Release 13.0

In Release 13.0 we have improved integration of data with old Drosophila gene identifiers from several sources, this information is now applied to a current FlyBase gene where possible. We have also added allele and phenotype information from FlyBase and miRNA target predictions from miRBase. Data from FlyBase is updated to the FB2008_05 release and other sources have been updated to the latest version. User interface improvements focus on uploading and saving lists. We have also launched a RESTful web service allowing queries to be run from scripts and remote sites.

Data integration

In this release we have made a major effort to update old identifiers for Drosophila genes that are provided by many data sources to match a current FlyBase identifier. We have done this with a synonym lookup, for example when we download data from a particular source that references gene CG12802 which is no longer a current gene identifier but is a synonym (an old identifier) for FBgn0250818. Where an old identifier did not match a single gene we did not load data for it. As a result we have improved data integration, you should see more data attached to current genes and no longer see old genes with data from only one source.

Data

We have added Drosophila allele and phenotype data from FlyBase and miRNA target predictions from miRBase. Data from FlyBase is updated to the FB2008_05 release and many other sources have been updated to the latest versions, new data are detailed below. For a complete list of all data included in FlyMine see the ‘Data’ tab above.

  • NEW - Drosophila melanogaster allele and phenoytype data from FlyBase.
  • NEW - Drosophila melanogaster predicted miRNA targets from miRBase.
  • UPDATE – three new RNAi screens added from DRSC.

Saving lists

We have enhanced creation of lists from results tables and fixed some selection issues.

  • NEW – a ‘Selection’ bar below the results table tracks objects that have been selected.
  • NEW – where the same object appears on multiple rows, selecting it once will select all rows even if on different pages.
  • FIX – performance of list creation from results improved.
  • FIX – selecting individual objects from multiple pages now works correctly.
  • FIX – selecting a whole column then de-selecting some rows now works as expected.

Web Services

We have begun to introduce RESTful web services to enable access to FlyMine data from scripts and other web sites. We are working on adding client APIs and further features.

  • It is now possible to run an XML query via a simple URL and get results as XML, or tab separated formats. See documentation for more.
  • All public template queries can be executed for any values and HTML results embedded in a remote web page. So if you run a web site presenting Drosophila data you can fetch results live from FlyMine to view alongside your own. Please contact us if you any questions about this. See documentation for more.

List upload

  • NEW – organism name is now displayed for issues on list confirmation page.
  • FIX – fixed problems uploading from a file on some versions of Safari.
  • FIX – improved performance and fixed unresponsive script errors when clicking ‘Add all’ with very large numbers (hundreds) of issues on upload confirmation page.
  • FIX – improved error messages for incorrect file names typed into file upload box.
  • FIX – improved disabling of paste/browse options on list upload page.

User interface

  • NEW – the List Analysis page menu bar has a ‘Find’ option to search for a particular identifier in the list.
  • NEW – the Lists tab now has a ‘Copy’ option. Select a list and type a new name to create a copy, or select multiple lists and they will be named automaticaly. You can copy public lists as well your own lists.
  • NEW – option to show/hide descriptions in the Template and List tabs.
  • NEW – widgets on List Analysis pages now show a count of objects that have no data for the widget.
  • FIX – linking to FlyBase with a list of genes from the List Analysis page now works with large lists.
  • NEW – link to FlyExpress with a list of genes from List Analsyis page.
  • NEW – added links to external databases in enrichment widgets.
  • NEW – link to BDGP in situ data from gene report pages.
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