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VT
2
The First Industrial-Strength
Philosophy
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IFOMIS
Institute for Formal Ontology
and Medical Information Science
http://ifomis.de
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Medicine
needs to find a way to enable the huge amounts of data resulting from formal trials and from informal clinical practice
to be (f)used together
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The problem
Different communities of medical researchers use different and often incompatible category systems in expressing the results of their work
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Example: Medical Nomenclature
MeSH (Medical Subject Headings):blood is a tissue
SNoMed (Systematized Nomenclature of Medicine):
blood is a fluid
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The solution
“ONTOLOGY”
Remover “Ontology Impedance”
But what does “ontology” mean?
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Two alternative readings
Ontologies are oriented around terms or concepts = currently popular IT conception
Ontologies are oriented around the entities in reality = traditional philosophical conception, embraced also by IFOMIS
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Ontology as a branch of philosophy
seeks to establish
the science of the kinds and structures of objects, properties, events, processes and relations in every domain of reality
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Ontology a kind of generalized chemistry or zoology
(Aristotle’s ontology grew out of biological classification)
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Aristotle
world’s first ontologist
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World‘s first ontology
(from Porphyry’s Commentary on Aristotle’s Categories)
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Linnaean Ontology
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Medical Diagnostic Ontology
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Ontology is distinguished from the special sciences
it seeks to study all of the various types of entities existing at all levels of granularity
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and to establish how they hang together to form a single whole (‘reality’ or ‘being’)
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Sources for ontological theorizing:
the study of ancient textsthought experiments (we are philosophers, after all)
the development of formal theories
the results of natural science
now also:
working with computers
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The existence of computers
and of large databases
allows us to express old philosophical problems in a new light
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Example: The Gene Ontology (GO)
hormone ; GO:0005179 %digestive hormone ; GO:0046659 %peptide hormone ; GO:0005180 %adrenocorticotropin ; GO:0017043 %glycopeptide hormone ; GO:0005181 %follicle-stimulating hormone ; GO:0016913
% = subsumption (lower term is_a higher term)
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as tree
hormone
digestive hormone peptide hormone
adrenocorticotropin glycopeptide hormone
follicle-stimulating hormone
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GO
is very useful for purposes of standardization in the reporting of genetic information
but it is not much more than a telephone directory of standardized designations organized into hierarchies
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GO deals with such basic ontological notions very
haphazardly
GO’s three main term-hierarchies are:component, function and process
But GO confuses functions with structures, and also with executions of functions
and has no clear account of the relation between functions and processes
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Moreover,
GO can in practice be used only by trained biologists
whether a GO-term stands in the subsumption relationship
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A still more important problemThere exist multiple databases:
GDB
Genome Database of Human Genome Project
GenBank
National Center for Biotechnology Information, Washington DC
etc.
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What is a gene?
GDB: a gene is a DNA fragment that can be transcribed and translated into a protein
GenBank: a gene is a DNA region of biological interest with a name and that carries a genetic trait or phenotype
GO uses ‘gene’ in its term hierarchy,but it does not tell us which of these definitions is correct
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How resolve such incompatibilities?
The Semantic Web Initiative
(Tim Berners-Lee, the inventor of the internet):
enforce terminological compatibility via standardized term hierarchies, with standardized definitions of terms
applied as meta-tags to websites
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The Semantic Web
The Web is a vast edifice of heterogeneous data sources
Needs the ability to query and integrate across different conceptual systems
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Metadata: the new Silver Bullet
We agree on a metadata standard for washing machines as concerns: size, capacity, energy consumption, water consumption, priceWe create machine-readable databases of our inventories and put them on the netA consumer can then query multiple sites simultaneously and thereby search the Internet for highly specific, reliable, context-sensitive results
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Cary Doctorow:
A world of exhaustive, reliable metadata would be a utopia.
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Problem 1: People lie
Meta-utopia is a world of reliable metadata. But poisoning the well can confer benefits to the poisoners
Metadata exists in a competitive world. Some people are crooks. Some people are cranks.
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Problem 2: People are lazy
Half the pages on Geocities are called “Please title this page”
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Problem 3: People are stupid
The vast majority of the Internet's users
(even those who are native speakers of English)
cannot spell or punctuate
Will internet users suddenly and en masse learn to accurately categorize their information according to whatever DL-hierarchy they're supposed to be using?
