underlying ontologies for biomedical work - the relation ontology (ro) and basic formal ontology...
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![Page 1: Underlying Ontologies for Biomedical work - The Relation Ontology (RO) and Basic Formal Ontology (BFO) Thomas Bittner SUNY Buffalo bittner3@buffalo.edu](https://reader037.vdocuments.mx/reader037/viewer/2022110322/56649d4c5503460f94a29e68/html5/thumbnails/1.jpg)
Underlying Ontologies for Biomedical work - The Relation Ontology (RO) and Basic Formal Ontology (BFO)
Thomas BittnerSUNY Buffalo
Disclaimer: I recycle many slides originally made by Barry Smith
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Overview
•Motivation
•BFO and RO
•Top-level categories and relations of BFO/RO
•Conclusions
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Why do we need a top-level ontology
such as Basic Formal Ontology
(BFO) ?
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Karen Eilbecksong.sf.netproperties and features of
nucleic sequencesSequence Ontology
(SO)
RNA Ontology Consortium(under development)three-dimensional RNA
structuresRNA Ontology
(RnaO)
Barry Smith, Chris Mungallobo.sf.net/relationshiprelationsRelation Ontology (RO)
Protein Ontology Consortium(under development)protein types and
modificationsProtein Ontology
(PrO)
Michael Ashburner, Suzanna Lewis, Georgios Gkoutos
obo.sourceforge.net/cgi-bin/ detail.cgi?
attribute_and_valuequalities of biomedical entities
Phenotypic Quality Ontology (PaTO)
Gene Ontology Consortiumwww.geneontology.orgcellular components, molecular functions, biological processes
Gene Ontology (GO)
FuGO Working Groupfugo.sf.netdesign, protocol, data
instrumentation, and analysis
Functional Genomics Investigation Ontology
(FuGO)
JLV Mejino Jr.,Cornelius Rosse
fma.biostr.washington.edu
structure of the human bodyFoundational 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 entitiesChemical 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
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Karen Eilbecksong.sf.netproperties and features of
nucleic sequencesSequence Ontology
(SO)
RNA Ontology Consortium
(under development)three-dimensional RNA structures
RNA Ontology(RnaO)
Barry Smith, Chris Mungallobo.sf.net/relationshiprelationsRelation Ontology (RO)
Protein Ontology Consortium(under development)protein types and
modificationsProtein Ontology
(PrO)
Michael Ashburner, Suzanna Lewis, Georgios Gkoutos
obo.sourceforge.net/cgi-bin/ detail.cgi?
attribute_and_valuequalities of biomedical entities
Phenotypic Quality Ontology (PaTO)
Gene Ontology Consortiumwww.geneontology.orgcellular components, molecular functions, biological processes
Gene Ontology (GO)
FuGO Working Groupfugo.sf.netdesign, protocol, data
instrumentation, and analysis
Functional Genomics Investigation Ontology
(FuGO)
JLV Mejino Jr.,Cornelius Rosse
fma.biostr.washington.edu
structure of the human bodyFoundational 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 entitiesChemical 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
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RELATION TO TIME
GRANULARITY
CONTINUANT
OCCURREN
T
INDEPENDENT
DEPENDENT
ORGAN
ANDORGANIS
M
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO
)
Organ
Function(F
MP,
CPRO
)
Phenotypic
Quality
(PaTO
)
Biological
Process(GO)
CELL
AND CELLULAR
COMPONENT
Cell
(CL)
Cellular Component(FMA, GO)
Cellula
r Function
(GO)
MOLECULE
Molecule
(ChEBI, SO,RnaO, PrO)
Molecular
Function
(GO)
Molecular
Process(GO)
Domain ontologies organized according to formal ontological
principles
![Page 7: Underlying Ontologies for Biomedical work - The Relation Ontology (RO) and Basic Formal Ontology (BFO) Thomas Bittner SUNY Buffalo bittner3@buffalo.edu](https://reader037.vdocuments.mx/reader037/viewer/2022110322/56649d4c5503460f94a29e68/html5/thumbnails/7.jpg)
Domain ontologies organized according to formal ontological
principles
RELATION TO TIME
GRANULARITY
CONTINUANT
OCCURREN
T
INDEPENDENT
DEPENDENT
ORGAN
ANDORGANIS
M
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO
)
Organ
Function(F
MP,
CPRO
)
Phenotypic
Quality
(PaTO
)
Biological
Process(GO)
CELL
AND CELLULAR
COMPONENT
Cell
(CL)
Cellular Component(FMA, GO)
