Making retrieval of axiom annotations for synonyms faster

[matentzn]

I learned now that I can use some blazing fast built-in method for obtaining basic metadata for terms. However, some typical use cases are not covered, including synonym provenance.

For example:

for entity, spv in adapter.synonym_property_values(mondo_terms):
            xrefs = "|".join(spv.xrefs)
            synonym_type = spv.synonymType
            synonym = spv.val
            predicate = spv.pred
            data_subsets.append({
                "id": entity,
                "synonym": synonym,
                "synonym_type": synonym_type,
                "xrefs": xrefs,
                "predicate": predicate,
                "group": mondo_group
            })

takes an enormous amount of time, similar to

runoak -i sqlite:tmp/mondo_paper.db aliases MONDO:0000001 --obo-model

While not using the obo-model (and therefore not getting xrefs etc) is instant. I think this is not just about synonyms - one of the main arguments for oak is that it is faster than SPARQL/OWL because it is using an SQL backend, and this should be true for axiom annotations in general, not just the primary annotations.

EDIT: This SPARQL query takes less than 5 seconds to run, for example, and its a pretty standard for my work. Its unclear how I can replicate this in OAK.

SELECT ?entity ?label ?synonym ?xref ?st1 ?st2 WHERE {
  ?entity rdfs:label ?label .
  ?ax owl:annotatedSource ?entity ;
         owl:annotatedProperty oboInOwl:hasExactSynonym ;
         owl:annotatedTarget ?synonym ;
         oboInOwl:hasDbXref ?xref .
  OPTIONAL {
  	?ax oboInOwl:hasSynonymType ?st1 .
  }
  OPTIONAL {
  	?ax oboInOwl:hasSynonymType ?st2 .
    FILTER(?st1!=?st2)
  }
  FILTER (isIRI(?entity) && STRSTARTS(str(?entity), "http://purl.obolibrary.org/obo/MONDO_"))
}