1 the future of disease ontology barry smith department of philosophy, university at buffalo...
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The Future of Disease Ontology
Barry SmithDepartment of Philosophy, University at Buffalo
National Center for Biomedical Ontology
http://ontology.buffalo.edu/smith
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Colors form a continuum
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colors form a prototyped continuum
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strategy of low hanging
fruit
focus on the foci
(cross-cultural,
lexicalized)
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Strategies for creating ontologies and terminologies
Ad hoc creation by each clinical or research community (à la UMLS)
versus
Coordinated creation of high quality reference ontologies in ways which serve reusability of clinical data and interoperability of with basic science
Ontologies as common railway gauge
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A simple rule
Use singular nouns
DiseaseDiseasesDisorderDisordersdisorderdisease
disordersdiseases
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Which strategy is more future proof?
Assumption: As time goes by the molecular/cellular basis of diseases will play an ever more important role in clinical medicine
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OBO Foundry
A subset of OBO ontologies whose developers agree in advance to accept a common set of principles designed to assure interoperability with basic science and support for logic-based reasoning
http://obofoundry.org
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OBO Foundry
– Gene Ontology– Cell Ontology– Sequence Ontology– RNA Ontology– PATO Phenotype Ontology– OBI Ontology of Biomedical Investigations
(née FuGO Functional Genomics Investigation Ontology)
– FMA– RO Relation Ontology
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GO’s three ontologies
molecular function
cellular component
biological process
continuant occurrent
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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)
Building out fron the original GO
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The ontology is open and available to be used by all.
The developers of the ontology agree in advance to collaborate with developers of other OBO Foundry ontology where domains overlap.
The ontology is in, or can be instantiated in, a common formal language.
The ontology possesses a unique identifier space within OBO.
The ontology provider has procedures for identifying distinct successive versions.
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The ontology has a clearly specified and clearly delineated content.
The ontology includes textual definitions for all terms.
The ontology is well-documented.
The ontology has a plurality of independent users.
The ontology uses relations which are unambiguously defined following the pattern of definitions laid down in the OBO Relation Ontology.
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ORTHOGONALITY
The developers commit to working with other Foundry members to ensure community convergence on a single controlled vocabulary for each domain.
REASON: if we annotate a database or body of literature with one high-quality biomedical ontology, we should be able to add annotations from a second such ontology without conflicts
INTEGRATION PRESUPPOSES ADDITIVITY
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Goal: when we annotate disease-related data
the disease terms we use should yield annotations which are logically consistent with – and even inferable from – other annotations using other OBO Foundry ontologies
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Foundational Model of Anatomy (FMA)
ontology of structural human anatomy
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FMAorganized in a graph-theoretical structure involving two sorts of links or edges:
is-a (= is a subtype of )
(pleural sac is-a serous sac)
part-of
(cervical vertebra part-of vertebral column)
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Pleural Cavity
Pleural Cavity
Interlobar recess
Interlobar recess
Mesothelium of Pleura
Mesothelium of Pleura
Pleura(Wall of Sac)
Pleura(Wall of Sac)
VisceralPleura
VisceralPleura
Pleural SacPleural Sac
Parietal Pleura
Parietal Pleura
Anatomical SpaceAnatomical Space
OrganCavityOrganCavity
Serous SacCavity
Serous SacCavity
AnatomicalStructure
AnatomicalStructure
OrganOrgan
Serous SacSerous Sac
MediastinalPleura
MediastinalPleura
TissueTissue
Organ PartOrgan Part
Organ Subdivision
Organ Subdivision
Organ Component
Organ Component
Organ CavitySubdivision
Organ CavitySubdivision
Serous SacCavity
Subdivision
Serous SacCavity
Subdivision
part
_of
is_a
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FMA follows formal rules for Aristotelian definitions
When A is_a B, the definition of ‘A ’ takes the form:
an A =Def. a B which C s...
a human being =Def. an animal which is rational
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Example
Cell =Def. an anatomical structure which consists of cytoplasm surrounded by a plasma membrane
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at every level of granularity
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The Gene Ontology
Cross-Species
Cross-Granularity
Impressive policies for maintenance
Has initiated logic-based reforms:relations to other ontologies
relations among GO’s 3 ontologies
Aristotelian definitions
enhanced treatment of granularity
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Multiple Inheritance
thing
car
blue thing
blue car
is_a is_a
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Multiple Inheritance
thing
car
blue thing
blue car
is_a1 is_a2
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is_a Overloading
Reasoning across ontologies demands that ontological relations (is_a, part_of, ...) have the same meanings in the different ontologies to be aligned.
