BioMart – biological queries made easy

doi:10.1186/1471-2164-10-22

BMC Genomics

Volume 10

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Smedley D
Haider S
Ballester B
Holland R
London D
Thorisson G
Kasprzyk A

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London D
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Kasprzyk A
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BioMart – biological queries made easy

Damian Smedley¹ , Syed Haider¹ , Benoit Ballester¹ , Richard Holland¹ , Darin London² , Gudmundur Thorisson³ and Arek Kasprzyk⁴

¹European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

²Institute for Genome Sciences & Policy (IGSP), Duke University CIEMAS, 101 Science Drive, DUMC Box 3382, Durham, NC 27708, USA

³Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK

⁴Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800 Toronto, Ontario, M5G 0A3, Canada

author email corresponding author email

BMC Genomics 2009, 10:22doi:10.1186/1471-2164-10-22


Published:	14 January 2009

Additional files

Additional file 1:

Sample Affymetrix Probe IDs. File of Affymetrix HG U95AV2 IDs for the BioMart example given in the paper.

Format: TXT Size: 5KB Download file

Additional file 2:

Use of BioMart within the Galaxy system. BioMart embedded in the Galaxy framework is used to retrieve the peptide sequence for the mouse Bambi gene (A). The peptide sequence is saved on the Galaxy server and then transmembrane domains identified in it by running tmap analysis (part of the EMBOSS package) also from within Galaxy (B). The downloaded results file shows two potential transmembrane segments (C).

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Additional file 3:

Cytoscape platform used to visualise a yeast protein interaction network. Annotation of the selected nodes in yellow is shown in the bottom pane and uses MartServices on our central portal to retrieve the GO annotation for each node.

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Additional file 4:

Taverna workflow demonstrating BioMart and web services interaction. Ensembl Gene IDs and EMBL IDs for a given set of genes (results of an Affymetrix microarray experiment) are recovered. The left hand panel shows a graphical depiction of the workflow in which the EMBL IDs are converted to KEGG IDs and then HTML links to marked up pathways using KEGG web services. The upper right panel shows the tabular results of the workflow with Ensembl Gene IDs mapped to KEGG pathway URLs. The bottom right panel shows one of these links with the mapped gene marked in red in the pathway.

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Additional file 5:

BioMart as a DAS server. Ensembl ContigView display showing a EMMA mouse strain archive track in blue (A). The data is served using the DAS protocol from a BioMart server in an external location to the rest of the Ensembl data. Ensembl GeneView showing Pancreatic Expression Database annotation (B). This annotation comes from a geneDAS source served by the BioMart server.

Format: DOC Size: 362KB Download file

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