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Datanator

General Information

Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.

Homepage https://www.datanator.info

Countries that developed this resource United States

Created in 2020

Taxonomic range

All

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: Datanator; Datanator; DOI: https://doi.org/10.25504/FAIRsharing.NmIgg9; Last edited: Sept. 24, 2020, 9:20 a.m.; Last accessed: Jan 18 2022 1:17 a.m.

Publication for citation Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior Yosef D. Roth, Zhouyang Lian, Saahith Pochiraju, Bilal Shaikh & Jonathan R. Karr; bioRxiv ; 2020.

This record is maintained by jonrkarr ORCID

Record added: May 22, 2020, 2:02 a.m.
Record updated: Sept. 24, 2020, 9:16 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.NmIgg9' by 'The FAIRsharing Team' at 09:16, 24 Sep 2020 (approved):

	'licences' has been modified:
		Before:
			Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)|https://github.com/KarrLab/datanator/blob/master/DATA_LICENSE|Data
			MIT Licence|https://github.com/KarrLab/datanator/blob/master/LICENSE|Software
		After:
			MIT Licence|https://opensource.org/licenses/mit|Software
			Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)|https://creativecommons.org/licenses/by-nc/4.0/|Data
		Added:
			MIT Licence|https://opensource.org/licenses/mit|Software
			Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)|https://creativecommons.org/licenses/by-nc/4.0/|Data
		Removed:
			Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)|https://github.com/KarrLab/datanator/blob/master/DATA_LICENSE|Data
			MIT Licence|https://github.com/KarrLab/datanator/blob/master/LICENSE|Software

	'onto_disciplines' has been modified:
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			Data Integration
			Metabolomics
			Molecular biology
			Omics
			Systems Biology
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			Biochemistry
			Data Integration
			Genomics
			Metabolomics
			Molecular biology
			Omics
			Systems Biology
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			Biochemistry
			Genomics
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	'onto_domains' has been modified:
		Before:
			Concentration
			RNA modification
			Reaction data
			modeling and simulation objective
		After:
			Concentration
			RNA modification
			Reaction data
			genome
			modeling and simulation objective
		Added:
			genome
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.NmIgg9' by 'jonrkarr' at 20:56, 23 Sep 2020 (approved):

	'licences' has been modified:
		Before:
			Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)|https://creativecommons.org/licenses/by-nc-nd/4.0/|Data
			MIT Licence|https://opensource.org/licenses/mit|Data
		After:
			Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)|https://github.com/KarrLab/datanator/blob/master/DATA_LICENSE|Data
			MIT Licence|https://github.com/KarrLab/datanator/blob/master/LICENSE|Software
		Added:
			Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)|https://github.com/KarrLab/datanator/blob/master/DATA_LICENSE|Data
			MIT Licence|https://github.com/KarrLab/datanator/blob/master/LICENSE|Software
		Removed:
			Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)|https://creativecommons.org/licenses/by-nc-nd/4.0/|Data
			MIT Licence|https://opensource.org/licenses/mit|Data

	'related_databases' has been modified:
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			MODOMICS
			BRENDA
			SABIO-RK Biochemical Reaction Kinetics Database
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			MODOMICS
			SABIO-RK Biochemical Reaction Kinetics Database
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		Removed:
			BRENDA

	'supportLinks' has been modified:
		Before:
			email|info@karrlab.org
			help|https://www.datanator.info/help
			online documentation|https://api.datanator.info
			online documentation|https://datanator.info/about
			online documentation|https://datanator.info/stats
		After:
			FAQ|https://www.datanator.info/help
			email|info@karrlab.org
			forum|https://github.com/KarrLab/datanator_frontend/issues
			help|https://www.datanator.info/help
			online documentation|https://datanator.info/about
			online documentation|https://api.datanator.info
			online documentation|https://datanator.info/stats
		Added:
			FAQ|https://www.datanator.info/help
			forum|https://github.com/KarrLab/datanator_frontend/issues
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	'publications' has been modified:
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		After:
			Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior|Yosef D. Roth, Zhouyang Lian, Saahith Pochiraju,  Bilal Shaikh & Jonathan R. Karr|bioRxiv|2020
		Added:
			Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior|Yosef D. Roth, Zhouyang Lian, Saahith Pochiraju,  Bilal Shaikh & Jonathan R. Karr|bioRxiv|2020
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	'dataProcesses' has been modified:
		Before:
			Web interface, data access, https://www.datanator.info
			Data download, data access, https://open.quiltdata.com/b/karrlab/packages/karrlab/datanator/
			Description of curation process, data curation, https://www.datanator.info/about
		After:
			Web interface, data access, https://www.datanator.info
			Data download, data access, https://doi.org/10.5281/zenodo.3971047
			Description of curation process, data curation, https://www.datanator.info/about
		Added:
			Data download, data access, https://doi.org/10.5281/zenodo.3971047
		Removed:
			Data download, data access, https://open.quiltdata.com/b/karrlab/packages/karrlab/datanator/