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Multiple Inheritance
thing
carblue
car #2947 is blue
is_a is_a
color
dark blue
is_a
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Multiple Inheritance
fracture
spiral fracturelimb
leg #29 has fracture #12
is_a is_a
anatomical structure
leg
is_a
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Multiple Inheritance
pharyngitis
infectious pharyngitis
heterogeneous cluster
disease instance #12 inheres in pharynx #29
is_a is_a
pharynx
is_a
anatomical structure
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Multiple Inheritance
is a source of errors
results are hard to maintain
serves as obstacle to integration with neighboring ontologies
hampers formulation of coherent definitions
contravenes orthogonality
no coherently defined levels
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Multiple Inheritance
can be easily dispensed with via normalization ???
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DO
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DO
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OBO Relation Ontology
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Three fundamental dichotomies
• types vs. instances
• continuants vs. occurrents
• dependent vs. independent
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Three fundamental dichotomies
• types vs. instances
• continuants vs. occurrents
• dependent vs. independent
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Glossary
Instance: A particular entity in spatio-temporal reality.
Type: A general kind instantiated by an open-ended totality of instances which share certain qualities and propensities in common of the sort that can be documented in scientific literature
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Glossary
Biological process instance: A change or complex of changes on the level of granularity of the cell or organism, mediated by one or more gene products.
Biological process type: A type of biological process instance.
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Cellular component instance: A part of a cell, including cellular structures, macromolecular complexes and spatial locations identified in relation to the cell
Cellular component type: A type of cellular component.
Glossary
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Molecular function instance: The propensity of a gene product instance to perform actions, such as catalysis or binding, on the molecular level of granularity.
Molecular function type: A type of molecular function instance (type of propensity)
Glossary
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SCIENCE TEXTS AREREPRESENTATIONS OF
TYPES IN REALITY
= of what is general in reality
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CLINICAL GUIDELINES ARE REPRESENTATIONS OF TYPES
IN REALITY
diseases, therapies, diagnostic procedures (measurements) are
generals, with particular instances
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ONTOLOGIES AREREPRESENTATIONS OF
TYPES IN REALITY
aka kinds, universals, categories, species, genera, ...
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siamese
mammal
cat
organism
substancetypes
animal
instances
frog
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two kinds of parthood
1. between instances:Mary’s heart part_of Marythis nucleus part_of this cell
2. between typeshuman heart part_of humancell nucleus part_of cell
“Relations in Biomedical Ontologies”, Genome Biology, Apr 2005
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Three fundamental dichotomies
• types vs. instances
• continuants vs. occurrents
• dependent vs. independent
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Continuants (aka endurants)– have continuous existence in time– preserve their identity through
change– exist in toto whenever they exist at
all
Occurrents (aka processes)– have temporal parts– unfold themselves in successive
phases– exist only in their phases
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You are a continuant
Your life is an occurrent
You are 3-dimensional
Your life is 4-dimensional
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Three fundamental dichotomies
• types vs. instances
• continuants vs. occurrents
• dependent vs. independent
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Dependent entities
require independent continuants as their bearers
There is no grin without a catThere is no run without a runnerThere is no pumping without a pumpThere is no kiss without a kisser and a kissee
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Dependent vs. independent continuants
Independent continuants (organisms, cells, molecules, environments)
Dependent continuants (qualities, shapes, roles, dispositions, propensities, functions)
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All occurrents are dependent entities
They are dependent on those independent continuants which are their participants (agents, patients, media ...)
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types
Continuant Occurrent
IndependentContinuant
DependentContinuant
instances
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Top-Level Ontology
ContinuantOccurrent
(always dependent on one or more
independent continuants)
IndependentContinuant
DependentContinuant
types
instances
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Top-Level Ontology
ContinuantOccurrent
IndependentContinuant
DependentContinuant
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= A representation of top-level types
Continuant Occurrent
IndependentContinuant
DependentContinuant
cell component
biological process
molecular function
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Continuant
IndependentContinuant
anatomy
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“On Carcinomas and Other Pathological Entities”, Comparative and Functional Genomics, Apr. 2006
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Top-Level Ontology
ContinuantOccurrent
IndependentContinuant
DependentContinuant
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= A representation of top-level types
Continuant Occurrent
IndependentContinuant
DependentContinuant
cell component
biological process
molecular function
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GO’s three ontologies
molecular function
cellular component
biological process
continuant
occurrent
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Functions, etc.
