from formal ontology to biomedical ontology
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From Formal Ontology to Biomedical Ontology. Biomereology. Barry Smith http://ifomis.org. Mereology as Formal Ontology. Logical Investigations (1900-01) Investigation III: On the Theory of Wholes and Parts. Husserl. Le śniewski Kotarbiński Tarski Grzegorczyk Woodger. - PowerPoint PPT PresentationTRANSCRIPT
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From Formal Ontology to Biomedical Ontology
Barry Smith
http://ifomis.org
Biomereology
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Mereology as Formal Ontology
Logical Investigations (1900-01)
Investigation III:
On the Theory of Wholes and Parts
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Husserl
Leśniewski
Kotarbiński
Tarski
Grzegorczyk
Woodger
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Cantor Leśniewski
Frege early Tarski
late Carnap (geometry of solids)
Grzegorczyk
(mereotopology)
set-theory as mereology as
principal instrument principal instrument
of formal ontology of formal ontology
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Hilbert Leśniewski
late Tarski Russell
Carnap early Tarski
Putnam Woodger
contemporary contemporary
model-theoretic realist ontology
semantics
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For Frege, Russell, Leśniewski, Wittgenstein, Quine …
logic is a zoology of facts
formal theories are theories of reality
with one intended interpretation: the world
tragicallyafter starting off on the right road
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Logic took a wrong turn
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(Tarski)
Carnap, Putnam, Goodman, etc.:
Forget reality!
Lose yourself in ‘models’!
“internal realism” ...
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Hilbert Leśniewski
late Tarski Russell
Carnap Wittgenstein
Putnam Quine
OLD: Logic as
Language
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Hilbert Leśniewski
late Tarski Russell
Carnap Wittgenstein
Putnam Quine
NEW: Logic as
Calculus
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Hilbert Leśniewski late Tarski Russell Carnap Wittgenstein Putnam Quine
OLD: Set-theory- based-model-theoretic semantics... possible worlds
blah blah
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Hilbert Leśniewski
late Tarski Russell
Carnap early Tarski
Putnam Woodger
NEW: Extreme
Mereotopological
Bio-Ontological Realism
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Husserl + Leśniewski
realist mereology-based ontology
+ universals
+ topology
+ relations
+ dependent entities
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Formal Ontology vs. Formal Logic
Formal ontology deals with formal ontological structures
Formal logic deals with formal logical structures
‘formal’ = domain-neutral
(obtain in all material spheres of reality)
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Formal Ontology
the theory of those ontological structures
(such as part-whole, universal-particular)
which apply to all domains whatsoever
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Formal Ontology vs. Formal Logic
Formal ontology deals with the interconnections of things
with objects and properties, parts and wholes, relations and collectives
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Formal-Ontological Categoriesobject
state of affairs
unity
plurality
boundary
dependent part
independent part
relation
are able to form complex structures in non-arbitrary, law-governed ways
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From Formal Ontology
to Biomedical Ontology
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Scales of anatomy
DNA
Protein
Organelle
Cell
Tissue
Organ
Organism
10-5 m
10-1 m
10-9 m
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Complexity of biological structures
30,000 genes in human
200,000 proteins
100s of cell types
100,000s of disease types
1,000,000s of biochemical pathways (including disease pathways)
A new golden age of classification
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A new golden age of classification
central importance of classes / types / kinds / universals / species
of independent objects
dependent objects
processes
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Different scientificcultures / terminologies
immunology
genetics
cell biology
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Fleck on Thought-Styles
the general structure of a thought-collective entails that the communication of thoughts within the collective, irrespective of content or logical justification, leads for sociological reasons to the reinforcement of the thought structure
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The problem of the unity of science
The logical positivist solution to this problem addressed a world in which sciences are identified with
printed textsWhat if sciences are identified with
information systems ?
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ProblemEach (clinical, pathological, genetic, proteomic, pharmacological …) information system uses its own classification system
How can we overcome the incompatibilities which become apparent when data from distinct sources needs to be combined?
