Web Service Datanator REST Us

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Overview

Provider:
api-datanator-info

Location:
United States Us

Submitter/Source:
Jonathan KarrUs (10 months ago)

Base URL:
https://api.datanator.info

Description(s):
by Jonathan Karr (10 months ago)

Datanator (https://www.datanator.info) is a toolkit for discovering the data needed to build, calibrate, and validate mechanistic models of cells. Datanator is composed of an integrated database of genomic and biochemical data, a web application for identifying relevant data for modeling a specific organism in a specific environmental condition, this REST API, and a Python library for programmatically discovering data for large models such as whole-cell models.

The Datanator REST API provides programmatic access to the Datanator integrated database of data for biochemical modeling. This includes metabolite concentrations, RNA half-lives, protein abundances, reaction rate constants, and other data. The query provides the ability to search the database for information about specific biochemical entities (e.g., metabolite, RNA, protein, reaction) in a specific organism in a specific environment (e.g., media, pH, temperature). To help users impute missing data, the API can retrieve data about the entity, organism, and environment of interest, as well as data about similar entities observed in similar organisms and similar environments, providing users “clouds” of data about the biochemistry of interest.

ELIXIR Description(s): Info
by Jonathan Karr (10 months ago)

Datanator (https://www.datanator.info) is a toolkit for discovering the data needed to build, calibrate, and validate mechanistic models of cells. The Datanator REST API provides programmatic access to Datanator’s integrated database of data for biochemical modeling.

License(s): Info
by Jonathan Karr (2 months ago)

Software: MIT License

by Jonathan Karr (2 months ago)

Data: CC-BY-NC License. Some of the data is available under more permissive terms. See here for more information.

by Jonathan Karr (2 months ago)

Database structure: CC0 License

Cost: Info
by Jonathan Karr (10 months ago)

Free

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Contact info: Info
by Jonathan Karr (10 months ago)
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Publications about this service: Info
by Jonathan Karr (2 months ago)

Roth YD, Lian Z, Pochiraju S, Shaikh B & Karr JR. Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior. bioRxiv, 2020.08.06.240051 (2020). DOI: 10.1101/2020.08.06.240051.

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