BridgeDb

General Information

BridgeDb is a framework and data repository for finding and mapping equivalent identifiers from various databases. BridgeDb provides a framework, live services, and identifier mapping files for genes, gene-variant, proteins, metabolites and interactions.

Homepage https://bridgedb.github.io

Countries that developed this resource Netherlands , United Kingdom , United States

Taxonomic range

Caenorhabditis elegans

Canis familiaris

Coronaviridae

Danio rerio

Drosophila melanogaster

Oryza sativa L. ssp. japonica

Pan troglodytes

Rattus norvegicus

Saccharomyces cerevisiae

Zea mays

Knowledge Domains

Subjects

User-defined Tags

COVID-19

How to cite this record FAIRsharing.org: BridgeDb; BridgeDb; DOI: https://doi.org/10.25504/FAIRsharing.5ry74y; Last edited: March 22, 2021, 1:03 p.m.; Last accessed: Apr 21 2021 5:34 p.m.

Publication for citation The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. van Iersel MP,Pico AR,Kelder T,Gao J,Ho I,Hanspers K,Conklin BR,Evelo CT; BMC Bioinformatics ; 2010; 10.1186/1471-2105-11-5;

This record is maintained by egonw ORCID

Record added: July 17, 2018, 9:45 a.m.
Record updated: March 22, 2021, 1:02 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.5ry74y' by 'The FAIRsharing Team' at 13:02, 22 Mar 2021 (approved):

	'standardsImplemented' has been modified:
		Before:
		After:
			Bioschemas
		Added:
			Bioschemas
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Edits to 'https://fairsharing.org/FAIRsharing.5ry74y' by 'The FAIRsharing Team' at 20:43, 19 Mar 2021 (approved):

	'supportLinks' has been modified:
		Before:
			help|https://bridgedb.github.io/pages/docs.html
			online documentation|https://github.com/bridgedb/
			tess training|https://tess.elixir-europe.org/materials/bridgedbr-tutorial-ce581787-b018-4a34-b161-5ed1b9cc8902
			tess training|https://tess.elixir-europe.org/materials/how-to-install-and-load-the-identifier-mapping-service-with-data-needed-for-gene-to-variant-and-variant-to-gene
			tess training|https://tess.elixir-europe.org/materials/bridgedbr-tutorial
			twitter|@BridgeDbProject
		After:
			TeSS training|https://tess.elixir-europe.org/materials/bridgedbr-tutorial-ce581787-b018-4a34-b161-5ed1b9cc8902
			TeSS training|https://tess.elixir-europe.org/materials/how-to-install-and-load-the-identifier-mapping-service-with-data-needed-for-gene-to-variant-and-variant-to-gene
			TeSS training|https://tess.elixir-europe.org/materials/bridgedbr-tutorial
			help|https://bridgedb.github.io/pages/docs.html
			online documentation|https://github.com/bridgedb/
			twitter|@BridgeDbProject
		Added:
			TeSS training|https://tess.elixir-europe.org/materials/bridgedbr-tutorial-ce581787-b018-4a34-b161-5ed1b9cc8902
			TeSS training|https://tess.elixir-europe.org/materials/how-to-install-and-load-the-identifier-mapping-service-with-data-needed-for-gene-to-variant-and-variant-to-gene
			TeSS training|https://tess.elixir-europe.org/materials/bridgedbr-tutorial
		Removed:
			tess training|https://tess.elixir-europe.org/materials/bridgedbr-tutorial-ce581787-b018-4a34-b161-5ed1b9cc8902
			tess training|https://tess.elixir-europe.org/materials/how-to-install-and-load-the-identifier-mapping-service-with-data-needed-for-gene-to-variant-and-variant-to-gene
			tess training|https://tess.elixir-europe.org/materials/bridgedbr-tutorial

	'description' has been modified:
		Before: BridgeDb is a framework and data repository for finding and mapping equivalent identifiers from various databases. BridgeDb has many facets: providing a framework, live services, and identifier mapping files for genes, gene-variant, proteins, metabolites and interactions. 
		After: BridgeDb is a framework and data repository for finding and mapping equivalent identifiers from various databases. BridgeDb provides a framework, live services, and identifier mapping files for genes, gene-variant, proteins, metabolites and interactions. 

