Release 0.93

Web interface

• New hints system displaying short help text at the top of pages. Hints are included by default but you can easily add your own, see Hints.
• Configuration errors in webconfig-model.xml are logged instead of throwing exception on deployment.
• The QueryBuilder now uses inner joins as the default when adding new fields to the view list
• Fixes to help text in the QueryBuilder
• Display informative error message if the superuser in the database doesn't match the superuser in the properties file.
• Removed the option to filter lists by tag on the template form, this made the interface clumsy and wasn't very useful
• Enrichment widgets - fixed rounding error, adding link to documentation on each widget.
• Use better MIME types for GFF3 and FASTA export - previously export links opened in a browser window for many users
  • now uses text/tab-separated-values for GFF3 and chemical/x-fasta for FASTA.
• Fix bug that allowed lists to be saved with empty names if only whitespace characters were entered
• Fixed bad interaction with saved list names and anti-spam JavaScript for the contact form.
• Link outs can post identifiers as multipart/form encrypted data, required for Reactome skypainter
• Option to include a link to the contact form just below the header ...

Bio/sources

new

See BioSources for details on how to add these sources to your mine.

• KEGG homologues
• Miranda - mirBase targets from the Sanger Institute.

updated

• UniProt converter
  • Improved memory management so converter can load larger files and works faster.
  • Restored the option to load the whole UniProt XML files.
• BioGRID
  • If organisms are specified in project.xml, process interactions with ONLY those organisms.
  • If organism is not specified in project.xml, process all files in data directory.
• OrthologueEvidence now has an evidence code and a publication collection.
• BioPAX
  • Doesn't throw an exception if a bad file names is found.
  • Synonyms now merging correctly.

Performance

• Fixes for several bugs that were causing slow export of very large data sets, export should now create temporary precomputed tables correctly to stage the data to be exported. Speed of export should be significantly improved.
• Better JavaScript and reduced HTML markup have made the list analysis page a bit faster to load.

Web services

• Embedded templates now use custom column descriptions as column headers if they have been configured.
• Option to fetch the release version of a Mine from the web service...

Web properties config

• OrthologueConverter? - Add links to other intermines to list analysis pages. See OrthologueConverter? for details.
• Meta tag properties can now be configured in web.properties. See WebProperties for more information. Example configuration:

  # in web.properties, populates meta tags 
  meta.keywords = microarray, bioinformatics, drosophila, genomics 
  meta.description = Integrated queryable database for Drosophila and Anopheles genomics 
  

• Mines can now link to Reactome's SkyPainter, an example entry from WebProperties:

  attributelink.reactomeListProt.Protein.7227.primaryIdentifier.list.url=http://www.reactome.org/cgi-bin/skypainter2?QUERY=<<attributeValue>>&SUBMIT=1&DB=gk_current
  attributelink.reactomeListProt.Protein.7227.primaryIdentifier.list.text=Reactome
  attributelink.reactomeListProt.Protein.7227.primaryIdentifier.list.usePost=true
  attributelink.reactomeListProt.Protein.7227.primaryIdentifier.list.enctype=multipart/form-data
  attributelink.reactomeListProt.Protein.7227.primaryIdentifier.list.delimiter=NEWLINE