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Stefan Schulz Holger Stenzhorn Martin Boeker

The Ontology of Biological Taxa. Stefan Schulz Holger Stenzhorn Martin Boeker. University Medical Center Freiburg (Germany) Institute of Medical Biometry and Medical Informatics. Definition Ontologies Representation [1] 2 3 4 5 Conclusion.

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Stefan Schulz Holger Stenzhorn Martin Boeker

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  1. The Ontology of Biological Taxa Stefan Schulz Holger Stenzhorn Martin Boeker University Medical Center Freiburg (Germany) Institute of Medical Biometry and Medical Informatics

  2. Definition Ontologies Representation [1] 2 3 4 5 Conclusion

  3. Definition Ontologies Representation [1] 2 3 4 5 Conclusion Biological Taxa: Definition

  4. Definition Ontologies Representation [1] 2 3 4 5 Conclusion Biological Taxa: Definition • Taxa (singular taxon): Hierarchically structured labels or ranks used for biological classification • Taxa can be attributed to organisms, populations, tissues, cells, cell components, and biological macromolecules • Most biological discourse is related to some taxa • Clarification taxa vs. species

  5. Definition Ontologies Representation [1] 2 3 4 5 Conclusion Examples for Taxa Taxon Chimpanzee Asian Elephant Drosophila (Rank) Kingdom Animalia Animalia Animalia Phylum Chordata Chordata Arthropoda Subphylum Vertebrata V ertebrata Class Mammalia Mammalia Insecta Order Primates Proboscidea Diptera Superfamily Elephantoidea Family Hominides Elephantidae Drosophilidae Subfamily Drosophilinae Genus Pan Elephas Drosophila Species Simia Elephas m aximus Drosophila trogl o dytes melanogaster

  6. Definition Ontologies Representation [1] 2 3 4 5 Conclusion Taxa and biomedial vocabularies • MeSH: 3,497 entries • Catalogue of Life: 1.75 M species by 2011 • NCBI taxonomy: 500,000 entries • UNIPROT: 17,467 entries • SNOMED CT: 27,400 entries • OBO: 30 out of 66 ontologies are taxon-specific • Nonspecific OBO ontologies: • GO : “spore wall assembly (sensu Fungi)“ “male tail morphogenesis (sensu Nematoda)” • CL: “non-visual cell (sensu Vertebrata)” “chemotactic amoeboid cell (sensu Mycetozoa)”

  7. Definition Ontologies Representation [1] 2 3 4 5 Conclusion The difficult concept of Species • No agreement on proper definition of the term “species” and its ontological status • 22 different conceptualizations of species • Popular: „group of organisms that can interbreed and produce fertile offspring (Mayr, 1969) “ • Theoretical sound, difficult to apply, not generally valid • Our approach: biological taxa need to be accounted for in biomedical ontologies, let alone whether they exist in nature or are merely (fiat) attributions by biologists

  8. Definition Ontologies Representation [1] 2 3 4 5 Conclusion

  9. Definition Ontologies Representation [1] 2 3 4 5 Conclusion Basic stipulations on ontologies Domain (Particulars)

  10. Definition Ontologies Representation [1] 2 3 4 5 Conclusion Hominid Basic stipulations on ontologies Ontology (Types) Domain (Particulars)

  11. Definition Ontologies Representation [1] 2 3 4 5 Conclusion Is_a Is_a Is_a Orangutan Gorilla Chimpanzee Instance_of Washoe Basic stipulations on ontologies Hominid Ontology (Types) Domain (Particulars)

  12. Definition Ontologies Representation [1] 2 3 4 5 Conclusion Instance_of Washoe Basic stipulations on ontologies Subtype (subclass) relation Is_a: Is_a (A, B) =defx: (instance_of (x, A)  instance_of (x, B)) Primate Is_a Type Hominid Ontology (Types) Is_a Is_a Is_a Orangutan Gorilla Chimpanzee Class Instantiation Domain (Particulars) Particular

  13. Definition Ontologies Representation [1] 2 3 4 5 Conclusion

  14. Definition Ontologies Representation [1] 2 3 4 5 Conclusion How to represent biological taxa?

  15. Definition Ontologies Representation[1] 2 3 4 5 Conclusion How to represent biological taxa? • Meta-Properties+ Intuitive- Instances of instances cannot be expressed by common representational formalisms (OWL, OBO) • Supertypes:+ Intuitive- Unintended inferences • Population instances+ Allows instantiation of abstract nodes (taxon, species, family…)- Requires A-Box extension (not expressible in OBO), - Only representation of organisms. • Qualities+ Flexible and intuitive- No place for abstract nodes • Qualia+ Abstract nodes can be represented as quality regions- Complex representation

