September, 2008

Release notes — No Comments
15
Sep 08

Release 15.0

In Release 15.0 we have updated data from FlyBase to release FB2008_08 and many sources are updated to the latest versions.

Data

Data from FlyBase is updated to the FB2008_08 release and many other sources have been updated to the latest versions, specific changes are detailed below. For a complete list of all data included in FlyMine see the ‘Data’ tab above.

  • NEW – FlyMine now loads all types interactions from the BioGRID for D. melanogaster, C. elegans and S. cerevisiae. Currently, no distinction is made between protein and genetic interactions. All of them (the ones from IntAct as well as the ones from the BioGRID) are now called ‘Interaction’. The Interaction Term allows to search for a particular interaction, eg phenotypic enhancement, two hybrid.
  • NEW – Affymetrix Probesets from the GeneChip D. melanogaster Genome 1.0 and 2.0 Arrays now have locations and mapped genes, obtained from the Ensembl database. FlyMine only loads probesets that match to at least one gene. More information on the Ensembl probeset mappings, can be found at Ensembl help
  • NEW – Loaded all aberrations from FlyBase including Drosdel deletions and they are now called ChromosomeStructureVariation. Each feature type is represented by a seperate sub-class: ChromosomalDeletion, ChromosomalDuplication, ChromosomalInversion, and ChromosomalTranslocation.
  • FIXED – The Ensembl id is correctly set for human genes.
  • NEW – Gene.flybaseFeatureType has been renamed to Gene.featureType.
  • FIXED – all MRNAs now have Translations.
  • FIXED – UTRs now have chromosome locations and appear in GBrowse.

Export

In this release, we’ve extended and improved the export system. We’ve optomised and configured the export process which has resulted in marked speed improvements. Also, we’ve added new functionality.

User interface

  • NEW – you can now have a dash in a list name
  • NEW – links on the allele list page directly to FlyBase
  • NEW – links on the allele list page to convert list to genes
  • FIXED – improved error handling throughout the site, including the QueryBuilder, template and query import pages
  • FIXED – the quick search now handles special characters correctly so you can search for any identifier, eg.
  • FIXED – selected records in your list stay highlighted even if you navigate away and then back to the list analysis page
  • FIXED – template form handles wildcards correctly
News — No Comments
8
Sep 08

Future of FlyMine

Dear FlyMine users,
We regret to announce that FlyMine will only be updated until December 2008/ January 2009. After that the final version will be kept live for as many years as it is still significantly used. Condolences would be appreciated and can be sent to support@flymine.org!
There are a couple of reasons for this change. Currently there is a great opportunity to develop a medically-focussed database using the InterMine system developed during the FlyMine project: we plan to generate a resource valuable to the broader biomedical research community and for which there will be little overlap with other resources worldwide. In addition, our most recent funding reviewers expressed concern at perceived overlap with FlyBase, leading us to re-evaluate where we could most effectively contribute.
Fortunately, FlyBase is keen to cover the loss of functionality provided to the Drosophila community either by adopting InterMine or by developing similar functionality themselves. In order to assess priorities for users we will be carrying out a survey jointly with FlyBase and encourage you to take part.
Drosophila data will still be available through the InterMine platform as part of the modENCODE project. In addition, the NIH is reviewing an application to incorporate InterMine functionality as part of the yeast (SGD), rat (RGD) and zebrafish (ZFIN) model organism databases.
During the FlyMine project our group developed the open source InterMine system, which is software used to create data warehouses with a flexible web interface. InterMine reduces the effort needed to build and maintain both small and large-scale data warehouses, while providing flexible querying, powerful operations on lists and integrated analysis tools.
InterMine has become a successful project in its own right and is being adopted by a growing number of groups for their own database projects. It has made real progress in enabling the creation of integrated databases and providing biologists with advanced functionality, and we will continue its development. We thank all users of FlyMine for contributing to this success by providing feedback and suggestions.
The FlyMine/ InterMine Team