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IMIA Working Group 6 Medical Concept Representation. Focus of Meeting:. New role of ontological research for new age of biomedical informatics. Scientific developments: foundational issues rather than operational questions. Long-term view: ensure development of robust

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IMIA Working Group 6 Medical Concept Representation

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Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

IMIA Working Group 6

Medical Concept Representation

Focus of Meeting:

  • New role of ontological research

    • for new age of biomedical informatics

Scientific developments:

foundational issues

rather than operational questions

  • Long-term view:

    • ensure development of robust

    • biomedical ontologies for the future


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

IMIA Working Group 6

Medical Concept Representation

The Foundational Role of Anatomy

for Biomedical Ontologies

Cornelius Rosse M.D., D.Sc.

S t r u c t u r a l I n f o r m a t i c s G r o u p

University of Washington


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

What will be the take home message?

What are the problems?

We have established biomedical informatics

Is it a service?

Is it a new biomedical science?

If a science

What is its theoretical foundation?

What is its methodology?

Are theory and ontological methodology applied in

the practice of biomedical informatics?

How do applications of theory and methodology supportinference about individuals (EHR)?


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

What will be the take home message?

What are the solutions?

  • Theoretical solution

    • Propose a theory for biomedical reality

    • derived from top-level ontologies

  • Methodological solution

    • Develop reference ontologies in

    • domains of empirical basic biomedical science

    • using sound methodology

    • Reuse reference ontologies in

    • application ontologies designed for

      • clinical specialties

      • biomedical research

      • education and training


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Case study: Cardiac Cycle


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Case study: Cardiac Cycle


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Case study: Cardiac Cycle

Atrial pressure


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Case study: Cardiac Cycle

Left ventricular pressure

Atrial pressure


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Case study: Cardiac Cycle

Left ventricular pressure

Left ventricular volume

Atrial pressure


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Case study: Cardiac Cycle

Left ventricular pressure

Aortic pressure

Left ventricular volume

Atrial pressure


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Case study: Cardiac Cycle

Left ventricular pressure

Aortic pressure

Left ventricular volume

Atrial pressure


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Case study: Cardiac Cycle

Left ventricular pressure

Aortic pressure

Left ventricular volume

Atrial pressure


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Movie


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Case study: Cardiac Cycle

Task:

Generate ontological representation

Resources

extant terminologies:

UMLS


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Cardiac Cycle in UMLS


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Cardiac Cycle in UMLS


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Cardiac Cycle in UMLS


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Cardiac Cycle in UMLS


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Movie


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Case study: Cardiac Cycle

Task:

Generate ontological representation of cardiac cycle

Resources

extant terminologies: UMLS

textbooks, literature

re-examination of cardiac cycle from ontological perspective


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Diversion!

Task:

Generate ontological representation of cardiac cycle

Resources

extant terminologies: UMLS

textbooks, literature

re-examination of cardiac cycle from ontological perspective


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Constitutents of Medical Science

Basic sciences Clinical sciences


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Constituents of Medical Science

Basic sciences Clinical sciences

PhysiologyInternal medicine

PathologyPediatrics

MicrobiologyPsychiatry

BiochemistryAnesthesiology

AnatomySurgery

macroscopicgeneral surgery

microscopicmaxillofacial surgery

embryologyotolaryngology

neuroanatomyneurosurgery


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Basic Sciences

Characteristics

Taught/learned during

first phase of professional training

Concerned with canonical knowledge

not data pertaining to individuals

Do not target specialties in clinical medicine

Need to be relearned in context of medical specialties

Purpose

Provide general understanding for

reasoning and managing data

pertaining to individuals


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Basic Sciences

Changing Environment

1960’s: curricular reform

1970’s: new biology


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Basic Sciences

Changing Environment

1960’s: curricular reform

1970’s: new biology

Medicine Biomedicine; Biomedical science


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Constituents of Biomedical Science

Basic sciences Clinical sciences

PhysiologyInternal medicine

PathologyPediatrics

MicrobiologyPsychiatry

BiochemistryAnesthesiology

AnatomySurgery

macroscopicgeneral surgery

microscopicmaxillofacial surgery

embryologyotolaryngology

neuroanatomyneurosurgery

Traditional

disciplines

New biologyNew medicine

molecular and cell biology molecular medicine

genomics, proteomics regenerative medicine

developmental biology translational medicine

systems biology nuclear medicine


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

What is Biomedical Informatics?

