Written in | Java |
---|---|
Operating system | Unix-like |
Available in | English |
Type | Federated database system |
License | LGPL |
Website |
useast |
BioMart is a community-driven project to provide a single point of access to distributed research data. The BioMart project contributes open source software and data services to the international scientific community. 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 as a data management solution [1] for the Human Genome Project. [2] Since then, BioMart has grown to become a multi-institute collaboration involving various database projects on five continents. [3] [4] [5] [6]
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 [7]
BioMart is a freely available, open-source, federated database system that provides unified access to disparate, geographically distributed data sources. [8] BioMart allows databases hosted on different servers to be presented seamlessly to users, facilitating collaborative projects. BioMart contains several levels of query optimization to efficiently manage large data sets, and offers a diverse selection of graphical user interfaces 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, [9] Galaxy, [10] Cytoscape, [11] and Taverna. [12]
There are around 40 BioMart data sources including the Atlas of UTR Regulatory Activity (AURA), the COSMIC cancer database, Ensembl Genomes, HapMap, InterPro, Mouse Genome Informatics (MGI), Rfam and UniProt. Access is provided by institutions including the European Bioinformatics Institute (EBI) and the Wellcome Trust Sanger Institute in the UK, Cold Spring Harbor Laboratory and the National Center for Biotechnology Information (NCBI) in the United States and French National Centre for Scientific Research (CNRS). [13] The BioMart Central Portal was established to provide a convenient single point of access to this growing pool of data sources. [3] [5] [6]
The BioMart tool is designed to help users save time by querying data from multiple genes or variants at once. BioMart is used for returning a large amount of focused data at once, being useful for Data mining, although it is recommended to limit queries to fewer than 500 inputs at a time. [14] Oftentimes, bioinformatics researchers need to perform many queries at once from multiple data sources. By using BioMart, the user saves a significant amount of time compared to manually inputting their search into multiple tools. [15]
These queries can be performed through the web interface, without requiring any programming experience, or programmatically, through tools like biomaRt using the R language interface. Common uses include ID conversions, retrieval of gene locations, and downloading sequences. [14]
There are four main steps to using BioMart through Ensembl, as listed below.
The associated video, Figure 1, demonstrates an example of navigating through these steps.
BioMart has available very powerful gene ID conversion functionality. By leveraging BioMart queries users can easily and conveniently collect many different IDs and other identifiers for hundreds of genes simultaneously, saving the user a significant time when compared to other tools. [16] When making a new BioMart query, filtering based on external reference IDs can be applied. [17] With this filtering option users can input external identifiers for genes including IDs from the databases of other organizations, gene names, and more. To decide which results are displayed, users select attributes corresponding to their desired identifiers. Attributes include IDs from many Ensembl databases, IDs from external databases such as those of NCBI, as well as many other identifiers. [17] Once the desired attributes are selected, obtaining the results of the BioMart query will display the corresponding identifiers for the input gene reference IDs. [16]
Below is a video that provides a demonstration of gene ID conversion with BioMart.
The BioMart interface on Ensembl allows for the combining of multiple data sets to allow a user to see the combined results of the multiple datasets selected. This User-friendly tool simplifies complex data integration by providing a simple to use interface to query and combine data from various biological data sources. This tool saves researchers considerable time and effort by automatically transforming data into standardized formats. BioMart also can apply powerful filters to the data set and has options to customize queries. Without BioMart, researchers would have to manually gather data from multiple sources, integrate that data with other sources and develop a way to process all the combined data. To use BioMart one can follow the step-by-step guide.
By following these steps (Figure 3), you'll be able to effectively combine multiple species datasets using BioMart in Ensembl and export the combined results for further analysis.
[18]
Users are able to view translated sequences, flanking sequences, introns, exons, and untranslated regions of genes in BioMart. [19] Users are able to tailor sequences to fit their use case, like including introns and UTRs for studying homology or for creating phylogenetic trees. The table output from this process also includes start and end positions and other helpful information. See Figure 6 for the screens used in this process and the output.
When viewing genes and transcripts, users can export a sequence to FASTA format with multiple options for what to include. The user can choose to display introns, exons, coding sequences, and/or untranslated regions, among other options. [21] This is useful in conjunction with other tools that take data in the FASTA format. A user can select and control what parts of a sequence they want to export, depending on what is being studied/researched, and output in the FASTA format. This output can then be used in other tools; such as sequence alignment tools, multiple sequence alignment tools, or phylogenetic tree building software.
