Underlying Ontologies for Biomedical work - The Relation Ontology (RO) and Basic Formal Ontology (BFO) Thomas Bittner SUNY Buffalo Disclaimer: I recycle many slides originally made by Barry Smith
Overview Motivation BFO and RO Top-level categories and relations of BFO/RO Conclusions
Why do we need a top-level ontology such as Basic Formal Ontology (BFO) ?
Karen Eilbecksong.sf.net properties and features of nucleic sequences Sequence Ontology (SO) RNA Ontology Consortium(under development) three-dimensional RNA structures RNA Ontology (RnaO) Barry Smith, Chris Mungall obo.sf.net/relationship relations Relation Ontology (RO) Protein Ontology Consortium (under development) protein types and modifications Protein Ontology (PrO) Michael Ashburner, Suzanna Lewis, Georgios Gkoutos obo.sourceforge.net/cgi -bin/ detail.cgi? attribute_and_value qualities of biomedical entities Phenotypic Quality Ontology (PaTO) Gene Ontology Consortium cellular components, molecular functions, biological processes Gene Ontology (GO) FuGO Working Groupfugo.sf.net design, protocol, data instrumentation, and analysis Functional Genomics Investigation Ontology (FuGO) JLV Mejino Jr., Cornelius Rosse fma.biostr.washington. edu structure of the human body Foundational Model of Anatomy (FMA) Melissa Haendel, Terry Hayamizu, Cornelius Rosse, David Sutherland, (under development) anatomical structures in human and model organisms Common Anatomy Refer- ence Ontology (CARO) Paula Dematos, Rafael Alcantara ebi.ac.uk/chebimolecular entities Chemical Entities of Bio- logical Interest (ChEBI) Jonathan Bard, Michael Ashburner, Oliver Hofman obo.sourceforge.net/cgi- bin/detail.cgi?cell cell types from prokaryotes to mammals Cell Ontology (CL) CustodiansURLScopeOntology
Karen Eilbecksong.sf.net properties and features of nucleic sequences Sequence Ontology (SO) RNA Ontology Consortium (under development) three-dimensional RNA structures RNA Ontology (RnaO) Barry Smith, Chris Mungall obo.sf.net/relationship relations Relation Ontology (RO) Protein Ontology Consortium (under development) protein types and modifications Protein Ontology (PrO) Michael Ashburner, Suzanna Lewis, Georgios Gkoutos obo.sourceforge.net/cgi -bin/ detail.cgi? attribute_and_value qualities of biomedical entities Phenotypic Quality Ontology (PaTO) Gene Ontology Consortium cellular components, molecular functions, biological processes Gene Ontology (GO) FuGO Working Groupfugo.sf.net design, protocol, data instrumentation, and analysis Functional Genomics Investigation Ontology (FuGO) JLV Mejino Jr., Cornelius Rosse fma.biostr.washington. edu structure of the human body Foundational Model of Anatomy (FMA) Melissa Haendel, Terry Hayamizu, Cornelius Rosse, David Sutherland, (under development) anatomical structures in human and model organisms Common Anatomy Refer- ence Ontology (CARO) Paula Dematos, Rafael Alcantara ebi.ac.uk/chebimolecular entities Chemical Entities of Bio- logical Interest (ChEBI) Jonathan Bard, Michael Ashburner, Oliver Hofman obo.sourceforge.net/cgi- bin/detail.cgi?cell cell types from prokaryotes to mammals Cell Ontology (CL) CustodiansURLScopeOntology Many partly independent efforts
Domain ontologies organized according to formal ontological principles RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT 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)
Domain ontologies organized according to formal ontological principles RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT 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)
FMA Domain ontologies specify the semantics of the vocabulary of a particular domain: RNAO ChEBI Cell Ontology PaTO
FMA RNAO ChEBI Cell Ontology PaTO Top-level ontology TLO All domain ontologies use the same top level notions
FMA RNAO ChEBI Cell Ontology PaTO Top-level ontology BFO All domain ontologies use the same top level notions Ontological principles
FMA RNAO ChEBI Cell Ontology PaTO BFO All domain ontologies use the same top level notions Diversity in the specifics Commonality in the foundations
FMA RNAO ChEBI Cell Ontology PaTO BFO All domain ontologies use the same top level notions Facilitates interoperatibility
FMA RNAO ChEBI Cell Ontology PaTO BFO All domain ontologies use the same top level notions Facilitates interoperatibility
FMA RNAO ChEBI Cell Ontology PaTO All domain ontologies use the same top level notions Shared Organizational, Scientific, and Ontological principles RO
More acronyms: BFO vs. BFO-FOL vs. BFO-DL vs. RO