Some dependent continuants are realizable
expression of a gene
application of a therapy
realization of a protocol
execution of a function
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The function of the heart is to pump blood
Not every activity (process) in an organism is the exercise of a function – there are – mal functionings
– side-effects (heart beating)
– accidents (external interference)
– background stochastic activity
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The FMA is a canonical representation
It is a computational representation of types and relations between types deduced from the qualitative observations of the normal human body
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The GO is a canonical representation
“The Gene Ontology is a computational representation of the ways in which gene products normally function in the biological realm”
Nucl. Acids Res. 2006: 34.
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GO’s three ontologies
molecular function
cellular component
biological process
continuant occurrent
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GO’s three+ ontologies
biological functions at
different levels of granularity
biological continuants =
cellular components +
FMA
biological processes (including molecular processes
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Top-Level Ontology
Continuant Occurrent
IndependentContinuant
DependentContinuant
Functioning Side-Effect,
Accident,Background Stochastic Process,
...Function
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Disease vs. Event
Myocardial infarction is not a disease
A disease is something realizable
Disease ≠ Realization
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Disease vs. Course of disease
Symptom-suppressant drugs demonstrate that a disease is not identical with any specific sequence or pattern of symptoms
Diseases are continuants that may exist even when their observable manifestations are not present
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Top-Level Ontology
Continuant Occurrent
IndependentContinuant
DependentContinuant
Functioning Course or history
of disease,mal-
functioningsFunction Disease
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Disease vs. symptom
Psoriasis as disease vs. psoriasis as manifestation (skin rash ...)
Cancer as disease vs. cancer as tumor
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Disease vs. Bearer of disease
A mushy brain is not a disease
A broken leg is not a disease
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types
Continuant Occurrent
IndependentContinuant
DependentContinuant
Function Disease
Functioning Side-Effect, Stochastic Process, ...
instances
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types
Continuant Occurrent
IndependentContinuant
DependentContinuant
Function Disease
Functioning Side-Effect, Stochastic Process, ...
Mary’s pneumonia Mary’s coughing
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Functions are continuant instances
The function of your heart begins to exist with the beginning to exist of your heart, and continues to exist, self-identically, until (roughly) your heart ceases to be able to respond if stimulated by your sympathetic and parasympathetic nervous systems
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Functions vs Functionings
the function of your heart = to pump blood in your body
this function is realized in processes of pumping blood
not all functions are realized (consider the function of this sperm ...)
not all functions are realized normally
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The Abnormality Theory of Disease
Disease is a state of a person which issues in abnormal behavior; something is an abnormal bodily or mental process if it does standard members of the human species some harm in standard circumstances;something does a person harm if it makes the person less able to live a good or worthwhile life.(Lawrie Reznek)
What are standard circumstances?What are states and how do they issue in consequences?
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"Defining Disease in the Genomics Era“, Larissa et al.
A disease is:
a state that places individuals at increased risk of adverse consequences.
genetic variations with no adverse consequences (like Gilbert's syndrome) will be interesting but inconsequential polymorphisms
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"Defining Disease in the Genomics Era“, Larissa et al.
A disease is:
a state that places individuals at increased risk of adverse consequences.
Where is the threshold for ‘adverse’ consequences (a) along the intensity dimension; (b) along the time dimension?
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A function is a disposition of a continuant to act in such a way as to contribute to the organism’s survival
states issue in consequences = continuants (e.g. cellular networks) have functions which are executed as patterns of functionings
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The function of the kidney is to clean blood
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Nephron
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Functional Segments
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Functions
functions based on shapes
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Low hanging fruit
Why we should not just talk about conditions
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What clinical medicine is for
to eliminate malfunctioning by fixing broken body parts
or to prevent the appearance of malfunctioning by intervening
or to alleviate the harmful consequences of this malfunctioning
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molecule cellular component
molecular function
cellularfunction
organism-level
biological function
organism
molecular process
cellularprocess
organism-level
process
functioningsfunctionings functionings
molecularlocation
cellular location
organism-level
location
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cell (types)
molecular function
(GO)
species
molecular process
cellular anatom
y
anatomy(fly, fish, human...)
cellularphysiology
organism-levelphysiology
ChEBI,Sequence,
RNA ...
