The BridgeDb framework

Egon Willighagen; Jonathan Mélius; Christian Brenninkmeijer; Stian Soiland-Reyes; Anwesha Bohler; Martina Kutmon; Andra Waagmeester; Alex Pico; Anders Riutta; Alasdair Gray; Christ Leemans; Colin Batchelor; Ola Spjuth; Nuno Nunes; Chris Evelo; Carole Goble

doi:10.7490/f1000research.1113101.1

The BridgeDb framework

Egon Willighagen, Jonathan Mélius, Christian Brenninkmeijer, Stian Soiland-Reyes, Anwesha Bohler, Martina Kutmon, Andra Waagmeester, Alex Pico, Anders Riutta, Alasdair Gray, Christ Leemans, Colin Batchelor, Ola Spjuth, Nuno Nunes, Chris Evelo, Carole Goble

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Research output: Contribution to conference › Poster

Abstract

What is BridgeDb? Biological systems consist of many thousands of genes, proteins, and metabolites. Our collective knowledge about these entities is collected in many hundreds of disparate databases, each focusing on particular themes of knowledge or types of experiments. Importantly, to capture this focus, each database uses its own definition of the key entities and have a matching collection of entity identifiers. Linking all these identifiers requires a flexible tool that provides identifier mappings (IDmaps) but that also knows about these complexities. BridgeDb (bridgedb.org) offer IDmaps and understands the difference between a gene, a DNA sequence, a microarray probe, and a protein. Likewise, it understands the difference between stereoisomers, protonation states, and compound classes for metabolites and other small molecules. Modules and plugins are available to use BridgeDb in many bioinformatics toolsets.

Original language	English
DOIs	https://doi.org/10.7490/f1000research.1113101.1
Publication status	Published - 8 Sept 2016
Event	ECCB 2016, The Hague - World Forum Convention Centre, The Hague, Netherlands Duration: 3 Sept 2016 → 7 Sept 2016 https://www.ebi.ac.uk/eccb/2016/

Conference

Conference	ECCB 2016, The Hague
Country/Territory	Netherlands
City	The Hague
Period	3/09/16 → 7/09/16
Internet address	https://www.ebi.ac.uk/eccb/2016/

Access to Document

10.7490/f1000research.1113101.1Licence: CC BY

Open-PHACTS An open integrated and sustainable chemistry, biology and pharmacology knowledge resource for drug discovery
Goble, C. (PI), Pettifer, S. (CoI), Stevens, R. (CoI), Gray, A. (Researcher), Soiland-Reyes, S. (Researcher) & Brenninkmeijer, C. (Researcher)
1/03/11 → 28/02/14
Project: Research

Cite this

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abstract = "What is BridgeDb? Biological systems consist of many thousands of genes, proteins, and metabolites. Our collective knowledge about these entities is collected in many hundreds of disparate databases, each focusing on particular themes of knowledge or types of experiments. Importantly, to capture this focus, each database uses its own definition of the key entities and have a matching collection of entity identifiers. Linking all these identifiers requires a flexible tool that provides identifier mappings (IDmaps) but that also knows about these complexities. BridgeDb (bridgedb.org) offer IDmaps and understands the difference between a gene, a DNA sequence, a microarray probe, and a protein. Likewise, it understands the difference between stereoisomers, protonation states, and compound classes for metabolites and other small molecules. Modules and plugins are available to use BridgeDb in many bioinformatics toolsets.",

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T1 - The BridgeDb framework

AU - Willighagen, Egon

AU - Mélius, Jonathan

AU - Brenninkmeijer, Christian

AU - Soiland-Reyes, Stian

AU - Bohler, Anwesha

AU - Kutmon, Martina

AU - Waagmeester, Andra

AU - Pico, Alex

AU - Riutta, Anders

AU - Gray, Alasdair

AU - Leemans, Christ

AU - Batchelor, Colin

AU - Spjuth, Ola

AU - Nunes, Nuno

AU - Evelo, Chris

AU - Goble, Carole

PY - 2016/9/8

Y1 - 2016/9/8

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AB - What is BridgeDb? Biological systems consist of many thousands of genes, proteins, and metabolites. Our collective knowledge about these entities is collected in many hundreds of disparate databases, each focusing on particular themes of knowledge or types of experiments. Importantly, to capture this focus, each database uses its own definition of the key entities and have a matching collection of entity identifiers. Linking all these identifiers requires a flexible tool that provides identifier mappings (IDmaps) but that also knows about these complexities. BridgeDb (bridgedb.org) offer IDmaps and understands the difference between a gene, a DNA sequence, a microarray probe, and a protein. Likewise, it understands the difference between stereoisomers, protonation states, and compound classes for metabolites and other small molecules. Modules and plugins are available to use BridgeDb in many bioinformatics toolsets.

U2 - 10.7490/f1000research.1113101.1

DO - 10.7490/f1000research.1113101.1

M3 - Poster

T2 - ECCB 2016, The Hague

Y2 - 3 September 2016 through 7 September 2016

ER -

The BridgeDb framework

Abstract

Conference

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Open-PHACTS An open integrated and sustainable chemistry, biology and pharmacology knowledge resource for drug discovery

Cite this