Reference Documents

The following documents describe technical aspects of the InterMine system. Many are references for particular APIs or file formats. For an introduction to the InterMine architecture see - TechnicalOverview.

Data loading and integration

• PrimaryKeys - reference for specifying and using primary keys
• PriorityConfig - configuration of data priorities between sources
• ModelDescription - formal description of the Model XML format
• Items XML format - formal description of the Items (data) XML format
• Items Java API - manipulating Items (data) in Java
• Perl API - manipulating Items (data) in Perl

ObjectStore

• ORMappingTool - about the ObjectStore object/relational mapping
• SimpleObjects - store simple data faster and use less disk space
• QueryPackage - how to query an ObjectStore
• IQL - syntax for OQL-like query language
• IQLExamples - some examples using IQL
• ResultsTuning - setting parameters for the query Results object
• OSInterMineCancellation - cancelling ObjectStore queries

The Model

• Model creation / model merging - how a data model is created for a mine

Build system

• DataIntegration - how the compilation and build system works
• AntTargets - a list of useful ant targets

SQL query optimiser

• Using the SQL query optimiser in other projects
• Implementation of the Optimiser cache

Technical Articles

• ResultsPrefetching - how the results pre-fetch system works
• FetchingRelatedObjects - fetching related objects in the Results object
  • solving the N + 1 reads problem
• ExplainPlans - SQL EXPLAIN plans in InterMine queries
• SafeObjectStore - safe implementation: Characteristics