BridgeDb identifier mapping service (variety of species)

BridgeDb is a platform for database identifier mapping, both simple identifiers (e.g. CHEBI:1234) and universal resource identifiers (URIs, e.g. http://identifiers.org/chebi/CHEBI:1234). It is the workhorse of data integration and supports the essential FAIR aspect of interoperability, with recent efforts adding detailed provenance and meaning to mappings (“scientific lenses”). BridgeDb provides the glue between bioinformatics processing pipeline blocks and has an OpenAPI-based interface. This service provides identifier mapping for metabolites and genes/proteins from a large variety of species.

For developers
For end-users
Type:
Database / data source, Service
Categories:
API Definitions for OpenRiskNet applications and data
Applicability domain:
Bioinformatics
Topic:
Identifier mapping
Targeted industry:
Chemicals, Drugs, Cosmetics, Food, Other consumer products
Targeted users:
Software Developers, Risk assessors, Researchers, Students, Data managers
Relevant OpenRiskNet case study:
AOPLink - Identification and Linking of Data related to AOPWiki

Provided by:
Maastricht University
Licence:
Apache 2.0 (None)
Login required:
No
Implementation status:
Available as web service
Integration status:
Integration in progress
Service integration operations completed:
Utilises the OpenRiskNet APIs to ensure that each service is accessible to our proposed interoperability layer.
Is annotated according to the semantic interoperability layer concept using defined ontologies.
Is containerised for easy deployment in virtual environments of OpenRiskNet instances.
Has documented scientific and technical background.
Is deployed into the OpenRiskNet reference environment.
Is listed in the OpenRiskNet discovery services.
Is listed in other central repositories like eInfraCentral, bio.tools and TeSS (ELIXIR).
Provides legal and ethical statements on how the service can be used.

Resources & Training

Tutorial
Workflow: Access TG-GATEs data for seleted compounds, select differentially expressed genes and identifier relevant pathways
Thomas Exner
13 Sep 2018
Abstract:
Example workflow based on OpenRiskNet tools - Pathway identification workflow related to DataCure and AOPlink case studies. This notebook downloads TG-Gates data of 4 compounds and selects genes overexpressed in all sample. The Affymetrix probe sets are then translated into Ensembl gene identifiers using the BridgeDB service and pathways associated with the genes are identified using the WikiPathways service.

Publisher: OpenRiskNet
Target audience: Risk assessors, Researchers, Data modellers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: EwC
Tutorial