Release 14.0

In Release 14.0 we have updated data from FlyBase to release FB2008_06 and many sources are updated to the latest versions. We have added an autocompletion feature for many constraints in template queries and QueryBuilder. This means that as you type, for example a GO term or protein domain name, suggested matches will be provided.

Data

Data from FlyBase is updated to the FB2008_06 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 - Drosophila genes now have a field ‘flyBaseFeatureType’ field for the gene type e.g. protein_coding, miRNA_gene.
  • NEW - D. melanogaster microRNATargets now have chromosome locations and appear in GBrowse.
  • FIX - C. elegans genes and proteins are now correctly linked to one another.
  • NEW – CRM and binding sites from REDfly now have an evidence field which contains information about the experiment.
  • FIX – More probesets from AffyMetrix are correctly mapped to genes, including those with predicted transcripts
  • NEW – A new tissue, the salivary gland, has been added to the FlyAtlas dataset.

Data integration

In this release we further improved the data integration system to update old identifiers for Drosophila genes that are provided by many data sources to match a current FlyBase identifier. We now include only current FlyBase genes that have a genome location (see 13.0 release notes for more details).

Data sources

Most data, including all genes and proteins, have been assigned a dataset. A dataset includes the source of the data, dataset name and URL, allowing you to quickly and easily find the origin of the data.

Autocompletion

Many name fields in template queries and the QueryBuilder now have type-ahead autocompletion to assist in selecting valid terms. As you start to type, possible matches are fetched from FlyMine; the text you have typed can match anywhere within the terms and multiple words can be matched. This is particularly useful for GO terms or protein domain names.

Removing list entries

It is now possible to remove entries from one of your lists. On the List Analysis page you can now select entries in the list and use the new ‘Edit’ menu to delete them from your list or add them to another existing list.

User interface

  • NEW – added linkouts for genes to BDGP in situ and for alleles to FlyBase
  • FIX – you can now access the lists and query history section of MyMine when not logged in. This allows you to delete your temporary lists.
  • FIX – GLEANR symbols are no longer low quality matches when using them to upload a list of Drosophila genes.
  • FIX – template and list search pages no longer reset the search term when using the back button.

Template web services

  • FIX – the ‘Show link with constraint values highlighted in red’ now highlights every value correctly
  • FIX – various javascript errors in Internet Explorer 6.0 have been fixed that prevented the results count from being updated.
  • NEW – results are returned with the correct file extension which makes it easier for programs to correctly open the file
  • FIX – you can now login while on the template web services page
  • FIX – template form correctly updates on error

Widgets

  • NEW – extra columns added to the widget export
  • FIX – enrichment widgets include more digits when displayed in scientific notation
  • FIX – enrichment widgets no longer overlap when displayed
  • NEW – statistical enrichment widgets now link to documentation on the method of calculation used
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