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relation-graph

Materialize OWL existential relations

Run

relation-graph --ontology-file uberon.owl --output-file relations.ttl --mode rdf --property 'http://purl.obolibrary.org/obo/BFO_0000050' --property 'http://purl.obolibrary.org/obo/BFO_0000051' --properties-file more_properties.txt

You can leave off the property and properties-file arguments; in that case all OWL object properties are used. The default mode is rdf; alternatively, the owl mode will output RDF, but as a valid OWL structure. The properties-file should look like this:

http://purl.obolibrary.org/obo/BFO_0000050
http://purl.obolibrary.org/obo/BFO_0000051

Note: Before running, you may need to increase the amount of memory available for Java. On UNIX style systems, this is done by setting the JAVA_OPTS environment variable. For example, to set the amount of memory to 16G, you would use this command: export JAVA_OPTS=-Xmx16G.

Full options

Usage: relation-graph [options]
  --usage  <bool>
        Print usage and exit
  --help | -h  <bool>
        Print help message and exit
  --ontology-file  <filename>
        Input OWL ontology
  --output-file  <filename>
        File to stream output triples to.
  --mode  <RDF|OWL|TSV>
        Configure style of triples to be output. RDF mode is the default; each existential relation is collapsed to a single direct triple. TSV mode outputs the same triples as RDF mode, but as TSV, compacting IRIs using an optional prefixes file.
  --property  <IRI>
        Property to restrict output relations to. Provide option multiple times for multiple properties. If no properties are provided (via CLI or file), then all properties found in the ontology will be used.
  --properties-file  <filename>
        File containing line-separated property IRIs to restrict output relations to. If no properties are provided (via CLI or file), then all properties found in the ontology will be used.
  --output-subclasses  <bool>
        Include entailed rdfs:subClassOf or owl:equivalentClass relations in output (default false)
  --reflexive-subclasses  <bool>
        When outputting rdfs:subClassOf, include relations to self for every class (default true)
  --equivalence-as-subclass  <bool>
        When outputting equivalent classes, output reciprocal rdfs:subClassOf triples instead of owl:equivalentClass triples (default true)
  --output-classes  <bool>
        Output any triples where classes are subjects (default true)
  --output-individuals  <bool>
        Output triples where individuals are subjects, with classes as objects (default false)
  --disable-owl-nothing  <bool>
        Disable inference of unsatisfiable classes by the whelk reasoner (default false)
  --prefixes  <filename>
        Prefix mappings to use for TSV output (YAML dictionary
  --obo-prefixes  <bool>
        Compact OBO-style IRIs regardless of inclusion in prefixes file
  --verbose  <bool>
        Set log level to INFO

Build

Install sbt (Scala Build Tool) on your system. For Mac OS X, it is easily done using Homebrew: brew install sbt. sbt requires a working Java installation, but you do not need to otherwise install Scala.

After sbt is installed, run sbt stage to create the executable. The executable is created in your cli/target/universal/stage/bin directory.