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balhoff committed Jun 7, 2023
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Expand Up @@ -65,7 +65,7 @@ The Ubergraph triplestore is organized into several named graphs.
- `http://reasoner.renci.org/ontology` — All the merged axioms from the input ontologies (logical axioms and annotation axioms), classified using `robot reason -r ELK`. Disjointness axioms are removed prior to reasoning. Include this graph if you want term labels.
- This graph also includes:
- Generated `rdfs:isDefinedBy` triples connecting ontology terms to their OBO namespace ontology IRI. For example, there is a triple `<http://purl.obolibrary.org/obo/FOO_0123456> rdfs:isDefinedBy <http://purl.obolibrary.org/obo/foo.owl>` for every term with OBO namespace "foo". Matching these triples is much faster than using `FILTER(STRSTARTS(STR(?term), "http://purl.obolibrary.org/obo/FOO_"))`.
- Precomputed information content score for each ontology class, based on the count of terms related to a given term via `rdfs:subClassOf` and [`part of`](http://purl.obolibrary.org/obo/BFO_0000050). The scores are `xsd:decimal` values scaled from `0` to `100` (e.g., a very specific term with no subclasses). Use the predicate `http://reasoner.renci.org/vocab/normalizedInformationContent` to retrieve IC scores.
- Precomputed information content score for each ontology class, based on the count of terms related to a given term via `rdfs:subClassOf` or any existential relation. The scores are `xsd:decimal` values scaled from `0` to `100` (e.g., a very specific term with no subclasses). Use the predicate `http://reasoner.renci.org/vocab/normalizedInformationContent` to retrieve IC scores.
- `http://reasoner.renci.org/redundant` — The complete inference closure for all subclass and existential relations. This includes all transitive, reflexive subclass relations. Within this graph, all predicates with the exception of `rdfs:subClassOf` imply an OWL existential relationship. For example, the triple:
- `CL:0000080 BFO:0000050 UBERON:0000179` ([circulating cell](http://purl.obolibrary.org/obo/CL_0000080)[part of](http://purl.obolibrary.org/obo/BFO_0000050)[haemolymphatic fluid](http://purl.obolibrary.org/obo/UBERON_0000179))

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