CHEBI Examples

• CHEBI Predicates
  • Citric acid and its ion forms
  • Citric acid
  • Citrate(3-)
  • Accessing CHEBI through OAK
  • Computing similarity
  • So what’s going on?
  • Always make use of the full range of edge types
  • Number of hops is often meaningless with ontologies
  • Calculating similarity using all predicates
  • Ontologies are not DAGs
  • So how do we handle these?
  • Relation Graph
  • SemSQL Builds have relation-graph pre-computed
  • OAK uses Relation Graph in semantic similarity
  • Relation Graph is only as good as its inputs
• CHEBI Slimmer
  • Initial setup
  • Set up vocabulary constants
  • All labels
  • Mappings
  • Various Relationships
  • Retrieve all Charge States
  • Find Conjugate Cliques
  • Calculate conjugate graph and strongly connected components
  • Lexical analysis
  • Analysis: Consistency check between lexically inferred cliques and asserted relationships
  • Create is-a map
  • Fetch Uniprot Synonyms
  • RHEA pH Mapping
  • Pick Canonical from Conjugate Cliques
  • Exclusion List
  • Generate Ontology