You can use this tool to convert OBO Flatfiles to OWL using custom translation patterns. The table below shows patterns for the OBO Relationship Ontology and some further examples. We plan to convert these relation definitions to OPPL2 in the future.
Please upload the ontology in the OBO Flatfile Format that you wish to convert to OWL.
Please download the library to do the conversion here: extOWL.tgz. Use the OBOTester class to test the library: java OBOTester infile outfile
You will need the Manchester OWL API in your classpath.
You can try malaria-owldef.obo with the tools we provide. This modified version of the Malaria Ontology includes an owldef definition for the realized-by relation.
We developed experimental software to convert OWL back to OBO-style relations, which you may wish to try owl2obo.tar.gz. You require the Hermit OWL reasoner in your classpath for this to work. We plan to make a proper software tool available in the future. There are also test results for Malaria Ontology (malaria.tar.gz) and a modified version of the Sequence Ontology including an integral-part-of statement (so.tar.gz).
|Relation (Class-Class)||OWLDEF Pattern|
|part-of||?X subclassOf part-of some ?Y|
|has-part||?X subclassOf has-part some ?Y|
|integral-part-of||(?X and not (part-of some ?Y)) or (?Y and not (has-part some ?X)) subclassOf Nothing|
|has-integral-part||(?X and not (has-part some ?Y)) or (?Y and not (part-of some ?X)) subclassOf Nothing|
|proper-part-of||?X subclassOf proper-part-of some ?Y|
|has-proper-part||?X subclassOf has-proper-part some ?Y|
|located-in||?X subclassOf located-in some ?Y|
|location-of||?X subclassOf location-of some ?Y|
|contained-in||?X subclassOf contained-in some ?Y|
|contains||?X subclassOf contains some ?Y|
|adjacent-to||?X subclassOf adjacent-to some ?Y|
|transformation-of||?X subclassOf transformation-of some ?Y|
|transformed-into||?X subclassOf transformed-into some ?Y|
|derives-from||?X subclassOf derives-from some ?Y|
|derived-into||?X subclassOf derived-into some ?Y|
|preceded-by||?X subclassOf preceded-by some ?Y|
|precedes||?X subclassOf precedes some ?Y|
|has-participant||?X subclassOf has-participant some ?Y|
|participates-in||?X subclassOf participates-in some ?Y|
|has-agent||?X subclassOf has-agent some ?Y|
|agent-in||?X subclassOf agent-in some ?Y|
|realized-by||?X subclassOf realized-by only ?Y|
|realizes||?X subclassOf realizes some ?Y|
|lacks-part||?X subclassOf not (has-part some ?Y)|
|has-function||?X subclassOf has-function some ?Y|
|lacks-function||?X subclassOf not (has-function some ?Y)|
|has-function-realized-by||?X subclassOf has-function some (realized-by only ?Y)|
Emphasized relations are not a part of the OBO Relationship Ontology. The derives-from and derived-into relation patterns are flawed, as there is not derives-from relation between individuals according to the OBO Relationship Ontology.
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