molgenis / molgenis-emx2

MOLGENIS EMX2, the latest version of the MOLGENIS data platform.
GNU Lesser General Public License v3.0
14 stars 18 forks source link

Turtle export classification of subclasses / individuals needs improvement #3066

Open AJKellmann opened 11 months ago

AJKellmann commented 11 months ago

What version of EMX2 are you using (see footer) v10.4.5-SNAPSHOT

Describe the bug In the rdf export some individuals are encoded as subclasses instead of individuals.

Some look like annotation properties

To Reproduce Steps to reproduce the behavior:

Download the TTL for the catalogue model
Load it in Protege
Review the class hierarchy

Expected behavior Individuals are not encoded as subclasses, but as individuals

Additional context Exporting RDF is still under active development, so we need to improve it step by step.

esthervanenckevort commented 10 months ago

Partially this is a data modelling issue. These are all modelled with the Ontology tables. Some of these definitely should not be modelled as Ontology tables (e.g. years). The bigger issue is that we can have multiple things in ontology tables and not a generic way of deciding what is in the ontology table. Is it a class with subclasses, a class with instances, properties? Unless we have a way to tell them apart any choice will have issues with those that don't fit that choice.