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

research data Data ( , ) are a collection of discrete or continuous value (semiotics), values that convey information, describing the quantity, qualitative property, quality, fact, statistics, other basic units of meaning, or simply sequences of symbols t ...

. The BioMart project contributes

open source software Open-source software (OSS) is Software, computer software that is released under a Open-source license, license in which the copyright holder grants users the rights to use, study, change, and Software distribution, distribute the software an ...

and data services to the international

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

. Although the BioMart software is primarily used by the

biomedical research Medical research (or biomedical research), also known as health research, refers to the process of using scientific methods with the aim to produce knowledge about human diseases, the prevention and treatment of illness, and the promotion of ...

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 as a data management solution for the

Human Genome Project The Human Genome Project (HGP) was an international scientific research project with the goal of determining the base pairs that make up human DNA, and of identifying, mapping and sequencing all of the genes of the human genome from both a ...

. Since then, BioMart has grown to become a multi-institute collaboration involving various database projects on five continents.

Integration with Ensembl

BioMart is a powerful tool for researchers and bioinformaticians that allows a user to export data from Ensembl, this could include data such as gene ID’s, gene positions, associated variations, protein domains and sequences. BioMArt allows the data to be exported into convenient file types like FASTA, XLS, CSV, TSV, HTML. Researchers can use the exported data in a variety of applications, including genomic studies, gene expression analysis, and comparative genomics. BioMart's intuitive interface enables users to customize queries to access specific data sets or features of interest easily

Software

BioMart is a freely available,

open-source Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use and view the source code, design documents, or content of the product. The open source model is a decentrali ...

federated database system A federated database system (FDBS) is a type of Meta (prefix), meta-database management system (DBMS), which transparently maps multiple autonomous Database management system, database systems into a single federated database. The constituent data ...

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 po ...

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

graphical user interface A graphical user interface, or GUI, is a form of user interface that allows user (computing), users to human–computer interaction, interact with electronic devices through Graphics, graphical icon (computing), icons and visual indicators such ...

s and

application programming interface An application programming interface (API) is a connection between computers or between computer programs. It is a type of software Interface (computing), interface, offering a service to other pieces of software. A document or standard that des ...

s 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,

Galaxy A galaxy is a Physical system, system of stars, stellar remnants, interstellar medium, interstellar gas, cosmic dust, dust, and dark matter bound together by gravity. The word is derived from the Ancient Greek, Greek ' (), literally 'milky', ...

Cytoscape Cytoscape is an Open-source software, open source bioinformatics software platform for Visualization (graphic), visualizing Metabolic network modelling, molecular interaction networks and integrating with gene expression profiles and other state da ...

, and

Taverna A taverna (; ) 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 establishment of tavernes ...

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 Somatic (biology), 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 ...

, Ensembl Genomes, HapMap, InterPro, Mouse Genome Informatics (MGI), Rfam 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 fro ...

. Access is provided by institutions including the European Bioinformatics Institute (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 organisation, non-profit British genomics and genetics research institute, primarily funded by the Wellcome Trust. It is l ...

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, botany, genomics, and quantitative biology. It is located in Laurel Hollow, New York, in Nassau County, on ...

and the

National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the 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 is lo ...

(NCBI) in the United States and

French National Centre for Scientific Research The French National Centre for Scientific Research (, , CNRS) is the French state research organisation and is the largest fundamental science agency in Europe. In 2016, it employed 31,637 staff, including 11,137 tenured researchers, 13,415 engi ...

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

References

{{Reflist

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