Written in | Java |
---|---|
Operating system | Unix-like |
Available in | English |
Type | Federated database system |
License | LGPL |
Website |
useast |
BioMart is a community-driven project to provide a single point of access to distributed research data. The BioMart project contributes open source software and data services to the international scientific community. 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 as a data management solution [1] for the Human Genome Project. [2] Since then, BioMart has grown to become a multi-institute collaboration involving various database projects on five continents. [3] [4] [5] [6]
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 [7]
BioMart is a freely available, open-source, federated database system that provides unified access to disparate, geographically distributed data sources. [8] BioMart allows databases hosted on different servers to be presented seamlessly to users, facilitating collaborative projects. BioMart contains several levels of query optimization to efficiently manage large data sets, and offers a diverse selection of graphical user interfaces 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, [9] Galaxy, [10] Cytoscape, [11] and Taverna. [12]
There are around 40 BioMart data sources including the Atlas of UTR Regulatory Activity (AURA), the COSMIC cancer database, Ensembl Genomes, HapMap, InterPro, Mouse Genome Informatics (MGI), Rfam and UniProt. Access is provided by institutions including the European Bioinformatics Institute (EBI) and the Wellcome Trust Sanger Institute in the UK, Cold Spring Harbor Laboratory and the National Center for Biotechnology Information (NCBI) in the United States and French National Centre for Scientific Research (CNRS). [13] The BioMart Central Portal was established to provide a convenient single point of access to this growing pool of data sources. [3] [5] [6]
The BioMart tool is designed to help users save time by querying data from multiple genes or variants at once. BioMart is used for returning a large amount of focused data at once, being useful for Data mining, although it is recommended to limit queries to fewer than 500 inputs at a time. [14] Oftentimes, bioinformatics researchers need to perform many queries at once from multiple data sources. By using BioMart, the user saves a significant amount of time compared to manually inputting their search into multiple tools. [15]
These queries can be performed through the web interface, without requiring any programming experience, or programmatically, through tools like biomaRt using the R language interface. Common uses include ID conversions, retrieval of gene locations, and downloading sequences. [14]
There are four main steps to using BioMart through Ensembl, as listed below.
The associated video, Figure 1, demonstrates an example of navigating through these steps.
BioMart has available very powerful gene ID conversion functionality. By leveraging BioMart queries users can easily and conveniently collect many different IDs and other identifiers for hundreds of genes simultaneously, saving the user a significant time when compared to other tools. [16] When making a new BioMart query, filtering based on external reference IDs can be applied. [17] With this filtering option users can input external identifiers for genes including IDs from the databases of other organizations, gene names, and more. To decide which results are displayed, users select attributes corresponding to their desired identifiers. Attributes include IDs from many Ensembl databases, IDs from external databases such as those of NCBI, as well as many other identifiers. [17] Once the desired attributes are selected, obtaining the results of the BioMart query will display the corresponding identifiers for the input gene reference IDs. [16]
Below is a video that provides a demonstration of gene ID conversion with BioMart.
The BioMart interface on Ensembl allows for the combining of multiple data sets to allow a user to see the combined results of the multiple datasets selected. This User-friendly tool simplifies complex data integration by providing a simple to use interface to query and combine data from various biological data sources. This tool saves researchers considerable time and effort by automatically transforming data into standardized formats. BioMart also can apply powerful filters to the data set and has options to customize queries. Without BioMart, researchers would have to manually gather data from multiple sources, integrate that data with other sources and develop a way to process all the combined data. To use BioMart one can follow the step-by-step guide.
By following these steps (Figure 3), you'll be able to effectively combine multiple species datasets using BioMart in Ensembl and export the combined results for further analysis.
[18]
Users are able to view translated sequences, flanking sequences, introns, exons, and untranslated regions of genes in BioMart. [19] Users are able to tailor sequences to fit their use case, like including introns and UTRs for studying homology or for creating phylogenetic trees. The table output from this process also includes start and end positions and other helpful information. See Figure 6 for the screens used in this process and the output.
When viewing genes and transcripts, users can export a sequence to FASTA format with multiple options for what to include. The user can choose to display introns, exons, coding sequences, and/or untranslated regions, among other options. [21] This is useful in conjunction with other tools that take data in the FASTA format. A user can select and control what parts of a sequence they want to export, depending on what is being studied/researched, and output in the FASTA format. This output can then be used in other tools; such as sequence alignment tools, multiple sequence alignment tools, or phylogenetic tree building software.