WebApollo: A Web-based Sequence Annotation Editor for Distributed Community Annotation

As genome sequencing becomes more efficient, annotation efforts must adapt to keep pace. With a larger reliance on contributions from domain specialists, the curation environment is shifting from a traditional centralized model to a geographically dispersed community annotation model—which requires new tools to support collaborative annotation. WebApollo is a successor to the original Apollo annotation editor and provides a web-based environment that allows multiple distributed users to edit and share sequence annotations. The WebApollo client is designed as an extension to JBrowse, a genome browser that provides a fast, highly interactive interface for visualizing genomic data. WebApollo allows users to create and modify transcript and exon structure via intuitive gestures, and also flags potential problems within these curated annotations. A server data broker allows dynamic access to genomic analyses results from both UCSC and Chado genome databases, and client code provides direct access to BAM data files to enable deep sequencing visualization. A server annotation editing engine handles edit logic and deals with the complexities of modifications in a biological context, where a single change can have multiple cascading effects (e.g., when splitting or merging transcripts). All edits are automatically stored persistently in the server, which ensures reliability and allows the client to show edit histories and provide full undo and redo functions. The server provides synchronized updates over multiple browser instances, so annotation edits are immediately visible to all users who are working on the same region. Additional information and code are available at http://gmod.org/wiki/WebApollo.

Public demo: http://icebox.lbl.gov:8080/WebApolloDemo