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

Re:Ontology for the life sciences: genes, proteins, diseases... by dan_fornika on Monday January 20, 2020 @06:48PM (#22103050)

I think the various OBOFoundry ontologies are at different stages of maturity. One of their design principles is interoperability, but I'm not sure how often one is able to reason effectively across ontologies unless great care is taken to ensure that logical axioms are sound.

I'm involved in a project[0] that has an aim to provide better data integration by using OBOFoundry ontologies, but it's been a challenge in practice to merge the software with the ontologies in a coherent way.

[0] https://www.irida.ca/data-integration/

[ Parent | on HN ]

Re:Ontology for the life sciences: genes, proteins, diseases... by jerven on Tuesday January 21, 2020 @01:55AM (#22104832)

There are a few which are really great. Basically my shortcut is Chris Mungall involved then it is logically and biologically ;) sound.

While we at SIB are more towards the RDF/SPARQL part of the spectrum (https://edu.sib.swiss/course/view.php?id=440). We do use OWL and obofoundry projects like Uberon and GO. For UniProt I took a lot of pain to make sure it is really compatible. We did the same for Rhea and ChEBI. This has paid of handsomely in new query capabilities.

[ Parent | on HN ]