Do Biolink category assignment to nodes here (rather than in PHENIO)

[caufieldjh]

Adding Biolink categories in PHENIO works: it derives category names from the Biolink schema and applies them to children in PHENIO.
Most of this relies on a sparql query: https://github.com/monarch-initiative/phenio/blob/main/src/sparql/bl-categories.ru

The original justification for this was to apply categories as upstream as possible, promoting reuse of an ontology with meaningful category assignments, even when used somewhere other than a KG.

This overall process has some disadvantages:

• It is slow and memory intensive
• It makes numerous mistakes:
  • it applies incorrect categories (Include QC step to check for multiple and/or conflicting Biolink categories monarch-initiative/phenio#22 , Node categories  #95)
  • it includes extra categories (Biolink merge brings in LinkML types monarch-initiative/phenio#37)
  • it induces punning (Adding biolink category induces punning monarch-initiative/phenio#32)
• It does not assign edge categories (see Include Biolink categories for relations monarch-initiative/phenio#70)

We can, instead, add categories as part of the KG transform.

[caufieldjh]

Note that the current KG transform adds many, but not all Biolink categories:

$ cut -f2 data/transformed/phenio/phenio_node_sources_nodes.tsv | sort | uniq -c | sort
      1 category
    117 biolink:SequenceVariant
   1101 biolink:Protein
   1775 biolink:Cell
   1854 biolink:OrganismTaxon
   4498 biolink:CellularComponent
   5616 biolink:ChemicalEntity
  12576 biolink:MolecularActivity
  15878 biolink:AnatomicalEntity
  17885 biolink:PhenotypicFeature
  27869 biolink:Disease
  30655 biolink:BiologicalProcess
 180234 biolink:NamedThing