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Slimmer configuration files
The main configuration file is a file with the suffix .props. The content consists of three lines, and may look something like:
owl=http://www.bioassayontology.org/bao/bao_complete.owl
iris=bao.iris
slimmed=http://purl.enanomapper.org/onto/external/bao-slim.owl
The owl= line indicates where the OWL file of the ontology to be slimmed is located. It is exactly this OWL file that is downloaded, loaded by the OWLAPI-based Slimmer utility, and slimmed.
The iris= line indicates the configuration file is found locally which defines which IRIs are to be included and excluded in the slimmed version of the ontology. The syntax of the .iris file is discussed below.
The slimmer= line specifies the file name under which the resulting slimmed ontology is saved. It is this file that is to be imported by the main eNanoMapper OWL file (with owl:import).
The .iris file configures the slicing of the ontology. It specifies which classes or class tress to include and which parts to exclude. For each included class it can also specify a new classes it subclasses. Each line in this file defines one instruction: one addition or one removal.
For example:
+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.
Thus, the first line in the above example shows that the term detection instrument is imported (from the BAO ontology) and made a subclass of the NPO_1436 class from the NPO ontoloy.