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BiGG Models

General Information

BiGG Models is a knowledgebase of genome-scale metabolic network reconstructions. BiGG Models integrates more than 70 published genome-scale metabolic networks into a single database with a set of standardized identifiers called BiGG IDs.

Homepage http://bigg.ucsd.edu

Countries that developed this resource United States

Created in 2010

Taxonomic range

All

Knowledge Domains

Subjects

User-defined Tags

Genome Scale Metabolic Model

Genome-scale network

How to cite this record FAIRsharing.org: BiGG Models; BiGG Models; DOI: https://doi.org/10.25504/FAIRsharing.va62ke; Last edited: Feb. 7, 2021, 9:11 p.m.; Last accessed: Oct 26 2021 10:47 a.m.

Publication for citation BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. King ZA,Lu J,Drager A,Miller P,Federowicz S,Lerman JA,Ebrahim A,Palsson BO,Lewis NE; Nucleic Acids Res ; 2015; 10.1093/nar/gkv1049;

This record is maintained by Andreas Dräger (draeger) ORCID

Record added: March 17, 2016, 11:24 a.m.
Record updated: Feb. 7, 2021, 9:10 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.va62ke' by 'The FAIRsharing Team' at 21:10, 07 Feb 2021 (approved):

	'publications' has been modified:
		Before:
			BiGG Models: A platform for integrating, standardizing and sharing genome-scale models|King ZA,Lu J,Drger A,Miller P,Federowicz S,Lerman JA,Ebrahim A,Palsson BO,Lewis NE|Nucleic Acids Res|2015
			BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions|Schellenberger J,Park JO,Conrad TM,Palsson BO|BMC Bioinformatics|2010
			BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.|King ZA,Lu J,Drager A,Miller P,Federowicz S,Lerman JA,Ebrahim A,Palsson BO,Lewis NE|Nucleic Acids Res|2015
		After:
			BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions|Schellenberger J,Park JO,Conrad TM,Palsson BO|BMC Bioinformatics|2010
			BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.|King ZA,Lu J,Drager A,Miller P,Federowicz S,Lerman JA,Ebrahim A,Palsson BO,Lewis NE|Nucleic Acids Res|2015
		Added:
		Removed:
			BiGG Models: A platform for integrating, standardizing and sharing genome-scale models|King ZA,Lu J,Drger A,Miller P,Federowicz S,Lerman JA,Ebrahim A,Palsson BO,Lewis NE|Nucleic Acids Res|2015

Edits to 'https://fairsharing.org/FAIRsharing.va62ke' by 'draeger' at 20:50, 07 Feb 2021 (approved):

	'publications' has been modified:
		Before:
			BiGG Models: A platform for integrating, standardizing and sharing genome-scale models|King ZA,Lu J,Drger A,Miller P,Federowicz S,Lerman JA,Ebrahim A,Palsson BO,Lewis NE|Nucleic Acids Res|2015
			BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions|Schellenberger J,Park JO,Conrad TM,Palsson BO|BMC Bioinformatics|2010
		After:
			BiGG Models: A platform for integrating, standardizing and sharing genome-scale models|King ZA,Lu J,Drger A,Miller P,Federowicz S,Lerman JA,Ebrahim A,Palsson BO,Lewis NE|Nucleic Acids Res|2015
			BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions|Schellenberger J,Park JO,Conrad TM,Palsson BO|BMC Bioinformatics|2010
			BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.|King ZA,Lu J,Drager A,Miller P,Federowicz S,Lerman JA,Ebrahim A,Palsson BO,Lewis NE|Nucleic Acids Res|2015
		Added:
			BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.|King ZA,Lu J,Drager A,Miller P,Federowicz S,Lerman JA,Ebrahim A,Palsson BO,Lewis NE|Nucleic Acids Res|2015
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.va62ke' by 'draeger' at 20:50, 07 Feb 2021 (approved):

