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

Abstract

Integrative research about multiple biochemical subsystems has significant potential to help advance biology, bioengineering and medicine. However, it is difficult to obtain the diverse data needed for integrative research. To facilitate biochemical research, we developed Datanator (https://datanator.info), an integrated database and set of tools for finding clouds of multiple types of molecular data about specific molecules and reactions in specific organisms and environments, as well as data about chemically-similar molecules and reactions in phylogenetically-similar organisms in similar environments. Currently, Datanator includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction rate constants about a broad range of organisms. Going forward, we aim to launch a community initiative to curate additional data. Datanator also provides tools for filtering, visualizing and exporting these data clouds. We believe that Datanator can facilitate a wide range of research from integrative mechanistic models, such as whole-cell models, to comparative data-driven analyses of multiple organisms.

Graphical Abstract

Datanator (https://datanator.info) is an integrated database of molecular data. To help investigators find relevant data for research even in the absence of direct measurements, Datanator includes tools for assembling "clouds" of measurements centered on a specific molecule or reaction in a particular organism that encompass measurements of similar molecules and reactions in similar organisms. Datanator is ideal for integrative and comparative analysis and modeling.

Figure 1.

Datanator encompasses several key types of molecular data about a wide range of organisms in a broad range of environments. (A) Number of measurements of each type of data. (B–D) Distributions of the genotype and environment of the measurements in the database. (E) Number of articles that Datanator integrates data from for each type of data.

Figure 2.

Datanator provides interactive tools for creating and visualizing clouds of data centered on specific molecules and reactions in specific organisms and environments. (A) Search form. (B–D) Search results grouped by class (metabolites, genes, or reaction). (E) Tables of clouds of potentially relevant measurements about a molecule or reaction. (F–H) Tools for filtering the data clouds. (I) Charts for visualizing the distributions of the data clouds.