What can InterMine Do?

The document explains what functionality you can expect from InterMine.

InterMine boasts a sophisticated, robust object-modeling system that allows for the modelling of complex biological phenomena. You can build and run complex queries accessing a database containing millions of objects.

Data Warehouse

  • Comprehensive build system allowing for the integration of data sets of varying size, complexity and quality.
  • Configurable, priority based integration - pick and choose which data you import.
  • Thoroughly optimised processes for greater speed and reliability.
  • Import biological data - InterMine comes equipped with data integration modules which load data from common biological formats
    • GFF3
    • FASTA
    • GO
    • UniProt
    • Psi
    • Chado
    • many more ...
  • Import your data - configure the model to add your own data
    • Add to the data model by editing an XML file
    • Everything else is auto-generated
  • Import anyone's data - import data from multiple sources
    • Configurable, priority based data integration system
    • FlyMine, which uses InterMine software, collects data from almost 50 sources.
  • Build system can be configured to make intermittent data dumps, saving time and effort.
  • Post-processing tasks can be run to manipulate the data after all data has been imported - calculating chromosome lengths, for example.

See: TechnicalOverview, IntegratingData

Web Interface

  • InterMine's web interface works 'out of the box', no programming is necessary.
  • Easily customise the webapp
    • You can customise display and functionality via the webapp or configuration files.
    • Configuration is easy and many items can be edited via the web interface.
      • Create and publish template queries
      • Add information to report pages
      • Control layout with tagging
    • Add tools by updating configuration files
      • Graphs
      • Widgets
      • GBrowse
      • External links
      • Data Categories
  • Intuitive user interface
    • QueryBuilder
      • Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources.
    • Lists
      • Upload data to create lists
      • Create lists from query results
      • Use lists in queries
      • Analyse lists using graphs and statistics
      • Operate on lists - union, intersect, and subtract
    • Saved user data
      • User data, such as lists and queries, are saved across sessions
      • Mark templates and lists of interest as a 'favourite'
    • QuickSearch
      • Allows users to browse the data available for any particular item in the database and, from there, to explore related items
      • Sophisticated filter technology on the templates and lists pages
    • Import/Export data
      • export and import queries, templates and lists
      • export results in several formats:
        • comma separated values (suitable for import into Excel)
        • tab separated values
        • Excel format
        • cytoscape SIF format
        • GFF3 format
        • FASTA format

See: FlyMine's tour for a detailed description of the interface.