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Biomart–Biological Queries Made Easy Damian Smedley, Syed Haider, Benoit Ballester, Richard Holland, Darin London, Gudmundur Thorisson, Arek Kasprzyk

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Biomart–Biological Queries Made Easy Damian Smedley, Syed Haider, Benoit Ballester, Richard Holland, Darin London, Gudmundur Thorisson, Arek Kasprzyk BioMart–biological queries made easy Damian Smedley, Syed Haider, Benoit Ballester, Richard Holland, Darin London, Gudmundur Thorisson, Arek Kasprzyk To cite this version: Damian Smedley, Syed Haider, Benoit Ballester, Richard Holland, Darin London, et al.. BioMart– biological queries made easy. BMC Genomics, BioMed Central, 2009, 10 (1), pp.22. 10.1186/1471- 2164-10-22. hal-01615162 HAL Id: hal-01615162 https://hal-amu.archives-ouvertes.fr/hal-01615162 Submitted on 19 Dec 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License BMC Genomics BioMed Central Software Open Access BioMart – biological queries made easy Damian Smedley1, Syed Haider1, Benoit Ballester1, Richard Holland1, Darin London2, Gudmundur Thorisson3 and Arek Kasprzyk*4 Address: 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 and 4Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800 Toronto, Ontario, M5G 0A3, Canada Email: Damian Smedley - [email protected]; Syed Haider - [email protected]; Benoit Ballester - [email protected]; Richard Holland - [email protected]; Darin London - [email protected]; Gudmundur Thorisson - [email protected]; Arek Kasprzyk* - [email protected] * Corresponding author Published: 14 January 2009 Received: 22 September 2008 Accepted: 14 January 2009 BMC Genomics 2009, 10:22 doi:10.1186/1471-2164-10-22 This article is available from: http://www.biomedcentral.com/1471-2164/10/22 © 2009 Smedley et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Biologists need to perform complex queries, often across a variety of databases. Typically, each data resource provides an advanced query interface, each of which must be learnt by the biologist before they can begin to query them. Frequently, more than one data source is required and for high-throughput analysis, cutting and pasting results between websites is certainly very time consuming. Therefore, many groups rely on local bioinformatics support to process queries by accessing the resource's programmatic interfaces if they exist. This is not an efficient solution in terms of cost and time. Instead, it would be better if the biologist only had to learn one generic interface. BioMart provides such a solution. Results: BioMart enables scientists to perform advanced querying of biological data sources through a single web interface. The power of the system comes from integrated querying of data sources regardless of their geographical locations. Once these queries have been defined, they may be automated with its "scripting at the click of a button" functionality. BioMart's capabilities are extended by integration with several widely used software packages such as BioConductor, DAS, Galaxy, Cytoscape, Taverna. In this paper, we describe all aspects of BioMart from a user's perspective and demonstrate how it can be used to solve real biological use cases such as SNP selection for candidate gene screening or annotation of microarray results. Conclusion: BioMart is an easy to use, generic and scalable system and therefore, has become an integral part of large data resources including Ensembl, UniProt, HapMap, Wormbase, Gramene, Dictybase, PRIDE, MSD and Reactome. BioMart is freely accessible to use at http:// www.biomart.org. Background to test and drive their research hypotheses. Typically, each In this post-genomics era, data of increasing volume and data source provides an advanced query interface on their complexity is being deposited into databases around the website to satisfy this requirement. However, each site has world. Biologists need to ask complex queries of this data its own solution and subsequently, the user has a learning Page 1 of 12 (page number not for citation purposes) BMC Genomics 2009, 10:22 http://www.biomedcentral.com/1471-2164/10/22 curve before they can start interacting with the data. A fur- tools and cross platform compatibility. These include ther problem the researcher has is that they often need to model organism databases such as Gramene [11], Dicty- query more than one data source, necessitating mastering base [12], Wormbase [13] and RGD (Rat Genome Data- more than one interface and having to cut and paste base) [14] as well as HapMap variation [15], pancreatic results between the sites. If the analysis involves high- expression database [16], Reactome pathways [17] and throughput data, this approach is not usually scalable. To PRIDE proteomic [18] databases (see Table 1 for the full overcome this problem, many groups rely on bioinforma- list). A wide variety of analyses and tasks are possible from ticians who can generate scripts to interact with the vary- the publicly available BioMarts, ranging from SNP (single ing programmatic interfaces of the different data sources. nucleotide polymorphism) selection for candidate gene They also often have to learn a number of different web screening, microarray annotation, cross-species analysis, services or application programmatic interfaces (APIs) for through to recovery of disease links, sequence variations each resource. A preferable solution would be to have and expression patterns. generic software that a biologist can use on top of any data source. BioMart[1] is such a solution. The range of interfaces is designed with both biologists and bioinformaticians in mind. The simplest way of que- BioMart is an open source data management system that rying BioMart is via the web interface called MartView comes with a range of query interfaces that allow users to (either on our central portal [2] or follow the links on our group and refine data based upon many different criteria. main page [1] to the individual sites). Programmatic In addition, the software features a built-in query opti- access is available via a Perl API or BioMart's web services miser for fast data retrieval. A BioMart installation can (MartServices). An important and novel feature of provide domain-specific querying of a single data source BioMart is that it offers "scripting at the click of a button". or function as a one-stop shop (web portal) to a wide A user can generate an API or MartServices script by build- range of BioMarts as our central portal [2] does. All ing up a query on the MartView website followed by a BioMart websites have the same look and feel (only vary- simple click of a button. All the interfaces allow the user ing in colour scheme and branding), which has obvious to build up biological queries by first selecting dataset(s) advantages to users moving between different resources. of interest, then the data to view and/or save (attributes), However, the power of the system comes from integrated some optional restrictions (filters) on the query and querying of the different BioMarts. If any datasets share finally the format for the data. common identifiers (such as Ensembl gene IDs or Uni- prot IDs) or even mappings to a common genome assem- Implementation bly, these can be used to link BioMarts together in Here we will describe a top-level view of the BioMart sys- integrated queries. Additionally, these datasets do not tem as the focus of this paper is on practical use of have to be located on the same server or even at the same BioMart rather than implementation and deployment. geographical location. This distributed solution has many Further documentation on these aspects can be found on advantages; not least of which is the fact that each site can the BioMart website http://www.biomart.org. BioMart is utilise their own domain expertise to deploy their designed around a simple, three tier architecture: BioMart. (i) The first tier consists of one or more relational data- BioMart also has the advantage of being integrated with bases. Each database may consist of one or more "marts", external software packages such as BioConductor [3], the which are schema compliant with BioMart definitions. Distributed Annotation System (DAS) [4], Galaxy [5], Each "mart" may hold a number of different datasets. The Cytoscape [6], Taverna [7]. This enables users to perform BioMart data model is a denormalised, query optimised integrated queries with non-BioMart data sources as well schema and can be deployed using Oracle, MySQL or as detailed analysis of the results. BioMart is also part of Postgres relational database management systems. Each the GMOD (Generic Model Organism Database) [8] suite dataset uses a reversed star model [10] where data map- of tools for building a model organism site. ping 1:1 with the central object being modelled is stored in a main table. Data mapping 1:n is stored in one or Originally developed for the Ensembl genome browser [9] more satellite, dimension tables. Two tools are provided as the EnsMart data warehouse [10], BioMart has now to build and configure the mart databases in the first tier: become a fully generic data integration solution. Although applicable to any type of data, BioMart is partic- • MartBuilder, to construct SQL statements that will trans- ularly suited for advanced searching of the complex form your schema into a mart.
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