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