	'dataProcesses' has been modified:
		Before:
			Search via Web Services, data access, https://bridgedb.github.io/pages/webservice.html
			Download All, data release, https://bridgedb.github.io/data/gene_database/
			Download A. gambiae data, data release, https://doi.org/10.5281/zenodo.3667670
			Download A. thaliana data, data release, https://doi.org/10.5281/zenodo.3667670
			Download B. subtilis data, data release, https://doi.org/10.5281/zenodo.3667670
			Download C. familiaris data, data release, https://doi.org/10.5281/zenodo.3667670
			Download C. elegans data, data release, https://doi.org/10.5281/zenodo.3667670
			Download B. taurus data, data release, https://doi.org/10.5281/zenodo.3667670
			Download E. coli data, data release, https://doi.org/10.5281/zenodo.3667670
			Download D. rerio data, data release, https://doi.org/10.5281/zenodo.3667670
			Download D. melanogaster data, data release, https://doi.org/10.5281/zenodo.3667670
			Download H. sapiens data, data release, https://doi.org/10.5281/zenodo.3667670
			Download G. zeae data, data release, https://doi.org/10.5281/zenodo.3667670
			Download G. gallus data, data release, https://doi.org/10.5281/zenodo.3667670
			Download P. troglodytes data, data release, https://doi.org/10.5281/zenodo.3667670
			Download O. japonica data, data release, https://doi.org/10.5281/zenodo.3667670
			Download M. musculus data, data release, https://doi.org/10.5281/zenodo.3667670
			Download Z. mays data, data release, https://doi.org/10.5281/zenodo.3667670
			Download S. cerevisiae data, data release, https://doi.org/10.5281/zenodo.3667670
			Download R. norvegicus data, data release, https://doi.org/10.5281/zenodo.3667670
		After:
			Search via Web Services, data access, https://bridgedb.github.io/pages/webservice.html
			Download All, data release, https://bridgedb.github.io/data/gene_database/
			Download A. gambiae data, data release, https://doi.org/10.5281/zenodo.3667670
			Download A. thaliana data, data release, https://doi.org/10.5281/zenodo.3667670
			Download B. subtilis data, data release, https://doi.org/10.5281/zenodo.3667670
			Download C. familiaris data, data release, https://doi.org/10.5281/zenodo.3667670
			Download C. elegans data, data release, https://doi.org/10.5281/zenodo.3667670
			Download B. taurus data, data release, https://doi.org/10.5281/zenodo.3667670
			Download E. coli data, data release, https://doi.org/10.5281/zenodo.3667670
			Download D. rerio data, data release, https://doi.org/10.5281/zenodo.3667670
			Download D. melanogaster data, data release, https://doi.org/10.5281/zenodo.3667670
			Download H. sapiens data, data release, https://doi.org/10.5281/zenodo.3667670
			Download G. zeae data, data release, https://doi.org/10.5281/zenodo.3667670
			Download G. gallus data, data release, https://doi.org/10.5281/zenodo.3667670
			Download P. troglodytes data, data release, https://doi.org/10.5281/zenodo.3667670
			Download O. japonica data, data release, https://doi.org/10.5281/zenodo.3667670
			Download M. musculus data, data release, https://doi.org/10.5281/zenodo.3667670
			Download Z. mays data, data release, https://doi.org/10.5281/zenodo.3667670
			Download S. cerevisiae data, data release, https://doi.org/10.5281/zenodo.3667670
			Download R. norvegicus data, data release, https://doi.org/10.5281/zenodo.3667670
			Download Interactions Data, data release, https://doi.org/10.6084/m9.figshare.135511761
			Download Complexes Data, data release, https://doi.org/10.6084/m9.figshare.12278810.v1
			Download Human Coronaviruses data, data release, https://doi.org/10.5281/zenodo.3860798
			Download Publications Data, data release, https://doi.org/10.6084/m9.figshare.13270523.v1
			Download Metabolites Data, data release, https://doi.org/10.6084/m9.figshare.13550384.v1
		Added:
			Download Interactions Data, data release, https://doi.org/10.6084/m9.figshare.135511761
			Download Complexes Data, data release, https://doi.org/10.6084/m9.figshare.12278810.v1
			Download Human Coronaviruses data, data release, https://doi.org/10.5281/zenodo.3860798
			Download Publications Data, data release, https://doi.org/10.6084/m9.figshare.13270523.v1
			Download Metabolites Data, data release, https://doi.org/10.6084/m9.figshare.13550384.v1
		Removed:

	'countries' has been modified:
		Before:
			Netherlands
		After:
			Netherlands
			United Kingdom
			United States
		Added:
			United Kingdom
			United States
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.5ry74y' by 'The FAIRsharing Team' at 20:40, 19 Mar 2021 (approved):

