Learn to use BioMart, a publicly available open source tool for management and querying of many types of biological data. It is widely used around the world for various projects. As a component of the use GMOD (Generic Model Organism Database) suite of tools, many projects and individuals contribute to the development of BioMart.

The main focus of this material will be the BioMart v0.7 Portal, and touches on other versions and installations of BioMart as well. The query interface allows users to assemble customized and complex queries of the underlying data sets that are accessible from this site.

Besides the Portal, researchers will find BioMart installed at many project sites. The solid and flexible foundation supports a huge range of species and data types. The various sites and versions may have some differences in their look or their data types, but understanding the basic functions of BioMart will serve users well at any site, or in third party tools developed around BioMart.

You will learn:

  • to perform effective, complex, and customized searches using BioMart datasets and filters
  • to obtain results with specified attributes and interact with the output
  • to identify BioMart installations and versions at other sites
  • ways to access the BioMart framework from other tools and third-party software
  • to interact with the new version of BioMart associated with the International Cancer Genome Consortium use (ICGC) project
TUTORIAL RELATED CONTENT

TUTORIALS

This tutorial is a part of the tutorial group Advanced Analysis and Queries. You might find the other tutorials in the group interesting:

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CATEGORIES

EBI : This category includes all resources maintained at the European Bioinformatics Institute (EBI)

Algorithms and Analysis : This category contains various tools that may help perform analysis of different genomics data types. This may include sequence alignment, large-scale or complex queries, motif finding, or comparative assessments.

Genome Databases (euk) : Genomic databases or repositories primarily aimed at eukaryotic organisms. Some may contain prokaryotic data as well.

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BIOMED CENTRAL

Recent BioMed Central research articles citing this resource

Buckberry Sam et al., Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation Human and rodent genomics. BMC Genomics (2017) doi:10.1186/s12864-016-3384-9

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Geuens Thomas et al., Mutant HSPB1 causes loss of translational repression by binding to PCBP1, an RNA binding protein with a possible role in neurodegenerative disease. Acta Neuropathologica Communications (2017) doi:10.1186/s40478-016-0407-3