VT

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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

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