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Basic Formal Ontology: A Common Standard

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Barry Smith
Barry Smith
EducaçãoTecnologia
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Lecture 7 Towards a Standard Upper Level Ontology
A shocking idea ,[object Object],[object Object]
Scientific ontologies have special features ,[object Object],[object Object]
For science, and thus for scientific ontologies, ,[object Object]
For scientific ontologies ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
For scientific ontologies ,[object Object],[object Object]
BFO ,[object Object],[object Object]
Three Fundamental Dichotomies ,[object Object],[object Object],[object Object],[object Object]
Continuant thing, quality … Occurrent process, event
depends_on Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality quality depends on bearer
depends_on Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality, … event depends on participant
instance_of Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality .... ..... ....... types instances
depends_on Continuant Occurrent process Independent Continuant thing Dependent Continuant quality .... ..... ....... temperature depends on bearer
3 kinds of (binary) relations ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Clark et al ., 2005 part_of is_a Definitions of relations Barry Smith, et al., “Relations in Biomedical Ontologies”, Genome Biology 2005, 6 (5), R46.
Type-level relations presuppose the underlying instance-level relations ,[object Object],[object Object],[object Object],[object Object]
Blinding Flash of the Obvious Continuant Occurrent (Process, Event) Independent Continuant Dependent Continuant How to create an ontology from the top down
Example: The Cell Ontology
Benefits of coordination ,[object Object],[object Object],[object Object],[object Object],[object Object]
Users of BFO ,[object Object],[object Object],[object Object],[object Object],[object Object]
Users of BFO ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Users of BFO ,[object Object],[object Object],[object Object],[object Object],[object Object]
Infectious Disease Ontology Consortium ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],OBO Open Biomedical Ontologies
The Open Biomedical Ontologies (OBO) Foundry RELATION TO TIME GRANULARITY CONTINUANT OCCURRENT INDEPENDENT DEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Biological Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO)
maintained by ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
inspired by ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
some important users ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Blinding Flash of the Obvious Continuant Occurrent (Process, Event) Independent Continuant Dependent Continuant How to create an ontology from the top down
Continuant Independent Continuant Dependent Continuant ..... ..... Non-realizable Dependent Continuant ( quality ) Realizable Dependent Continuant ( function , role , disposition )
Realizable dependent continuants ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],continuants
Their realizations ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],occurrents
Continuant Independent Continuant Dependent Continuant ..... ..... Non-realizable Dependent Continuant ( quality ) Realizable Dependent Continuant ( function , role , disposition )
realization depends_on realizable Continuant Occurrent Independent Continuant bearer Dependent Continuant disposition .... ..... ....... Process of realization
Specific Dependence ,[object Object],[object Object],[object Object],[object Object]
depends_on Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality .... ..... ....... temperature depends on bearer
The (Aristotelian) Ontological Sextet Substances Quality entities Processes Universals Substance-universals Quality-universals Process-universals Particulars Individual Substances Quality-instances (Tropes…) Process-instances
 
