positively_regulates mappings (boomer analysis)

[balhoff]

• biolink:acts_upstream_of_positive_effect EquivalentTo acts upstream of, positive effect (most probable) 0.8
• biolink:entity_positively_regulates_entity EquivalentTo directly positively regulates activity of (most probable) 0.8
• biolink:acts_upstream_of_or_within EquivalentTo acts upstream of or within, positive effect (most probable) 0.8
• biolink:positively_regulates ProperSuperClassOf acts upstream of, positive effect (most probable) 0.8
• biolink:process_positively_regulates_process EquivalentTo positively regulates (most probable) 0.8
• biolink:positively_regulates ProperSuperClassOf directly positively regulates (most probable) 0.8
• biolink:positively_regulates ProperSuperClassOf acts upstream of or within, positive effect (most probable) 0.8
• biolink:positively_regulates ProperSuperClassOf positively regulates 0.06
• biolink:entity_positively_regulates_entity ProperSubClassOf acts upstream of, positive effect (most probable) 0.8

[balhoff]

(Some explanation in #806)

Issues to address:

• RO:0002213 is skos:exactMatch for two different biolink terms (biolink:process_positively_regulates_process should be the winner)
• Missing hierarchy relation between biolink:acts_upstream_of_positive_effect and biolink:acts_upstream_or_within
• Incompatible ranges for biolink:entity_positively_regulates_entity and RO:0004034 (not in picture, just my assertion)

[nlharris]

is this something you could address with a PR, @balhoff?

[vincentvialard]

Missing hierarchy relation between biolink:acts_upstream_of_positive_effect and biolink:acts_upstream_or_within

PR https://github.com/biolink/biolink-model/pull/1190 fixes something related, but this specific issue can not be solved simply because we are facing a case of multiple inheritance: Source: https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http://purl.obolibrary.org/obo/RO_0004034

But it drawed my attention to the hierarchy, and there is a mismatch in biolink where acts upstream of or within is a subpredicate of acts upstream of:

  acts upstream of or within:
    is_a: acts upstream of
    domain: gene or gene product
    range: biological process
    annotations:
      canonical_predicate: true
    exact_mappings:
      - RO:0002264

So I guess a much bigger rework than my patch is required.