  16. Definition Ontologies Representation[1] 2 3 4 5 Conclusion Washoe World (Particulars)

  17. Definition Ontologies Representation[1] 2 3 4 5 Conclusion Taxon Meta-Ontology (Meta-Properties) Is_a Is_a Is_a Species Order Family Instance_of Instance_of Instance_of Instance_of Washoe Primate Is_a Hominid Ontology (Types) Is_a Is_a Is_a Orangutan Gorilla Chimpanzee World (Particulars)

  18. Definition Ontologies Representation[1] 2 3 4 5 Conclusion How to represent biological taxa? • Meta-Properties+ Intuitive- Instances of instances cannot be expressed by common representational formalisms (OWL, OBO) • Supertypes:+ Intuitive- Unintended inferences • Population instances+ Allows instantiation of abstract nodes (taxon, species, family…)- Requires A-Box extension (not expressible in OBO), - Only representation of organisms. • Qualities+ Flexible and intuitive- No place for abstract nodes • Qualia+ Abstract nodes can be represented as quality regions- Complex representation

  19. Definition Ontologies Representation 1 [2] 3 4 5 Conclusion How to represent biological taxa? • Meta-Properties+ Intuitive- Instances of instances cannot be expressed by common representational formalisms (OWL, OBO) • Supertypes:+ Intuitive- Unintended inferences • Population instances+ Allows instantiation of abstract nodes (taxon, species, family…)- Requires A-Box extension (not expressible in OBO), - Only representation of organisms. • Qualities+ Flexible and intuitive- No place for abstract nodes • Qualia+ Abstract nodes can be represented as quality regions- Complex representation

  20. Definition Ontologies Representation 1 [2] 3 4 5 Conclusion Taxon Meta-Ontology (Meta-Properties) Is_a Is_a Is_a Species Order Family Instance_of Instance_of Instance_of Instance_of Washoe Primate Is_a Hominid Ontology (Types) Is_a Is_a Is_a Orangutan Gorilla Chimpanzee World (Particulars)

  21. Definition Ontologies Representation 1 [2] 3 4 5 Conclusion Washoe Taxon Ontology (Types) Is_a Is_a Is_a Species Order Family Is_a Is_a Primate Is_a Hominid Is_a Is_a Is_a Orangutan Gorilla Chimpanzee World (Particulars) Instance_of

  22. Definition Ontologies Representation 1 [2] 3 4 5 Conclusion How to represent biological taxa? • Meta-Properties+ Intuitive- Instances of instances cannot be expressed by common representational formalisms (OWL, OBO) • Supertypes:+ Intuitive- Unintended inferences • Population instances+ Allows instantiation of abstract nodes (taxon, species, family…)- Requires A-Box extension (not expressible in OBO), - Only representation of organisms. • Qualities+ Flexible and intuitive- No place for abstract nodes • Qualia+ Abstract nodes can be represented as quality regions- Complex representation

  23. Definition Ontologies Representation 1 2 [3] 4 5 Conclusion How to represent biological taxa? • Meta-Properties+ Intuitive- Instances of instances cannot be expressed by common representational formalisms (OWL, OBO) • Supertypes:+ Intuitive- Unintended inferences • Population instances+ Allows instantiation of abstract nodes (taxon, species, family…)- Requires A-Box extension (not expressible in OBO), - Only representation of organisms. • Qualities+ Flexible and intuitive- No place for abstract nodes • Qualia+ Abstract nodes can be represented as quality regions- Complex representation

  24. Definition Ontologies Representation 1 2 [3] 4 5 Conclusion Has_granular_part Class of Chimpanzees Taxon Is_a Is_a Is_a Species Order Family ChimpanzeePopulation Chimpanzee World (Particulars)

  25. Definition Ontologies Representation 1 2 [3] 4 5 Conclusion Has_granular_part chimp1 chimp2 Taxon Is_a Is_a Is_a Species Order Family ChimpanzeePopulation Chimpanzee World (Particulars) Class of Chimpanzees