Cellula
r Function
(GO)
MOLECULE
Molecule
(ChEBI, SO,RnaO, PrO)
Molecular
Function
(GO)
Molecular
Process(GO)
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FMA
Domain ontologies specify the semantics of the vocabulary of a particular domain:
RNAO ChEBI
Cell OntologyPaTO
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FMA
RNAO ChEBI
Cell OntologyPaTO
Top-level ontology
TLO
All domain ontologies use the same top level notions
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FMA
RNAO ChEBI
Cell OntologyPaTO
Top-level ontology
BFO
All domain ontologies use the same top level notions
Ontologicalprinciples
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FMA
RNAO ChEBI
Cell OntologyPaTO
BFO
All domain ontologies use the same top level notions
Diversity in the specifics
Commonalityin the foundations
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FMA
RNAO ChEBI
Cell OntologyPaTO
BFO
All domain ontologies use the same top level notions
Facilitates interoperatibility
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FMA
RNAO ChEBI
Cell OntologyPaTO
BFO
All domain ontologies use the same top level notions
Facilitates interoperatibility
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FMA
RNAO ChEBI
Cell OntologyPaTO
All domain ontologies use the same top level notions
SharedOrganizational,Scientific, and Ontologicalprinciples
RO
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More acronyms: BFO vs. BFO-FOL vs. BFO-DL vs. RO
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Kinds of Ontologies
Terms
General Logic
Thesauri
formalTaxonomies
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, [email protected]
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Ontologies:logical inferences
Non-ontologies:no logical inferences
Kinds of Ontologies
Terms
General Logic
Thesauri
formalTaxonomies
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
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Kinds of Ontology Languages
General Logic
Description Logics
(DAML+OIL)
Tradeoff betweenexpressive power and computability
How well canwe specify intendedmeaning of terms
What can we compute automatically
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Kinds of Ontology Languages
General Logic
Description Logics
(DAML+OIL)
Tradeoff betweenexpressive power and computability
How well canwe specify intendedmeaning of terms
What can we compute automatically
![Page 20: Underlying Ontologies for Biomedical work - The Relation Ontology (RO) and Basic Formal Ontology (BFO) Thomas Bittner SUNY Buffalo bittner3@buffalo.edu](https://reader037.vdocuments.mx/reader037/viewer/2022110322/56649d4c5503460f94a29e68/html5/thumbnails/20.jpg)
Kinds of Ontology Languages
General Logic
Description Logics
(DAML+OIL)
Tradeoff betweenexpressive power and computability
How well canwe specify intendedmeaning of terms
What can we compute automatically
![Page 21: Underlying Ontologies for Biomedical work - The Relation Ontology (RO) and Basic Formal Ontology (BFO) Thomas Bittner SUNY Buffalo bittner3@buffalo.edu](https://reader037.vdocuments.mx/reader037/viewer/2022110322/56649d4c5503460f94a29e68/html5/thumbnails/21.jpg)
We need BOTH kinds of languages
General Logic
Description Logics
(DAML+OIL)
Tradeoff betweenexpressive power and computability
How well canwe specify intendedmeaning
What can we compute automatically
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Computational representations of BFO
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Computational representations of BFO
• BFO-FOL• ‘implementation’ of
BFO in first order logic
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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
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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 oncomputation based on logically verified principles
computational efficiency of a DLneeded
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BFO vs. RO
• RO = Relation ontology
• RO is a sub-set of BFO-DL that has been included in the OBO framework of ontologies
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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
