Ontology for the life sciences: genes, proteins, diseases, all expressed in OWL

Re:Ontology for the life sciences: genes, proteins, diseases... by jakeogh on Monday January 20, 2020 @04:15PM (#22102148)

Is 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

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Re:Ontology for the life sciences: genes, proteins, diseases... by chrismungall on Tuesday January 21, 2020 @11:28PM (#22114635)

For a general purpose OWL python library there is OWLReady2 and 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/

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-fri... and 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)

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Re:Ontology for the life sciences: genes, proteins, diseases... by haddr on Monday January 20, 2020 @04:48PM (#22102348)

Jena API was quite common to use with Java, and RDFLib for python.

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Re:Ontology for the life sciences: genes, proteins, diseases... by rzzzt on Monday January 20, 2020 @05:57PM (#22102766)

OWL API is also a contender in the Java libraries category: https://github.com/owlcs/owlapi

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