News

For all our latest news and updates view our timeline below

2017

Congratulations to Pfizer group on their latest publication in Nature Methods

January 4th 2016

We would like to congratulate Pfizer group on their latest publication in Nature Methods entitled "OASIS: web-based platform for exploring cancer multi-omics data"

You can read the publication online using the link below:

OASIS: web-based platform for exploring cancer multi-omics data

2016

Hosting Migration

December 10th 2015

We are currently in the process of migrating hosting, during which time the BioMart community portal will be temporarily unavailable.

However, you can still access BioMart services at any of the BioMart community servers. The list of those servers can be found on the

community page

The link to the server can be found under 'Database' heading. For example, if you are interested in using the latest Ensembl release through BioMart web interface simply click on 'Ensembl' and the link will take you to http://www.ensembl.org/biomart/martview. If you are a user of biomaRt (a part of the Bioconductor library) change the host from 'www.biomart.org' to 'www.ensembl.org'. Similar procedure can be used for all the other community servers.

We apologise for any inconvenience caused.

BioMart community portal temporarily unavailable

November 9th 2015

The BioMart community portal is temporarily unavailable while we look for new hosting options. If this is something you feel you would like to help with then please email arek.kasprzyk@gmail.com

However, in the meantime, you can still access BioMart services at any of the BioMart community servers. The list of those servers can be found on the

community page

The link to the server can be found under 'Database' heading. For example, if you are interested in using the latest Ensembl release through BioMart web interface simply click on 'Ensembl' and the link will take you to http://www.ensembl.org/biomart/martview. If you are a user of biomaRt (a part of the Bioconductor library) change the host from 'www.biomart.org' to 'www.ensembl.org'. Similar procedure can be used for all the other community servers.

We apologise for any inconvenience caused.

Latest updates to BioMart Portals 0.9 and 0.7

October 28th 2015

The BioMart Portals have been updated with the latest version of the following databases:

  • Ensembl
  • Ensembl Genomes
  • Uniprot
  • VectorBase
  • Vega

Latest updates to BioMart Portals 0.9 and 0.7

August 07th 2015

The BioMart Portals have been updated with the latest version of the following databases:

  • Ensembl
  • Ensembl Genomes
  • Uniprot
  • WormBase Parasite
  • VectorBase

Latest updates to BioMart Portals 0.9 and 0.7

June 11th 2015

The BioMart Portals have been updated with the latest version of the following databases:

  • ensembl
  • vega
  • vectorbase
  • uniprot
  • pompeu fabra university regulatory genomics datasets

We would like to welcome three new community members

April 22nd 2015

  • Fantom 5

    RIKEN Center for Life Science Technologies (CLST), Japan.

    The FANTOM5 project mapped a promoter level expression atlas in human and mouse. The FANTOM5 BioMart instance provides the set of promoters along with annotation.

  • Dapper

    Department of Genetics, University of Cambridge, Cambridge, UK

    Mass spec identified protein interaction networks in Drosophila cell cycle regulation

  • WormBase ParaSite

    EBI UK

    Parasitic worms (helminths) are responsible for more than a billion human infections globally and have a devastating impact on livestock and agriculture.

Latest updates to BioMart Portals 0.9 and 0.7

April 12th 2015

The BioMart Portals have been updated with the latest version of the following databases:

  • dapper
  • ensembl
  • ensembl genomes
  • fantom
  • vector base
  • vega
  • worm parasite

Latest updates to BioMart Portals 0.9 and 0.7

January 29th 2015

The BioMart Portals have been updated with the latest version of the following databases:

  • ensembl
  • ensembl genomes
  • urgi
  • uniprot
  • vega
2015

Latest updates to BioMart Portals 0.9 and 0.7

October 30th 2014

The BioMart Portals have been updated with the latest version of the following databases:

  • ensembl
  • ensembl genomes
  • uniprot

Latest updates to BioMart Portals 0.9 and 0.7

July 3rd 2014

The BioMart Portals have been updated with the latest version of the following databases:

  • urgi
  • vectorbase
  • phytozome
  • uniprot
  • ensembl genomes

BioMart release v0.9 and our new website

May 20th 2014

The latest version of BioMart includes support for data analysis and visualisation tools. The first of the BioMart tools has already been implemented and is accessible from

www.biomart.org

This tool enables enrichment analysis of genes in all Ensembl species and a broad range of gene identifiers for each species are also available. Furthermore, the tool supports cross-species analysis using Ensembl homology data. Finally, the enrichment tool facilitates analysis of BED files containing genomic features such as Copy Number Variations (CNVs) or Differentially Methylated Regions (DMRs).

The latest BioMart release comes with the new version of the REST and SOAP APIs. These APIs are available for testing at central.biomart.org. Third party developers who are currently using REST or SOAP version 0.7 are encouraged to start testing and transitioning to 0.9. The two servers providing access to BioMart data through REST and SOAP (version 0.7 and version 0.9) will be running in parallel to provide support for easy transition. The Enrichment tool is also accessible programmatically through 0.9 REST/SOAP interface.

