Community annotation of the zebrafish genome: a wiki solution

Rajeshwari Meli, Meenakshi Sharma, Ashok Patowary, Abhiranjan Prasad, Mukesh Lalwani, Jayant Maini, A Ramcharan Singh, Gaurav Kumar, Vaibhav Jadhav, Vinod Scaria, Sridhar Sivasubbu
Institute of Genomics and Integrative Biology, Mall Road, Delhi - 110007, India

An enormous amount of information on a genomics scale is available for Zebrafish (Danio rerio), which is a well-studied model organism for Human diseases. However, a majority of this annotation is scattered in obscure data sources, which are not easily amenable for large-scale and integrative analysis. To integrate the zebrafish centric genomics information into a unified resource we have developed 'FishMap' - A platform for storage, display and retrieval of genomic information of zebrafish. This database provides a centralized, web accessible, integrated resource for common access to this data while allowing sophisticated data mining queries. The datasets in FishMap have been methodically collected from various resources and supplementary information of publications and mapped to the zebrafish genome. The data is organized into nine major sections, which include Comparative Genomics, Mapping and Sequencing, Gene and Gene Predictions, Expression and Regulation, and Variation and Repeats.

In addition to an integrated genomics database, FishMap aims to provide shared genomics resources for community annotation of the zebrafish genome on the lines of the 'wiki' called the 'Zebrafish GenomeWiki'. Members of the zebrafish community can annotate, comment and edit existing data sets using the Zebrafish GenomeWiki portal. The Zebrafish GenomeWiki will permit community experts and individual investigators to add the latest genomics information and discuss alternative annotations there by speeding up the fine annotation the zebrafish genome.

FishMap is built on the Gbrowse, which is a part of the Generic Model Organism Database Consortium Project. The database is amenable to programmatic access through the Distributed Annotation System (DAS) as well as BioMoby protocols, thus making it a central community resource that can be integrated with existing data mining and analysis workflows. We hope FishMap together with the Zebrafish GenomeWiki would be an integral resource for community participation in zebrafish genomics. The resource is freely available at URL: http://miracle.igib.res.in/fishmap OR http://fishmap.igib.res.in/