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. 2014 Jul 1:3:148.
doi: 10.12688/f1000research.4521.1. eCollection 2014.

BridgeDb app: unifying identifier mapping services for Cytoscape

Jianjiong Gao  1 , Chao Zhang  2 , Martijn van Iersel  3 , Li Zhang  4 , Dong Xu  5 , Nikolaus Schultz  6 , Alexander R Pico  7
Affiliations

BridgeDb app: unifying identifier mapping services for Cytoscape

Jianjiong Gao et al. F1000Res. .

Abstract

The BridgeDb app for Cytoscape allows users to map and annotate identifiers of genes, proteins and metabolites in the context of biological networks. The app greatly simplifies the identifier mapping process in Cytoscape by providing a unified interface to different mapping resources and services. The app also provides a programming interface via Cytoscape Commands that can be utilized for identifier mapping by other Cytoscape apps. In this article we provide a technical guide to the BridgeDb app for mapping identifiers in Cytoscape.

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Conflict of interest statement

Competing interests: No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. BridgeDb app implementation.
Figure 2.
Figure 2.. NOA app utilizing BridgeDb app services for gene ontology annotation.
See this image and copyright information in PMC

References

    1. Shannon P, Markiel A, Ozier O, et al. : Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504 10.1101/gr.1239303 - DOI - PMC - PubMed
    1. van Iersel MP, Pico AR, Kelder T, et al. : The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. BMC bioinformatics. 2010;11(1):5 10.1186/1471-2105-11-5 - DOI - PMC - PubMed
    1. Kasprzyk A, Keefe D, Smedley D, et al. : EnsMart: a generic system for fast and flexible access to biological data. Genome Res. 2004;14(1):160–169 10.1101/gr.1645104 - DOI - PMC - PubMed
    1. Berriz GF, Roth FP: The Synergizer service for translating gene, protein and other biological identifiers. Bioinformatics. 2008;24(19):2272–2273 10.1093/bioinformatics/btn424 - DOI - PMC - PubMed
    1. Côté RG, Jones P, Martens L, et al. : The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. BMC bioinformatics. 2007;8(1):401 10.1186/1471-2105-8-401 - DOI - PMC - PubMed

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