UNMIREOT

Tools to identify, diagnose, and semi-automatically repair hidden contradictions in biomedical ontologies.

Running the tool

To run the tool to combine an ontology with its imports closure (so, if you want to combine two or more ontologies, simply add an additional import declaration for each one you wish to include, and then run this script on it):

$ groovy merge_imports.groovy ontology.owl

To check an ontology for unsatisfiable classes, and to diagnose causes of those unsatisfiable classes:

$ groovy quick_repair.groovy ontology.owl output_dir/

Two other tools are:

• explain.groovy creates a justification for every unsatisfiable class in an ontology
• repair.groovy uses the naive black box algorithm to diagnose/repair an ontology (i.e. examines every unsatisfiable class)

In both cases, you'll only want to use these if you have a relatively small ontology.

Experimental results

The result of the analysis over OBO Foundry can be found in obo/.

• obo/core/results.json Every unsatisfiable class in the OBO Foundry meta-ontology, and its justification.
• obo/results.json contains a list of OBO ontologies, and the results of an attempt to combine it with the repaired OBO Foundry meta-ontology. Either contains an inconsistency message, a loading error, or the number of unsatisfiable classes upon successful combination.
• obo/results/ one subdirectory for each OBO ontology+OBO core combination with unsatisfiable classes, containing:
  • out.log The output of the quick_repair script
  • results.json Each axiom removed, and which classes doing so made satisfiable
• obo/axioms.json All of the axioms removed for all OBO ontologies, and which classes they made satisfiable.
• obo/axiom_counts.json Each of the axioms removed from the OBO ontologies, and how many classes it made satisfiable. Interestingly, some of these are zero - that's because every class it affected had another indepdendent cause for its unsatisfiability.
• obo/rmcounts.json Each OBO ontology, and the number of axioms that had to be removed from it to made all of its classes unsatisfiable (UPHENO 37!!)
• obo/classes.json Every unsatisfiable class found, and which ontologies it was unsatisfiable in.

Recreating the experiment

Obtaining the ontologies

Please note: these instructions may not be perfect. This has been adapted from a highly experimental setup. If you have any issues, please open an issue

You can also find the files used to run the experiment there. You will have to obtain your own ontology files, though. The ontologies.yml file downloaded from the OBO Foundry at the time of the experiment is provided, but the download links will give you newer versions of those ontologies than the ones analysed in the original experiment, so the results may differ somewhat. All snippets in this section assume you start from the obo/ subdirectory. To create a simple bash script to download all of the ontology files in the ontologies.yml file, you can run:

mkdir ontologies
groovy tools/format_download.groovy
cd ontologies
chmod a+x get_ontologies.sh
./get_ontologies.sh

OBO Foundry

Because it's relatively small, the repaired OBO Foundry meta-ontology is provided in obo/core/obofoundry_core_fixed.owl. You can recreate this part of the experiment by copying the ontologies/bfo.owl file into core/, then manually editing that file so that it contains these lines in its owl:Ontology closure (sorry, didn't make a script for that):

<owl:imports rdf:resource="http://purl.obolibrary.org/obo/chebi.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/doid.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/pato.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/po.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/xao.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/zfa.owl"/>

Then, you can run:

groovy ../quick_repair.groovy core/bfo.owl core/

This will create your core/results.json with each axiom that had to be removed, and each unsatisfiable class it repaired, and the coherent OBO foundry meta-ontology in core/fixed.owl.

OBO Ontologies

If you want to recreate the OBO ontologies experiment, note that it will overwrite the given result files. First, you will have to fill obo/ontologies/ with the ontologies you're interested in, then run the following (Note, if you generated your own core above, you'll have to change the first argument to core/fixed.owl):

groovy combine_each_folder.groovy core/obofoundry_core_fixed.owl ontologies/

This will combine each ontologies in obo/ontologies with the OBO Foundry meta-ontology, and run a satisfiability check on each of them. The results, including which ontologies were unloadable, inconsistent, and numbers of unsatisfiable classes, will be recorded in obo/results.json. The combined ontologies will be stored in obo/combos. You can then run the quick repair algorithm on them individually, or create a simple bash script to do so for you:

groovy make_bash.groovy
chmod a+x run_all.sh
./run_all.sh

Be advised, that to completely recreate the experiment, for all OBO ontologies, will take a long time and a lot of computational power. When it's done, there will be an obo/results directory, with subdirectories for each combination, including the output of the script, axioms removed, and a coherent version of the ontology. You can then collate all the results to generate the axioms.json, axiom_counts.json, rmcounts.json, and classes.json results files, and view overall axiom counts etc with:

groovy collate_results.groovy

You can also run the create_association.groovy file, to create a TSV showing the relationship between the number of unsatisfiable classes in each OBO ontology and the number of axioms that had to be removed from it to repair them all.