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Two distinct kinds of entities
universals particulars
types tokens
classes instances
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Mishainstances
Tom
Instance-of Instance-of
substance
siamese
Is-acat
Is-amammal
Is-aanimal
Is-aorganism
Is-a
Human being
Is-a
Universals,classes,types
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Particulars:Continuants vs. occurrents
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Persistent entities
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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
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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
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Continuants have
spatial parts
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Occurrents (processes) have spatio-temporal parts
t i m e
process
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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
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RELATION TO TIME
GRANULARITY
CONTINUANT
OCCURREN
T
INDEPENDENT
DEPENDENT
ORGAN
ANDORGANIS
M
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO
)
Organ
Function(F
MP,
CPRO
)
Phenotypic
Quality
(PaTO
)
Biological
Process(GO)
CELL
AND CELLULAR
COMPONENT
Cell
(CL)
Cellular Component(FMA, GO)
Cellula
r Function
(GO)
MOLECULE
Molecule
(ChEBI, SO,RnaO, PrO)
Molecular
Function
(GO)
Molecular
Process(GO)
Ontologies organized according to ontological
principles
![Page 38: Underlying Ontologies for Biomedical work - The Relation Ontology (RO) and Basic Formal Ontology (BFO) Thomas Bittner SUNY Buffalo bittner3@buffalo.edu](https://reader037.vdocuments.mx/reader037/viewer/2022110322/56649d4c5503460f94a29e68/html5/thumbnails/38.jpg)
38
Kinds of continuants
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
Independent
continuants
(substances)
Dependent
continuants
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39
Kinds of continuants
Independent
continuants
(substances)
Dependent
continuants
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40
Kinds of continuants
Independent
continuants
(substances)
Dependent
continuants
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41
Kinds of continuants
Independent
continuants
(substances)
Dependent
continuants
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture. •the yellow color of this car•the maximal speed of this car
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Kinds of continuants
Independent
continuants
(substances)
Dependent
continuants
•the mass of this planet•its disposition to sustain life
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43
Kinds of continuants
Independent
continuants
(substances)
Dependent
continuants
•the mass of this molecule•its disposition to engage in chemical reactions
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RELATION TO TIME
GRANULARITY
CONTINUANT
OCCURREN
T
INDEPENDENT
DEPENDENT
ORGAN
ANDORGANIS
M
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO
)
Organ
Function(F
MP,
CPRO
)
Phenotypic
Quality
(PaTO
)
Biological
Process(GO)
CELL
AND CELLULAR
COMPONENT
Cell
(CL)
Cellular Component(FMA, GO)
Cellula
r Function
(GO)
MOLECULE
Molecule
(ChEBI, SO,RnaO, PrO)
Molecular
Function
(GO)
Molecular
Process(GO)
Ontologies organized according to ontological
principles
![Page 45: Underlying Ontologies for Biomedical work - The Relation Ontology (RO) and Basic Formal Ontology (BFO) Thomas Bittner SUNY Buffalo bittner3@buffalo.edu](https://reader037.vdocuments.mx/reader037/viewer/2022110322/56649d4c5503460f94a29e68/html5/thumbnails/45.jpg)
RELATION TO TIME
GRANULARITY
CONTINUANT
OCCURREN
T
INDEPENDENT
DEPENDENT
ORGAN
ANDORGANIS
M
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO
)
Organ
Function(F
MP,
CPRO
)
Phenotypic
Quality
(PaTO
)
Biological
Process(GO)
CELL
AND CELLULAR
COMPONENT
Cell
(CL)
Cellular Component(FMA, GO)
Cellula
r Function
(GO)
MOLECULE
Molecule
(ChEBI, SO,RnaO, PrO)
Molecular
Function
(GO)
Molecular
Process(GO)
Ontologies organized according to ontological
principles
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Universals and particulars(cont.)
