Ontobio assoc_rdfgen does not hand NOT annotations ("negated" in the association json)

biolink / ontobio

python library for working with ontologies and ontology associations

https://ontobio.readthedocs.io/en/latest/

BSD 3-Clause "New" or "Revised" License

118 stars 30 forks source link

Ontobio assoc_rdfgen does not hand NOT annotations ("negated" in the association json) #286

Open dougli1sqrd opened 5 years ago

dougli1sqrd commented 5 years ago

The RDF GO-CAM generation from association code in assoc_rdfgen does not handle NOT annotations. Currently there are GO Rules that refer to annotations being NOT annotations. But this is not represented when translated from associations.

In order to more accurately represent the data, let's build a model based on negated field.

cmungall commented 5 years ago

Represent as ComplementOf https://github.com/geneontology/noctua/issues/524

dustine32 commented 5 years ago

If it helps, I have some example RDF for this captured in Noctua and documented here https://github.com/geneontology/gocamgen/issues/20#issuecomment-459474560

dustine32 commented 3 years ago

This change https://github.com/biolink/ontobio/commit/50e38f25e440ee61c3df4e6f9fbb2951609f3c04 provides the emit function for NOT (aka complementOf) in assoc_rdfgen.py. Just need to hook it up to assoc_rdfgen's CamRdfTransform.translate() if we still wanted to handle these here: https://github.com/biolink/ontobio/blob/c66f2030530eaa4e9c5335d0bf7c6d24f094beb1/ontobio/rdfgen/assoc_rdfgen.py#L214