The Ontology of Biological Taxa

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Presentation transcript:

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

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

Biological Taxa: Definition 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

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

Taxa and biomedial vocabularies 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)”

The difficult concept of Species 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

Definition Ontologies Representation [1] 2 3 4 5 Conclusion

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

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

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

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

Definition Ontologies Representation [1] 2 3 4 5 Conclusion

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

How to represent biological taxa? 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

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

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

How to represent biological taxa? 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

How to represent biological taxa? 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

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

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

How to represent biological taxa? 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

How to represent biological taxa? 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

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

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

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

How to represent biological taxa? 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

How to represent biological taxa? 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

Qualities in Upper Ontologies 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

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

?? Definition Ontologies Representation 1 2 3 [4] 5 Conclusion Quality Is_a Taxon_Quality Is_a Kingdom_Animalia_Quality Is_a Phylum_Chordata_ Quality Is_a Class_Mammalia Quality Is_a Order_Primatae Quality q3 Is_a Family_Hominides Quality q4 Is_a Species_Simia T. Quality Species Homo S. Quality World (Particulars) q2 q1 q7 q6 q5 Hela Cell

How to represent biological taxa? 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

How to represent biological taxa? 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

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

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

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

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

How to represent biological taxa? 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

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

Preferred Representations 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

Preferred Representations 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

Preferred Representations 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”

Preferred Representations 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”

Definition Ontologies Representation 1 2 3 4 [5] Conclusion

Summary Favored representation: Taxa are qualities Two flavors: 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

Use cases Embedded in top-level ontology BioTop 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

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