Presentation is loading. Please wait.

Presentation is loading. Please wait.

The Ontology of Biological Taxa

Published byBryan George Modified over 8 years ago

Similar presentations

Presentation on theme: "The Ontology of Biological Taxa"— Presentation transcript:

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 Biological Taxa: Definition
Definition Ontologies Representation [1] Conclusion Biological Taxa: Definition

4 Biological Taxa: Definition
Definition Ontologies Representation [1] 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 Taxa and biomedial vocabularies
Definition Ontologies Representation [1] Conclusion Taxa and biomedial vocabularies MeSH: 3,497 entries Catalogue of Life: 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 The difficult concept of Species
Definition Ontologies Representation [1] 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 Basic stipulations on ontologies
Definition Ontologies Representation [1] Conclusion Basic stipulations on ontologies Domain (Particulars)

10 Basic stipulations on ontologies
Definition Ontologies Representation [1] Conclusion Basic stipulations on ontologies Hominid Ontology (Types) Domain (Particulars)

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

12 Basic stipulations on ontologies
Definition Ontologies Representation [1] 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

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

14 How to represent biological taxa?
Definition Ontologies Representation [1] Conclusion How to represent biological taxa?

15 How to represent biological taxa?
Definition Ontologies Representation [1] 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
World (Particulars) Washoe

17 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

18 How to represent biological taxa?
Definition Ontologies Representation [1] 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 How to represent biological taxa?
Definition Ontologies Representation 1 [2] 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
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

21 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

22 How to represent biological taxa?
Definition Ontologies Representation 1 [2] 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 How to represent biological taxa?
Definition Ontologies Representation 1 2 [3] 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 Chimpanzee Population
Definition Ontologies Representation 1 2 [3] Conclusion Taxon Is_a Is_a Is_a Order Family Species Has_granular_part Chimpanzee Population Chimpanzee Class of Chimpanzees World (Particulars)

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

26 Chimpanzee Population
Definition Ontologies Representation 1 2 [3] 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

27 How to represent biological taxa?
Definition Ontologies Representation 1 2 [3] 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 How to represent biological taxa?
Definition Ontologies Representation [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 Qualities in Upper Ontologies
Definition Ontologies Representation [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 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

32 How to represent biological taxa?
Definition Ontologies Representation [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 How to represent biological taxa?
Definition Ontologies Representation [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
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

37 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

38 How to represent biological taxa?
Definition Ontologies Representation [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 Preferred Representations
Definition Ontologies Representation [5] Conclusion Preferred Representations

40 Preferred Representations
Definition Ontologies Representation [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 Preferred Representations
Definition Ontologies Representation [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 Preferred Representations
Definition Ontologies Representation [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 Preferred Representations
Definition Ontologies Representation [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 Summary Favored representation: Taxa are qualities Two flavors:
Definition Ontologies Representation [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 Use cases Embedded in top-level ontology BioTop
Definition Ontologies Representation [5] Conclusion Use cases Embedded in top-level ontology BioTop Demonstration taxon quality hierarchy “taxdemo” in 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 Acknowledgements: The Ontology of Biological Taxa
Stefan Schulz Holger Stenzhorn Martin Boeker Alan Rector, Manchester Michel Dumontier, Ottawa anonymous reviewers

Download ppt "The Ontology of Biological Taxa"

Similar presentations

Classification CP Biology.

Classification CP Biology.
1 Institute of Medical Biometry und Medical Informatics, University Medical Center Freiburg, Germany 2 AVERBIS GmbH, Freiburg, Germany 3 Paediatric Hematology.

1 Institute of Medical Biometry und Medical Informatics, University Medical Center Freiburg, Germany 2 AVERBIS GmbH, Freiburg, Germany 3 Paediatric Hematology.
Schulz S, Boeker M – BioTopLite – An Upper Level Ontology for the Life Sciences – ODLS 2013 BioTopLite : An Upper Level Ontology for the Life Sciences.

Schulz S, Boeker M – BioTopLite – An Upper Level Ontology for the Life Sciences – ODLS 2013 BioTopLite : An Upper Level Ontology for the Life Sciences.
Bio. 230 --- Classification, Taxonomy, Nomenclature.