normal(functionings)
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pathophysiology
pathoanatomy(fly, fish, human ...)
pathological(malfunctionings)
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pathophysiology
pathoanatomy(fly, fish, human ...)
pathological(dispositional
malfunctionings)
disease
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Pathoanatomy
not: disease of anatomical structure
but: disease of pathonatomical structure
Types of pathoanatomical structures:
malshapen limbs
pathological formations (tumors)
disturbed networks
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Some pathoanatomical structures are not associated with a risk of adverse consequences (‘disorders’)
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Fiat vs. bona fide boundaries
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Fiat vs. Bona Fide Boundaries
Fiat boundary Physical boundary
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Colorado exists
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Tumors exist
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everything here is an independent continuant
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structure vs. formation = bona fide vs. fiat boundaries
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malgrowths
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disease and anatomical damage
prokaryotic organisms do not have diseases
eukaryotic cells have a high number of different types of dispositions and form complex networks (such as the human brain) which can be damaged in ways which give rise to adverse effects
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(Lou)
polio, ALS, myasthenia gravis, muscular distrophy begin with changes in the structures of certain cells (this we know)
if these changes lead to distortions in the network which compromise the viability of the organism, then the organism has a disease
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Action item
Add molecular and cellular networks to the domain anatomy
Create a new discipline of network pathoanatomy
extend anatomy to networksextend pathoanatomy to types of disturbed
networks
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pathoanatomy
There are malshaped networks and malshaped things (deformities)
and also genetic malmutations
which give rise to malfunctionings, behavioral abnormalities
The networks function
The malshaped network malfunctions
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Boorse
Health is conformity to normal species design (as statistically determined).
(Biostatistical Theory)
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Boorse
disease =def. an impairment of normal functional ability
What Is Disease? J. M. Humber, R. F. Almeder, Eds., Humana Press, Totowa, NJ, 1997.
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from Larissa, et al. Science 2001
To be considered a DISEASE, the genotypic or phenotypic state of the patient must have the potential for adverse consequences. In Gilbert's syndrome, there is an asymptomatic elevation of liver enzymes in response to stress, but this condition is not considered a DISEASE because it does not lead to adverse consequences. The World Health Organization's valuable classification of adverse consequences includes physical or psychological impairment, activity restrictions, and/or role limitations. The inclusion of role limitations is particularly important because it acknowledges the sociological consequences of DISEASE in terms of shortening the quantity of life or disturbing its quality. When determining states that are associated with DISEASE, the challenge is to describe potential adverse outcomes comprehensively and explicitly. Because an adverse consequence in one culture may not be viewed as such in another, this consideration must take into account different ethnic and cultural beliefs. For example, whereas menopause is considered a medical condition in North America, in other cultures it is viewed as a normal aspect of aging.
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from Larissa, et al. Science 2001
The human genome sequence is likely to reveal many harmless genetic variations that will turn out not to be associated with DISEASE. Until we resolve questions about polymorphisms, incomplete penetrance of genetic mutations, and the contribution of environmental factors to DISEASE etiology, we will not be able to assess the probability of adverse consequences associated with a particular gene abnormality. There is little doubt that many genetic variations will have no consequences and, like those in individuals with Gilbert's syndrome, will be interesting but inconsequential polymorphisms. Until a mutation is shown to demonstrate a defined risk of developing adverse consequences, individuals carrying that mutation should not be considered DISEASEd. Defining adverse consequences and determining the risk of myriad small genetic variations is a mammoth task. But it is only with this information that clinicians can accurately define the term DISEASE in the genomics era, and in so doing, be able to advise their patients appropriately.
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Enc Brit 1an impairment of the normal state of an organism that interrupts or modifies its vital functions. A brief discussion of disease follows. The subject is treated in a variety of articles. For a general discussion of human, animal, and plant diseases, see disease. For a discussion
of diseases categorized according to their cause or transmission, see infection; nutritional disease; occupational disease. For a discussion of diseases associated with particular stages of human development, see childhood disease and disorder; growth; development. For a discussion of malignancy, which may affect any organ or tissue in the body, see cancer. For a discussion of disease-causing organisms such as viruses, bacteria, and parasites, see bacteria; virus. For a discussion of bodily defenses against disease, see immune system. For a discussion of the diagnosis and treatment of disease, see diagnosis; therapeutics; drug; medicine, history of. For a discussion of diseases affecting particular organs, tissues, or processes, see blood disease; cardiovascular disease; digestive system disease; endocrine system, human; renal system disease; skin disease; metabolic disease; muscle disease; nervous system disease; reproductive system disease; respiratory disease; eye disease and ear disease; connective tissue disease. For a discussion of neuroses and psychoses, see mental disorder. For a discussion of alcoholism and other drug addictions, see alcohol consumption.