Kinds of Ontologies Terms General Logic Thesauri formal Taxonomies Frames (OKBC) Data Models (UML, STEP) Description Logics (DAML+OIL) Principled, informal hierarchies ad hoc Hierarchies (Yahoo!) structured Glossaries XML DTDs Data Dictionaries (EDI) ‘ordinary’ Glossaries XML Schema DB Schema Glossaries & Data Dictionaries MetaData, XML Schemas, & Data Models Formal Ontologies & Inference Thesauri, Taxonomies Michael Gruninger,
Ontologies: logical inferences Non-ontologies: no logical inferences Kinds of Ontologies Terms General Logic Thesauri formal Taxonomies Frames (OKBC) Data Models (UML, STEP) Description Logics (DAML+OIL) Principled, informal hierarchies ad hoc Hierarchies (Yahoo!) structured Glossaries XML DTDs Data Dictionaries (EDI) ‘ordinary’ Glossaries XML Schema DB Schema
Kinds of Ontology Languages General Logic Description Logics (DAML+OIL) Tradeoff between expressive power and computability How well can we specify intended meaning of terms What can we compute automatically
Kinds of Ontology Languages General Logic Description Logics (DAML+OIL) Tradeoff between expressive power and computability How well can we specify intended meaning of terms What can we compute automatically
Kinds of Ontology Languages General Logic Description Logics (DAML+OIL) Tradeoff between expressive power and computability How well can we specify intended meaning of terms What can we compute automatically
We need BOTH kinds of languages General Logic Description Logics (DAML+OIL) Tradeoff between expressive power and computability How well can we specify intended meaning What can we compute automatically
Computational representations of BFO
BFO-FOL ‘implementation’ of BFO in first order logic
Computational representations of BFO BFO-DL ‘implementation’ of BFO in the description logic OWL (Ontology WEB language) BFO-FOL ‘implementation’ of BFO in first order logic
Computational representations of BFO BFO-DL ‘implementation’ of BFO in OWL BFO-FOL ‘implementation’ of BFO in first order logic Focus on logically sound formulation of ontological principles high expressive power of FOL needed Focus on computation based on logically verified principles computational efficiency of a DL needed
26 BFO vs. RO RO = Relation ontology RO is a sub-set of BFO-DL that has been included in the OBO framework of ontologies
27 What is ‘in’ the Relation Ontology (RO) ??? Logically verified terminology that is relevant to the OBO-framework terminology for top-level categories terminology for top-level relations
Two distinct kinds of entities universalsparticulars typestokens classesinstances
Misha instances Tom Instance-of substance siamese Is-a cat Is-a mammal Is-a animal Is-a organism Is-a Human being Is-a Universals, classes, types
Particulars: Continuants vs. occurrents
Persistent entities
Continuant Persists through time in virtue of being wholly present at every time at which it exists at all. I exist in full at this moment in time
Persistent entities Continuant Persists through time in virtue of being wholly present at every time at which it exists at all. I exist in full at this moment in time Occurrent Evolve over time Do not exist in full at any given moment This presentation does not exist in full right now
Continuants have spatial parts
Occurrents (processes) have spatio-temporal parts t i m e process
Continuants do NOT have spatio- temporal parts I am a continuant The first 5-minute phase of my existence is not a spatio-temporal part of me It is a spatio-temporal part of my life My life is a process
Ontologies organized according to ontological principles RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT 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)
38 Kinds of continuants Independent continuants (substances) Dependent continuants
39 Kinds of continuants Independent continuants (substances) Dependent continuants
40 Kinds of continuants Independent continuants (substances) Dependent continuants
41 Kinds of continuants Independent continuants (substances) Dependent continuants the yellow color of this car the maximal speed of this car
42 Kinds of continuants Independent continuants (substances) Dependent continuants the mass of this planet its disposition to sustain life
43 Kinds of continuants Independent continuants (substances) Dependent continuants the mass of this molecule its disposition to engage in chemical reactions
Ontologies organized according to ontological principles RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT 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)
Ontologies organized according to ontological principles RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT 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)
Universals and particulars (cont.)