Specifically dependent continuants ,[object Object],[object Object],[object Object],[object Object]
the particular case of redness (of a particular fly eye) the universal red instantiates an instance of an eye (in a particular fly) the universal eye instantiates depends on
the particular case of redness (of a particular fly eye) red instantiates an instance of an eye (in a particular fly) eye instantiates depends on color anatomical structure is_a is_a
depends_on Continuant Occurrent process Independent Continuant thing Dependent Continuant quality .... ..... ....... temperature depends on bearer
Specifically Dependent Continuants Specifically Dependent Continuant Quality, Pattern Realizable Dependent Continuant if the bearer ceases to exist, then its quality, function, role ceases to exist the color of my skin the function of my heart to pump blood my weight
The Open Biomedical Ontologies (OBO) Foundry RELATION TO TIME GRANULARITY CONTINUANT OCCURRENT INDEPENDENT DEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Biological Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO)
rationale of OBO Foundry coverage CONTINUANT OCCURRENT INDEPENDENT DEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Organism-Level Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) Cellular Process (GO) MOLECULE Molecule (ChEBI, SO, RNAO, PRO) Molecular Function (GO) Molecular Process (GO) GRANULARITY RELATION TO TIME
Continuant Independent Continuant Specifically Dependent Continuant ..... ..... Quality Realizable Dependent Continuant ( function , role , disposition )
Specific Dependence ,[object Object],[object Object],[object Object],[object Object]
Generically Dependent Continuants Generically Dependent Continuant Information Object Gene Sequence if one bearer ceases to exist, then the entity can survive, because there are other bearers (copyability) the pdf file on my laptop the DNA (sequence) in this chromosome
Continuant Independent Continuant Specifically Dependent Continuant ..... ..... Quality Realizable Dependent Continuant ( function , role , disposition )
Realizable dependent continuants ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],continuants
Their realizations ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],occurrents
Generically Dependent Continuant Realizable Role Information Artifact Sequence… Continuant Occurrent Independent Continuant Specifically Dependent Continuant Quality Disposition Functioning Function
Role (Externally-Grounded Realizable Entity) ,[object Object],[object Object],[object Object]
Disposition (Internally-Grounded Realizable Entity) ,[object Object],[object Object],[object Object]
Function (A Disposition Designed or Selected For) ,[object Object],[object Object],[object Object],[object Object]
The parts of the organism have functions ,[object Object]
What is a Disease? ,[object Object],[object Object],[object Object],[object Object]
Four distinct classificatory tasks ,[object Object],[object Object],[object Object],[object Object]
Four distinct BFO categories ,[object Object],[object Object],[object Object],[object Object]
Disposition ,[object Object],[object Object],[object Object],[object Object],[object Object]
Disorder ,[object Object]
Disorder ,[object Object],[object Object],[object Object],[object Object],[object Object]
Disorder ,[object Object],[object Object],[object Object]
[object Object],[object Object]
Big Picture
[object Object],[object Object],[object Object],etiological process produces disorder bears disposition realized_in pathological process produces abnormal bodily features recognized_as signs & symptoms interpretive process produces diagnosis used_in
Elucidation of Primitive Terms ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Definitions - Foundational Terms ,[object Object],[object Object],[object Object]
Dispositions and Predispositions ,[object Object],[object Object],[object Object]
Cirrhosis - environmental exposure ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Influenza - infectious ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],But the disorder also induces normal physiological processes (immune response) that can results in the elimination of the disorder (transient disease course).
Huntington’s Disease - genetic ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Benefits of coordination ,[object Object],[object Object],[object Object],[object Object]
Why GO is so successful ,[object Object],[object Object],[object Object],[object Object]
Benefits of BFO ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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Basic Formal Ontology: A Common Standard

