An InterMine model describes the classes available to the InterMine system and their relationships. The model is used to generate the database tables, the Java class files and the web application.
A model can be described using a model file. The model can be either read from one file or built up from several files using "model merging". An example of a single file model is used in the "testmine".
An InterMine datamine is built from sources. Each source can contribute to the data model and also provides data. When a mine is built with the
./gradlew builddb command, the model is created from small "additions" file contributed by each source. Specifically, the model is created by reading the
project.xml file and merging the model fragment from each addition file for each source.
Other additions files (i.e. not from sources) can be explicitly merged by setting the
extra.model.paths.end properties in the
project.properties of your
dbmodel directory. An example from FlyMine's
so_additions.xml will be merged first and
'chado-db-stock_additions.xml will be merged after all other model fragments.
Note that bio-model's
core.xml model fragment is always used as a base for the merging - everything will be merge into the classes in
From the uniprot source (
Final, merged, model definition:
The resulting class has all attributes of the
core.xml and from
uniprot_additions.xml. Note that in uniprot we don't need to declare a base class for
Protein (like as
extends="BioEntity") as the base class from
core.xml is merged into the final class.
Previously the data model was merged from all data sources' additions XML file (plus the SO terms, core and genomic additions). This is no longer true. Since each source is in its own JAR now, the data model is self-contained for each data source. Therefore, if you reference a class in your data parser, it must be present in the additions file.
Alternatively, you can specify a single data model file that will be merged into each source:
This setting will merge the specified additions file, e.g.
MY-MINE_additions.xml, into the data model for everyone of your mine's data sources.