BFO and Ontology Design Principles
Barry Smith
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How is the OBO Foundry organized?
• Top-Level: Basic Formal Ontology (BFO)• Mid-Level: IAO, OBI, OGMS ...• Domain-Level: Foundry Bio-Ontologies
Anatomy Ontology(FMA*, CARO)
Environment
Ontology(EnvO)
Infectious Disease
Ontology(IDO*)
Biological Process
Ontology (GO*)
Cell Ontology
(CL)
CellularComponentOntology
(FMA*, GO*) Phenotypic Quality
Ontology(PaTO)
Subcellular Anatomy Ontology (SAO)Sequence Ontology
(SO*) Molecular Function
(GO*)Protein Ontology(PRO*) OBO Foundry Modular Organization 3
top level
mid-level
domain level
Information Artifact Ontology
(IAO)
Ontology for Biomedical Investigations
(OBI)
Ontology of General Medical Science
(OGMS)
Basic Formal Ontology (BFO)
BFO: the very top
Continuant Occurrent(Process, Event)
IndependentContinuant
DependentContinuant
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RELATION TO TIME
GRANULARITY
CONTINUANT OCCURRENT
INDEPENDENT DEPENDENT
ORGAN ANDORGANISM
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO)
OrganFunction
(FMP, CPRO) Phenotypic
Quality(PaTO)
Biological Process
(GO)CELL AND CELLULAR
COMPONENT
Cell(CL)
Cellular Compone
nt(FMA, GO)
Cellular Function
(GO)
MOLECULEMolecule
(ChEBI, SO,RnaO, PrO)
Molecular Function(GO)
Molecular Process
(GO)
CONTINUANT OCCURRENT
INDEPENDENT DEPENDENT
ORGAN ANDORGANISM
Organism(NCBI
Taxonomy)
Anatomical Entity
(FMA, CARO)
OrganFunction
(FMP, CPRO) Phenotypic
Quality(PaTO)
Organism-Level Process
(GO)
CELL AND CELLULAR
COMPONENT
Cell(CL)
Cellular Compone
nt(FMA, GO)
Cellular Function
(GO)
Cellular Process
(GO)
MOLECULEMolecule
(ChEBI, SO,RnaO, PrO)
Molecular Function(GO)
Molecular Process
(GO)
obofoundry.org
GRANULARITY
RELATION TO TIME
BFO & GO
continuant occurrent
biological processes
independentcontinuant
cellular component
dependentcontinuant
molecular function
Basic Formal Ontology
Continuant Occurrent
process, eventIndependentContinuant
thing
DependentContinuant
quality
.... ..... .......
types
instances
Experience with BFO in building ontologies provides
• a community of skilled ontology developers and users (user group has 120 members)
• associated logical tools • documentation for different types of users• a methodology for building conformant
ontologies by starting with BFO and populating downwards
Example: The Cell Ontology
:.
Users of BFOPharmaOntology (W3C HCLS SIG)
MediCognos / Microsoft Healthvault
Cleveland Clinic Semantic Database in Cardiothoracic Surgery
Major Histocompatibility Complex (MHC) Ontology (NIAID)
Neuroscience Information Framework Standard (NIFSTD) and Constituent Ontologies
Interdisciplinary Prostate Ontology (IPO)
Nanoparticle Ontology (NPO): Ontology for Cancer Nanotechnology Research
Neural Electromagnetic Ontologies (NEMO)
ChemAxiom – Ontology for Chemistry
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:.
Users of BFOGO Gene Ontology
CL Cell Ontology
SO Sequence Ontology
ChEBI Chemical Ontology
PATO Phenotype (Quality) Ontology
FMA Foundational Model of Anatomy Ontology
ChEBI Chemical Entities of Biological Interest
PRO Protein Ontology
Plant Ontology
Environment Ontology
Ontology for Biomedical Investigations
RNA Ontology
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:.
Users of BFOOntology for Risks Against Patient Safety (RAPS/REMINE)
eagle-i an VIVO (NCRR)
IDO Infectious Disease Ontology (NIAID)
National Cancer Institute Biomedical Grid Terminology (BiomedGT)
US Army Biometrics Ontology
US Army Command and Control Ontology
Sleep Domain Ontology
Subcellular Anatomy Ontology (SAO)
Translaftional Medicine On (VO)
Yeast Ontology (yOWL)
Zebrafish Anatomical Ontology (ZAO)
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:.
DOLCE, SUMO, Cyc
DOLCE: (Largely) extends BFO, but built to support ‘linguistic and cognitive engineering’
SUMO: No dependent continuants (so: no diabetes, no temperature instances); SUMO has its own tiny biology (‘body-covering’, ‘fruit-Or-vegetable’)
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:.