  • 1. Lecture 7 Towards a Standard Upper Level Ontology
  • 2.
  • 3.
  • 4.
  • 5.
  • 6.
  • 7.
  • 8.
  • 9. Continuant thing, quality … Occurrent process, event
  • 10. depends_on Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality quality depends on bearer
  • 11. depends_on Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality, … event depends on participant
  • 12. instance_of Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality .... ..... ....... types instances
  • 13. depends_on Continuant Occurrent process Independent Continuant thing Dependent Continuant quality .... ..... ....... temperature depends on bearer
  • 14.
  • 15. Clark et al ., 2005 part_of is_a Definitions of relations Barry Smith, et al., “Relations in Biomedical Ontologies”, Genome Biology 2005, 6 (5), R46.
  • 16.
  • 17. Blinding Flash of the Obvious Continuant Occurrent (Process, Event) Independent Continuant Dependent Continuant How to create an ontology from the top down
  • 18. Example: The Cell Ontology
  • 19.
  • 20.
  • 21.
  • 22.
  • 23.
  • 24.
  • 25. The Open Biomedical Ontologies (OBO) Foundry RELATION TO TIME GRANULARITY CONTINUANT OCCURRENT INDEPENDENT DEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Biological Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO)
  • 26.
  • 27.
  • 28.
  • 29. Blinding Flash of the Obvious Continuant Occurrent (Process, Event) Independent Continuant Dependent Continuant How to create an ontology from the top down
  • 30. Continuant Independent Continuant Dependent Continuant ..... ..... Non-realizable Dependent Continuant ( quality ) Realizable Dependent Continuant ( function , role , disposition )
  • 31.
  • 32.
  • 33. Continuant Independent Continuant Dependent Continuant ..... ..... Non-realizable Dependent Continuant ( quality ) Realizable Dependent Continuant ( function , role , disposition )
  • 34. realization depends_on realizable Continuant Occurrent Independent Continuant bearer Dependent Continuant disposition .... ..... ....... Process of realization
  • 35.
  • 36. depends_on Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality .... ..... ....... temperature depends on bearer
  • 37. The (Aristotelian) Ontological Sextet Substances Quality entities Processes Universals Substance-universals Quality-universals Process-universals Particulars Individual Substances Quality-instances (Tropes…) Process-instances
  • 38.  
  • 39.
  • 40. the particular case of redness (of a particular fly eye) the universal red instantiates an instance of an eye (in a particular fly) the universal eye instantiates depends on
  • 41. the particular case of redness (of a particular fly eye) red instantiates an instance of an eye (in a particular fly) eye instantiates depends on color anatomical structure is_a is_a
  • 42. depends_on Continuant Occurrent process Independent Continuant thing Dependent Continuant quality .... ..... ....... temperature depends on bearer
  • 43. Specifically Dependent Continuants Specifically Dependent Continuant Quality, Pattern Realizable Dependent Continuant if the bearer ceases to exist, then its quality, function, role ceases to exist the color of my skin the function of my heart to pump blood my weight
  • 44. The Open Biomedical Ontologies (OBO) Foundry RELATION TO TIME GRANULARITY CONTINUANT OCCURRENT INDEPENDENT DEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Biological Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO)
  • 45. rationale of OBO Foundry coverage CONTINUANT OCCURRENT INDEPENDENT DEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Organism-Level Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) Cellular Process (GO) MOLECULE Molecule (ChEBI, SO, RNAO, PRO) Molecular Function (GO) Molecular Process (GO) GRANULARITY RELATION TO TIME
  • 46. Continuant Independent Continuant Specifically Dependent Continuant ..... ..... Quality Realizable Dependent Continuant ( function , role , disposition )
  • 47.
  • 48. Generically Dependent Continuants Generically Dependent Continuant Information Object Gene Sequence if one bearer ceases to exist, then the entity can survive, because there are other bearers (copyability) the pdf file on my laptop the DNA (sequence) in this chromosome
  • 49. Continuant Independent Continuant Specifically Dependent Continuant ..... ..... Quality Realizable Dependent Continuant ( function , role , disposition )
  • 50.
  • 51.
  • 52. Generically Dependent Continuant Realizable Role Information Artifact Sequence… Continuant Occurrent Independent Continuant Specifically Dependent Continuant Quality Disposition Functioning Function
  • 53.
  • 54.
  • 55.
  • 56.
  • 57.
  • 58.
  • 59.
  • 60.
  • 61.
  • 62.
  • 63.
  • 64.
  • 66.
  • 67.
  • 68.
  • 69.
  • 70.
  • 71.
  • 72.
  • 73.
  • 74.
  • 75.

Notas do Editor

  1. In the following discussion: Classes are in upper case ‘ A ’ is the class Instances are in lower case ‘ a ’ is a particular instance
  2. The gene ontology consortium develops ontologies and makes annotation of gene products to those ontologies. The ontologies are databases containing sets of biological processes, molecular functions, and cellular components and the relationships between them. Annotators within the consortium use these ontologies to categorise gene products. During my talk today I’m going to explain about the uses of GO and give a more detailed explanation of the ontolgoies and of the system of annotation. Then Harold Drabkin is going to talk in more detail about annotation and about how you can submit annotations of your own gene products of interest.