	'organizations' has been modified:
		Before:
		After:
			Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, the Netherlands|https://www.maastrichtuniversity.nl/research/bioinformatics|Maintains
			Gladstone Institute of Cardiovascular Disease, San Francisco, USA|https://gladstone.org/science/cardiovascular-disease-institute|Maintains
			University of Missouri, USA|http://missouri.edu/|Maintains
			Heriot-Watt University, Edinburgh, United Kingdom|https://www.hw.ac.uk/|Maintains
			The University of Manchester, Manchester, UK|http://www.manchester.ac.uk/|Maintains
		Added:
			Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, the Netherlands|https://www.maastrichtuniversity.nl/research/bioinformatics|Maintains
			Gladstone Institute of Cardiovascular Disease, San Francisco, USA|https://gladstone.org/science/cardiovascular-disease-institute|Maintains
			University of Missouri, USA|http://missouri.edu/|Maintains
			Heriot-Watt University, Edinburgh, United Kingdom|https://www.hw.ac.uk/|Maintains
			The University of Manchester, Manchester, UK|http://www.manchester.ac.uk/|Maintains
		Removed:

	'accessPoints' has been modified:
		Before:
			REST|https://webservice.bridgedb.org/|OpenAPI 
		After:
			REST|https://bridgedb.github.io/pages/webservice.html|BridgeDB Web Services
		Added:
			REST|https://bridgedb.github.io/pages/webservice.html|BridgeDB Web Services
		Removed:
			REST|https://webservice.bridgedb.org/|OpenAPI 

	'supportLinks' has been modified:
		Before:
			forum|https://groups.google.com/forum/#!forum/bridgedb-discuss
			help|https://tess.elixir-europe.org/materials/bridgedbr-tutorial
		After:
			help|https://bridgedb.github.io/pages/docs.html
			online documentation|https://github.com/bridgedb/
			tess training|https://tess.elixir-europe.org/materials/bridgedbr-tutorial-ce581787-b018-4a34-b161-5ed1b9cc8902
			tess training|https://tess.elixir-europe.org/materials/how-to-install-and-load-the-identifier-mapping-service-with-data-needed-for-gene-to-variant-and-variant-to-gene
			tess training|https://tess.elixir-europe.org/materials/bridgedbr-tutorial
			twitter|@BridgeDbProject
		Added:
			help|https://bridgedb.github.io/pages/docs.html
			online documentation|https://github.com/bridgedb/
			tess training|https://tess.elixir-europe.org/materials/bridgedbr-tutorial-ce581787-b018-4a34-b161-5ed1b9cc8902
			tess training|https://tess.elixir-europe.org/materials/how-to-install-and-load-the-identifier-mapping-service-with-data-needed-for-gene-to-variant-and-variant-to-gene
			tess training|https://tess.elixir-europe.org/materials/bridgedbr-tutorial
			twitter|@BridgeDbProject
		Removed:
			forum|https://groups.google.com/forum/#!forum/bridgedb-discuss
			help|https://tess.elixir-europe.org/materials/bridgedbr-tutorial

	'name' has been modified:
		Before: BridgeDb Metabolite ID Mappings database
		After: BridgeDb

	'licences' has been modified:
		Before:
			Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication|https://creativecommons.org/publicdomain/zero/1.0/|Data
			Apache License 2.0|http://www.apache.org/licenses/LICENSE-2.0|Software
		After:
			Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication|https://creativecommons.org/publicdomain/zero/1.0/|Data
			Apache License 2.0|http://www.apache.org/licenses/LICENSE-2.0|Software
			EMBL-EBI Terms of Use|http://www.ebi.ac.uk/about/terms-of-use|Data
		Added:
			EMBL-EBI Terms of Use|http://www.ebi.ac.uk/about/terms-of-use|Data
		Removed:

	'tools' has been modified:
		Before:
			BridgeDb|2.2|https://bridgedb.org/
			PathVisio|3.1|https://pathvisio.org/
		After:
			BridgeDB Java Library||https://github.com/bridgedb/BridgeDb/releases
		Added:
			BridgeDB Java Library||https://github.com/bridgedb/BridgeDb/releases
		Removed:
			BridgeDb|2.2|https://bridgedb.org/
			PathVisio|3.1|https://pathvisio.org/

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

	'onto_domains' has been modified:
		Before:
		After:
			molecular interaction
		Added:
			molecular interaction
		Removed:

