Update in progress: note to all users. FAIRsharing is always available for you to search and discover databases, standards and data policies. However, for producers of these resources who maintain or wish to add new records, please note that editing is disabled until September while we migrate our data to our new, improved system. Read our blog post or get in touch with us for more details.

US Department of Energy Systems Biology Knowledgebase

Abbreviation:KBase

Recommended

General Information

KBase is the first large-scale bioinformatics system that enables users to upload their own data, analyze it (along with collaborator and public data), build increasingly realistic models, and share and publish their workflows and conclusions. KBase aims to provide a knowledgebase: an integrated environment where knowledge and insights are created and multiplied.

Homepage https://www.kbase.us

Countries that developed this resource United States

Created in 2012

Taxonomic range

All

Knowledge Domains

Subjects

In the following recommendations:

How to cite this record FAIRsharing.org: KBase; US Department of Energy Systems Biology Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.jsxqrk; Last edited: Oct. 12, 2020, 11:28 a.m.; Last accessed: Aug 02 2021 12:43 a.m.

Publication for citation The DOE Systems Biology Knowledgebase (KBase) View ORCID ProfileAdam P. Arkin, Rick L Stevens, Robert W Cottingham, Sergei Maslov, Christopher S Henry, Paramvir Dehal, Doreen Ware, Fernando Perez, Nomi L Harris et.al...; bioRxiv ; 2016; doi.org/10.1101/096354;

This record is maintained by KBase (kbaseoutreach)

Record added: Feb. 23, 2017, 11:05 a.m.
Record updated: Oct. 12, 2020, 11:22 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.jsxqrk' by 'The FAIRsharing Team' at 11:22, 12 Oct 2020 (approved):

	'taxonomies' has been modified:
		Before:
		After:
			All
		Added:
			All
		Removed:

	'onto_disciplines' has been modified:
		Before:
		After:
			Bioinformatics
			Systems Biology
		Added:
			Bioinformatics
			Systems Biology
		Removed:

	'dataProcesses' has been modified:
		Before:
		After:
			Search & Submit (Free Login Required), data access, https://narrative.kbase.us/#login
		Added:
			Search & Submit (Free Login Required), data access, https://narrative.kbase.us/#login
		Removed:

	'onto_domains' has been modified:
		Before:
		After:
			Workflow
		Added:
			Workflow
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.jsxqrk' by 'kbaseoutreach' at 16:19, 11 Aug 2020 (approved):

	'licences' has been modified:
		Before:
			KBase Terms and Condition|https://kbase.us/terms-and-conditions/|Data
			KBasePrivacy Policy|https://kbase.us/privacy-policy/|Data
		After:
			KBase Terms and Condition|https://www.kbase.us/terms-and-conditions/|Data
			KBasePrivacy Policy|https://www.kbase.us/privacy-policy/|Data
		Added:
			KBase Terms and Condition|https://www.kbase.us/terms-and-conditions/|Data
			KBasePrivacy Policy|https://www.kbase.us/privacy-policy/|Data
		Removed:
			KBase Terms and Condition|https://kbase.us/terms-and-conditions/|Data
			KBasePrivacy Policy|https://kbase.us/privacy-policy/|Data

	'supportLinks' has been modified:
		Before:
			FAQ|https://kbase.us/frequently-asked-questions/
			forum|https://kbase.us/using-the-kbase-help-board/
			online documentation|https://kbase.us/wp-content/uploads/2017/02/KBase-Brochure_1Feb2017.pdf
			online documentation|http://worldcomp-proceedings.com/proc/p2014/BIC3092.pdf
			twitter|@DOEKbase
		After:
			FAQ|https://docs.kbase.us/getting-started/faq
			forum|https://www.kbase.us/support/
			online documentation|https://docs.kbase.us/
			training|https://www.kbase.us/learn/
			twitter|@DOEKbase
		Added:
			FAQ|https://docs.kbase.us/getting-started/faq
			forum|https://www.kbase.us/support/
			online documentation|https://docs.kbase.us/
			training|https://www.kbase.us/learn/
		Removed:
			FAQ|https://kbase.us/frequently-asked-questions/
			forum|https://kbase.us/using-the-kbase-help-board/
			online documentation|https://kbase.us/wp-content/uploads/2017/02/KBase-Brochure_1Feb2017.pdf
			online documentation|http://worldcomp-proceedings.com/proc/p2014/BIC3092.pdf

	'related_databases' has been modified:
		Before:
			National Microbiome Data Collaborative
		After:
			IMG/M: the integrated metagenome data management and comparative analysis system
			CyVerse Data Common Repository
			National Microbiome Data Collaborative
		Added:
			IMG/M: the integrated metagenome data management and comparative analysis system
			CyVerse Data Common Repository
		Removed:

	'miriam_id' has been modified:
		Before: None
		After: 

	'organizations' has been modified:
		Before:
			United States Department of Energy, Office of Science, USA|http://science.energy.gov/ber/|Funds
			Lawrence Berkeley National Laboratory (LBNL), CA, USA|http://www.lbl.gov/about/|Maintains
		After:
			United States Department of Energy, Office of Science, USA|http://science.energy.gov/ber/|Funds
			Lawrence Berkeley National Laboratory (LBNL), CA, USA|http://www.lbl.gov/about/|Maintains
			Argonne National Laboratory, Lemont, IL, USA|http://www.anl.gov|Maintains
			Oak Ridge National Lab|https://www.ornl.gov/|Maintains
			Brookhaven National Laboratory|https://www.bnl.gov/world/|Maintains
		Added:
			Argonne National Laboratory, Lemont, IL, USA|http://www.anl.gov|Maintains
			Oak Ridge National Lab|https://www.ornl.gov/|Maintains
			Brookhaven National Laboratory|https://www.bnl.gov/world/|Maintains
		Removed:

Support

General

FAQ	Getting started and FAQs
forum	Support
online documentation	KBase Documentation
training	Learn how to use KBase
twitter	KBase

Additional Information

Contact

Adam Arkin ORCID

Tools

No tools defined

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Data Access

Search & Submit (Free Login Required)

https://narrative.kbase.us/#login

Publications

The DOE Systems Biology Knowledgebase (KBase)

View ORCID ProfileAdam P. Arkin, Rick L Stevens, Robert W Cottingham, Sergei Maslov, Christopher S Henry, Paramvir Dehal, Doreen Ware, Fernando Perez, Nomi L Harris et.al...
bioRxiv 2016

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

No syntax standards defined

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

Implementing Policies

Credit

Record Maintainer

This record is maintained by KBase (kbaseoutreach)

Funds

United States Department of Energy, Office of Science, USA (Government body)

Maintains

Lawrence Berkeley National Laboratory (LBNL), CA, USA (Government body) Lead
Argonne National Laboratory, Lemont, IL, USA (Government body)
Oak Ridge National Lab
Brookhaven National Laboratory (Government body)

Grant Number(s)

DE-AC02-05CH11231 (United States Department of Energy, Office of Science, USA)
DE-AC02-06CH11357 (United States Department of Energy, Office of Science, USA)
DE-AC02-98CH10886 (United States Department of Energy, Office of Science, USA)
DE-AC05-00OR22725 (United States Department of Energy, Office of Science, USA)

US Department of Energy Systems Biology Knowledgebase

We need your help!

Developed by

Contact Us

About FAIRsharing