Cyc:ConceivingSomething_BiologicalReproductionEvent =def a collection of events; a sub-collection of BiologicalReproductionEvent. In each conceivingSomething_BiologicalReproduction Event, someone becomes pregnant.
Cyc:The immaculate conception =def. The ConceivingSomething_BiologicalReproductionEvent in which Mary_MotherOfJesus was conceived. Catholic dogma holds that Mary (unlike Jesus) was conceived by conventional biological means, but that GodOfAbrahamIsaacAndJacob interceded at the time of her conception to keep her free from the stain of original sin, or ‘immaculate’.
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Basic Formal Ontology
continuant occurrent
independentcontinuant
dependentcontinuant
organism
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Continuants
• continue to exist through time, preserving their identity while undergoing different sorts of changes
• independent continuants – objects, things, ...
• dependent continuants – qualities, attributes, shapes, potentialities ...
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Occurrents
• processes, events, happenings– your life– this process of accelerated cell
division
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Qualitiestemperatureblood pressuremass...
are continuantsthey exist through time while undergoing changes
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Qualitiestemperature / blood pressure /
mass ...are dimensions of variation within the structure of the entitya quality is something which can change while its bearer remains one and the same
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A Chart representing how John’s temperature
changes
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A Chart representing how John’s temperature
changes
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BFO: The Very Top
continuant
independentcontinuant
dependentcontinuant
quality
occurrent
temperature 26
Blinding Flash of the Obvious
independentcontinuant
dependentcontinuant
quality
temperature types
instances
organism
John John’s
temperature 27
Blinding Flash of the Obvious
independentcontinuant
dependentcontinuant
quality
temperature types
instances
organism
John John’s
temperature 28
Blinding Flash of the Obvious
temperature types
instances
organism
John John’s
temperature .
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inheres_in
temperature types
instances
John’s temperature
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37ºC37.1º
C37.5º
C37.2º
C37.3º
C37.4º
C
instantiates at t1
instantiates at t2
instantiates at t3
instantiates at t4
instantiates at t5
instantiates at t6
human types
instances
John
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embryo
fetus adultneonat
einfant child
instantiates at t1
instantiates at t2
instantiates at t3
instantiates at t4
instantiates at t5
instantiates at t6
Temperature subtypesDevelopment-stage
subtypes
are threshold divisions (hence we do not have sharp boundaries, and we have a certain degree of choice, e.g. in how many subtypes to distinguish, though not in their ordering)
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independentcontinuant
dependentcontinuant
quality
temperature types
instances
organism
John John’s
temperature
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independentcontinuant
dependentcontinuant
quality
temperature
organism
John John’s
temperature
occurrent
process
course of temperature
changes
John’s temperature history
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independentcontinuant
dependentcontinuant
quality
temperature
organism
John John’s
temperature
occurrent
process
life of an organism
John’s life
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BFO: The Very Top
continuant occurrent
independentcontinuant
dependentcontinuant
quality disposition
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BFO: The Very Top
continuant
independentcontinuant
dependentcontinuant
qualityfunctionroledisposition
occurrent
disposition- of a glass vase, to shatter if dropped- of a human, to eat - of a banana, to ripen- of John, to lose hair
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dispositionif it ceases to exist, then its bearer and/or its immediate surrounding environment is physically changedits realization occurs when its bearer is in some special physical circumstancesits realization is what it is in virtue of the bearer’s physical make-up
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function - of liver: to store glycogen- of birth canal: to enable transport- of eye: to see- of mitochondrion: to produce ATP
not optional; reflection of physical makeup of bearer
role optional:exists because the bearer is in some special natural, social, or institutional set of circumstances in which the bearer does not have to be
role - bearers can have more than one role
person as student and staff member- roles often form systems of mutual dependence
husband / wife first in queue / last in queuedoctor / patient
host / pathogen
role of some chemical compound: to serve as analyte in an experiment
of a dose of penicillin in this human child: to treat a disease
of this bacteria in a primary host: to cause infection
independentcontinuant
dependentcontinuant
function
to seeeye
John’s eye function of John’s eye: to see
occurrent
process
process of seeing
John seeing
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Particulars and Universals
me this walking
my left leg
this leg moving
to makeme walk
human being
living creature
walkingleg moving
legfunction
process
Instance-of at t
Instance-of
Instance-ofat t
Instance-ofat t
Instance-of
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instanceOf at t2 instanceOf at t1
instanceOf at t2
The importance of temporal indexing
#1’s stomach
benigntumor
instanceOf at t1
#4
malignanttumor
partOf at t1
stomach
partOf at t2
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Continuants and Occurrents
me this walking
my left leg
this leg moving
to makeme walk
human being
living creature
walkingleg moving
legfunction
process
Instance-ofat t
Instance-of
Instance-ofat t
Instance-ofat t
Instance-of
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Independent versus dependent
Independent entities
Do not require any other entity to exist to enable their own existence
Dependent entities
Require the existence of some other entity for their existence
me this walking
my left leg
this leg moving
to makeme walk
Independentcontinuants Dependent
continuantsOccurrents
(are all dependent)
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Dependent continuants
• Realized– Quality: redness (of blood)
• Realizable– Function: to flex (of knee joint)– Role: student– Power: boss– Disposition: brittleness (of a bone)
Realizations flexing
studying
ordering
breaking
continuants occurrents
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Relation Ontology
ContinuantOccurrent
process, event
IndependentContinuant
~ thing
DependentContinuant
.... ..... .......