Misha substance instances Tom Instance-of substance siamese Is-a cat Is-a mammal Is-a animal Is-a organism Is-a Human being Is-a substance- Universals
Accidents: Species and instances quality color red scarlet R232, G54, B24 Barry Smith Universals among dependent continuants Is-a this individual token of redness (this token redness – here, now) Inst-Of
Of dependent continuants Universals and particulars Accidents: Species and instances substance animal mammal human Irishman this individual token man Of independent continuants
Substance universals Ontologies organized according to ontological principles RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT 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)
Quality/func tion universals Ontologies organized according to ontological principles RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT 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)
52 What is ‘in’ the Relation Ontology (RO) ??? Logically verified terminology that is relevant to the OBO-framework terminology for top-level categories terminology for top-level relations
53 What is ‘in’ the Relation Ontology (RO) ??? Logically verified terminology that is relevant to the OBO-framework terminology for top-level categories terminology for top-level relations
Misha instances Tom Instance-of substance siamese Is-a cat Is-a mammal Is-a animal Is-a organism Is-a Human being Is-a is-a relation between Unive rsals
Misha instances Tom Instance-of substance siamese Is-a cat Is-a mammal Is-a animal Is-a organism Is-a Human being Is-a is-a relation between Unive rsals Human Being is-a mammal Every instance of Human Being is also an instance of mammal
Misha instances Tom Instance-of hasPet isPetOf substance siamese Is-a cat Is-a mammal Is-a animal Is-a organism Is-a Human being Is-a is-a relation between Unive rsals IsPetOf
Instance-level relations universal-level relations Misha instances Tom Instance-of hasPet isPetOf cat Human being Universals HasPet IsPetOf
Universal parthood: Human anatomy The universal human body The universal human head Human heads are parts of human bodies
Universal parthood Human-heads Human-bodies Part-of
Universal parthood Human-heads Human-bodies HasPart
The semantics of universal parthood X PART-OF Y iff For every instance x of X there exists an instance y of Y such that x part-of y AND For every instance y of Y there exists an instance x of X such that x part-of y
General framework for defining universal-level relations in terms of relations between individuals R all-some (A, B) =: ∀ x (Inst(x, A) → ∃ y( Inst(y, B) & Rxy)) For every instance x of A there is some instance y of B such that R(x,y) holds R some-all (A, B) =: ∀ y (Inst(y, B) → ∃ x( Inst(x, A) & Rxy)) For every instance y of B there is some instance x of A such that R(x,y) holds R all-all (A, B) =: R all-some (A, B) & R some-all (A, B) R can be ANY binary relation
63 Important Individual-level relations
Independent Continuant Occurrent Dependent Continuant You, me, This molecule, My cat Misha Individual-level relations
Independent Continuant Occurrent Dependent Continuant My temperature (now) My height My role as a presenter Individual-level relations
Independent Continuant Occurrent Dependent Continuant Processes: My life, My presenting this talk Individual-level relations
Independent Continuant Occurrent Dependent Continuant Part-of My heart part-of my body Montana part-of United States Individual-level relations
Independent Continuant Occurrent ParticipatesIn Part-of the runner participates in the racing process the molecule participates in the diffusion process Dependent Continuant Individual-level relations
Dependent Continuant Independent Continuant Occurrent ParticipatesIn Part-of the racing involves racers the diffusion process involves molecules Involves Individual-level relations
Independent Continuant Occurrent Dependent Continuant ParticipatesIn Part-of the first 10 minutes of the presentation are part of the presentation my childhood is part of my life Involves Individual-level relations
Independent Continuant Occurrent Dependent Continuant ParticipatesIn RealizationOf PartOf The power of a catalytic RNA to catalyze a reaction is realized through a complex process of binding substrates in the correct orientation and stabilizing reaction intermediates The role of antibiotics in treating infections is realized via the killing of bacteria Involves Individual-level relations
Independent Continuant Occurrent Dependent Continuant ParticipatesIn RealizationOf PartOf A warming process yields a rise in temperature The tenure process yields a rise in John’s status Involves Changes quality Individual-level relations
Independent Continuant Occurrent Dependent Continuant ParticipatesIn InheresIn RealizationOf Part-of PartOf Your height inheres in you The role the antibiotics inheres in the antibiotics Involves Changes quality Individual-level relations
Independent Continuant Occurrent Dependent Continuant ParticipatesIn InheresIn RealizationOf Part-of PartOf Involves Changes quality Individual-level relations
Time-dependent relations ternary relations time as parameter R xyt the relation R holds between x and y and t My left hand is (individual) part of my left arm now Time-independent relations binary relations R xy the relation R holds between x and y Left Human Hand is part of Left Human Body (Canonical anatomy) Relations among independent persistent entities
76 Conclusions
FMA RNAO ChEBI Cell Ontology PaTO Based upon the top-level ontology BFO RO All domain ontologies use the same top level notions
Karen Eilbecksong.sf.net properties and features of nucleic sequences Sequence Ontology (SO) RNA Ontology Consortium(under development) three-dimensional RNA structures RNA Ontology (RnaO) Barry Smith, Chris Mungall obo.sf.net/relationship relations Relation Ontology (RO) Protein Ontology Consortium (under development) protein types and modifications Protein Ontology (PrO) Michael Ashburner, Suzanna Lewis, Georgios Gkoutos obo.sourceforge.net/cgi -bin/ detail.cgi? attribute_and_value qualities of biomedical entities Phenotypic Quality Ontology (PaTO) Gene Ontology Consortium cellular components, molecular functions, biological processes Gene Ontology (GO) FuGO Working Groupfugo.sf.net design, protocol, data instrumentation, and analysis Functional Genomics Investigation Ontology (FuGO) JLV Mejino Jr., Cornelius Rosse fma.biostr.washington. edu structure of the human body Foundational Model of Anatomy (FMA) Melissa Haendel, Terry Hayamizu, Cornelius Rosse, David Sutherland, (under development) anatomical structures in human and model organisms Common Anatomy Refer- ence Ontology (CARO) Paula Dematos, Rafael Alcantara ebi.ac.uk/chebimolecular entities Chemical Entities of Bio- logical Interest (ChEBI) Jonathan Bard, Michael Ashburner, Oliver Hofman obo.sourceforge.net/cgi- bin/detail.cgi?cell cell types from prokaryotes to mammals Cell Ontology (CL) CustodiansURLScopeOntology
Domain ontologies organized according to formal ontological principles RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT 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)