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Solution:
“Ontology”
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Compare:
1) pure mathematics (theories of structures such as order, set, function, mapping) employed in every domain
2) applied mathematics, applications of these theories = re-using the same definitions, theorems, proofs in new application domains
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Three levels of ontology
1) formal ontology (mereology, mereotopology, …)
2) domain ontologies = Foundational Model of Anatomy, Gene
Ontology, Unified Medical Language System, SNOMED
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Biomereology must be rich enough to deal with time and
change
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Leśniewski’s mereology
grew out of his concerns with the foundations of mathematics
LIKE SET THEORY, IT DOES NOT TAKE ACCOUNT OF TIME
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The Problem
The tumor developed in John’s lung over 25 years
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The Problem
____ developed in _____ over 25 years
process
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The Problem
The tumor developed in the lung over 25 years
substances
things
objects
continuants
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The Problem
The tumor developed in the lung over 25 years
WHAT IS PART OF WHAT
IS NOT DETERMINATE
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The Problem
The tumor developed in the lung over 25 years
substances
GLUING THESE TOGETHER MEREOLOGICALLY YIELDS ONTOLOGICAL MONSTERS
processes
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Substances and processes exist in time in different ways
substance
t i m
e
process
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SNAP vs SPAN
Endurants vs perdurants
Continuants vs occurrents
In preparing an inventory of reality
we keep track of these two different kinds of entities in two different ways
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Fourdimensionalism
– only processes exist
– time is just another dimension, analogous to the three spatial dimensions
– substances are analyzed away as worms/fibers within the four-dimensional plenum
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There are no substances
Bill Clinton does not exist
Rather: there exists within the four-dimensional plenum a continuous succession of processes which are
similar in a Billclintonizing sort of way
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Fourdimensionalism solves the problems of
universal applicability of mereology
indeterminacy of parthood
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Fourdimensionalism (the SPAN perspective) is right in
everything it says
But incomplete
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The response to anyone who believes that fourdimensionalism is
the whole truth about reality is:
see a doctor
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The response to anyone who believes that fourdimensionalism is
the whole truth about reality is:
see any organism
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Bio-Ontology requires two orthogonal applications of
mereology
A fourdimensional ontology
supplemented by a threedimensional ontology of
continuant entities
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How can a threedimensional ontology solve the problem of
determinacy of parthood
PARTHOOD AT AN INSTANT IS DETERMINATE
take an assay of what exists in the three spatial dimensions always at some specific instant of time
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The 4D and 3D ontologies represent two complementary views
of the same rich and messy reality
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DNA
Protein
Organelle
Cell
Tissue
Organ
Organism
10-5 m
10-1 m
Scales of anatomy
10-9 m
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A new golden age of classification
central importance of classes / types / kinds / universals / species
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and of is-a hierarchies
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cars
Cadillacs blue cars
blue Cadillacs
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Confusions about ‘is-a’ and ‘part-of’ in bio-ontologies
Unified Medical Language System
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The UMLS Semantic Network
a US Federal Government ontology designed to unify all biomedical terminologies
59what are the nodes in this graph?
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linguistic entities
≈ meanings
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UMLS SN
is_a =def.
if one item ‘is_a’ another item then the first item is more specific in meaning than the second item
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Fruit
Orange
VegetableSimilarTo
ApfelsineSynonymWith
NarrowerThan
Goble & Shadbolt
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How can concepts/meanings figure as relata of relations such as
disrupts or contained in?