	'dataProcesses' has been modified:
		Before:
		After:
			Search via Web Services, data access, https://bridgedb.github.io/pages/webservice.html
			Download All, data release, https://bridgedb.github.io/data/gene_database/
			Download A. gambiae data, data release, https://doi.org/10.5281/zenodo.3667670
			Download A. thaliana data, data release, https://doi.org/10.5281/zenodo.3667670
			Download B. subtilis data, data release, https://doi.org/10.5281/zenodo.3667670
			Download C. familiaris data, data release, https://doi.org/10.5281/zenodo.3667670
			Download C. elegans data, data release, https://doi.org/10.5281/zenodo.3667670
			Download B. taurus data, data release, https://doi.org/10.5281/zenodo.3667670
			Download E. coli data, data release, https://doi.org/10.5281/zenodo.3667670
			Download D. rerio data, data release, https://doi.org/10.5281/zenodo.3667670
			Download D. melanogaster data, data release, https://doi.org/10.5281/zenodo.3667670
			Download H. sapiens data, data release, https://doi.org/10.5281/zenodo.3667670
			Download G. zeae data, data release, https://doi.org/10.5281/zenodo.3667670
			Download G. gallus data, data release, https://doi.org/10.5281/zenodo.3667670
			Download P. troglodytes data, data release, https://doi.org/10.5281/zenodo.3667670
			Download O. japonica data, data release, https://doi.org/10.5281/zenodo.3667670
			Download M. musculus data, data release, https://doi.org/10.5281/zenodo.3667670
			Download Z. mays data, data release, https://doi.org/10.5281/zenodo.3667670
			Download S. cerevisiae data, data release, https://doi.org/10.5281/zenodo.3667670
			Download R. norvegicus data, data release, https://doi.org/10.5281/zenodo.3667670
		Added:
			Search via Web Services, data access, https://bridgedb.github.io/pages/webservice.html
			Download All, data release, https://bridgedb.github.io/data/gene_database/
			Download A. gambiae data, data release, https://doi.org/10.5281/zenodo.3667670
			Download A. thaliana data, data release, https://doi.org/10.5281/zenodo.3667670
			Download B. subtilis data, data release, https://doi.org/10.5281/zenodo.3667670
			Download C. familiaris data, data release, https://doi.org/10.5281/zenodo.3667670
			Download C. elegans data, data release, https://doi.org/10.5281/zenodo.3667670
			Download B. taurus data, data release, https://doi.org/10.5281/zenodo.3667670
			Download E. coli data, data release, https://doi.org/10.5281/zenodo.3667670
			Download D. rerio data, data release, https://doi.org/10.5281/zenodo.3667670
			Download D. melanogaster data, data release, https://doi.org/10.5281/zenodo.3667670
			Download H. sapiens data, data release, https://doi.org/10.5281/zenodo.3667670
			Download G. zeae data, data release, https://doi.org/10.5281/zenodo.3667670
			Download G. gallus data, data release, https://doi.org/10.5281/zenodo.3667670
			Download P. troglodytes data, data release, https://doi.org/10.5281/zenodo.3667670
			Download O. japonica data, data release, https://doi.org/10.5281/zenodo.3667670
			Download M. musculus data, data release, https://doi.org/10.5281/zenodo.3667670
			Download Z. mays data, data release, https://doi.org/10.5281/zenodo.3667670
			Download S. cerevisiae data, data release, https://doi.org/10.5281/zenodo.3667670
			Download R. norvegicus data, data release, https://doi.org/10.5281/zenodo.3667670
		Removed:

	'publications' has been modified:
		Before:
		After:
			The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services.|van Iersel MP,Pico AR,Kelder T,Gao J,Ho I,Hanspers K,Conklin BR,Evelo CT|BMC Bioinformatics|2010
		Added:
			The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services.|van Iersel MP,Pico AR,Kelder T,Gao J,Ho I,Hanspers K,Conklin BR,Evelo CT|BMC Bioinformatics|2010
		Removed:

	'related_databases' has been modified:
		Before:
			WikiPathways
		After:
			WikiPathways
			Ensembl
			The Human Metabolome Database
		Added:
			Ensembl
			The Human Metabolome Database
		Removed:

	'shortname' has been modified:
		Before: BridgeDb Metabolite ID Mappings database
		After: BridgeDb

	'taxonomies' has been modified:
		Before:
			Not applicable
		After:
			Anopheles gambiae
			Arabidopsis thaliana
			Bacillus subtilis
			Bos taurus
			Caenorhabditis elegans
			Canis familiaris
			Coronaviridae
			Danio rerio
			Drosophila melanogaster
			Escherichia coli
			Gallus gallus
			Gibberella zeae
			Homo sapiens
			Mus musculus
			Oryza sativa L. ssp. japonica
			Pan troglodytes
			Rattus norvegicus
			Saccharomyces cerevisiae
			Zea mays
		Added:
			Anopheles gambiae
			Arabidopsis thaliana
			Bacillus subtilis
			Bos taurus
			Caenorhabditis elegans
			Canis familiaris
			Coronaviridae
			Danio rerio
			Drosophila melanogaster
			Escherichia coli
			Gallus gallus
			Gibberella zeae
			Homo sapiens
			Mus musculus
			Oryza sativa L. ssp. japonica
			Pan troglodytes
			Rattus norvegicus
			Saccharomyces cerevisiae
			Zea mays
		Removed:
			Not applicable

