Touring Ensembl: A practical guide to genome browsing

The number of databases in molecular biological fields has rapidly increased to provide a large-scale resource. Though valuable information is available, data can be difficult to access, compare and integrate due to different formats and presentations of web interfaces. This paper offers a practical guide to the integration of gene, comparative genomic, and functional genomics data using the Ensembl website at http://www.ensembl.org

Advanced Genomic Data Mining

As data banks increase their size, one of the current challenges in bioinformatics is to be able to query them in a sensible way. Information is contained in differen

URLs for additional information.

<p>URLs for additional information.</p

R output (using <i>biomaRt</i> library) providing CodeLink bioarray IDs and their mappings to Ensembl transcripts (<i>chr: start-end position</i>), as explained in the text.

<p>R output (using <i>biomaRt</i> library) providing CodeLink bioarray IDs and their mappings to Ensembl transcripts (<i>chr: start-end position</i>), as explained in the text.</p

BioMart can join different datasets, in this case Reactome and UniProt to identify enzymes involved in carbohydrate metabolism.

<p>BioMart can join different datasets, in this case Reactome and UniProt to identify enzymes involved in carbohydrate metabolism.</p

Screenshot displaying BioMart embedded in the Galaxy framework.

<p>Screenshot displaying BioMart embedded in the Galaxy framework.</p

BioMart libraries available in the Central Server.

<p>BioMart libraries available in the Central Server.</p

Diagram depicting the way different applications interact with data mining tools.

<p>The boxed area shows the topics discussed in this paper. BioMart's Central Server coordinates access to different databases: on the left-hand side, Galaxy interacts with BioMart by means of URL-based queries, allowing interaction with the UCSC Genome Browser and its Table Browser; while on the right interaction with Ensembl and its API is shown. Other platforms such as BioConductor rely on Web services (<i>MartService</i>) to retrieve information from the BioMart system. Additionally, BioMart is compliant with the DAS protocol <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000121#pcbi.1000121-Dowell1" target="_blank">[34]</a> and can be queried by means of a Perl API, <i>biomart-perl</i>, as well as a Java API, <i>martj</i>.</p