Slimmer is a slim tool to slim ontologies as part of ontology integration. It allows users to provide configuration files that specify which parts of an ontology should be kept and/or removed, allowing to just select parts of the ontology you like. Rewiring the ontology is part of the features, allowing you to define new super terms.

Configuring the slimming

The configuration of the slimming of an ontology consists of two files. The first file is a Java properties file, listing the ontology, a pointer to the second configuration file, and the URI of the output ontology. Details are found at https://github.com/enanomapper/slimmer/wiki/Slimmer-configuration-files and in https://enanomapper.github.io/tutorials/Added%20ontology%20terms/README.html

For example:

owl=http://www.bioassayontology.org/bao/bao_complete.owl iris=bao.iris slimmed=http://purl.enanomapper.org/onto/external/bao-slim.owl

The second, .iris file configures the slicing of the ontology:

+D(http://purl.bioontology.org/ontology/npo#NPO_1436):http://www.bioassayontology.org/bao#BAO_0000697 detection instrument +D(http://purl.obolibrary.org/obo/IAO_0000030):http://www.bioassayontology.org/bao#BAO_0000179 endpoint +D(http://purl.obolibrary.org/obo/OBI_0000070):http://www.bioassayontology.org/bao#BAO_0000015 bioassay

This configuration file uses a custom syntax which is briefly explained here. By default it removes all content.

The first character indicates if the something needs to be included (+) or excluded from a previously defined inclusion (-). The second character indicates whether a whole upper (U) or down (D) tree should be included or excluded. After the colon the URI of the resource is given to be in- or excluded, followed by a user-oriented comment. Finally, before the colon and in brackets an optional superclass of this resource can be specified, possibly from other ontologies.

Compile

shell mvn clean compile assembly:single

Run

shell java -cp target/slimmer-1.0.0-SNAPSHOT-jar-with-dependencies.jar com.github.enanomapper.Slimmer src/main/resources

Funding

The project has had contributions from various European Commission projects. The eNanoMapper project was funded by the European Union’s Seventh Framework Programme for research, technological development and demonstration (FP7-NMP-2013-SMALL-7) under grant agreement no. 604134. NanoCommons has received funding from European Union Horizon 2020 Programme (H2020) under grant agreement nº 731032. NanoSolveIt has received funding from European Union Horizon 2020 Programme (H2020) under grant agreement no. 814572.