	'homepage' has been modified:
		Before: https://www.bridgedb.org/mapping-databases/hmdb-metabolite-mappings/
		After: https://bridgedb.github.io

	'description' has been modified:
		Before: Metabolite identifier mapping database for small chemical compounds, based on curated information from HMDB, ChEBI, and Wikidata.
		After: BridgeDb is a framework and data repository for finding and mapping equivalent identifiers from various databases. BridgeDb has many facets: providing a framework, live services, and identifier mapping files for genes, gene-variant, proteins, metabolites and interactions.

Edits to 'https://fairsharing.org/FAIRsharing.5ry74y' by 'The FAIRsharing Team' at 10:59, 23 Feb 2021 (approved):

	'contact' has been modified:
		Before: Denise Slenter
		After: 

	'contactORCID' has been modified:
		Before: 0000-0001-8449-1318
		After:

Edits to 'https://fairsharing.org/FAIRsharing.5ry74y' by 'The FAIRsharing Team' at 10:37, 07 Apr 2020 (approved):

	'user_defined_tags' has been modified:
		Before:
		After:
			COVID-19
		Added:
			COVID-19
		Removed:

In Collections

EOSC-Life

Bioschemas

COVID-19 Resources

RDA Covid-19 WG Resources

Support

General

help	Documentation
online documentation	GitHub Project
twitter	@BridgeDbProject

TeSS training resources

BridgeDbR Tutorial

How to install and load the Identifier Mapping Service with data needed for gene-to-variant and variant-to-gene

BridgeDbR Tutorial

Tools

BridgeDB Java Library

https://github.com/bridgedb/BridgeDb/releases

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Applies to: Database software

Apache License 2.0

Data Release

Download All	https://bridgedb.github.io/data/gene_database/
Download A. gambiae data	https://doi.org/10.5281/zenodo.3667670
Download A. thaliana data	https://doi.org/10.5281/zenodo.3667670
Download B. subtilis data	https://doi.org/10.5281/zenodo.3667670
Download C. familiaris data	https://doi.org/10.5281/zenodo.3667670
Download C. elegans data	https://doi.org/10.5281/zenodo.3667670
Download B. taurus data	https://doi.org/10.5281/zenodo.3667670
Download E. coli data	https://doi.org/10.5281/zenodo.3667670
Download D. rerio data	https://doi.org/10.5281/zenodo.3667670
Download D. melanogaster data	https://doi.org/10.5281/zenodo.3667670
Download H. sapiens data	https://doi.org/10.5281/zenodo.3667670
Download G. zeae data	https://doi.org/10.5281/zenodo.3667670
Download G. gallus data	https://doi.org/10.5281/zenodo.3667670
Download P. troglodytes data	https://doi.org/10.5281/zenodo.3667670
Download O. japonica data	https://doi.org/10.5281/zenodo.3667670
Download M. musculus data	https://doi.org/10.5281/zenodo.3667670
Download Z. mays data	https://doi.org/10.5281/zenodo.3667670
Download S. cerevisiae data	https://doi.org/10.5281/zenodo.3667670
Download R. norvegicus data	https://doi.org/10.5281/zenodo.3667670
Download Interactions Data	https://doi.org/10.6084/m9.figshare.135511761
Download Complexes Data	https://doi.org/10.6084/m9.figshare.12278810.v1
Download Human Coronaviruses data	https://doi.org/10.5281/zenodo.3860798
Download Publications Data	https://doi.org/10.6084/m9.figshare.13270523.v1
Download Metabolites Data	https://doi.org/10.6084/m9.figshare.13550384.v1

Data Access

Search via Web Services

https://bridgedb.github.io/pages/webservice.html

REST Web Services

BridgeDB Web Services

https://bridgedb.github.io/pages/webservice.html

Publications

The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services.

van Iersel MP,Pico AR,Kelder T,Gao J,Ho I,Hanspers K,Conklin BR,Evelo CT
BMC Bioinformatics 2010

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

Bioschemas

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 egonw ORCID

Maintains

Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, the Netherlands (University)
Gladstone Institute of Cardiovascular Disease, San Francisco, USA (Research institute)
University of Missouri, USA (University)
Heriot-Watt University, Edinburgh, United Kingdom (University)
The University of Manchester, Manchester, UK (University)

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