The issue: nodes with the biolink:OntologyClass category get mapped to biolink:NamedThing, but there are more specific mappings available for them in the input graph edges.
A run of universalizer on kg-phenio like this:
$ universalizer run ~/kg-phenio/data/merged/ -u
produces this output:
Input path: /home/harry/kg-phenio/data/merged/
Will update categories.
Found these graph files:['/home/harry/kg-phenio/data/merged/merged-kg_nodes.tsv', '/home/harry/kg-phenio/data/merged/merged-kg_edges.tsv']
Retrieving entity names in /home/harry/kg-phenio/data/merged/merged-kg_nodes.tsv...
Found 28758 unexpected identifiers.
Will normalize 27106 identifiers.
Wrote IRI maps to /home/harry/kg-phenio/data/merged/update_id_maps.tsv.
Retrieving categories in /home/harry/kg-phenio/data/merged/merged-kg_nodes.tsv...
Found 430307 unexpected categories.
Will normalize 171124 categories.
Wrote category maps to /home/harry/kg-phenio/data/merged/update_category_maps.tsv.
Updated 171124 nodes.
Complete.
The processed edgefile does not contain the biolink:category edges, as expected.
The category mapfile, however (update_category_maps.tsv) doesn't include any category maps beyond biolink:NamedThing.
Correspondingly, the processed nodefile doesn't include more specific category mappings than that (one node here):
ENVO:01001570 biolink:NamedThing terrestrial ecoregion An ecoregion which is located on a landmass. Graph
The issue: nodes with the
biolink:OntologyClass
category get mapped tobiolink:NamedThing
, but there are more specific mappings available for them in the input graph edges.A run of universalizer on kg-phenio like this:
produces this output:
The processed edgefile does not contain the
biolink:category
edges, as expected. The category mapfile, however (update_category_maps.tsv
) doesn't include any category maps beyondbiolink:NamedThing
. Correspondingly, the processed nodefile doesn't include more specific category mappings than that (one node here):That should be
biolink:EnvironmentalFeature
.