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Is https://bitbucket.org/jibalamy/owlready2/src/default/ https://bitbucket.org/jibalamy/owlready2/src/default/ the standard py lib for accessing these? Is ther
by jakeogh 7y ago
Is https://bitbucket.org/jibalamy/owlready2/src/default/ https://bitbucket.org/jibalamy/owlready2/src/default/ the standard py lib for accessing these?
Is there a recent tutorial on querying the ontology from the terminal? I found a few on yt, this one is 5y old: https://www.youtube.com/watch?v=5DCS9LE-8rE https://www.youtube.com/watch?v=5DCS9LE-8rE
- haddr 7y agoJena API was quite common to use with Java, and RDFLib for python.
- rzzzt 7y agoOWL API is also a contender in the Java libraries category: https://github.com/owlcs/owlapi https://github.com/owlcs/owlapi
- chrismungall 7y agoFor a general purpose OWL python library there is OWLReady2 and funowl: https://github.com/hsolbrig/funowl https://github.com/hsolbrig/funowl For a Python library that intends to provide a level of abstraction more appropriate to bioinformatics use cases see https://github.com/biolink/ontobio/ https://github.com/biolink/ontobio/ The ontology data model for this is based more on obograph json than on OWL. See https://douroucouli.wordpress.com/2016/10/04/a-developer-friendly-json-exchange-format-for-ontologies/ https://douroucouli.wordpress.com/2016/10/04/a-developer-fri... and https://douroucouli.wordpress.com/2016/10/04/a-developer-friendly-json-exchange-format-for-ontologies/ https://douroucouli.wordpress.com/2016/10/04/a-developer-fri... Of course, it's always possible to use an RDF level library such as rdflib, but this can be low-level for OWL. Even simple bio-ontologies often make frequent use of existential restrictions and axiom annotations. And of course it's possible to use a python-jvm bridge to access the fully featured java OWL API. (I am involved in both ontobio and funowl)