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balhoff merged 1 commit into from
Feb 7, 2022
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Update README.md #97

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20 changes: 19 additions & 1 deletion README.md
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Expand Up @@ -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`;
Expand All @@ -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 <bool>
Print usage and exit
--help | -h <bool>
Print help message and exit
--ontology-file <string>
--output-file <string>
--mode <output mode>
--property <string*>
--properties-file <string?>
--output-subclasses <boolean value>
--reflexive-subclasses <boolean value>
--equivalence-as-subclass <boolean value>
```

## 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.

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