search

biolink / kgx

KGX is a Python library for exchanging Knowledge Graphs
https://kgx.readthedocs.io
BSD 3-Clause "New" or "Revised" License
116 stars 28 forks source link

Add Plant Trait Ontology to obograph_source.py #305

Open diatomsRcool opened 3 years ago

diatomsRcool commented 3 years ago

Is your feature request related to a problem? Please describe. When I transform the Plant Ontology and the Plant Trait Ontology from json to tsv, everything is labeled as biolink:NamedThing.

Describe the solution you'd like I would like for kgx to correctly transform the entities in the Plant Ontology as either biolink:AnatomicalEntity or biolink:LifeStage and entities in the Plant Trait Ontology as biolink:PhenotypicFeature. This could include hard coding that all entities in TO are biolink:PhenotypicFeature, same as with HPO. PO will be trickier because it contains anatomical entities and growth stages.

Describe alternatives you've considered For the moment, I can adjust the ontology files to make this work, but it would be better if these ontologies were appropriately included. If I can change the OBONameSpace used in the ontology files, I am willing to do that, but I don't know what the acceptable values are.

Additional context See https://github.com/diatomsRcool/eco-kg/issues/10

deepakunni3 commented 3 years ago

@diatomsRcool Thanks for raising this issue. I have had this on my todo for a while now :)

I'll take a look and report back how to do this more efficiently and systematically.

justaddcoffee commented 3 years ago

As @caufieldjh mentions above, we are running into this in kg-obo too, it's not a show-stopper though - lots or possibly all transformed OBO ontologies have nodes that are all of type biolink:NamedThing.

I'm curious what strategy we could use to get more specific node types