The BioMart community portal: an innovative alternative to large, centralized data repositories.

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations

The blast query form allows to search the contigs as a database using as input sequence(s) in Fasta format.

<p>Others parameters which can be used in this query are blast program (blastn, blastx), expected value and maximum number of outputs to be shown. The blast results are shown in a table allowing to add new contigs as favorite. Ticking the alignment checkbox enables to browse the alignment results.</p

The Venn diagram shows the number of contigs shared between libraries and the specific ones.

<p>It has been built using libraries alignment data. To build a new diagram the user has to select the libraries he wants to have in each pool (from two to five). If the user clicks on a figure in the graph the list of corresponding contigs will appear in the list box on the right hand side. Clicking on the contig names redirects to the corresponding page.</p

Variants overview figures.

<p>From the main variant page, graphics synthesizing informations on the variant set can be displayed. The presented graphs are InDels size distribution (top) and Indels annotations pie chart (bottom).</p

The sequence view provides informations such as nucleotide content and longest open reading frame (ORF).

<p>The possible starts are presented in green, stops in red and ORFs in blue. The query form permits different actions on the sequence such as extraction, reverse complementation, translation in different frames, ORF presentation and text search.</p

Contigs overview figures.

<p>From the main contig page, graphics synthesizing informations on the contig set can be displayed. The presented graphs are contigs depth versus size plot (top-left), contigs length distribution (top-right), contig best annotations pie chart (bottom-left) and libraries mapping bar chart (bottom-right). All graphics can be printed or downloaded in four different formats (PNG, JPEG, PDF, SVG).</p

The BioMart Community Portal: An Innovative Alternative to Large, Centralized Data Repositories

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.This article is from Nucleic Acids Research 43 (2015): W589, doi:10.1093/nar/gkv350. Posted with permission.</p