User profiles for Dagmar Waltemath

Dagmar Waltemath

Professor of Medical Informatics
Verified email at uni-greifswald.de
Cited by 2607

Controlled vocabularies and semantics in systems biology

M Courtot, N Juty, C Knüpfer, D Waltemath… - Molecular systems …, 2011 - embopress.org
The use of computational modeling to describe and analyze biological systems is at the heart
of systems biology. Model structures, simulation descriptions and numerical results can be …

SBML Level 3: an extensible format for the exchange and reuse of biological models

SM Keating, D Waltemath, M König, F Zhang… - Molecular systems …, 2020 - embopress.org
Abstract Systems biology has experienced dramatic growth in the number, size, and
complexity of computational models. To reproduce simulation results and reuse models, …

[HTML][HTML] Reproducible computational biology experiments with SED-ML-the simulation experiment description markup language

D Waltemath, R Adams, FT Bergmann, M Hucka… - BMC systems …, 2011 - Springer
Background The increasing use of computational simulation experiments to inform modern
biological research creates new challenges to annotate, archive, share and reproduce such …

[HTML][HTML] Minimum information about a simulation experiment (MIASE)

D Waltemath, R Adams, DA Beard… - PLoS computational …, 2011 - journals.plos.org
Reproducibility of experiments is a basic requirement for science. Minimum Information (MI)
guidelines have proved a helpful means of enabling reuse of existing work in modern …

[HTML][HTML] COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

…, M Scharm, S Soiland-Reyes, D Waltemath… - BMC …, 2014 - Springer
Background With the ever increasing use of computational models in the biosciences, the
need to share models and reproduce the results of published studies efficiently and easily is …

The systems biology markup language (SBML): language specification for level 3 version 2 core release 2

…, R Sheriff, LP Smith, D Waltemath… - Journal of integrative …, 2019 - degruyter.com
Computational models can help researchers to interpret data, understand biological functions,
and make quantitative predictions. The Systems Biology Markup Language (SBML) is a …

Democratizing knowledge representation with BioCypher

…, MT Strauss, D Turei, E Ulusoy, D Waltemath… - Nature …, 2023 - nature.com
Biomedical data are amassed at an ever-increasing rate, and machine learning tools that
use prior knowledge in combination with biomedical big data are gaining much traction 1, 2. …

[HTML][HTML] Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative

…, CJ Myers, F Schreiber, D Waltemath… - … in bioengineering and …, 2015 - frontiersin.org
The Computational Modeling in Biology Network (COMBINE) is a consortium of groups
involved in the development of open community standards and formats used in computational …

The systems biology markup language (SBML): language specification for level 3 version 2 core

…, S Sahle, JC Schaff, LP Smith, D Waltemath… - Journal of integrative …, 2018 - degruyter.com
Computational models can help researchers to interpret data, understand biological functions,
and make quantitative predictions. The Systems Biology Markup Language (SBML) is a …

[HTML][HTML] Initiatives, concepts, and implementation Practices of the findable, accessible, interoperable, and reusable data principles in health data stewardship: Scoping …

ET Inau, J Sack, D Waltemath, AA Zeleke - Journal of Medical Internet …, 2023 - jmir.org
Background Thorough data stewardship is a key enabler of comprehensive health research.
Processes such as data collection, storage, access, sharing, and analytics require …