Edits to 'https://fairsharing.org/FAIRsharing.NmIgg9' by 'The FAIRsharing Team' at 13:39, 15 Jun 2020 (approved):

	'licences' has been modified:
		Before:
			Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)|https://creativecommons.org/licenses/by-nc-nd/4.0/|Data
			The MIT License (MIT)|https://opensource.org/licenses/mit|Data
		After:
			Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)|https://creativecommons.org/licenses/by-nc-nd/4.0/|Data
			MIT Licence|https://opensource.org/licenses/mit|Data
		Added:
			MIT Licence|https://opensource.org/licenses/mit|Data
		Removed:
			The MIT License (MIT)|https://opensource.org/licenses/mit|Data

Edits to 'https://fairsharing.org/FAIRsharing.NmIgg9' by 'The FAIRsharing Team' at 13:37, 15 Jun 2020 (approved):

	'licences' has been modified:
		Before:
			Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)|https://open.quiltdata.com/b/karrlab/packages/karrlab/datanator/tree/latest/LICENSE|Data
			MIT|https://github.com/KarrLab/datanator/blob/master/LICENSE|Software
		After:
			Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)|https://creativecommons.org/licenses/by-nc-nd/4.0/|Data
			The MIT License (MIT)|https://opensource.org/licenses/mit|Data
		Added:
			Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)|https://creativecommons.org/licenses/by-nc-nd/4.0/|Data
			The MIT License (MIT)|https://opensource.org/licenses/mit|Data
		Removed:
			Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)|https://open.quiltdata.com/b/karrlab/packages/karrlab/datanator/tree/latest/LICENSE|Data
			MIT|https://github.com/KarrLab/datanator/blob/master/LICENSE|Software

Edits to 'https://fairsharing.org/FAIRsharing.NmIgg9' by 'The FAIRsharing Team' at 16:04, 09 Jun 2020 (approved):

	'taxonomies' has been modified:
		Before:
			Not applicable
		After:
			All
		Added:
			All
		Removed:
			Not applicable

	'supportLinks' has been modified:
		Before:
			email|info@karrlab.org
			help|https://www.datanator.info/help
			online documentation|https://api.datanator.info
		After:
			email|info@karrlab.org
			help|https://www.datanator.info/help
			online documentation|https://api.datanator.info
			online documentation|https://datanator.info/about
			online documentation|https://datanator.info/stats
		Added:
			online documentation|https://datanator.info/about
			online documentation|https://datanator.info/stats
		Removed:

	'onto_domains' has been modified:
		Before:
			modeling and simulation objective
		After:
			Concentration
			RNA modification
			Reaction data
			modeling and simulation objective
		Added:
			Concentration
			RNA modification
			Reaction data
		Removed:

Support

General

FAQ	FAQ
support email	Email address
forum	Issue tracker
help	Tutorial
online documentation	About Datanator
online documentation	REST API documentation
online documentation	Statistics

Additional Information

Contact

Jonathan Karr ORCID

Tools

No tools defined

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)

Applies to: Database software

MIT Licence

Data Curation

Description of curation process

https://www.datanator.info/about

Data Access

Web interface	https://www.datanator.info
Data download	https://doi.org/10.5281/zenodo.3971047

REST Web Services

REST API

https://api.datanator.info/

Publications

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

Yosef D. Roth, Zhouyang Lian, Saahith Pochiraju, Bilal Shaikh & Jonathan R. Karr
bioRxiv 2020

Link to Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

BpForms Grammar

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by jonrkarr ORCID

Funds

National Institute of General Medical Sciences (NIGMS), Bethesda, MD, USA (Government body)
National Institute of Biomedical Imaging and Bioengineering (NIBIB), USA (Government body)

Maintains

Karr Lab (Lab) Lead

Grant Number(s)

P41EB023912 (National Institute of Biomedical Imaging and Bioengineering (NIBIB), USA)
R35GM119771 (National Institute of General Medical Sciences (NIGMS), Bethesda, MD, USA)

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