From 4c4ecc6bacd2c83390e58517bc6e555e3de8a06f Mon Sep 17 00:00:00 2001 From: Jim Balhoff Date: Mon, 7 Feb 2022 11:23:19 -0500 Subject: [PATCH] Update README.md --- README.md | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 6f2956f..b9be252 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ Materialize OWL existential relations ## Run ```bash -relation-graph --ontology-file uberon.owl --non-redundant-output-file nonredundant.ttl --redundant-output-file redundant.ttl --mode rdf --property 'http://purl.obolibrary.org/obo/BFO_0000050' --property 'http://purl.obolibrary.org/obo/BFO_0000051' --properties-file more_properties.txt +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`; @@ -17,6 +17,24 @@ 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 + Print usage and exit + --help | -h + Print help message and exit + --ontology-file + --output-file + --mode + --property + --properties-file + --output-subclasses + --reflexive-subclasses + --equivalence-as-subclass +``` + ## Build Install `sbt` (Scala Build Tool) on your system. For Mac OS X, it is easily done using [Homebrew](http://brew.sh): `brew install sbt`. `sbt` requires a working Java installation, but you do not need to otherwise install Scala.