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docs/using-and-reusing.md

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@@ -206,6 +206,23 @@ The [ontorat.txt](https://github.com/OHSU-Library/obo-tutorial/blob/master/examp
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On the Ontorat website you can "Load Settings File" with this file to fill in the settings, then "Specify input data file" with a "File upload", and use `qtt.txt`. Then click "Get OWL (RDF/XML) Output File". The resulting OWL file is [ontorat.owl](https://github.com/OHSU-Library/obo-tutorial/raw/master/examples/ontorat.owl). I changed the "Ontology IRI" for this file using Protégé to something more sensible than the default.
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### Extracting Ontology Modules with ROBOT
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Sometimes you want to import too many terms for OntoFox, but the target ontology is too large to import all of it. Thre's a tool you can use in this case: OBO [ROBOT](http://robot.obolibrary.org/). ROBOT is like a Swiss Army Knife for ontology manipulation. It can do many things, including the steps we just did with OntoFox and Ontorat. Here we are going to use it to filter a source ontology down to a smaller subset and then we will extract the terms we want into a module.
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Download [Uberon](http://purl.obolibrary.org/obo/uberon/ext.owl) to the examples directory.
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Filter Uberon to part_of and has_part
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`robot filter --input ext.owl --term BFO:0000050 --term BFO:0000051 --output uberon-subset.owl`
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Extract Uberon terms
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`obot extract --method STAR --input uberon-subset.owl --term-file uberon-terms.txt --output uberon-mod.owl`
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The result is the uberon-module.owl file, with all the terms listed in uberon-terms.txt and all their part_of/has_part dependencies.
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### Importing Ontologies with Protégé
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OBO ontologies are part of the web of linked data. Using terms from other ontologies means making links to resources across the web. Another form of linking is *import*: you can import another complete ontology or OWL file into your own ontology.
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![Protégé import screenshot](import.png)
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### Extracting Ontology Modules with ROBOT
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Sometimes you want to import too many terms for OntoFox, but the target ontology is too large to import all of it. Thre's a tool you can use in this case: OBO [ROBOT](http://robot.obolibrary.org/). ROBOT is like a Swiss Army Knife for ontology manipulation. It can do many things, including the steps we just did with OntoFox and Ontorat. Here we are going to use it to filter a source ontology down to a smaller subset and then we will extract the terms we want into a module.
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Download [Uberon](http://purl.obolibrary.org/obo/uberon/ext.owl) to the examples directory.
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Filter Uberon to part_of and has_part
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`robot filter --input ext.owl --term BFO:0000050 --term BFO:0000051 --output uberon-subset.owl`
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Extract Uberon terms
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`obot extract --method STAR --input uberon-subset.owl --term-file uberon-terms.txt --output uberon-mod.owl`
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The result is the uberon-module.owl file, with all the terms listed in uberon-terms.txt and all their part_of/has_part dependencies.
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### Editing Ontologies by Hand
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