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Problem 4: Metrics influence results
raw MHz scores privilege Intel's CISC chips over Motorola's RISC chips.
Every player in a metadata standards body will want to emphasize their high-scoring axes
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Problem 5: Multiple descriptions
We impart informationHe chattersThey gossip
Requiring everyone to use the same vocabulary to describe their material denudes the cognitive landscape, enforces homogeneity in ideas.
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Problem 6: Ontology Impedance
= semantic mismatch between ontologies being merged
This problem recognized in Semantic Web literature:
http://ontoweb.aifb.uni-karlsruhe.de/About/Deliverables/ontoweb-del-7.6-swws1.pdf
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Solution 1: treat it as (inevitable) ‘impedance’
and learn to find ways to cope with the disturbance which it brings
Suggested here:
http://ontoweb.aifb.uni-karls-ruhe.de/Ab-out/Deliverables/ontoweb-del-7.6-swws1.pdf
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Solution 2: resolve the impedance problem on a case-by-case basis
Suppose two databases are put on the web.
Someone notices that "where" in the friends table and "zip" in a places table mean the same thing.
http://www.w3.org/DesignIssues/Semantic.html
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Both solutions fail
1. treating mismatches as ‘impedance’ inappropriate in an area like medicine
and ignores the problem of error propagation
2. resolving impedance on a case-by-case basis defeats the very purpose of the Semantic Web
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Problem 5: Multiple descriptions
Requiring everyone to use the same vocabulary to describe their material not always practicable especially in the medical domain
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Clinicians
often do not use category systems at all – they use unstructured text
from which useable data has to be extracted in a further step
Reasons for this: every case is different, much patient data is context-dependent
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Proposed IFOMIS solution
distinguish two separate tasks:
- the task of developing computer applications capable of running in real time
- the task of developing an expressively rich framework of a sort which will allow us to resolve incompatibilities between definitions
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different terminology systems
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need not interconnect at all
for example they may relate to entities of different granularity
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we cannot make incompatible terminology-systems interconnect
just by looking at concepts, or knowledge or language
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we cannot make incompatible terminology-systems interconnect
or by staring at the terminology systems themselves
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to decide which of a plurality of competing definitions to accept
we need some tertium quid
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we need, in other words,
to take the world itself into account
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BFO
= basic formal ontology
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BFO
ontology is defined not as the ‘standardization’ or ‘specification’ of conceptualizations
(not as a branch of knowledge or concept engineering)
but as an inventory of the entities existing in reality
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The BFO framework
will solve the problem of ontological impedance and provide tools for quality-control on the output of computer applications
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BFO not a computer application
but a Reference Ontology
(something like old-fashioned metaphysics)
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Reference Ontology
a theory of a domain of entities in the world
based on realizing the goals of maximal expressiveness and adequacy to reality
sacrificing computational tractability for the sake of representational adequacy
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Reference Ontology
a theory of the tertium quid
– called reality –
needed to hand-callibrate database/terminology systems
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Methodology
Get ontology right first
(realism; descriptive adequacy; rather powerful logic);
solve tractability problems later
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A reference ontology
is a theory of reality
But how is this possible?
How can we get beyond our concepts?
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Answer:
draw on 2 millennia of philosophical research • pertaining to realism, scepticism, error,
theory change, and the language/concept/world relation
• pertaining to the structure of reality itself at different levels of granularity
APPLY THE RESULTS TO THE DOMAIN OF MEDICAL REALITY
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try to find ways to look at the same objects at different levels
of granularity:
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and also:
look not at concepts, representations, of a passive observer
but rather at agents (clinicians) acting in the world
taking account of the tacit knowledge of reality which the domain experts possess
GO useable only by biologists, because only they know how given terms function in given contexts
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The Reference Ontology Community
IFOMIS (Leipzig) Laboratories for Applied Ontology
(Trento/Rome, Turin)Foundational Ontology Project (Leeds)Ontology Works (Baltimore)Ontek Corporation (Buffalo/Leeds)Language and Computing (L&C)
(Belgium/Philadelphia)
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Domains of Current Work
IFOMIS Leipzig: Medicine, Bioinformatics
Laboratories for Applied Ontology
Trento/Rome: Ontology of Cognition/Language
Turin: Law
Foundational Ontology Project: Space, Physics
Ontology Works: Genetics, Molecular Biology
Ontek Corporation: Biological Systematics
Language and Computing: Natural Language Understanding
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Recall:
GDB: a gene is a DNA fragment that can be transcribed and translated into a protein
Genbank: a gene is a DNA region of biological interest with a name and that carries a genetic trait or phenotype
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Ontology
‘fragment’, ‘region’, ‘name’, ‘carry’, ‘trait’, ‘type’
... ‘part’, ‘whole’, ‘function’, ‘inhere’, ‘substance’ …
are ontological terms in the sense of traditional (philosophical) ontology
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BFOnot just a system of categoriesbut a formal theory with definitions, axioms, theoremsdesigned to provide the resources for
reference ontologies for specific domainsof sufficient richness that terminological incompatibilities can be resolved intelligently rather than by brute force
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Two basic oppositions
Granularity (of molecules, genes, cells, organs, organisms ...)