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Swimming is healthy and contains 8 letters
67UMLS Semantic Network
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Vitamin
Injury or Poisoning
causes
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Bacterium
Experimental Model of Disease
causes
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Manufactured Object
Disease or Syndromecauses
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Biomedical or Dental Material
Mental or Behavioral
Dysfunctioncauses
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The Gene Ontology
a ‘controlled vocabulary’
designed to standardize annotation of genes and gene products
used by over 20 genome database and many other groups in academia and industry
and methodology much imitated
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A part_of B =def A can be part of B
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The Gene Ontology
menopause part_of death
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GO: ‘within’
lytic vacuole within a protein storage vacuole is-a protein storage vacuole
interval within a football match is-a football match
embryo within a uterus is-a uterus
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GO: ‘extrinsic to’
extrinsic to membrane part-of membrane
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these people need our help
formal-ontological help
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WoodgerThe Axiomatic Method in Biology
part_of
earlier_than
derives_by_division_or_fusion_from
environment_of
is_a_cell
is_a_male_gamete
is_a_female_gamete
is_a_whole_organism
is_an_organized_unity
is_a_genetic_property
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Material Primitives
part_of
earlier_than
derives_by_division_or_fusion_from
environment_of
is_a_cell
is_a_male_gamete
is_a_female_gamete
is_a_whole_organism
is_an_organized_unity
is_a_genetic_property
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Formal Primitives
part_of
earlier_than
derives_by_division_or_fusion_from
environment_of
is_a_cell
is_a_male_gamete
is_a_female_gamete
is_a_whole_organism
is_an_organized_unity
is_a_genetic_property
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Formal Primitives
part_of
earlier_than
derives_by_division_or_fusion_from
environment_of
is_a_cell
is_a_male_gamete
is_a_female_gamete
is_a_whole_organism
is_an_organized_unity
is_a_genetic_property
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Open Biological Ontologies Consortium
http://obo.sourceforge.net/
OBO library of controlled vocabularies developed for shared use across different biological domains.
Gene Ontology plus: Cell Ontology, Sequence Ontology, etc.
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Open Biological Ontologies Consortium
European Bioinformatics Institute, Cambridge
Jackson Labs, Bar Harbor, Maine
Berkeley Genetics,
Edinburgh Mouse Atlas Project
IFOMIS, Saarbrücken
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OBO Relations Ontology:is_apart_ofdevelops_ fromderives_ from located_atparticipates_inadjacent_tocontained_inprecedeshas_function
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Woodger’s Formal Primitives
part_of
earlier_than
derives_by_division_or_fusion_from
environment_of
is_a_cell
is_a_male_gamete
is_a_female_gamete
is_a_whole_organism
is_an_organized_unity
is_a_genetic_property
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Foundational Model of Anatomy Reference Ontology
a graph-theoretical structure involving two sorts of links or edges:
is-a (= is a subtype of )
(auditory ossicle is-a bone)
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
88Pleural Cavity
Pleural Cavity
Pleura(Wall of Sac)
Pleura(Wall of Sac)
Pleural SacPleural Sac
Parietal Pleura
Parietal Pleura
Anatomical SpaceAnatomical Space
OrganCavityOrganCavity
Serous SacCavity
Serous SacCavity
AnatomicalStructure
AnatomicalStructure
OrganOrgan
Serous SacSerous Sac TissueTissue
Organ PartOrgan Part
Organ Subdivision
Organ Subdivision
Organ Component
Organ Component
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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
Serous SacCavity
Serous SacCavity Serous SacSerous Sac
MediastinalPleura
MediastinalPleura
TissueTissueOrgan Subdivision
Organ Subdivision
Organ Component
Organ Component
Serous SacCavity
Subdivision
Serous SacCavity
Subdivision
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The Anatomy Reference Ontology
a coherent theory of part-of as a relation between classes / types must be based on a (mereological) theory of part-of as a relation between instances
Mary’s heart part-of Mary
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Taking the instance-level part_of as primitive
we can define:
A part_of B = any instance of A is part_of some instance of B
nucleus part_of cell
but not:
testis part_of human
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from A part_of B we cannot infer that B has_part A
human_testis part_of human
but not
human has_part human testis
running has_part breathing
but not
breathing part_of running
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Scales of anatomy
DNA
Protein
Organelle
Cell
Tissue
Organ
Organism
10-5 m
10-1 m
10-9 m
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Institute for Formal Ontology and Medical Information Science
http://ifomis.org
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Buffalo Center for Ontological Research
Two tenure-track faculty positions in ontology
http://ontology.buffalo.edu/bcor
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The End