Bubastis is a tool for detecting asserted logical differences between two ontologies, such as between versions.
Bubastis is available as a web application at http://www.ebi.ac.uk/efo/bubastis/. There is documentation on how to use the Bubasists web application here http://www.ebi.ac.uk/fgpt/sw/bubastis/index.html.
The Bubasist Java library can be built using maven.
mvn clean package
Usage:
java -jar bubastis.jar parameters:
(required) -ontology1 location of ontology 1 either a URL for an ontology on the web or a local file location in obo or owl format. Typically the older version of the ontologies being compared
(required) -ontology2 location of ontology 2 either a URL or local file location of an obo or owl format ontology. Typically the newer version of the ontologies being compared.
(optional) -output location of output file to send results, default is to console.
(optional) -format required format of diff report, default is plain text, value 'xml' will produce xml
(optional) -xslt for xml version of the diff report this will insert an xslt location into the header for rendering these in a customised manner in a web page. Value should be location of xslt file.
Examples:
Loading two files locally and outputting results to console:
java -jar bubastis.jar -ontology1 "H://obi_nov_08.owl" -ontology2 "H://obi_jan_09.owl"
Loading two files locally and output results to xml file with an xslt location inserted into header
java -jar bubastis.jar -ontology1 "H://obi_nov_08.owl" -ontology2 "H://obi_jan_09.owl" -output "H://OBIdiff.xml" -format xml -xslt "./stylesheets/bubastis.xslt"
Loading one file locally and one from the web and outputting results to plain text:
java -jar bubastis.jar -ontology1 "H://disease_ontology_version_1.owl" -ontology2 "http://www.disease.org/diseaseontology_latest.owl" -output "C://my_diff.txt"