I was wondering if anybody could give me some pointers on how to parse an OWL ontology with available tools.
I would like to generate an output file based on the ChEBI ontology, to get all the terms associated with specific compounds, both direct and indirect annotations. The CheEBI ontology is available from http://www.ebi.ac.uk/chebi/downloadsForward.do
For example, methotrexate (http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:44185) is annotated as dicarboxylic acid (http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3A35692). However dicarboxylic acid is itself a carboxylic acid (http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3A33575). I would like to return an annotation to both dicarboxylic acid and carboxylic acid for methotrexate.
My only experience with ontologies is with GO, and for parsing that I use various bioconductor packages in R, so any help greatly appreciated.