Propose QEdge.negated and Edge.negated

[edeutsch]

Addresses #281

[edeutsch]

2021-12-16 DECISION: Hold until BioLink finalizes their process.

[cmungall]

Negation and predicate hierarchies

Consider:

1. Query: A NOT interacts-with B
2. KP Assertion: A NOT phosphorylates B

(where phosphorylates is a subpredicate of interacts-with)

What is the interpretation of 1?

• 1a: Loose interpretation: Find all negative statements relating A and B, where the relationship is some kind of interaction relationship
• 1b: Strict logical interpretation: What statements explicitly make the claim that A does not interact-with B

For 1a, (loose interpretation) implementors should include all assertion A NOT R B, where R is a reflexive transitive subproperty of interacts-with, i.e. the same algorithm as for positive assertions. Here assertion 2 WOULD be returned

For 1b, implementors essentially invert the procedure for positive statements. Here assertion 2 WOULD NOT be returned

We can also explore the reverse situation

1 . Query: A NOT phosphorylates B
2. KP Assertion: A NOT interacts-with B

Here 2 is logically entailed by 1

Negation and class hierarchies

1. Query: ?drug NOT has-side effect coughing
2. KP assertion: drugA NOT has-effect respiratory-system-phenotype (i.e. no respiratory system phenotypes)
3. ontology: coughing subClassOf respiratory-system-phenotype

Under the logical interpretation, 1 is entailed by 2 and 3, so drugA will be returned. Note this involves reversing the traversal direction for a positive query

[edeutsch]

Closing in favor of a more comprehensive PR #407