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OWL for annotators

OWL for annotators. David Osumi - Sutherland. What is OWL?. Web Ontology Language Can express everything in OBO and more . Certified web standard Fast reasoning software allows: automated ontology building; error checking; queries . I’m an annotator, why should I care about OWL?.

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OWL for annotators

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  1. OWL for annotators David Osumi-Sutherland

  2. What is OWL? • Web Ontology Language • Can express everything in OBO and more. • Certified web standard • Fast reasoning software allows: • automated ontology building; error checking; queries

  3. I’m an annotator, why should I care about OWL? • OBO is OWL • OBO 1.4 spec defines OBO as a mapping to OWL. • OWL reasoning is used by GO to: • Automate classification during ontology building • Check for errors (inconsistencies) in ontology and annotations • Drive TermGenie • Tell you how annotation extensions fold

  4. I’m an annotator, why should I care about OWL? • OBO is OWL • OBO 1.4 spec defines OBO as a mapping to OWL. • OWL reasoning is used by GO to: • Automate classification during ontology building • Check for errors (inconsistencies) in ontology and annotations • Drive TermGenie • Tell you how annotation extensions fold YOU CAN’T KNOW HOW AN ANNOTATION EXTENSION WILL FOLD WITHOUT ASKING A REASONER!

  5. What is an ontology ? A classification appendage antenna wing forewing hindwing

  6. OBO-OWL cheat sheet: classification OWL: antenna SubClassOfappendage OBO: antennais_a appendage

  7. Relationships record necessary conditions for class membership Being part of a thoracic segment is a necessary condition of being in the class leg ‘leg’ SubClassOfpart_ofsome thoracic segment part_ofsome ‘thoracic segment leg wing

  8. class – class relationships are quantified • Class:Class relationships are many to many • Does the relation apply to all or just some of the class ? • we specify this with quantifiers: • some ∃: there exists, • ∀: for all, all, only, every

  9. relationships between classes use quantifiers • OBO (quantifiers hidden) • name: leg • relationship: part_ofthoracic segment • OWL (MS): • leg SubClassOfpart_ofsome ‘thoracic segment’

  10. Directionality and quantifiers ✔ ‘wing’ SubClassOfpart_ofsome thoracic segment ✗ ‘thoracic segment’ SubClassOfhas_partsome ‘wing’ has_partsome wing thoracic segment

  11. Defining necessary and sufficient conditions for class membership • English • Any appendage that is part of some thoracic segment is a thoracic appendage • OWL • thoracic appendage EquivalentTo‘appendage’ and part_ofsome thoracic segment • OBO • name: thoracic appendage • intersection_of: appendage • intersection_of: part_ofthoracic segment part_ofsomethoracic segment thoracic appendage appendage

  12. part_ofsome ‘thoracic segment’ appendage wing wing thoracic appendage wing part_ofsome‘thoracic segment' thoracic appendage appendage

  13. How automated classification helpsontology building • Record • one classification (is_a) • relationships (necessary conditions for class membership) • Reason: • To find what other classifications are applicable +ve: It is very hard to find all relevant classifications by hand. -ve: Only works if relations well defined and understood

  14. We don’t need to make a class to express a concept in OWL • Just as in annotation extensions

  15. Some relations entail others negatively regulates regulates regulates some ‘cell division’ negatively_regulatessome ‘cell division’ X X

  16. Rules IFXregulates Y AND Y part_ofZ X regulates Z

  17. IFXregulates Y AND Y part_ofZ X regulates Z regulates some Y part_ofsome Z Y X regulates some Z X

  18. Annotation extension -> OWL

  19. Folding folding

  20. Unfolding

  21. OWL translation of C16 with multiple clauses Note – not nested Sometimes reasoning will give classifications you might not expect.

  22. OWL translation of C16 finding equivalent GO terms AE equivalent to existing term

  23. TermGenie examples TG: regulation of cell adhesion involved in retrograde extension is_a: GO:0010975 {is_inferred="true"} ! regulation of neuron projection development is_a: GO:0030155 {is_inferred="true"} ! regulation of cell adhesion

  24. The reasons for inferred classification can be complicated

  25. Take home messages • If you understand the relations you use then the classification should look after itself. • Except in the most trivial cases, you can’t work out how an annotation extension will fold. • Tooling support may be necessary to help understand the implications of annotation extensions

  26. Tooling support for Annotation Extensions • A web tool to allow annotators to find how extensions will fold, check for equivalence, etc?

  27. PROBABLY WON’T USE SLIDES FROM HERE ON

  28. ERROR MESSAGES ARE YOUR FRIENDS! – They tell you you’ve screwed up before you get embarrassing emails complaining that you’ve screwed up

  29. Some classes don’t intersect OWL DisjointWithOBO: disjoint_from X Y X Y ✗

  30. Some classes don’t intersect cellular component molecular function nucleus kinase activity kinase activity ✗ nucleus is_akinase activity nucleus subClassOfkinase activity nucleus

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