Representing negative knowledge in the semantic web is an open problem. This post is going to be a living document where I keep notes on use cases, potential solutions, and awful hacks.

SSSOM

In the Simple Standard for Sharing Ontological Mappings (SSSOM), we decided to represent negative knowledge by adding a modifier onto a predicate. This means that a semantic mapping known to be false gets represented like this in TSV:

subject_id	subject-label	predicate_id	predicate_modifier	object_id	object_label	mapping_justification
CHEBI:8925	ryanodine	skos:exactMatch	Not	mesh:D031309	Ryania	semapv:ManualMappingCuration

Since SSSOM is heavily tied to the OBO community, this gets turned into RDF with the following axiom:

[] a owl:Axiom ;
    owl:annotatedSubject CHEBI:8925 ;
    owl:annotatedProperty skos:exactMatch ;
    owl:annotatedObject mesh:D031309 ;
    sssom:predicate_modifier sssom:NegatedPredicate .

It’s debated whether asserting an axiom also requires the assertion of the triple itself CHEBI:8925 skos:exactMatch mesh:D031309, however, in this case, it’s clear that triples represent true knowledge, so we would not want to concretize it.

RDF Surfaces

Damien Goutte-Gattat made me aware of RDF Surfaces in a discussion on a SSSOM PR. To summarize his comment, RDF surfaces create a part of an RDF graph that contains negated assertions, something like:

@prefix log: <http://www.w3.org/2000/10/swap/log#> .
@prefix FBbt: <http://purl.obolibrary.org/obo/FBbt_> .
@prefix UBERON: <http://purl.obolibrary.org/obo/FBbt_> .
@prefix skos: http://www.w3.org/2004/02/skos/core#> .

(_:x) log:onNegativeSurface {
  FBbt:00004508 skos:exactMatch UBERON:0000056 .
} .

This paper is still under review and also might be of limited use because it uses sneaky N3 syntax { } which are used to express formulae.

I haven’t actually gone out to do a deep survey on this. If you are aware of something relevant, please let me know.