FlyMine 31.0

We are happy to announce we have a released a new version of FlyMine.  We have updated some data sets, added a few new features and fixed some bugs.

Human Readable Labels

The labels for the data in FlyMine come from the field and table names from the database.

We have updated this to use user-friendly labels instead in an effort to make the labels more human readable.

Open ID

You can now log in to FlyMine using your Gmail or Yahoo account.  Simply click on the “Log in” link and follow the intructions.

Region Search

  • Additional parameter allows users to extend regions at both sides
  • Can create lists by feature types for all results or for an individual region
  • Results show gene symbols as well as DB identifier
  • Fixed by when exporting a long list of objects to galaxy caused a “Request-URI Too Large” error
  • Now works correctly with subclasses

Web Services

  • NEW: region search The ability to search for genomic features by interval (the Regions tab of the web-app) has been exposed as a web-service resource. Region data can be converted to lists, or downloaded directly as GFF3, FASTA or BED.
  • NEW: token authentication A new authentication mechanism has been introduced which has advantages over the current system of sending username and password details. The use of tokens means that users can authenticate requests without having to send their username and password, thus minimising chances of these being compromised. Tokens can be replaced without having to change login details, or indeed disabled entirely, meaning web-service access to user data can be forbidden on a user-by-user basis. This authentication mechanism is to be preferred to the current mechanism. One important benefit is the ability to make authenticated requests (for dealing with lists for instance) from the browser.
  • NEW: Ruby client Our commitment to supporting the range of languages used by bio-informatians has been extended to Ruby, which has a growing community based around the Bio-Ruby project. The Ruby client libraries are available from [https://rubygems.org/gems/intermine rubygems.org]. For documentation please visit [http://www.intermine.org/docs/ruby-docs].
  • NEW: Exporting BED from webservice queries In addition to GFF3 and FASTA, the BED biological standard format is supported from web-service queries.
  • NEW: Column summary data The column summary data (visible when clicking on the ? icon on a results table) is now available via web-services when passing the ”’summaryPath”’ parameter to a query or template results request.
  • NEW: Code generation The ability to generate code to run queries is now available programmatically via a web-service. Please see the WebService wiki page for details.

Export

  • New export format – BED
  • Fixed bugs that caused export to fail when:
    • feature didn’t have location info
    • sequence feature was not the root class, eg. Pathways.genes
    • all columns of an outer join are removed

Report Pages

We have added new widgets to the report pages:

  • Publications displayer orders by number of genes mentioned
  • New Pathways displayer shows pathways from other Mines for orthologues of current gene
  • New RGD disease displayer shows disease ontology terms from RatMine for orthologues of current gene
  • New viewer shows interactions, GO terms etc on publication report page

Data

  • New species from OMIM: human, rat and mouse.
  • YeastMine is now live, so we have removed yeast data from FlyMine, including publication, pathways, GO and interaction data.

Network Displayer

  • Added help text for different file types
  • Large datasets are now handled correctly. If there are too many interactions (> 2000) a link to download the data is shown instead of the displayer:
    The network contains more than 2000 elements, the interaction can become sluggish in the displayer.
    Please [Download the network data] and import it to [Cytoscape desktop] and use Force-Directed Layout
    to view or [view interaction data] in a table.

Templates

  • Radio buttons stay checked when selecting/deselecting list constraint
  • Clicking on the “query >” breadcrumb to get back to the template form works correctly
  • Editing constraints for nested classes (eg. Gene > homologue > organism) doesn’t break model browser
  • In query builder, “Show results” button greyed out and not clickable anymore
  • After editing a template, if the user clicked on a template on the home page they would be directed to the previous template they had been editing.
  • Can now import template queries containing “ONE OF” constraints
  • Added option to delete trackers to the template import form. This allows superusers to export/import templates from other Mines, but save the usage information.
  • Fixed error when running a template with a bag constraint in an attribute and a lookup constraint in its parent

Miscellaneous

  • FIX – keyword search now handles booleans correctly
  • FIX – pathway widget correctly filters for KEGG pathways
  • UPDATE – widget data easier to download
  • UPDATE – list upload form has default organism selected, leading to less issues when uploading lists
  • FIX – links to other mines is cleverer, so results appear faster
  • FIX – report pages are now cached speeding up loading times
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