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.
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
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 right-hand panel
- Better support in backwards compatibility to handle linkouturl and default filter displayname
- Bug fixes
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
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
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)
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.
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.