smartniz/ubergraph

Integrated OBO ontology store

Ubergraph

Integrated OBO ontology triplestore

• Merged set of mutually referential OBO ontologies:
  • Uberon anatomy
  • Cell Ontology (CL)
  • Gene Ontology (GO)
  • Biospatial Ontology (BSPO)
  • Phenotype and Trait Ontology (PATO)
  • Human Phenotype Ontology (HPO)
  • Mammalian Phenotype Ontology (MP)
  • Fission Yeast Phenotype Ontology (FYPO)
  • Monarch Disease Ontology (MONDO)
  • Chemical Entities of Biological Interest (ChEBI)
  • Relations Ontology (RO)
  • Environmental conditions, treatments and exposures ontology (ECTO)
  • Environment Ontology (ENVO)
  • Ontology for Biomedical Investigations (OBI)
  • Medical Action Ontology (MAXO)
  • Evidence and Conclusion Ontology (ECO)
  • NCBI Taxonomy (slim version)
  • Experimental Factor Ontology (EFO)
  • Protein Ontology (PRO)
  • NCIt OBO Edition (NCIT)
• Precomputed OWL classification (class hierarchy)
• Materialized “class relations” from existential property restrictions (in separate named graphs)
• Blazegraph RDF triplestore; SPARQL query interface

Query

SPARQL endpoint: https://stars-app.renci.org/ubergraph/sparql

• Query interface in YASGUI: https://api.triplydb.com/s/_26lcKdBY

Graph organization

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. 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 • part of • haemolymphatic fluid)

  is shorthand for the OWL axiom

  • circulating cell SubClassOf (part of some haemolymphatic fluid)

• http://reasoner.renci.org/nonredundant — Triples in this graph are a subset of, and have the same semantics as, the "redundant" graph, pruned according to several redundancy rules.

• https://biolink.github.io/biolink-model/ — RDF rendering of the Biolink model, as well as triples connecting ontology terms to Biolink categories (derived from mappings in Biolink model), using the predicate https://w3id.org/biolink/vocab/category.

• http://reasoner.renci.org/ontology/closure — The transitive reflexive subclass closure only, no existential relations. This graph may be removed, since these triples are all in http://reasoner.renci.org/redundant.

Support

Development of Ubergraph has been supported by the NCATS Biomedical Data Translator project, as well as by RENCI.