Bio Classification, Taxonomy, Nomenclature.
Animals Chapter 1 Section 1. Classification Kingdom Phylum Class Order Family Genus Species.

Animals Chapter 1 Section 1. Classification Kingdom Phylum Class Order Family Genus Species.
Classification Biology History Carolus Linnaeus (1707–1778) was born. His great work, the Systema Naturae, ran through twelve editions during his lifetime.

Classification Biology History Carolus Linnaeus (1707–1778) was born. His great work, the Systema Naturae, ran through twelve editions during his lifetime.
Clades and Classes. Classification Methods By ecology By form By ancestry.

Clades and Classes. Classification Methods By ecology By form By ancestry.
Towards a Computational Paradigm for Biological Structure Stefan Schulz Department of Medical Informatics University Hospital Freiburg (Germany) Udo Hahn.

Towards a Computational Paradigm for Biological Structure Stefan Schulz Department of Medical Informatics University Hospital Freiburg (Germany) Udo Hahn.
Ontology Notes are from:

Ontology Notes are from:
What is an Ontology? AmphibiaTree 2006 Workshop Saturday 8:45–9:15 A. Maglia.

What is an Ontology? AmphibiaTree 2006 Workshop Saturday 8:45–9:15 A. Maglia.
Ontology-based Convergence of Medical Terminologies: SNOMED CT and ICD-11 Institute for Medical Informatics, Statistics and Documentation, Medical University.

Ontology-based Convergence of Medical Terminologies: SNOMED CT and ICD-11 Institute for Medical Informatics, Statistics and Documentation, Medical University.
Developing an OWL-DL Ontology for Research and Care of Intracranial Aneurysms – Challenges and Limitations Holger Stenzhorn, Martin Boeker, Stefan Schulz,

Developing an OWL-DL Ontology for Research and Care of Intracranial Aneurysms – Challenges and Limitations Holger Stenzhorn, Martin Boeker, Stefan Schulz,
Taxonomic ontologies: Bridging phylogenetic and taxonomic history Peter Midford University of Kansas Phenoscape Project.

Taxonomic ontologies: Bridging phylogenetic and taxonomic history Peter Midford University of Kansas Phenoscape Project.
The Foundational Model of Anatomy and its Ontological Commitment(s) Stefan Schulz University Medical Center, Freiburg, Germany FMA in OWL meeting November.

The Foundational Model of Anatomy and its Ontological Commitment(s) Stefan Schulz University Medical Center, Freiburg, Germany FMA in OWL meeting November.
Stefan Schulz Medical Informatics Research Group

Stefan Schulz Medical Informatics Research Group
Of 39 lecture 2: ontology - basics. of 39 ontology a branch of metaphysics relating to the nature and relations of being a particular theory about the.

Of 39 lecture 2: ontology - basics. of 39 ontology a branch of metaphysics relating to the nature and relations of being a particular theory about the.
Alignment of the UMLS Semantic Network with BioTop Methodology and Assessment Stefan Schulz University Medical Center, Freiburg, Germany Elena Beisswanger.

Alignment of the UMLS Semantic Network with BioTop Methodology and Assessment Stefan Schulz University Medical Center, Freiburg, Germany Elena Beisswanger.
Semantic Species Taxonomy Shima Izadpanahi CMPE583 Term project.

Semantic Species Taxonomy Shima Izadpanahi CMPE583 Term project.
A CompuGroup Software GmbH, Koblenz, Germany b IMBI, University Medical Center Freiburg, Germany c Semfinder AG, Kreuzlingen, Switzerland d OntoMed Research.

A CompuGroup Software GmbH, Koblenz, Germany b IMBI, University Medical Center Freiburg, Germany c Semfinder AG, Kreuzlingen, Switzerland d OntoMed Research.
Classification of Organisms BIO 138 - Ch. 17. Ch. 17, section 1: Classification of Organisms -Taxonomy is the science of describing, naming, and classifying.

Classification of Organisms BIO Ch. 17. Ch. 17, section 1: Classification of Organisms -Taxonomy is the science of describing, naming, and classifying.

Similar presentations

Ads by Google