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Related Experiment Video

Updated: Dec 1, 2025

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Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior.

Yosef D Roth1, Zhouyang Lian1, Saahith Pochiraju1

  • 1Icahn Institute for Data Science and Genomic Technology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1255 5th Avenue, Suite C2, New York, NY 10029, USA.

Nucleic Acids Research
|November 11, 2020
PubMed
Summary
This summary is machine-generated.

Datanator is a new database and toolset that makes it easier to find diverse molecular data for integrative research in biology and medicine. It helps researchers access and analyze complex biological datasets more efficiently.

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Area of Science:

  • Biochemistry
  • Systems Biology
  • Bioinformatics

Background:

  • Integrative research across biochemical subsystems is crucial for advancing biology, bioengineering, and medicine.
  • Acquiring diverse data for such integrative studies presents a significant challenge.

Purpose of the Study:

  • To develop an integrated database and toolset, Datanator, to facilitate the retrieval of multi-modal molecular data for biochemical research.
  • To enable researchers to find data on specific molecules, reactions, organisms, and environments, as well as chemically and phylogenetically similar entities.

Main Methods:

  • Datanator integrates various molecular data types including metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction rate constants.
  • The database covers a broad range of organisms and environments.
  • Tools are provided for filtering, visualizing, and exporting curated data clouds.

Main Results:

  • Datanator provides access to diverse biochemical data, including metabolite concentrations, RNA and protein modifications, and reaction kinetics.
  • The platform facilitates the discovery of data clouds for specific and related molecular entities across various organisms.
  • Tools for data manipulation and visualization are integrated within the Datanator system.

Conclusions:

  • Datanator significantly lowers the barrier to accessing and utilizing diverse biochemical data for integrative research.
  • The database and tools are expected to accelerate the development of mechanistic models, such as whole-cell models, and comparative analyses across multiple organisms.