	'publications' has been modified:
		Before:
			BiGG Models: A platform for integrating, standardizing and sharing genome-scale models|King ZA,Lu J,Drger A,Miller P,Federowicz S,Lerman JA,Ebrahim A,Palsson BO,Lewis NE|Nucleic Acids Res|2015
			BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions|Schellenberger J,Park JO,Conrad TM,Palsson BO|BMC Bioinformatics|2010
		After:
			BiGG Models: A platform for integrating, standardizing and sharing genome-scale models|King ZA,Lu J,Drger A,Miller P,Federowicz S,Lerman JA,Ebrahim A,Palsson BO,Lewis NE|Nucleic Acids Res|2015
			BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions|Schellenberger J,Park JO,Conrad TM,Palsson BO|BMC Bioinformatics|2010
			BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.|King ZA,Lu J,Drager A,Miller P,Federowicz S,Lerman JA,Ebrahim A,Palsson BO,Lewis NE|Nucleic Acids Res|2015
		Added:
			BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.|King ZA,Lu J,Drager A,Miller P,Federowicz S,Lerman JA,Ebrahim A,Palsson BO,Lewis NE|Nucleic Acids Res|2015
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.va62ke' by 'The FAIRsharing Team' at 15:10, 04 Feb 2021 (approved):

	'organizations' has been modified:
		Before:
			U.S. Department of Energy|http://genomicscience.energy.gov/datasharing/|Funds
			European Commission|http://ec.europa.eu/|Funds
			Novo Nordisk Foundation, Denmark|http://www.novonordiskfonden.dk/en|Funds
			University of California, San Diego, CA, USA|http://www.ucsd.edu|Maintains
			U.S. National Library of Medicine|https://www.nlm.nih.gov/|Funds
			National Science Foundation (NSF), USA|https://www.nsf.gov/|Funds
		After:
			U.S. Department of Energy|http://genomicscience.energy.gov/datasharing/|Funds
			European Commission|http://ec.europa.eu/|Funds
			Novo Nordisk Foundation, Denmark|http://www.novonordiskfonden.dk/en|Funds
			U.S. National Library of Medicine|https://www.nlm.nih.gov/|Funds
			National Science Foundation (NSF), USA|https://www.nsf.gov/|Funds
			University of California, San Diego, CA, USA|http://www.ucsd.edu|Maintains
			Systems Biology Research Group, University of California San Diego, USA|https://systemsbiology.ucsd.edu/|Maintains
		Added:
			Systems Biology Research Group, University of California San Diego, USA|https://systemsbiology.ucsd.edu/|Maintains
		Removed:

	'supportLinks' has been modified:
		Before:
			schema file|https://github.com/SBRG/bigg_models
			twitter|@ucsd_sbrg
		After:
			online documentation|https://github.com/sbrg/bigg_models
			twitter|@ucsd_sbrg
		Added:
			online documentation|https://github.com/sbrg/bigg_models
		Removed:
			schema file|https://github.com/SBRG/bigg_models

	'description' has been modified:
		Before: BiGG is a freely compendium of published genome-scale metabolic networks, combined into a single database. NCBI genome annotations are used to map genes, and metabolites are linked to many external databases such as KEGG, PubChem as well as others..
		After: BiGG Models is a knowledgebase of genome-scale metabolic network reconstructions. BiGG Models integrates more than 70 published genome-scale metabolic networks into a single database with a set of standardized identifiers called BiGG IDs.

	'licences' has been modified:
		Before:
			MIT Licence|https://opensource.org/licenses/mit|Data
		After:
			BIGG Licence|http://bigg.ucsd.edu/license#license|Data
		Added:
			BIGG Licence|http://bigg.ucsd.edu/license#license|Data
		Removed:
			MIT Licence|https://opensource.org/licenses/mit|Data

	'onto_disciplines' has been modified:
		Before:
			Life Science
		After:
			Life Science
			Metabolomics
		Added:
			Metabolomics
		Removed:

	'onto_domains' has been modified:
		Before:
			Pathway or network prediction
		After:
			Prediction and recognition
			network model
		Added:
			Prediction and recognition
			network model
		Removed:
			Pathway or network prediction

