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Principles of Ontology Development: Making Definitions Computable

Learn how to create computable definitions using reasoning, formal concept analysis, and logical definitions in biology ontology to enhance visualization and integration. Use reasoners for ontology authoring and quality control efficiently.

jeremy-benjamin
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Principles of Ontology Development: Making Definitions Computable

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  1. Principles and Practice of Ontology Development: Making Definitions Computable Chris Mungall LBL

  2. Why make definitions computable? • Doing the work all by yourself is hard, boring and error prone • Automate using reasoning • Bonus: • Makes the definitions easier for humans • Enables better visualization

  3. Biology is modular, most ontology classes are compositional phalanx p pf ph distal phalanx proximal phalanx pp dp autopod hand foot ppf dpf dph pph (adapted from diagram by David Hill and Joel Richardson)

  4. History • “Cross-products” • Hill, D. P. and Blake, J. A. and Richardson, J. E. and Ringwald M: Extension and integration of the gene ontology (GO): combining GO vocabularies with external vocabularies. Genome Res 2002 • Formal Concept Analysis • Description Logics 1980s-present • Galen – Rector et al • GONG – Wroe, Stevens et al

  5. Logical definitions • Genus-differentia form • Text definition is genus-differentia form • Distal phalanx of hand: • “A distal phalanx that is part of a hand.” • or “A distal phalanx[ID:2]that is part of a hand[ID:3].” • OWL: • ‘distal phalanx of hand’ EquivalentTo ‘distal phalanx’and part_ofsome hand • OBO-Format • [Term] • id: ID:1 ! distal phalanx of hand • intersection_of: ID:2 ! distal phalanx • intersection_of: part_of ID:3 ! hand

  6. Editing logical definitions • OBO-Edit • Cross-product tab • Genus • Differentia • Parent Editor • select links to make them ‘intersections’ • Protégé 4 • Equivalent Classes • Enter expression

  7. Using a reasoner • Given: • ‘distal phalanx of hand’ EquivalentTo ‘distal phalanx’ and part_ofsome hand • ‘phalanx of hand’ EquivalentTo phalanxand part_ofsome hand • ‘distal phalanx’ is_a phalanx • A reasoner can infer that: • ‘distal phalanx of hand’ is_a ‘phalanx of hand’ dp ph dph

  8. Uses of a reasoner • Ontology authoring • Time saving • Automatically inferring is_a polyhierarchy • Quality Control • detecting inconsistencies • Data integration and discovery • Less applications… so far

  9. Reasoners • OBO-Edit • Rule Based Reasoner • OWL Reasoners (Protégé 4) • Pellet • FaCT++ • HermiT

  10. Difference between OBO and OWL reasoning • OBO format expresses a subset of OWL • We thought this would be enough for most users • But this turned out not to be true • E.g. Lacks part • See talk later today • Sufficient for basic anatomical classification

  11. Modularity and external ontologies • Modularity principle: • Multiple orthogonal ontologies • Use classes from O1 as building blocks in O2 • E.g. • astrocyte differentiation • anucleate cell • BUT: Can pose problems for large external ontologies • CHEBI • PRO

  12. Import • application can choose to follow import chain • if it doesn’t, then there are dangling references • the full import closure can be large! CL GO-BP imports ontology based application

  13. Large Import Closure CL GO-BP AO GO-CC PRO CHEBI ontology based application

  14. Bridge files • current solution used by NIF, GO CL BP BP-xp-CL more advanced application basic application

  15. MIREOT - Minimal Information for Retrieval of External Ontology Terms • current solution used by OBI, PRO, hemo-CL BP CL (full) CL subset copy • ontology author “MIREOT”s in subset of external ontology

  16. Deploying cell.obo • Typical User • inferred links materialized • external ontology links removed • Advanced User • asserted links only • external links present • minimal external classes included

  17. Ontology publishing pipeline cell_edit.obo cell_public.obo cell_basic.obo reasoner filter GO/PRO/etc subset GO/PRO/etc subset obo2owl obo2owl obo2owl cell_edit.owl cell_public.owl cell_basic.owl reasoner filter GO/PRO/etc subset GO/PRO/etc subset

  18. Summary • Many ontologies are seeing the benefits of using computable definitions • e.g. fly anatomy • GO slow to adopt, lots of legacy issues to work out • Better to employ them from the outset • DC_CL • Hemo_CL

  19. END

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