universals
particulars
has_participant
inheres_in instance_of (at t)
isa isa
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t t tinstanceOf
The essential pieces
materialobject
spacetimeregion
mesome
temporal region
my life
my 4D STR
some spatialregion
coursespatialregion
temporalregion
dependent continuant
some quality
located-in at t
at t
participantOf at t occupies
projectsOn
projectsOn at t
OGMSOntology for General Medical
Science
http://code.google.com/p/ogms
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• ontology for the representation of– diseases, signs, symptoms
– clinical processes
– diagnosis, treatment and outcomes
• fundamental idea:– a disease is a disposition rooted in some
(physical) disorder in the organism
Ontology of General Medical Science (OGMS)
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Motivation
• Clarity about:– disease etiology and progression
– disease and the diagnostic process
– phenotype and signs/symptoms
– entities in reality and observations of sucn entities
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Physical Disorder
:.
Physical Disorder
– independent continuantfiat object part
A causally linked combination of physical components of the extended organism that is clinically abnormal.
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Clinically abnormal
– (1) not part of the life plan for an organism of the relevant type (unlike aging or pregnancy),
– (2) causally linked to an elevated risk either of pain or other feelings of illness, or of death or dysfunction, and
– (3) such that the elevated risk exceeds a certain threshold level.*
*Compare: baldness57
Big Picture
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Pathological Process=def. A bodily process that is a manifestation of a disorder and is clinically abnormal.
Disease =def. – A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
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Cirrhosis - environmental exposure
• Etiological process - phenobarbitol-induced hepatic cell death– produces
• Disorder - necrotic liver– bears
• Disposition (disease) - cirrhosis– realized_in
• Pathological process - abnormal tissue repair with cell proliferation and fibrosis that exceed a certain threshold; hypoxia-induced cell death– produces
• Abnormal bodily features– recognized_as
• Symptoms - fatigue, anorexia• Signs - jaundice, enlarged spleen
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Influenza - infectious
• Etiological process - infection of airway epithelial cells with influenza virus
– produces
• Disorder - viable cells with influenza virus
– bears
• Disposition (disease) - flu
– realized_in
• Pathological process - acute inflammation
– produces
• Abnormal bodily features
– recognized_as
• Symptoms - weakness, dizziness
• Signs - fever 61
Dispositions and Predispositions
All diseases are dispositions; not all dispositions are diseases.
Predisposition to Disease
=def. – A disposition in an organism that constitutes an increased risk of the organism’s subsequently developing some disease.
