Medicine of Greifswald) ; nfdi4health - German National Research Data Infrastructure for Personal Health Data (University Medicine of Greifswald)
Related items
- Projects (8)
- Institutions (3)
- Investigations (1+1)
- Studies (1+1)
- Assays (1+1)
- Data files (1+2)
- Models (1+2)
- SOPs (0+1)
- Publications (10)
- Presentations (10+1)
nfdi4health aims to create the most comprehensive inventory of German epidemiological, public health and clinical trial data to date. It builds a centralised data catalogue with elaborate search functionalities, sophisticated data access management, and a data analysis toolbox, while respecting stringent requirements for privacy concerning personal health data. Standardisation services ensure a high degree of interoperability. Use cases covering prototypical study types and areas of research show
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Programme: nfdi4health - German National Research Data Infrastructure for Personal Health Data
Public web page: https://www.nfdi4health.de
Start date: 1st Jul 2020
Organisms: Homo sapiens
This project bundles information about COVID-19 related studies and tools in Germany. It intends to provide an information hub for the different initiatives, their aims, their processes, standards and study protocols, as well as their available data and metadata.
It is initiated by the German National Research Data Infrastructure for Personal Health Data (nfdi4health), a consortium that plans to establish a concept for a federated research data infrastructure for personal health data in Germany.
...
Salmon farmed on modern feeds contains less of the healthy, long-chain fatty acids (EPA and DHA) than before. Up until the turn of the millennium, farmed salmon were fed fish oil as a replacement for their omega-3 rich natural prey. However, fish oil is now a scarce resource, and more than half of the fat in modern feeds comes from plant oils that are inexpensive, but devoid of long-chain omega-3 fatty acids. How can we increase the omega-3 content of salmon on sustainable feeds?
One option is
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Programme: The Digital Salmon
Public web page: http://tinyurl.com/genosysfat
Organisms: Danio rerio, Salmo salar, Oncorhynchus mykiss
Programme: COMBINE (Computational Modeling in Biology Network)
Public web page: https://multicellml.org/
Organisms: Not specified
The GMDS project group bundles activities for health-related FAIR data infrastructures in the fields of biomedical research, clinical data management and medical informatics in Germany. It aims at providing a platform for information exchange about best practice for and implementation of FAIR data management in these fields and constructing a network of FAIR data managements providers in these fields. Through bridging between providers and potential users of such data management platforms within
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Programme: German Association for Medical Informatics, Biometry and Epidemiology (GMDS)
Public web page: https://gmds.de/aktivitaeten/medizinische-informatik/projektgruppenseiten/faire-dateninfrastrukturen-fuer-die-biomedizinische-informatik/
Start date: 28th Feb 2019
End date: 27th Feb 2022
Organisms: Not specified
The Systems Biology Service Center of de.NBI (de.NBI-SysBio) provides bioinformatics support and a standards-based data management for systems biology projects, with focus on the provenance of experimental results and on the reproducibility of modeling experiments, as well as high-quality curated biochemical data to modelers and experimentalists.
The node concentrates on two tools for the data management in life sciences research: SEEK, a catalogue for storage, registration and exchange of data
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Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: Not specified
Organisms: Not specified
Public showcase and collection of training material
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: http://www.denbi.de
Organisms: Not specified
The workshop focuses on the publication, curation, retrieval, and usage of kinetic data from the reaction kinetics database SABIO-RK and on the use of data in modeling. There will be experience reports from scientists who successfully used experimental data to formulate or verify biological hypotheses with the computer, and you will experience how experimental data can be used with computational models.
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: http://www.h-its.org/event/kinetics-on-the-move/
Snapshots: No snapshots
Person responsible: Ron Henkel
Snapshots: No snapshots
Investigation: Hands-on: Model Management in SEEK
Investigation: Hands-on: Model Management in SEEK
Study: Hands-On: Tyson1991 - Cell Cycle 6 var
Organisms: No organisms
Models: BIOMD0000000005 from BioModels Database
SOPs: No SOPs
Data files: SEDML for BIOMD0000000005
Creators: Ron Henkel, Dagmar Waltemath
Submitter: Ron Henkel
Investigations: Hands-on: Model Management in SEEK
This is BIOMD0000000005.
Creators: Ron Henkel, Dagmar Waltemath
Submitter: Ron Henkel
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Not specified
Investigations: Hands-on: Model Management in SEEK
Studies: Hands-On: Tyson1991 - Cell Cycle 6 var
Modelling analyses: BIOMD0000000005 - Tyson1991 - Cell Cycle 6 var
Abstract (Expand)
Authors: Dagmar Waltemath, Martin Golebiewski, Michael L Blinov, Padraig Gleeson, Henning Hermjakob, Michael Hucka, Esther Thea Inau, Sarah M Keating, Matthias König, Olga Krebs, Rahuman S Malik-Sheriff, David Nickerson, Ernst Oberortner, Herbert M Sauro, Falk Schreiber, Lucian Smith, Melanie I Stefan, Ulrike Wittig, Chris J Myers
Date Published: 29th Jun 2020
Publication Type: Journal
Citation: Journal of Integrative Bioinformatics 0(0)
Abstract (Expand)
Authors: Falk Schreiber, Björn Sommer, Tobias Czauderna, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris Myers, David Nickerson, Dagmar Waltemath
Date Published: 29th Jun 2020
Publication Type: Journal
Citation: Journal of Integrative Bioinformatics 0(0)
Abstract (Expand)
Authors: N. J. Stanford, M. Scharm, P. D. Dobson, M. Golebiewski, M. Hucka, V. B. Kothamachu, D. Nickerson, S. Owen, J. Pahle, U. Wittig, D. Waltemath, C. Goble, P. Mendes, J. Snoep
Date Published: 12th Oct 2019
Publication Type: Journal
PubMed ID: 31602618
Citation: Methods Mol Biol. 2019;2049:285-314. doi: 10.1007/978-1-4939-9736-7_17.
