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Biolink Model 2.0 Migration Guide

Chemical Hierarchy for Biolink-Model 2.0.0

  • Refactor of the ‘Molecular Entity’ and ‘Chemical Substance’ classes and hierarchy.
  • ‘Genomic Entity’ is now a ‘mixin’ rather than a class.
  • ‘Chemical Substance’ class is deprecated in favor of ‘Small Molecule’ (child of ‘Molecular Entity’).
  • New classes: ‘Chemical Entity’, ‘Chemical Mixture’, ‘Complex Chemical Mixture’, ‘Small Molecule Entity’, ‘Polypeptide’, ‘Nucleic Acid Entity’.
  • ‘Gene’ now is a child of ‘Nucleic Acid Entity’.
  • ‘Nucleic Acid Entity’ now groups DNA, RNA, etc.
  • ‘Protein’ is a child of ‘Polypeptide’.
  • ‘Carbohydrate’, ‘FoodComponent’, and ‘Metabolite’ are deprecated.
  • New classes: ‘Information Resource’
  • New association slots (edge properties): ‘knowledge source’, ‘primary knowledge source’, ‘original knowledge source’, ‘aggregator knowledge source’, ‘supporting data source’

reaction_image_cont reaction_image

  • New association classes: ‘Reaction To Participant Association’, ‘Reaction To Catalyst Association’.
  • New predicates (and inverses): ‘catalyzes’, ‘has substrate’, ‘consumes’.
  • EC numbers help define the ‘Molecular Activity’ class.


  • added inverses for the majority of biolink predicates.
  • primary direction of predicate tagged with ‘biolink:canonical_predicate’.

Deprecated items removed

  • assciation_id, edge label, association type, disease or phenotypic feature association to location association.