BioMart is a community-driven project to provide a single point of access to distributed

research data In the pursuit of knowledge, data (; ) is a collection of discrete values that convey information, describing quantity, quality, fact, statistics, other basic units of meaning, or simply sequences of symbols that may be further interpreted. ...

. The BioMart project contributes

open source software Open-source software (OSS) is computer software that is released under a license in which the copyright holder grants users the rights to use, study, change, and distribute the software and its source code to anyone and for any purpose. Open ...

and data services to the international

scientific community The scientific community is a diverse network of interacting scientists. It includes many " sub-communities" working on particular scientific fields, and within particular institutions; interdisciplinary and cross-institutional activities are als ...

. Although the BioMart software is primarily used by the biomedical research community, it is designed in such a way that any type of data can be incorporated into the BioMart framework. The BioMart project originated at the

European Bioinformatics Institute The European Bioinformatics Institute (EMBL-EBI) is an Intergovernmental Organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wel ...

as a data management solution for the Human Genome Project. Since then, BioMart has grown to become a multi-institute collaboration involving various database projects on five continents.

Software

BioMart is a freely available, open-source,

federated database system A federated database system (FDBS) is a type of meta- database management system (DBMS), which transparently maps multiple autonomous database systems into a single federated database. The constituent databases are interconnected via a computer netw ...

that provides unified access to disparate, geographically distributed data sources. BioMart allows databases hosted on different servers to be presented seamlessly to users, facilitating collaborative projects. BioMart contains several levels of

query optimization Query optimization is a feature of many relational database management systems and other databases such as NoSQL and graph databases. The query optimizer attempts to determine the most efficient way to execute a given query by considering the p ...

to efficiently manage large data sets, and offers a diverse selection of

graphical user interface The GUI ( "UI" by itself is still usually pronounced . or ), graphical user interface, is a form of user interface that allows users to interact with electronic devices through graphical icons and audio indicator such as primary notation, inst ...

s and application programming interfaces to allow queries to be performed in whatever manner is most convenient for the user. BioMart's capabilities are extended by integration with several widely used software packages such as

Bioconductor Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology. Bioconductor is based primarily on the statistical R programm ...

, Galaxy,

Cytoscape Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression profiles and other state data. Additional features are available as plugins. Plugins are availabl ...

, and

Taverna A taverna (Greek: ταβέρνα) is a small Greek restaurant that serves Greek cuisine. The taverna is an integral part of Greek culture and has become familiar to people from other countries who visit Greece, as well as through the establishme ...

Data sources and community

There are around 40 BioMart data sources including the Atlas of UTR Regulatory Activity (AURA), the

COSMIC cancer database COSMIC is an online database of somatically acquired mutations found in human cancer. Somatic mutations are those that occur in non-germline cells that are not inherited by children. COSMIC, an acronym of ''Catalogue Of Somatic Mutations In Cancer ...

Ensembl Ensembl genome database project is a scientific project at the European Bioinformatics Institute, which provides a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other v ...

Genomes,

HapMap The International HapMap Project was an organization that aimed to develop a haplotype map (HapMap) of the human genome, to describe the common patterns of human genetic variation. HapMap is used to find genetic variants affecting health, disease a ...

InterPro InterPro is a database of protein families, protein domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterise them. The contents of InterPro c ...

Mouse Genome Informatics Mouse Genome Informatics (MGI) is a free, online database and bioinformatics resource hosted by The Jackson Laboratory, with funding by the National Human Genome Research Institute (NHGRI), the National Cancer Institute (NCI), and the Eunice Kenne ...

(MGI),

Rfam Rfam is a database containing information about non-coding RNA (ncRNA) families and other structured RNA elements. It is an annotated, open access database originally developed at the Wellcome Trust Sanger Institute in collaboration with Jane ...

and

UniProt UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from ...

. Access is provided by institutions including the

(EBI) and the

Wellcome Trust Sanger Institute The Wellcome Sanger Institute, previously known as The Sanger Centre and Wellcome Trust Sanger Institute, is a non-profit British genomics and genetics research institute, primarily funded by the Wellcome Trust. It is located on the Wellcome G ...

in the UK,

Cold Spring Harbor Laboratory Cold Spring Harbor Laboratory (CSHL) is a private, non-profit institution with research programs focusing on cancer, neuroscience, plant biology, genomics, and quantitative biology. It is one of 68 institutions supported by the Cancer Centers ...

and the

National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The ...

(NCBI) in the United States and

French National Centre for Scientific Research The French National Centre for Scientific Research (french: link=no, Centre national de la recherche scientifique, CNRS) is the French state research organisation and is the largest fundamental science agency in Europe. In 2016, it employed 31,63 ...

(CNRS). The BioMart Central Portal was established to provide a convenient single point of access to this growing pool of data sources.

References

{{Reflist, 2

External links

DATABASE Issue dedicated to BioMart

* ttp://biomart.org/ BioMart Project home page
BioMart Users mailing list
Bioinformatics software Biological databases Data warehousing products Free software projects Science and technology in Cambridgeshire South Cambridgeshire District