Disease most commonly is caused by the invasion of an organism by one or more outside agents. Typically the infectious organisms are microorganisms (e.g., bacteria, viruses, and fungi), but they also can include larger organisms such as parasitic worms or nonliving but harmful substances such as toxins or ionizing radiation. Disease also may result from changes within the organism—an anatomical fault (congenital or acquired) or a physiological malfunction (e.g., diabetes mellitus, in which the body fails to secrete or adequately utilize insulin, a hormone that regulates blood-sugar levels). Other diseases are a combination of external and internal factors. An organism's failure to adapt to changes in its environment can produce damaging changes within it. Physiological malfunctions and disturbances of normal growth can be induced by changes of diet or by invasion of microorganisms or other agents.
Nearly all organisms are able to defend themselves against most diseases. Humans and other vertebrates have developed two strategies of resistance, called immunity, to invading agents: nonspecific immunity, which is present in all vertebrates at birth; and specific immunity, which is acquired only after stimulation by the presence of a certain microbe or its products (e.g., the virus that causes chicken pox). Immunity also can be stimulated artificially in humans or other animals by inoculating them with microorganisms that have been killed (as in typhoid vaccine) or weakened (attenuated) ones (as in measles vaccine), which produce the defensive immune reaction without causing the disease.
Sometimes an organism's defensive reaction to invasion by an outside agent can become part of the disease. The crippling of the lungs produced by tuberculosis is caused partly by the destruction of lung tissue by the invading microorganism (in humans, usually Mycobacterium tuberculosis) and partly by the fibrous tissue that the body lays around the infection in a defensive reaction. Disorders of the immune response itself can produce autoimmune disease (e.g., rheumatoid arthritis) in which the immune response is triggered not by an outside invader but by the body's own tissues, which some cells fight against and try to reject. The immune system also can be disabled by an invading microorganism, as is the case with the disease AIDS.
Not all organisms that invade another produce disease. Some can establish a mutually beneficial relationship with their host without impairing its vital systems; for example, the bacteria that live in the gastrointestinal tracts of humans and other vertebrates make possible the digestive processes of their hosts. In addition, organisms that are pathogenic to one species may be harmless to another.
A disease that becomes established in an organism usually requires some form of treatment. In most cases, treatment consists of administering drugs that kill the causative agent, restore any physiological or biochemical imbalances that have occurred, or control the symptoms caused by the agent so that the affected organism can continue to function. Other forms of treatment include moving the diseased organism to another environment or removing the diseased parts from the organism.
The most effective way to control disease is by preemptory prevention. The best method is to eliminate a disease-causing organism from the environment, such as by killing pathogens or parasites contaminating a water supply. Also effective is the disruption of a pathogen's transmission from one organism to another, either by avoiding contact with body tissues or fluids that harbour a pathogen or by eliminating an intermediary vector (e.g., killing the mosquitoes that transmit malaria to humans). Disease also may be prevented by removing a susceptible organism from an unhealthful environment, strengthening the organism's defenses by making it healthier, or vaccination.
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everything here is an independent continuant
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Functions are beneficial
those processes which are the realizations of a biological function Z are (in normal circumstances) beneficial to the organism
( such as to sustain the organism in existence)
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Functions
This is a screwdriver
This is a good screwdriver
This is a broken screwdriver
This is a heart
This is a healthy heart
This is an unhealthy heart
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Prototypes
good functioning (sound anatomy)
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Departures from Prototypes
reasonable functioning
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Poor functioning
poor functioning
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Malfunctioning
malfunctioning
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Death?
