adding more x-bte annotation for v3 Monarch API

[colleenXu]

In #774, we migrated to the new v3 Monarch API (using the /association endpoint). This is one of the #774 (comment) that may be useful to do.

• investigate the new query options? subject/object category, taxon, namespace: example
  • look at what adds coverage, is good to have as separate operations (namespace, species context?). For example, is there cell-level/organelle-level gene-expression info?
• annotating more MetaEdges (not covered by past operations)

click to see MetaEdges

• Chem to Pathway: unclear how helpful this is, since chemicals seem generic (water, ADP, ATP...). Example. 1 Predicate: participates_in
  • their prefix Reactome differs from what we use (REACT)...so this may require extra post-processing support
    (depends on how helpful setting the subject/object namespace is)
  • unclear if other Pathway namespaces exist
• Gene to Pathway: previously chose not to annotate because MyGene also covers this info. Also has prefix issue (see Chem to Pathway above). 1 Predicate: participates_in
• Gene to GO BiologicalProcess (989349 items): previously chose not to annotate because MyGene also covers this info. Each kind has multiple possible predicates, lots of diff primary knowledge sources
  • actively_involved_in (797927)
  • acts_upstream_of_or_within (180729)
  • acts_upstream_of (9327)
  • acts_upstream_of_or_within_positive_effect (507)
  • acts_upstream_of_positive_effect (506)
  • acts_upstream_of_or_within_negative_effect (178)
  • acts_upstream_of_negative_effect (175)
• Gene to GO MolecularActivity (848151 items): see notes for BiologicalProcess above
  • enables (841330)
  • contributes_to (6821)
• Gene to GO CellularComponent (745837 items): see notes for BiologicalProcess above
  • located_in (502225)
  • active_in (145515)
  • part_of (94049)
  • colocalizes_with (4048)
• Gene to Gene ortholog: previously chose not to annotate because MyGene also covers this info. 1 predicate (orthologous_to, 551383 hits). Seems to be 1 primary knowledge source (panther)

[colleenXu]

Very useful info - the csv here: monarch-initiative/monarch-app#675 (comment)

Has some breakdown by namespace + category, but not taxon.