  26. Definition Ontologies Representation 1 2 [3] 4 5 Conclusion HominidPopulation Has_granular_part Is_a Hominid_max Taxon Is_a Is_a Is_a Species Order Family ChimpanzeePopulation Chimpanzee Is_a World (Particulars) Class of Chimpanzees Chimp_max

  27. Definition Ontologies Representation 1 2 [3] 4 5 Conclusion How to represent biological taxa? • Meta-Properties+ Intuitive- Instances of instances cannot be expressed by common representational formalisms (OWL, OBO) • Supertypes:+ Intuitive- Unintended inferences • Population instances+ Allows instantiation of abstract nodes (taxon, species, family…)- Requires A-Box extension (not expressible in OBO), - Only representation of organisms. • Qualities+ Flexible and intuitive- No place for abstract nodes • Qualia+ Abstract nodes can be represented as quality regions- Complex representation

  28. Definition Ontologies Representation 1 2 3 [4] 5 Conclusion How to represent biological taxa? • Meta-Properties+ Intuitive- Instances of instances cannot be expressed by common representational formalisms (OWL, OBO) • Supertypes:+ Intuitive- Unintended inferences • Population instances+ Allows instantiation of abstract nodes (taxon, species, family…)- Requires A-Box extension (not expressible in OBO), - Only representation of organisms. • Qualities+ Flexible and intuitive- No place for abstract nodes • Qualia+ Abstract nodes can be represented as quality regions- Complex representation

  29. Definition Ontologies Representation 1 2 3 [4] 5 Conclusion Qualities in Upper Ontologies • BFO : “A dependent continuant that is exhibited if it inheres in an entity or categorical property. Examples: the color of a tomato, the ambient temperature of air, the circumference shape of a nose, the mass of a piece of gold, the weight of a chimpanzee” • DOLCE : “…the basic entities we can perceive or measure: shapes, colors, sizes, sounds, smells, as well as weights, lengths, electric charges” • The relation inheres_in links qualities to their bearers

  30. Definition Ontologies Representation 1 2 3 [4] 5 Conclusion Hela Cell

  31. Definition Ontologies Representation 1 2 3 [4] 5 Conclusion ?? q4 q3 q2 q1 q7 q6 q5 Quality Is_a Taxon_Quality Is_a Kingdom_Animalia_Quality Is_a Phylum_Chordata_Quality Is_a Class_MammaliaQuality Is_a Order_PrimataeQuality Is_a Family_HominidesQuality Is_a Species_Simia T.Quality Species Homo S.Quality World (Particulars) Hela Cell

  32. Definition Ontologies Representation 1 2 3 [4] 5 Conclusion How to represent biological taxa? • Meta-Properties+ Intuitive- Instances of instances cannot be expressed by common representational formalisms (OWL, OBO) • Supertypes:+ Intuitive- Unintended inferences • Population instances+ Allows instantiation of abstract nodes (taxon, species, family…)- Requires A-Box extension (not expressible in OBO), - Only representation of organisms. • Qualities+ Flexible and intuitive- No place for abstract nodes • Qualia+ Abstract nodes can be represented as quality regions- Complex representation

  33. Definition Ontologies Representation 1 2 3 4 [5] Conclusion How to represent biological taxa? • Meta-Properties+ Intuitive- Instances of instances cannot be expressed by common representational formalisms (OWL, OBO) • Supertypes:+ Intuitive- Unintended inferences • Population instances+ Allows instantiation of abstract nodes (taxon, species, family…)- Requires A-Box extension (not expressible in OBO), - Only representation of organisms. • Qualities+ Flexible and intuitive- No place for abstract nodes • Qualia+ Abstract nodes can be represented as quality regions- Complex representation

  34. Definition Ontologies Representation 1 2 3 4 [5] Conclusion q1 q2

  35. Definition Ontologies Representation 1 2 3 4 [5] Conclusion Taxon Quality Is_a Order Quality Is_a Family Quality Species Quality q1 q2

  36. Definition Ontologies Representation 1 2 3 4 [5] Conclusion q1 Taxon Quality Primatae Region Is_a Order Quality Is_a Part-of Hominides Region Family Quality Part-of Species Quality Simia T. Region Has-location some q2

