Knowledgebase · FAIRsharing
BridgeDb
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.
- Website
- Record in FAIRsharing (doi:10.25504/FAIRsharing.5ry74y)
- Subjects: Biology, Chemistry, Metabolomics, Systems Biology
Documentation, events and training
bio.tools API and tool documentation
- BridgeDb (same homepage)
TeSS Training materials (10)
- Downloading all currently released BridgeDb identifier mapping databases
- Making BridgeDb Derby files with Groovy (linked to the bio.tools entry)
- BridgeDb: Mapping Gene Identifiers
- Information about chemicals (linked to the bio.tools entry)
- Identifier mapping with Cytoscape (linked to the bio.tools entry)
- BridgeDb-Matlab Usage Instructions
- BridgeDbR Tutorial
- How to install and load the Identifier Mapping Service with data needed for gene-to-variant and variant-to-gene (linked to the bio.tools entry)
- #metawinterschool contribution by BiGCaT
- BridgeDbR Tutorial (linked to the bio.tools entry)
TeSS Events (1)
- ELIXIR Fluxomics Training School 2021 2021-10-04
Taxila Training materials (1)
FAIR4ChemNL Training materials (1)
What is known per question
The questions of the decision tree, with what FAIRsharing says about this repository. ✓ supported, ✗ excluded, ? not known. Your own answers are marked.
What kind of data do you want to archive?
- ? Spectra
- ? Crystal structures
- ? Computational chemistry
- ? Catalysis
- ? Compounds and reactions
- ? Bioassays and chemical biology
- ? Materials and polymers
- ? Images and microscopy
- ? Something else
Subjects: Biology; Chemistry; Metabolomics; Systems Biology
Domains: molecular interaction
Does the journal or publisher you publish with require or recommend a repository?
- ? Yes
- ? No
- ? I do not know
FAIRsharing has no information on this.
Which discipline does your data belong to?
FAIRsharing has no information on this.
Which publisher?
FAIRsharing has no information on this.
Does your funder have requirements for where data is archived?
- ? Yes
- ? No
- ? I do not know
FAIRsharing has no information on this.
Which funder?
FAIRsharing has no information on this.
Does your institution offer a data repository?
- ? Yes
- ? No
- ? I do not know
Organisations: University of Manchester (maintains); ELIXIR Europe (associated_with); ELIXIR Netherlands (associated_with); Heriot-Watt University, Edinburgh, United Kingdom (maintains); University of Missouri, USA (maintains); Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, the Netherlands (maintains); Gladstone Institute of Cardiovascular Disease, San Francisco, USA (maintains)
Which institution?
FAIRsharing has no information on this.
Can your data be shared openly?
- ✓ Yes, openly available
- ? Yes, after an embargo
- ✗ Only with restrictions
Data access: open
Data deposition: not applicable
How large is your dataset?
- ? Less than 1 GB
- ? 1 GB to 50 GB
- ? 50 GB to 1 TB
- ? More than 1 TB
FAIRsharing has no information on this.
Why can the data not be open?
- ? It contains personal data
- ? Commercial or intellectual property reasons
- ? Safety or security concerns
- ? A data sharing agreement limits it
FAIRsharing has no information on this.
Under which license do you want to share the data?
- ✓ CC0 / public domain
- ? CC BY
- ? Another open license
- ? Not decided yet
Licences: Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication; EMBL-EBI Terms of Use; Apache License 2.0
Do you need a persistent identifier, such as a DOI, for citing the data?
- ? Yes, a DOI
- ? Any persistent identifier will do
- ? No
FAIRsharing has no information on this.
Must the data be stored in a specific region?
- ? In the European Union
- ? In a specific country
- ✓ No preference
Country: Netherlands; United Kingdom; United States
Must archiving be free of charge?
- ? Yes, free only
- ? A fee is fine
FAIRsharing has no information on this.
Which country?
✓ 3 of 15 in the list ✗ excludes 12
Country: Netherlands; United Kingdom; United States