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Understanding OWL for Annotators: A Guide to Web Ontology Language and OBO Integration

This guide introduces annotators to OWL (Web Ontology Language), emphasizing its significance in ontology building, error checking, and automated classification processes. OWL, a certified web standard, enables the expression of complex relationships and concepts that go beyond OBO, which is effectively a mapping to OWL as per the OBO 1.4 specification. The document discusses how OWL reasoning can help automate classification, check for errors, and enhance tools like TermGenie, while offering insights into the implications of annotation extensions. Understanding OWL is essential for successful annotation practices.

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Understanding OWL for Annotators: A Guide to Web Ontology Language and OBO Integration

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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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