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HNPCC - genetic pre-disposition• Etiological process - inheritance of a mutant mismatch repair gene
– produces• Disorder - chromosome 3 with abnormal hMLH1
– bears• Disposition (disease) - Lynch syndrome
– realized_in• Pathological process - abnormal repair of DNA mismatches
– produces• Disorder - mutations in proto-oncogenes and tumor suppressor genes with
microsatellite repeats (e.g. TGF-beta R2)– bears
• Disposition (disease) - non-polyposis colon cancer– realized in
• Symptoms (including pain)
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Influenza - infectious
• Etiological process - infection of airway epithelial cells with influenza virus
– produces
• Disorder - viable cells with influenza virus
– bears
• Disposition (disease) - flu
– realized_in
• Pathological process - acute inflammation
– produces
• Abnormal bodily features
– recognized_as
• Symptoms - weakness, dizziness
• Signs - fever
Symptoms & Signs used_in
Interpretive process produces
Hypothesis - rule out influenza suggests
Laboratory tests produces
Test results - elevated serum antibody titers used_in
Interpretive process produces
Result - diagnosis that patient X has a disorder that bears the disease flu
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
• Etiological process - inheritance of >39 CAG repeats in the HTT gene– produces
• Disorder - chromosome 4 with abnormal mHTT– bears
• Disposition (disease) - Huntington’s disease– realized_in
• Pathological process - accumulation of mHTT protein fragments, abnormal transcription regulation, neuronal cell death in striatum– produces
• Abnormal bodily features– recognized_as
• Symptoms - anxiety, depression• Signs - difficulties in speaking and
swallowing
Symptoms & Signs used_in
Interpretive process produces
Hypothesis - rule out Huntington’s suggests
Laboratory tests produces
Test results - molecular detection of the HTT gene with >39CAG repeats used_in
Interpretive process produces
Result - diagnosis that patient X has a disorder that bears the disease Huntington’s disease
HNPCC - genetic pre-disposition• Etiological process - inheritance of a mutant mismatch repair
gene– produces
• Disorder - chromosome 3 with abnormal hMLH1– bears
• Disposition (disease) - Lynch syndrome– realized_in
• Pathological process - abnormal repair of DNA mismatches– produces
• Disorder - mutations in proto-oncogenes and tumor suppressor genes with microsatellite repeats (e.g. TGF-beta R2)– bears
• Disposition (disease) - non-polyposis colon cancer
Cirrhosis - environmental exposure
• Etiological process - phenobarbitol-induced hepatic cell death
– produces
• Disorder - necrotic liver
– bears
• Disposition (disease) - cirrhosis
– realized_in
• Pathological process - abnormal tissue repair with cell proliferation and fibrosis that exceed a certain threshold; hypoxia-induced cell death
– produces
• Abnormal bodily features
– recognized_as
• Symptoms - fatigue, anorexia
• Signs - jaundice, splenomegaly
Symptoms & Signs used_in
Interpretive process produces
Hypothesis - rule out cirrhosis suggests
Laboratory tests produces
Test results - elevated liver enzymes in serum used_in
Interpretive process produces
Result - diagnosis that patient X has a disorder that bears the disease cirrhosis
Systemic arterial hypertension
• Etiological process – abnormal reabsorption of NaCl by the kidney
– produces
• Disorder – abnormally large scattered molecular aggregate of salt in the blood
– bears
• Disposition (disease) - hypertension
– realized_in
• Pathological process – exertion of abnormal pressure against arterial wall
– produces
• Abnormal bodily features
– recognized_as
• Symptoms - headaches, dizziness
• Signs – elevated blood pressure
Symptoms & Signs used_in
Interpretive process produces
Hypothesis - rule out hypertension suggests
Laboratory tests produces
Test results - used_in
Interpretive process produces
Result - diagnosis that patient X has a disorder that bears the disease hypertension
Type 2 Diabetes Mellitus• Etiological process –
– produces• Disorder – abnormal pancreatic beta
cells and abnormal muscle/fat cells– bears
• Disposition (disease) – diabetes mellitus– realized_in
• Pathological processes – diminished insulin production , diminished muscle/fat uptake of glucose
– produces• Abnormal bodily features
– recognized_as• Symptoms – polydipsia, polyuria,
polyphagia, blurred vision• Signs – elevated blood glucose and
hemoglobin A1c
Symptoms & Signs used_in
Interpretive process produces
Hypothesis - rule out diabetes mellitus suggests
Laboratory tests – fasting serum blood glucose, oral glucose challenge test, and/or blood hemoglobin A1c produces
Test results - used_in
Interpretive process produces
Result - diagnosis that patient X has a disorder that bears the disease type 2 diabetes mellitus
Type 1 hypersensitivity to penicillin• Etiological process – sensitizing of mast
cells and basophils during exposure to penicillin-class substance
– produces• Disorder – mast cells and basophils with
epitope-specific IgE bound to Fc epsilon receptor I
– bears• Disposition (disease) – type I
hypersensitivity– realized_in
• Pathological process – type I hypersensitivity reaction
– produces• Abnormal bodily features
– recognized_as• Symptoms – pruritis, shortness of breath• Signs – rash, urticaria, anaphylaxis
Symptoms & Signs used_in
Interpretive process produces
Hypothesis - suggests
Laboratory tests – produces
Test results – occasionally, skin testing used_in
Interpretive process produces
Result - diagnosis that patient X has a disorder that bears the disease type 1 hypersensitivity to penicillin
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Disease vs. Disease course
Disease =def. – A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
Disease course =def. – The aggregate of processes in which a disease disposition is realized.
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coronary heart disease
John’s coronary heart disease
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asymptomatic (‘silent’) infarction
early lesions and small
fibrous plaques
stable angina
surface disruption of plaque
unstable angina
instantiates at t1
instantiates at t2
instantiates at t3
instantiates at t4
instantiates at t5
time
independentcontinuant
dependentcontinuant
disposition
diseasedisorder
John’s disordered
heart
John’s coronary heart
disease
occurrent
process
course of disease
course of John’s disease
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