OWLDEF method and software

Web frontend

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.


Download

Stable

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.

Development

Convert OWL to OBO

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).

OBO to OWL in Crossproduct definitions

A developmental version of our conversion software is here: obo2owlcp.jar. To use, replace the obo2owl.jar above with this jar file and use the OBOTester to convert OBO files. The difference in obo2owlcp.jar is that only one variable is used and the owldef definition must be an OWL class description, not an OWL class axiom. This allows to convert OBO files that include formal definitions to OWL. We provide an example conversion of the Human Phenotype Ontology: hpo-in-owl.owl.

Pattern definitions

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.

License

All our software is distributed under the Modified BSD License:

Copyright (c) 2010, European Bioinformatics Institute
All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.