About the Track Hub Registry


Due to their size, efficient integration of large external data sources into genome browsers is a long-standing challenge, which has recently grown in complexity in parallel with the growth of NGS and other high throughput technologies, as well as the rapid evolution from one to many reference genomes. For more than a decade, the Distributed Annotation System (DAS) has been the workhorse for integration of external data sources into genome browsers. However, DAS was not developed to serve data for very high feature densities, querying large feature-rich genomic regions, or providing fast zooming functionality.

The UCSC Genome Bioinformatics group has recently developed the more efficient track hub technology and indexed BigBed, BigWig files. Track data hubs represent a way to collate related data sets through a single attachable URL for presentation as a single entity. These data sets are provided in binary indexed file formats (e.g. bigBed, bigWig, BAM, VCF) supporting both partial downloads and caching, significantly improving performancs over DAS. They can be hosted on a simple HTTP or FTP server reducing the cost of setup and maintenance. Track data hubs provides an efficient mechanism for visualising remotely hosted Internet-accessible collections of genome annotations on genome browsers.

The track hub specification is provided here.

Both UCSC and Ensembl have developed initial support for this technology, but there are still limitations for many users, and Ensembl's support has remained incomplete so far. Integration of track hubs into the Ensembl and UCSC genome browsers involved the copy-paste of a known URL. Discovery is based on word of mouth or the provision of manually curated portal pages hosted by the genome browsers. We believe this system is unmaintainable, as the current growth in data volume in bioinformatics applies not only to the size and density of datasets, but also to their number. The number of public track hubs is increasing, largely because of the explosion of next generation sequencing data. Better interfaces are thus required for users to effectively explore available data sources and find those relevant for their research.

The Track Hub Registry is designed to overcome these challenges. It is conceived as a centralised repository for registering and discovering publicly accessible track data hubs, to allow third parties willing to share their data to advertise their services, and to make it easier for researchers around the workd to discover and use hubs containing different types of genomic research data. The Registry provides an intuitive and easy to use search interface, and RESTful APIs for registering and searching track hubs, checking if a track hub is still available and obtain information which can be used by genome browsers to build convenient interfaces.

Funding

The Track Hub Registry is supported by funding from the BBSRC (ProteoGenomics: Dynamic Linkage of Genomes and Proteomes through Ensembl and ProteomeXchange; BB/L024225/1), the Wellcome Trust (WT095908 and WT098051) and the European Molecular Biology Laboratory.

Status:

API v0.8.2, UI v0.9.1


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