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
In Release 17.0 we have updated data from FlyBase to release FB2009_05 and many sources are updated to the latest versions.
Data from FlyBase is updated to the FB2009_05 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 natural_transposable_element features from FlyBase chado.
- FIX – Fixed bug that caused some proteins from FlyBase not to be loaded.
- UPDATE – Create synonyms for FlyBase proteins discarded because they have an identical sequence to a protein already stored in the database.
- UPDATE – Added seven new FlyAtlas tissues.
- FIX – Added datasets and long names to FlyBase interactions.
- FIX – Added datasets to protein domains from InterPro.
- FIX – Fixed bug that prevented the loading of self-self interactions from IntAct and BioGRID.
- UPDATE – Added symbol to identifiers to show in HTML title, eg changed ‘Report page: FBgn0000606’ to ‘Gene report for eve (FBgn0000606)’
- NEW – Added link from list analysis and report pages to modMine.
- FIX – Improved performance of templates page in MyMine.
- FIX – Fixed bug encountered when trying to access the list web services.
- UPDATE – Changed the orientation of the FlyAtlas widget to increase readability.
- UPDATE – Improved error messages generated by the web services.
- UPDATE – Improved messages given when arriving to FlyMine from another website.
- FIX – Fixed link to QueryBuilder on home page.
- UPDATE – GOTerm now autocompletes in the QueryBuilder.
- FIX – Fixed bug in bulk download query for Anopheles homologues.
In Release 16.0 we have updated data from FlyBase to release FB2009_04 and many sources are updated to the latest versions, the way we include proteins has been redesigned so that all isoforms from UniProt are loaded. We have introduced a significant new feature to querying (‘outer joins’) and improved general query and export performance.
Data from FlyBase is updated to the FB2009_04 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.
- UPDATE – We now include all isoforms of proteins from UniProt.
- UPDATE – Gene Ontology (GO) data assigned to genes has been re-modelled to now include relationship types between terms. Genes no longer have an allGoAnnotation collection to model transitive closure of the ontology, instead use the GoAnnotation.relations.parents collection.
- NEW – We now load deficiencies/deletions and aberrations from FlyBase
- FIX – TransposableElementInsertionSite features now have orientations, these are displayed in GBrowse.
- FIX – Rat genes now have synonyms, organisms and datasets correctly attached
- FIX – Drosophila mRNA now have synonyms and datasets correctly attached
- FIX – ESTs now have locations
- FIX – Dmel proteins from UniProt are correctly attached to genes.
- FIX – All genes and proteins now have a datasource.
- UPDATE – Cytological location data now available
- UPDATE – Proteins and transcripts are now linked
- NEW – Predicted miRNA targets
- NEW – Drosophila development ontology
- NEW – Synonyms now have datasets, so you can tell who is using which identifier.
- UPDATE – Anopheles proteins now loaded for correct strain.
- UPDATE -Â Apis mellifera genome removed.
In a major update to the query system it is now possible to choose whether columns include information that must be present to produce a row in the results or should just be shown if a value is present. This is best illustrated with an example. Consider an organism that has a thousand genes but only 900 are known to code for a protein. In FlyMine there would be 1000 genes and 900 of them would be related to a protein. You can now query for genes and related proteins in two ways:
- ‘inner join’ – You create a query with two columns, the first for the gene identifier, the second with the protein identifier. Only 900 rows are return, those that don’t have a protein aren’t included. This is how all queries worked before this release.
- ‘outer join’ – You create the same query but specify the gene to protein relationship as an ‘outer join’. This will return all 1000 genes in the first column and have empty cells in the second column for the 100 genes that don’t have a protein.
Organise your lists
You can now apply aritrary tags to your saved lists both on the list analysis page and in MyMine. Tags can be any label you like to help you categorise your saved information, one list can have multiple tags applied. You can filter lists by tag from the Lists view page.
Improvements to the internals of InterMine have made exporting large datasets significantly faster – you should find download speeds around an order of magnitude better.
- NEW – web service API is available.
- FIX – Creating a list after converting between orthologues now works.
- NEW – link to ArrayExpress atlas is available on certain report pages.
- NEW – link to FlyBase appears on list analysis pages for alleles and insertions.
- FIX – Foreign characters display properly
- FIX – Chromosome distribution widget now excludes rubbish chromosomes from its calculations.
- FIX – 404 error page improved.
- FIX – List information on the report page is now at the top, for increased visibility
- FIX – Export display issues fixed for Internet Explorer.
- FIX – Fixed some slow algorithms displaying results data.
- FIX – Fixed error in “Add Column” function where there are no extra columns to add.
- FIX – Fixed “View all” button on Sequence residues.
- UPDATE – Export now has column headings at the top.
- FIX – Performance of widget queries improved.
- FIX – Wildcards in queries are exported correctly.
- UPDATE – Collection sizes are updated using AJAX on report pages.
- UPDATE – UTRs now present in GBrowse