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.
Highlights
Cytoscape is an integrated network visualization tool and analysis platform[1,2]
The following reviewer comments are addressed in this version: * Clarification about relationship to and reliance upon BridgeDb project app, databases and web services. * Updates to Table 1 and caption * Clarification of persistent selection behavior in graphical user interface (GUI) * Added Use Case 3: Identifiers and symbols * Explanation of "force single" * Example of R code with and without the custom function” * Clarification on how regular expressions are used for data source inference * Consistent references to “Uniprot-TrEMBL” * Described how results are added to Table Panel * Changed “singular” to “single” * Updated documentation on available species See referee reports
This problem has been addressed by the BridgeDB project[3], which created clients and services to translate between various identifiers
Summary
Any reports and responses or comments on the article can be found at the end of the article. The following reviewer comments are addressed in this version: * Clarification about relationship to and reliance upon BridgeDb project app, databases and web services. * Updates to Table 1 and caption * Clarification of persistent selection behavior in GUI * Added Use Case 3: Identifiers and symbols * Explanation of "force single" * Example of R code with and without the custom function” * Clarification on how regular expressions are used for data source inference * Consistent references to “Uniprot-TrEMBL” * Described how results are added to Table Panel * Changed “singular” to “single” * Updated documentation on available species See referee reports The following reviewer comments are addressed in this version: * Clarification about relationship to and reliance upon BridgeDb project app, databases and web services. * Updates to Table 1 and caption * Clarification of persistent selection behavior in GUI * Added Use Case 3: Identifiers and symbols * Explanation of "force single" * Example of R code with and without the custom function” * Clarification on how regular expressions are used for data source inference * Consistent references to “Uniprot-TrEMBL” * Described how results are added to Table Panel * Changed “singular” to “single” * Updated documentation on available species See referee reports
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