Version: 4.0.0

Project XML

This document describes the InterMine project XML file. This file is located in the mine directory and determines:

  • the Mine's data model
  • which data sources are loaded during a build

The project XML file has two sections:

<sources>#

The <source> elements list and configure the data sources to be loaded, each one has a type that corresponds to the name of the bio-source artifact (jar) which includes parsers to retrieve data and information on how it will be integrated. The name can be anything and can be the same as type, using a more specific name allows you to define specific integration keys. Each source also has a version. If one is not provided, the default InterMine version will be used.

<source> elements can have several properties: src.data.dir, src.data.file and src.data.includes . They are all used to define locations of files that the source should load. Different parser types accept different properties, see the two links below for the full list and example project XML entries.

<post-processing>#

Specific operations can be performed on the Mine once data is loaded, these are listed here as <post-process> elements. For details on which postprocesses are available, see Post processing

Versions#

Each data source has its own version. See Data Source Versions for details on how to version your own data sources and how to specify which versions to use.

Data model#

The data model is generated by iterating though each project listed in the project XML file and retrieving its additions.xml file. This file is then merged into the other additions files. There is also an optional "Global" additions file, see Model Merging for details.

Examples#

For an example project XML file, see Biotestmine's project.xml file.

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