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Principles and Practice of Ontology Development: Making Definitions Computable

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

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Principles and Practice 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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