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Mishasubstanceinstances
Tom
Instance-of Instance-of
substance
siamese
Is-acat
Is-amammal
Is-aanimal
Is-aorganism
Is-a
Human being
Is-a
substance-Universals
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Accidents: Species and instances
quality
color
red
scarlet
R232, G54, B24
Barry Smith
Universals among dependent continuants
Is-a
Is-a
Is-a
Is-a
this individual token of redness (this token redness – here, now)
Inst-Of
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Of dependent continuants
Universals and particulars
Accidents : Species and instances
substance
animal
mammal
human
Irishman
this individual token man
Of independent continuants
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RELATION TO TIME
GRANULARITY
CONTINUANT
OCCURREN
T
INDEPENDENT
DEPENDENT
ORGAN
ANDORGANIS
M
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO
)
Organ
Function(F
MP,
CPRO
)
Phenotypic
Quality
(PaTO
)
Biological
Process(GO)
CELL
AND CELLULAR
COMPONENT
Cell
(CL)
Cellular Component(FMA, GO)
Cellula
r Function
(GO)
MOLECULE
Molecule
(ChEBI, SO,RnaO, PrO)
Molecular
Function
(GO)
Molecular
Process(GO)
Substance universals
Ontologies organized according to ontological
principles
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RELATION TO TIME
GRANULARITY
CONTINUANT
OCCURREN
T
INDEPENDENT
DEPENDENT
ORGAN
ANDORGANIS
M
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO
)
Organ
Function(F
MP,
CPRO
)
Phenotypic
Quality
(PaTO
)
Biological
Process(GO)
CELL
AND CELLULAR
COMPONENT
Cell
(CL)
Cellular Component(FMA, GO)
Cellula
r Function
(GO)
MOLECULE
Molecule
(ChEBI, SO,RnaO, PrO)
Molecular
Function
(GO)
Molecular
Process(GO)
Quality/function universals
Ontologies organized according to ontological
principles
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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
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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
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Mishainstances
Tom
Instance-of Instance-of
substance
siamese
Is-acat
Is-amammal
Is-aanimal
Is-aorganism
Is-a
Human being
Is-a
is-a relation betweenUniversals
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Mishainstances
Tom
Instance-of Instance-of
substance
siamese
Is-acat
Is-amammal
Is-aanimal
Is-aorganism
Is-a
Human being
Is-a
is-a relation betweenUniversals
Human Beingis-amammal
Every instanceof Human Beingis also an instanceof mammal
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Mishainstances
Tom
Instance-of Instance-of
hasPet
isPetOf
substance
siamese
Is-acat
Is-amammal
Is-aanimal
Is-aorganism
Is-a
Human being
Is-a
is-a relation betweenUniversals
IsPetOf
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Instance-level relations
universal-level relations
Mishainstances
Tom
Instance-of Instance-of
hasPet
isPetOf
cat
Human being
Universals
HasPet
IsPetOf
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Universal parthood:
Human anatomy
The universal human body
The universalhuman head Human heads
are parts of human bodies
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Universal parthood
Human-headsHuman-bodies
Part-of
Part-of
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Universal parthood
Human-headsHuman-bodies
HasPart
HasPart
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The semantics of universal parthood
X PART-OF Y iffFor every instance x of X there exists an instance y of Y such thatx part-of y
ANDFor every instance y of Y there exists an instance x of X such thatx part-of y
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General framework for defining universal-level relations in terms of relations between individuals
Rall-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
Rsome-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
Rall-all(A, B) =: Rall-some(A, B) & Rsome-all(A, B)
R can be ANY binary relation
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63
Important Individual-level relations
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IndependentContinuant
Occurrent
DependentContinuant
You, me,This molecule,My cat Misha
Individual-level relations
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IndependentContinuant
Occurrent