	'user_defined_tags' has been modified:
		Before:
		After:
			Genome Scale Metabolic Model
			Genome-scale network
		Added:
			Genome Scale Metabolic Model
			Genome-scale network
		Removed:

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

	'dataProcesses' has been modified:
		Before:
			Manually, data curation, 
		After:
			Download, data release, http://bigg.ucsd.edu/data_access
			Advanced Search, data access, http://bigg.ucsd.edu/advanced_search
		Added:
			Download, data release, http://bigg.ucsd.edu/data_access
			Advanced Search, data access, http://bigg.ucsd.edu/advanced_search
		Removed:
			Manually, data curation, 

	'accessPoints' has been modified:
		Before:
			REST|http://bigg.ucsd.edu/web_api|http://bigg.ucsd.edu/api/v2/
		After:
			REST|http://bigg.ucsd.edu/data_access|http://bigg.ucsd.edu/api/v2/
		Added:
			REST|http://bigg.ucsd.edu/data_access|http://bigg.ucsd.edu/api/v2/
		Removed:
			REST|http://bigg.ucsd.edu/web_api|http://bigg.ucsd.edu/api/v2/

Edits to 'https://fairsharing.org/FAIRsharing.va62ke' by 'The FAIRsharing Team' at 18:06, 03 Sep 2016 (approved):

	'description' has been modified:
		Before: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models.
		After: BiGG is a freely compendium of published genome-scale metabolic networks, combined into a single database. NCBI genome annotations are used to map genes, and metabolites are linked to many external databases such as KEGG, PubChem as well as others.. Related databases have changed:  Previous values: biodbcore-000306: A repository of mathematical models of biological and biomedical systems biodbcore-000740: JWS Online biodbcore-000755: MetaNetX New values:  biodbcore-000306: A repository of mathematical models of biological and biomedical systems biodbcore-000740: JWS Online biodbcore-000755: MetaNetX biodbcore-000455: PubChem biodbcore-000663: Kyoto Encyclopedia of Genes and Genomes

In Collections

Systems Medicine

Support

General

online documentation	GitHub Project
twitter	@ucsd_sbrg

Additional Information

Contact

Zachary A. King ORCID

Tools

Escher

http://escher.github.io/

1.0

Access / Retrieve Data

Conditions of Use

Applies to: Data use

BIGG Licence

Data Release

Download

http://bigg.ucsd.edu/data_access

Data Access

Advanced Search

http://bigg.ucsd.edu/advanced_search

REST Web Services

http://bigg.ucsd.edu/api/v2/

http://bigg.ucsd.edu/data_access

Publications

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

Schellenberger J,Park JO,Conrad TM,Palsson BO
BMC Bioinformatics 2010

View Paper (PubMed) View Publication

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.

King ZA,Lu J,Drager A,Miller P,Federowicz S,Lerman JA,Ebrahim A,Palsson BO,Lewis NE
Nucleic Acids Res 2015

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

Minimal Information Required In the Annotation of Models

Terminology Artifacts

No semantic standards defined

Models and Formats

Systems Biology Markup Language

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 Andreas Dräger (draeger) ORCID

Funds

U.S. Department of Energy (Government body)
European Commission (Government body)
Novo Nordisk Foundation, Denmark (Company)
U.S. National Library of Medicine (Government body)
National Science Foundation (NSF), USA (Government body)

Maintains

University of California, San Diego, CA, USA (University)
Systems Biology Research Group, University of California San Diego, USA (Lab) Lead

Grant Number(s)

332020 (European Commission)
DE-SC0004917 (U.S. Department of Energy)
DE-SC0008701 (U.S. Department of Energy)
DE-SC0008701 (U.S. Department of Energy)
DGE-1144086 (National Science Foundation (NSF), USA)
NNF 132150- 002 (Novo Nordisk Foundation, Denmark)
R21 HD080682 (U.S. National Library of Medicine)

BiGG Models

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