SNAP vs. SPAN
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SNAP vs. SPAN
Two different ways of existing in time:
continuing to exist (of organisms, their qualities, roles, functions, conditions)
occurring (of processes)
SNAP vs. SPAN = Anatomy vs. Physiology
SNAP: Entities existing in toto at a time
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Three kinds of SNAP entities
1. Independent: Substances, Objects, Things
2. Dependent: Qualities, Functions, Conditions, Roles
3. Spatial regions
SNAP: Dependent
SNAP-Spatial Region
SNAP-Independent
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SPAN: Entities occurring in time
SPANEntity extended in time
Portion of Spacetime
Fiat part of process *First phase of a clinical trial
Spacetime worm of 3 + Tdimensions
occupied by life of organism
Temporal interval *projection of organism’s life
onto temporal dimension
Aggregate of processes *Clinical trial
Process[±Relational]
Circulation of blood,secretion of hormones,course of disease, life
Processual Entity[Exists in space and time, unfolds
in time phase by phase]
Temporal boundary ofprocess *
onset of disease, death
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SPAN: Dependent (Processes)
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SPAN: Spatiotemporal Regions
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Realization (SNAP-SPAN)
the execution of a plan
the expression of a function
the exercise of a role
the realization of a disposition
the course of a disease
the application of a therapy
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SNAP dependent entities and their SPAN realizations
plan
function
role
disposition
disease
therapy
SNAP
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SNAP dependent entities and their SPAN realizations
execution
expression
exercise
realization
course
application
SPAN
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More examples:
performance of a symphonyprojection of a filmexpression of an emotionutterance of a sentenceincrease of body temperaturespreading of an epidemicextinguishing of a forest firemovement of a tornado
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BFO = SNAP/SPAN + Theory of Granular Partitions +
theory of universals and instances
theory of part and whole
theory of boundaries
theory of functions, powers, qualities, roles
theory of environments, contexts
theory of spatial and spatiotemporal regions
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MedO: medical domain ontologyuniversals and instances and normativity
theory of part and whole and absence
theory of boundaries/membranes
theory of functions, powers, qualities, roles, (mal)functions, bodily systems
theory of environments: inside and outside the organism
theory of spatial and spatiotemporal regions: anatomical mereotopology
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MedO: medical domain ontologytheory of granularity: relations between
molecule ontology
gene ontology
cell ontology
anatomical ontology
etc.
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IFOMIS project
collaborate with L&C to show how an ontology constructed on the basis of philosophical principles can help in overhauling and validating L&C’s large terminology-based medical ontology LinkBase®
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Testing the BFO/MedO approach
within a software environment for NLP of unstructured patient records
collaborating with
Language and Computing nv (www.landcglobal.be)
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L&C
LinKBase®: world’s largest terminology-based ontology
with mappings to UMLS, SNOMED, etc.
+ LinKFactory®: suite for developing and managing large terminology-based ontologies
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LinKBase
LinKBase still lacking a formal theorylacking a formal theory• BFO and MedO designed to add better
reasoning capacity • by tagging LinKBase domain-entitiesdomain-entities with
corresponding BFO/MedO categories• by constraining links within LinKBase
according to the theory of granular partitionsaccording to the theory of granular partitions
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L&C’s long-term goal
Transform the mass of unstructured patient records into a gigantic medical experiment
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IFOMIS’s long-term goal
Build a robust high-level BFO-MedO framework
THE WORLD’S FIRST INDUSTRIAL-STRENGTH PHILOSOPHY
which can serve as the basis for an ontologically coherent unification of medical knowledge and terminology
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END
http://ontologist.com
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