Finally, the BioMart website has been completely redesigned to cater for a better user experience. The re-organised layout, incorporation of new functionality, such as the "quick tool access" and the use of subtle animation makes for clearer navigation and greater site interactivity.

Latest version of Ensembl and VectorBase now available

March 7th 2014

You can access the new versions of Ensembl and VectorBase through the BioMart Portal

Latest version of Ensembl, Ensembl Genomes, Uniprot and Vector Base now available

February 7th 2014

You can access the new versions of Ensembl, Ensembl Genomes, Uniprot and Vector Base through the BioMart Portal

2014

Latest version of Uniprot and Ensembl Genomes now available

September 27th 2013

You can access the new versions of Uniprot and Ensembl Genomes through the BioMart Portal

Latest version of Ensembl now available

September 18th 2013

You can access the new versions of Ensembl through the BioMart Portal

We would like to welcome our newest community member - Institut Nationale de Recherche Agronomique.

August 26th 2013

Please visit our community page for more information on Institut Nationale de Recherche Agronomique (INRA).

Latest updates to Uniprot, VectorBase, COSMIC, Pancreatic Expression Database and Ensembl Genomes also available

August 26th 2013

You can access the new versions of Ensembl Genomes, Uniprot, COSMIC, Pancreatic Expression Database and Vectorbase through the BioMart Portal

New versions of Ensembl, Uniprot, Phytozome, Vectorbase, Gramene, Pancreatic Expression Database and Reactome now available

July 15th 2013

You can access the new versions of Ensembl, Uniprot, Phytozome, Vectorbase, Gramene, Pancreatic Expression Database and Reactome through the BioMart Portal

Ensembl 71, Ensembl Genomes 18, Cosmic 64, Vega 51, UniProt and ICGC Dataset Version 12 now available

June 1st 2013

You can access the new versions of Ensembl 71, Ensembl Genomes 18, Cosmic 64, Vega 51 and UniProt through the BioMart Portal

ICGC Dataset Version 12 can be accessed through the Cancer Portal:

http://dcc.icgc.org/web/

2013

Ensembl Genomes Release 16 now available

Nov 26th 2012

You can access Ensembl Genomes Release 16 through the BioMart Portal

Ensembl Release 69 database now available

Nov 26th 2012

You can access Ensembl Release 16 through the BioMart Portal

ICGC Release 10 now available through Cancer Portal

Nov 8th 2012

Release 10! New Spain CLL methylation data. 18 TCGA DBs updated & 2 new DBs. Updates to UK Breast and MDS. 432 new genomes, 7,022 in total. Click the link below for more info:

http://dcc.icgc.org/web/

Predictive Models of Gene Regulation from High-Throughput Epigenomics Data now available

Oct 11th 2012

Research in the Computational Gene Regulation group within the Research Unit on Biomedical Informatics focuses on the development of computational methods to study the mechanisms of regulation of gene expression.

This group is also part of the European network of excellence on alternative splicing EURASNET.

"Predictive Models of Gene Regulation from High-Throughput Epigenomics Data" research paper can be accessed below:

http://www.hindawi.com/journals/cfg/2012/284786/#B34

GWAS Central available through BioMart Portal

Oct 3rd 2012

GWAS Central provides a centralized compilation of summary level findings from genetic association studies, both large and small.

RhesusBase now available through BioMart Portal

Sept 16th 2012

RhesusBase is a knowledgebase developed by Peking university to facilitate the primate research community.

The database was developed on the basis of the BioMart 0.8 framework to customize and facilitate data download.

It has also recently been featured in an article in Nucleic Acid Research:

http://nar.oxfordjournals.org/content/early/2012/09/08/nar.gks835.full

ICGC release 9 available through Cancer Portal

Aug 31st 2012

12 TCGA database updated and 6 new databases, includes new data from MAGIC and PedBrain projects. Data from 3,029 new genomes, 6,590 in total.

Rfam now available through BioMart Portal

Aug 16th 2012

Rfam database of non-coding RNA families has been included into http://central.biomart.org

The Rfam BioMart may be found at:

http://xfam-biomart.sanger.ac.uk/

Additional BioMarts for other Xfam resources, such as Pfam are currently in development and will be included in due course.

Release 68 Ensembl avaiable through BioMart Portal

Jul 31st 2012

This release includes the new mouse assembly (GRCm38) as well as updated patches for the human assembly (GRCh37.p8).

We introduce the Chinese softshell turtle (Pelodiscus sinensis) as a new species and update the Dog genome to CanFam3.1.

The ground squirrel has been renamed to Ictidomys tridecemlineatus in line with recent taxonomic reassessments.

