In Release 22.0 we have updated data from FlyBase to release FB2009_10 and updated several data sets to their most recent versions. In addition we have added GO annotation for protein domains from InterPro and a microRNA widget to list analysis pages which shows enrichment of microRNAs targetting the genes in a list. Please see the data section of FlyMine for more details.
- NEW – GO annotation for protein domains (from interpro)
- NEW: microRNA widget on list analysis pages, showing enrichment of microRNAs targetting the genes in a list.
In Release 21.0 we have updated data from FlyBase to release FB2009_09 and updated several data sets to their most recent versions. Please see the data section of FlyMine for more details.
- NEW – Curated pathways from FlyReactome
- FIX: Template query name and description no longer disappear when paging through results.
- NEW: We’ve added an option to download data in compressed format.
- FIX: Lines of text don’t wrap in the middle of words on results pages.
- FIX: Attribute types are consistently displayed in the QueryBuilder.
- NEW: Added a display option on widgets to view all widget data in a separate table.
- NEW: Added an option to select dataset (KEGG or Reactome) on pathway enrichment widget.
- NEW: Added a description to widget queries.
- NEW: Added a widget displaying the predicted binding sites (from the Tiffin data) enriched in the upstream intergenic region of genes in the list.
In Release 20.0 we have updated data from FlyBase to release FB2009_08 and updated several data sets to their most recent versions. Also we have added pathways from Reactome for fly, yeast and worm. We’ve added a pathway enrichment widget to each gene list analysis page. Please see the pathways section of FlyMine for more details. In addition, we have added new data for CDNA clones and fixed a few minor bugs in the webapp.
In Release 19.0 we have updated data from FlyBase to release FB2009_07 and many other data sources have been updated to the latest versions. In particular, experimentally determined protein structures for D. melanogaster from PDB have been updated, adding a further 39 known structures.
Good News – FlyMine is now funded by the NHGRI and so will continue to be updated and developed until at least 2011. Please continue to give us your ideas and feedback.
FlyMine 18.1 contains no new data but fixes several issues with advanced QueryBuilder features and rare export problems. All other functionality remains the same.
The technical details:
- The Query Overview in the top right pane is now more consistently ordered.
- Constraint Logic: queries with multiple sets of OR constraints now work correctly, subsequent OR constraints were being ignored.
- Constraint Logic: removing constraints no longer resets all operations from OR to AND, and no longer removes brackets.
- ‘loop queries’ and outer joins now work correctly together, loop constraints are not permitted across outer joins.
- New constraints added to the query always default to inner joins.
- Paths are no longer added to the Query Overview when you cancel adding a constraint
- Fixed a bug where export failed in some cases with complex queries.
- Exported column headings now use the description if this has been specified in a Template Query – to match the results table behaviour.
- The column description for the root node is no longer lost when exporting.
- Rows are no longer duplicated when exporting a query with multiple outer joined collections that each contain only one row.
- Removing the column the original query was sorted by no longer gives an error when exporting.
In Release 18.0 we have updated data from FlyBase to release FB2009_06 and many sources are updated to the latest versions.
Data from FlyBase is updated to the FB2009_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 – Added orthologues from TreeFam
- FIX – Fixed bug that caused some genes and protein domains to lose their names.
- UPDATE – Added a goterm.parents collection to make querying easier.
- UPDATE – Orthologues between the 12 Drosophila species now come directly from FlyBase rather than the orginal Clark-Eisen analysis (PMID: 17994087).
- FIX – Favourite star on my mine page for templates
- NEW – Added sign up for mailing list when creating account
- FIX – Several QueryBuilder bugs, regarding a combination of loop queries and outer joins
- UPDATE – The order of the QueryBuilder summary no longer changes when join styles change. We’ve implemented a better way of ordering paths:
- that ignores the difference between inner and outer joins
- the puts attributes before references and collections
- orders alphabetically within attributes/refs/collections