Basic Formal Ontology: A Common Standard
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The document discusses the Basic Formal Ontology (BFO), a top-level ontology intended to support information integration in scientific research. BFO defines three fundamental dichotomies: continuant vs. occurrent, independent vs. dependent, and type vs. instance. It also distinguishes between specifically dependent continuants like qualities and realizable dependent continuants like functions. The goal of BFO is to provide a framework for building consistent lower-level ontologies in a reusable manner.
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Basic Formal Ontology: A Common Standard
- 1. Lecture 7 Towards a Standard Upper Level Ontology
- 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
- 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.
- 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
- 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)
- 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 )
- 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
- 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
- 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 )
- 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 )
- 52. Generically Dependent Continuant Realizable Role Information Artifact Sequence… Continuant Occurrent Independent Continuant Specifically Dependent Continuant Quality Disposition Functioning Function
- 65. Big Picture
Editor's Notes
- In the following discussion: Classes are in upper case ‘ A ’ is the class Instances are in lower case ‘ a ’ is a particular instance
- 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.