Phytozome v8.0 available through BioMart Portal

Jul 1st 2012

Version 8 includes 21 genomes assembled and/or annotated at the JGI, and 9 externally produced genomes.

Also included are early release access to the Panicum virgatum (switchgrass) genome and annotation, as well as the unannotated assembly of the Cotton D Genome.

Update genomes include Eucalyptus, Aquilegia, and the grasses maize, rice and Brachypodium. New JGI genomes include the aforementioned Panicum virgatum genome, as well as Capsella rubella,and Phaseolus vulgaris, while the external genomes Brassica rapa, flax, and apple make their first appearance in Phytozome.

2012

New BioMart Website Released

Nov 16th 2011

We are pleased to announce the release of the new BioMart website, which has been completely redesigned with improved functionality and graphics. Your feedback is welcome and appreciated.

DATABASE Special Issue Dedicated to BioMart

Nov 11th 2011

BioMart is a unique open source data federation technology that provides unified access to distributed databases storing a wide range of data. This DATABASE issue recognizes BioMart's outstanding contributions to bioinformatics and documents the achievements of the BioMart community, which has grown impressively over the last ten years to become what it is today, a collaboration between numerous database projects on five continents: Asia, Australia, Europe, North America and South America.

http://oxfordjournals-marketing.oup.com/q/1MozDkVONg1Q1p/wv

BioMart v 0.8 rc6

May 10th 2011

This release candidate offers the following features:

  • Supports rudimentary Semantic Web features: OWL-ontologies and SPARQL-queries (details in Section 11.5, "Semantic Web" in the user manual)
  • Automated command line deployment tool for ICGC nodes
  • MartConfigurator (MC) supports importing configuration (sources and/or access points) from other 0.8 portal configuration xml file
  • Improved usability in MC including list view of the access points in the left-hand panel
  • Better support in backwards compatibility to handle linkouturl and default filter displayname
  • Bug fixes

BioMart v 0.8 rc5

Mar 11th 2011

This release candidate offers the following features:

  • client APIs: Java, REST, SOAP (details in user manual section 11)
  • full plugin support including both client and server side components
  • update of materialized mart is now fully supported
  • better support for virtual mart (schema update and basic manipulations)
  • improvement of MC usability
  • user manual includes a dedicated section about ICGC deployment

BioMart v 0.8 rc4

Feb 1st 2011

This release is tested on Mac OS X (Leopard and Snow Leapord), Linux (Debian 4.1.1-21), Java 6. See docs for details.

This release candidate offers the following features:

  • Materialize for 5 database platforms (MySQL, Oracle, PgSQL, MS SQL, DB2)
  • Secure access for BioMart server to server communication
  • Third party plugins framework for GUI developers
  • Improved configuration management
2011

BioMart v 0.8 rc3

Dec 18th 2010

The 0.8 release candidate 3 is now available for deployer testing. The new BioMart version is a Java based, out-of-the-box single integrated application to facilitate mart building, configuration and web server deployment.

This release candidate offers the following features:

  • Support for 5 database platforms (MySQL, Oracle, PgSQL, MS SQL, DB2)
  • Virtual Marts (non-materialised querying against source database)
  • A range of different web interfaces from Basic Form to Advanced Querying interfaces (MartAnalysis, MartForm, MartWizard, MartExplorer) and a Report page (MartReport)
  • Backwards compatibility for BioMart 0.7 sources
  • Secure access
  • Multi-dataset linking with Link-Indices for faster and scalable joins
  • Processor framework for specialised data visualisations (e.g charts)

Features not available yet:

  • Full Mbuilder component including source schema modifications
  • Updates
  • Processors (Genomic Sequence, GFF, DAS, WSDL, Gzip, Excel)
2010

BioMart v 0.7

May 14th 2008

This release candidate offers the following features:

  • MartBuilder is now a fully featured application with enhanced layout for schema transformation. It can also run in a server/client mode making it possible to monitor the mart building process through a MartRunner component.
  • MartView layout has been improved. Programmatic access has been extended to include URL API functionality and mapping from XML queries to URL API. The long outstanding problem with MartEditor templates has been fixed.
2008

BioMart v 0.6

June 15th 2007

This release candidate offers the following features:

  • BioMart can now be used as a 1.5 DAS annotation server. The server can be configured using standard BioMart configuration tools without requiring to do any additional programming.
  • MartView comes with an improved layout and better interactivity. The response times for the results panel have been considerably improved for datasets with large configuration, and the results come with an 'unique rows' option. In addition to the existing web service XML button, MartView now features a Perl button which shows the query in Perl API format.
  • MartBuilder now allows you to execute, monitor and control your transformation SQL remotely. Improved schema diagrams provide more compact overviews, and improved dataset diagrams provide a clearer picture of the dataset structure. In addition, the user has more options for modifying created datasets and better information about them in 'explain dataset' and 'explain table' dialogs.
2007