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Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies usually requires flexible and versatile tools to manipulate them efficiently, in particular for enriching their axiomatic content. The Ontology Pre Processor Language (OPPL) is an OWL-based language for automating the changes to be performed in an ontology. OPPL augments the ontologists' toolbox by providing a more efficient and less error-prone mechanism, for enriching a biomedical ontology, than the one obtained by a manual treatment.


OPPL-Galaxy is a wrapper on top of OPPL that can be used within Galaxy. The functionality delivered by OPPL (i.e. automated ontology manipulation) can be combined along with the tools and workflows devised within the Galaxy framework, resulting in an enhancement of OPPL.

Several use cases are provided (see Uses cases) in order to demonstrate OPPL-Galaxy's capability for enriching, modifying and querying biomedical ontologies.

Coupling OPPL-Galaxy with other bioinformatics tools of the Galaxy framework results in a system that it is more than the sum of its parts: OPPL-Galaxy opens a new dimension of analyses and exploitation of biomedical ontologies, including automated reasoning, paving the way towards advanced biological data analyses.

OPPL-Galaxy architecture

The inner circle, in the figure below, represents the OPPL wrapper and the outer one Galaxy. Galaxy deals with the data and the parameters that will be passed to the OPPL wrapper. In order to pass, for instance, an ontology to the OPPL wrapper, the ontology must be first uploaded to Galaxy (or passed to it as the output of another Galaxy tool). Also, Galaxy deals with the output of the OPPL wrapper: the output can be redirected to other Galaxy tools or downloaded and saved as an standalone file. The OPPL wrapper coordinates the OPPL API (to parse the OPPL script and execute it), the OWL API (to read/write ontologies from stdin/to stdout and perform changes) and the chosen reasoner (to perform inferences).

OPPL-Galaxy architecture

Public instance

We provide a public instance of Galaxy with OPPL-Galaxy installed on it, including the Galaxy tools related to OPPL-Galaxy like ONTO-toolkit and NCBO-Galaxy: