Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 Jun 11:7:725.
doi: 10.12688/f1000research.14807.2. eCollection 2018.

Identifier Mapping in Cytoscape

Adam Treister  1 , Alexander R Pico  1
Affiliations

Identifier Mapping in Cytoscape

Adam Treister et al. F1000Res. .

Abstract

Identifier Mapping, the association of terms across disparate taxonomies and databases, is a common hurdle in bioinformatics workflows. The idmapper app for Cytoscape simplifies identifier mapping for genes and proteins in the context of common biological networks. This app provides a unified interface to different identifier resources accessible through a right-click on the table's column header. It also provides an OSGi programming interface via Cytoscape Commands and CyREST that can be utilized for identifier mapping in scripts and other Cytoscape apps, and supports integrated Swagger documentation.

Keywords: BridgeDb; Cytoscape; ID Mapping; Identifiers.

PubMed Disclaimer

Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Simplified dialog for ID Mapping.
Four options are presented to the user when accessing idmapper from within the Cytoscape GUI, each with common default or inferred values to reduce the number of steps required of the user.
Figure 2.
Figure 2.. Swagger documented function.
The functionality of idmapper is contained in this single function: map column.
See this image and copyright information in PMC

References

    1. Cline MS, Smoot M, Cerami E, et al. : Integration of biological networks and gene expression data using Cytoscape. Nat Protoc. 2007;2(10):2366–2382. 10.1038/nprot.2007.324 - DOI - PMC - PubMed
    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;11:5. 10.1186/1471-2105-11-5 - DOI - PMC - PubMed
    1. Gao J, Zhang C, van Iersel M, et al. : BridgeDb app: unifying identifier mapping services for Cytoscape [version 1; referees: 2 approved]. F1000Res. 2014;3:148. 10.12688/f1000research.4521.1 - DOI - PMC - PubMed
    1. Szklarczyk D, Morris JH, Cook H, et al. : The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res. 2017;45(D1):D362–D368. 10.1093/nar/gkw937 - DOI - PMC - PubMed

Publication types

LinkOut - more resources