not functioning at all
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Not functioning at all
leads to death modulo internal factors:
plasticity
redundancy (2 kidneys)
criticality of the system involved
external factors:
prosthesis (dialysis machines, oxygen tent)
special environments
assistance from other organisms
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Disease = remoteness from prototypical functioning
disease
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Ontology of Disease
Diseases are, like functions, dependent continuants
They are states or conditions which endure for a certain time and have a course or history, which is an occurrent
Disease instances = Mary’s pneumonia
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Need to take time into account
a forty year old man with rapidly dividing, highly invasive, cancerous prostate cells has the disease prostate cancer
a ninety year old man with slowly dividing cancerous prostate cells does not have the disease prostate cancer
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A 90 year old man with Alzheimers probably had Alzheimers undiagnosed at the age of 40
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The FMA is a canonical representation
but it recognizes also variant anatomical structures (e.g. coronary arteries or bronchopulmonary segments which deviate from the canonical anatomical pattern of organization)
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canonical life Gestalten
+ variant life Gestalten (vegetarians)
+ pathological life Gestalten (serial murderers)
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Model organisms
you can buy a mouse with the prototypical mouse Bauplan according to a precise specification
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Just as there are 2 x n canonical Baupläne for human beings (male
and female at n successive stages)
so there may be different canonical life plans for different types of human beings (in different types of contexts)
what are the different types?
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What is a canonical environment?
What is a canonical family?
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From Embryontology to GerontologyConceptionDevelopmentBirthInfancyToddlerdomEarly ChildhoodChildhoodAdolescenceEarly AdulthoodMiddle ageOld age Death
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What does every human canonical life involve?
9 months of development (here the plan is very determinate)
birthinfancytoddlerdomlater: acquisition of consciousness, languagecycles of waking, sleeping; eating and not
eatingdeath
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The organizing principle of complex living systems
a life-like system =def. any compact system containing an order and distribution of sustaining nonlinear limit cycle oscillators, and a related system of algorithmic guide mechanisms, that is capable of regulating its interior conditions for a considerable range of ambient environmental conditions so as to permit its own satisfactory preservative operation
Iberall, A. S. and McCulloch, W. S. The organizing principle of complex living systems. Journal of Basic Engineering. 290-294. June 1969.
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Iberall and McCulloch
An essential characteristic of a living system is its marginal instability. Its principal dynamic properties are that it hungers, feeds, and can move or creep so that it can continue to hunger, feed, and move or creep.
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Iberall and McCulloch 20 action modes:Action Modes % of timeSleeps 30Eats 5Drinks 1Voids 1Sexes 3Works 25Rests (no motor activity, indifferent internal sensory flux) 3Talks 5Attends (indifferent motor activity, involved sensory activity) 4Motor practices (runs, walks, plays, etc.) 4Angers 1Escapes (negligible motor and sensory input) 1“Anxioius-es” 2”Euphorics” 2Laughs 1Aggresses 1Fears, fights, flights 1Interpersonally attends (body, verbal or sensory contact) 8Envies 1Greeds 1 Total: 100% +/- 20% of time involvement
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Functions
an entity has a biological function if and only if it is part of an organism and has a disposition to act reliably in such a way as to contribute to the organism’s survival
doesn’t apply to sperm
doesn’t apply to carcinomatous lung
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Revised formulation
an entity has a biological function if and only if it is part of an organism and has a disposition to act reliably in such a way as to contribute to the organism’s realization of the canonical life plan for an organism of the relevant species
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What clinical medicine is for
to bring the patient back in the direction of the canonical life for an organism of his stage of development
cure = pulling you all the way back
life extension (can take you beyond the canonical life)
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Disease (Some Hypotheses)
• an anatomical structure in an organism has a certain function
• this structure has become pathological– growths, pathogens, genetically determined
deformations
• and so malfunctions in ways which fall outside the species-typical range for an organism in this stage of development (= outside the canonical life)
• and brings a high risk of adverse consequences
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Disease = remoteness from prototypical functioning modulo stage
of development and environment
disease
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A new proposed definition
X has a disease =def.
i. X departs from the canonical life plan appropriate for X‘s stage of development and environment
ii. this departure brings (causally) risk of adverse consequences for X
iii. this departure is rooted in an enduring pathoanatomical distortion
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To apply this definition
we do not need to know the nature of the pathoanatomical distortion in every type of case
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Implications for disease ontology
Focus on specific focal families of diseases* where we can specify relevant pathoanatomical entities (including cellular networks ...) and relevant types of disturbances
A classification of diseases is a classification of those patterns of pathoanatomical disturbance which give rise to adverse consequences
*Ignore the common cold; ignore syndromes
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Implications for disease ontology
Follow the principle of low-hanging fruit
Have these specifications created and validated by human experts
Take the structure and work with SNOMED for importing further content
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United States
Colorado
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Abnormality rooted in generalized pathoanatomy
disease
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Abnormality rooted in generalized pathoanatomy
disease
Enduring phenotypic abnormality
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DO
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