DependentContinuant
My temperature (now)My heightMy role as a presenter
Individual-level relations
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IndependentContinuant
Occurrent
DependentContinuant
Processes:My life,My presenting this talk
Individual-level relations
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IndependentContinuant
Occurrent
DependentContinuant
Part-of
• My heart part-of my body• Montana part-of United States
Individual-level relations
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IndependentContinuant
Occurrent
ParticipatesIn
Part-of
• the runner participates in the racing process• the molecule participates in the diffusion process
DependentContinuant
Individual-level relations
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DependentContinuant
IndependentContinuant
Occurrent
ParticipatesIn
Part-of
• the racing involves racers• the diffusion process involves molecules
Involves
Individual-level relations
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IndependentContinuant
Occurrent
DependentContinuant
ParticipatesIn
Part-of
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
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IndependentContinuant
Occurrent
DependentContinuant
ParticipatesIn RealizationOf
PartOf
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
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IndependentContinuant
Occurrent
DependentContinuant
ParticipatesIn RealizationOf
PartOf
PartOf
• A warming process yields a rise in temperature•The tenure process yields a rise in John’s status
Involves
Changesquality
Individual-level relations
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IndependentContinuant
Occurrent
DependentContinuant
ParticipatesIn
InheresIn
RealizationOf
Part-of
PartOf
• Your height inheres in you• The role the antibiotics inheres in the antibiotics
Involves
Changesquality
Individual-level relations
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IndependentContinuant
Occurrent
DependentContinuant
ParticipatesIn
InheresIn
RealizationOf
Part-of
PartOf
Involves
Changesquality
Individual-level relations
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• 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
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76
Conclusions
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FMA
RNAO ChEBI
Cell OntologyPaTO
Basedupon thetop-level ontologyBFO
RO
All domain ontologies use the same top level notions
![Page 78: Underlying Ontologies for Biomedical work - The Relation Ontology (RO) and Basic Formal Ontology (BFO) Thomas Bittner SUNY Buffalo bittner3@buffalo.edu](https://reader037.vdocuments.mx/reader037/viewer/2022110322/56649d4c5503460f94a29e68/html5/thumbnails/78.jpg)
Karen Eilbecksong.sf.netproperties and features of
nucleic sequencesSequence Ontology
(SO)
RNA Ontology Consortium(under development)three-dimensional RNA
structuresRNA Ontology
(RnaO)
Barry Smith, Chris Mungallobo.sf.net/relationshiprelationsRelation Ontology (RO)
Protein Ontology Consortium(under development)protein types and
modificationsProtein Ontology
(PrO)
Michael Ashburner, Suzanna Lewis, Georgios Gkoutos
obo.sourceforge.net/cgi-bin/ detail.cgi?
attribute_and_valuequalities of biomedical entities
Phenotypic Quality Ontology (PaTO)
Gene Ontology Consortiumwww.geneontology.orgcellular components, molecular functions, biological processes
Gene Ontology (GO)
FuGO Working Groupfugo.sf.netdesign, protocol, data
instrumentation, and analysis
Functional Genomics Investigation Ontology
(FuGO)
JLV Mejino Jr.,Cornelius Rosse
fma.biostr.washington.edu
structure of the human bodyFoundational 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 entitiesChemical 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
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RELATION TO TIME
GRANULARITY
CONTINUANT
OCCURREN
T
INDEPENDENT
DEPENDENT
ORGAN
ANDORGANIS
M
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO
)
Organ
Function(F
MP,
CPRO
)
Phenotypic
Quality
(PaTO
)
Biological
Process(GO)
CELL
AND CELLULAR
COMPONENT
Cell
(CL)
Cellular Component(FMA, GO)
Cellula
r Function
(GO)
MOLECULE
Molecule
(ChEBI, SO,RnaO, PrO)
Molecular
Function
(GO)
Molecular
Process(GO)
Domain ontologies organized according to formal ontological
principles