About OPPL-Galaxy
OPPL-Galaxy can be used to execute an OPPL script against an ontology, generating a new ontology. OPPL (Ontology Pre Processor Language) is a high level scripting language, based in the Manchester OWL Syntax, to automate the manipulation of an ontology. An OPPL script (See test.oppl) defines a query to be performed against the ontology, and some actions (Adding or removing axioms) that affect the entities that will be retrieved. Those entities can be named or defined by a variable. OPPL is a powerful method for defining and executing modelling patterns that are repeated in an ontology, saving time and energy.
Usage
An ontology and an OPPL file are needed (test.owl and test.oppl can be used as samples, both available in the bundle). Load both with Get Data >> Upload File from your computer, or redirect from another Galaxy tool. OPPL-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS. In case the loaded ontology includes OWL imports, OPPL-Galaxy will try to resolve them.
The reasoner can be Pellet, HermiT, FaCT++ or Elk.
The output ontology can be OBO or OWL (RDF/XML).
More information
Galaxy public instance with OPPL-Galaxy pre-installed:
OPPL-Galaxy Examples:
http://biordf.org/OPPL-Galaxy/
OPPL examples:
http://oppl2.sourceforge.net/taggedexamples/
Links of interest:
http://www.w3.org/TR/owl2-manchester-syntax/
http://code.google.com/p/factplusplus/
Citation
Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Erick Antezana. OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL. In Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences, SWAT4LS 2011, pages 12–19, ACM 2012.
Contact
Please send any request or comment to mikel.egana.aranguren@gmail.com.