  37. Definition Ontologies Representation 1 2 3 4 [5] Conclusion q1 TaxonRegion Is_a Is_a Is_a FamilyRegion OrderRegion SpeciesRegion Taxon Quality Primatae Region Is_a Order Quality Is_a Part-of Hominides Region Family Quality Part-of Species Quality Simia T. Region Has-location some q2

  38. Definition Ontologies Representation 1 2 3 4 [5] Conclusion How to represent biological taxa? • Meta-Properties+ Intuitive- Instances of instances cannot be expressed by common representational formalisms (OWL, OBO) • Supertypes:+ Intuitive- Unintended inferences • Population instances+ Allows instantiation of abstract nodes (taxon, species, family…)- Requires A-Box extension (not expressible in OBO), - Only representation of organisms. • Qualities+ Flexible and intuitive- No place for abstract nodes • Qualia+ Abstract nodes can be represented as quality regions- Complex representation

  39. Definition Ontologies Representation 1 2 3 4 [5] Conclusion Preferred Representations

  40. Definition Ontologies Representation 1 2 3 4 [5] Conclusion Preferred Representations • Meta-Properties+ Intuitive- Instances of instances cannot be expressed by common representational formalisms (OWL, OBO) • Supertypes:+ Intuitive- Unintended inferences • Population instances+ Allows instantiation of abstract nodes (taxon, species, family…)- Requires A-Box extension (not expressible in OBO), - Only representation of organisms. • Qualities+ Flexible and intuitive- No place for abstract nodes • Qualia+ Abstract nodes can be represented as quality regions- Complex representation

  41. Definition Ontologies Representation 1 2 3 4 [5] Conclusion Preferred Representations • Meta-Properties+ Intuitive- Instances of instances cannot be expressed by common representational formalisms (OWL, OBO) • Supertypes:+ Intuitive- Unintended inferences • Population instances+ Allows instantiation of abstract nodes (taxon, species, family…)- Requires A-Box extension (not expressible in OBO), - Only representation of organisms. • Qualities+ Flexible and intuitive- No place for abstract nodes • Qualia+ Abstract nodes can be represented as quality regions- Complex representation

  42. Definition Ontologies Representation 1 2 3 4 [5] Conclusion Preferred Representations • Meta-Properties+ Intuitive- Instances of instances cannot be expressed by common representational formalisms (OWL, OBO) • Supertypes:+ Intuitive- Unintended inferences • Population instances+ Allows instantiation of abstract nodes (taxon, species, family…)- Requires A-Box extension (not expressible in OBO), - Only representation of organisms. • Qualities+ Flexible and intuitive- No place for abstract nodes • Qualia+ Abstract nodes can be represented as quality regions- Complex representation “BFO”

  43. Definition Ontologies Representation 1 2 3 4 [5] Conclusion Preferred Representations • Meta-Properties+ Intuitive- Instances of instances cannot be expressed by common representational formalisms (OWL, OBO) • Supertypes:+ Intuitive- Unintended inferences • Population instances+ Allows instantiation of abstract nodes (taxon, species, family…)- Requires A-Box extension (not expressible in OBO), - Only representation of organisms. • Qualities+ Flexible and intuitive- No place for abstract nodes • Qualia+ Abstract nodes can be represented as quality regions- Complex representation “DOLCE”

  44. Definition Ontologies Representation 1 2 3 4 [5] Conclusion

  45. Definition Ontologies Representation 1 2 3 4 [5] Conclusion Summary • Favored representation: Taxa are qualities • Two flavors: • Subtype hierarchies of qualities • Inclusion hierarchies of quality regions • Compatible with OBO / OWL-DL • Qualities can inhere in populations, organisms, body parts, biomolecules (“sensu”) • Compatible with Mayr’s concept of species as populations: each taxon quality corresponds to exactly one group of organisms

  46. Definition Ontologies Representation 1 2 3 4 [5] Conclusion Use cases • Embedded in top-level ontology BioTop • Demonstration taxon quality hierarchy “taxdemo” in http://purl.org/biotop • NCBI taxonomy converted into OWL-DL taxon quality hierarchy (Dumontier Lab, Carleton University, Canada) • Suggested formalism for the organism hierarchy redesign of SNOMED CT

  47. The Ontology of Biological Taxa Acknowledgements: Stefan Schulz Holger Stenzhorn Martin Boeker Alan Rector, Manchester Michel Dumontier, Ottawa anonymous reviewers

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