Abstract (Expand)
Authors: Falk Schreiber, Björn Sommer, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Matthias König, Chris Myers, David Nickerson, Dagmar Waltemath
Date Published: 13th Jul 2019
Publication Type: Journal
Citation: Journal of Integrative Bioinformatics 16(2)
Abstract (Expand)
Authors: Maxwell Lewis Neal, Matthias König, David Nickerson, Göksel Mısırlı, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael T Cooling, Daniel L Cook, Sharon Crook, Miguel de Alba, Samuel H Friedman, Alan Garny, John H Gennari, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nick Juty, Chris Myers, Brett G Olivier, Herbert M Sauro, Martin Scharm, Jacky L Snoep, Vasundra Touré, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath
Date Published: 1st Mar 2019
Publication Type: Journal
DOI: 10.1093/bib/bby087
Citation: Briefings in Bioinformatics 20(2):540-550
Abstract
Authors: Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Nicolas Le Novère, Chris Myers, David Nickerson, Björn Sommer, Dagmar Waltemath
Date Published: 29th Mar 2018
Publication Type: Journal
Citation: Journal of Integrative Bioinformatics 15(1)
Abstract (Expand)
Authors: Chris J. Myers, Gary Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novere, David P. Nickerson, Falk Schreiber, Dagmar Waltemath
Date Published: 1st Dec 2017
Publication Type: InProceedings
Citation: 2017 Winter Simulation Conference (WSC),pp.884-895,IEEE
Abstract (Expand)
Authors: F. Schreiber, G. D. Bader, P. Gleeson, M. Golebiewski, M. Hucka, N. Le Novere, C. Myers, D. Nickerson, B. Sommer, D. Walthemath
Date Published: 12th Feb 2017
Publication Type: Not specified
PubMed ID: 28187405
Citation: J Integr Bioinform. 2016 Dec 18;13(3):289. doi: 10.2390/biecoll-jib-2016-289.
Abstract (Expand)
Authors: M. I. Stefan, S. J. Edelstein, N. Le Novere
Date Published: 31st Jul 2008
Publication Type: Not specified
PubMed ID: 18669651
Citation: Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10768-73. doi: 10.1073/pnas.0804672105. Epub 2008 Jul 31.
Abstract
Authors: Thomas H. Crouch, Claude B. Klee
Date Published: 1st Aug 1980
Publication Type: Not specified
DOI: 10.1021/bi00557a009
Citation: Biochemistry 19(16) : 3692
Hint Task 4. Please refer to the related task sheet: https://fairdomhub.org/presentations/251
Creators: Ron Henkel, Dagmar Waltemath
Submitter: Ron Henkel
Hint Task 5. Please refer to the related task sheet: https://fairdomhub.org/presentations/251
Creators: Ron Henkel, Dagmar Waltemath
Submitter: Ron Henkel
Hint Task 9A. Please refer to the related task sheet: https://fairdomhub.org/presentations/251
Creators: Ron Henkel, Dagmar Waltemath
Submitter: Ron Henkel
Hint Task 9. Please refer to the related task sheet: https://fairdomhub.org/presentations/251
Creators: Ron Henkel, Dagmar Waltemath
Submitter: Ron Henkel
The paper by Tyson for the Hands-on Model Management in SEEK. Please refer to the related task sheet: https://fairdomhub.org/presentations/251
Creators: Ron Henkel, Dagmar Waltemath
Submitter: Ron Henkel
Presentation at the 10th anniversary of SABIO-RK, Heidelberg 2016
Creator: Dagmar Waltemath
Submitter: Dagmar Waltemath
Here you find the Tasks for todays Hands-on Model Management in SEEK session
Creators: Ron Henkel, Dagmar Waltemath
Submitter: Ron Henkel
Written by Martin Scharm (University of Rostock), Ron Henkel (University of Rostock), Dagmar Waltemath (University of Rostock), Olaf Wolkenhauer (University of Rostock, Stellenbosch University), and presented by Martin Scharm (University of Rostock) as part of the Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015.
Creators: Natalie Stanford, Dagmar Waltemath, Olaf Wolkenhauer, Ron Henkel, Martin Scharm (University of Rostock)
Submitter: Natalie Stanford
Written and presented by Dagmar Waltemath (University of Rostock) as part of the Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015.
Creators: Natalie Stanford, Dagmar Waltemath
Submitter: Natalie Stanford
Prepared and presented by Carole Goble (University of Manchester), Wolfgang Mueller (HITS), Dagmar Waltermath (University of Rostock), at the Reproducible and Citable Data and Models Workshop, Warnemünde, Germany. September 14th - 16th 2015.
Creators: Natalie Stanford, Wolfgang Müller, Carole Goble, Dagmar Waltemath
Submitter: Natalie Stanford