Basic sciences Clinical sciences

PhysiologyInternal medicine

PathologyPediatrics

MicrobiologyPsychiatry

BiochemistryAnesthesiology

AnatomySurgery

macroscopicgeneral surgery

microscopicmaxillofacial surgery

embryologyotolaryngology

neuroanatomyneurosurgery

Traditional

disciplines

New biologyNew medicine

molecular and cell biology molecular medicine

genomics, proteomics regenerative medicine

developmental biology translational medicine

systems biology nuclear medicine

Biomedical Informatics


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

What will be the take home message?

What are the problems?

We have established biomedical informatics

Is it a service?

Is it a new biomedical science?

If a science

What is its theoretical foundation?

What is its methodology?

Are theory and ontological methodology applied in

the practice of biomedical informatics?

How do applications of theory and methodology supportinference about individuals (EHR)?


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Attributes of Science

Science has

a.) theories on basis of which hypotheses can be formulated

b.) methodology which can test the hypotheses

Best hope: Ontology


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Need for theories and methodology

What is ontology ?

Smith (1996):

“the science which deals with the nature and organization of reality”

Grenon, Smith & Goldberg (2004)

“An ontology grasps the entities which exist within a given portion of the world at a given level of generality. It includes a taxonomy of the types of entities and relations that exist in that portion of the world seen from a given perspective.”

Ontological theories

derive from the philosophy of reality

Ontological methodology

creates an artifact which depicts a portion of the world

seen from a given perspective


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Need for theories and methodology

What is ontology ?

first meaning:

Smith (1996):

“the science which deals with the nature and organization of reality

Grenon, Smith & Goldberg (2004)

“An ontology grasps the entities which exist within a given portion of the world at a given level of generality. It includes a taxonomy of the types of entities and relations that exist in that portion of the world seen from a given perspective.”

second meaning:

an artifact

projects to a given domain of reality

created through the application of

principles and methods of ontological science


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Why base an ontology on reality?

Ambiguity

  • any domain discourse is full with it

  • humans are adapt at dealing with it

    - printed page tolerates it

  • computational inference will be

    crippled by it


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Why base an ontology on reality?

Ambiguity

  • any domain discourse is full with it

  • humans are adapt at dealing with it

    - printed page tolerates it

  • computational inference will be

    crippled by it

    Conclusion:

    - we have to base ontology on reality

    - need to take a new look at reality


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

What kinds of ontologies are there?

  • Formal, top-level ontologies

  • 2. Domain reference ontologies

  • 3. Terminology-based application ontologies


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

What kinds of ontologies are there?

  • Formal, top-level ontologies:DOLCE, BFO

    • domain-independent theories

    • framework of axioms and definitions

    • high degree of representational accuracy

    • designed to be used as controls on other types of ontologies


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

What kinds of ontologies are there?

  • Formal, top-level ontologies:DOLCE, BFO

    • domain-independent theories

    • framework of axioms and definitions

    • high degree of representational accuracy

    • designed to be used as controls on other types of ontologies

  • 2. Domain reference ontologies:FMA

    • declare a theory about a particular domain of reality

    • make use of methods of top-level ontologies

    • general purpose resources

    • generalize to other domains

    • anatomy generalizes to physiology, surgery


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

What kinds of ontologies are there?

  • Formal, top-level ontologies:DOLCE, BFO

    • domain-independent theories

    • framework of axioms and definitions

    • high degree of representational accuracy

    • designed to be used as controls on other types of ontologies

  • 2. Domain reference ontologies:FMA

    • declare a theory about a particular domain of reality

    • make use of methods of top-level ontologies

    • general purpose resources

    • generalize to other domains

    • anatomy generalizes to physiology, surgery

  • 3. Terminology-based application ontologies:

  • GO, other OBO, SNOMED, MeSH

    • systems of terms

    • purpose-built

    • designed to meet particular needs

    • annotating databases, medical data


Basic formal ontology

Basic Formal Ontology

Entities

Occurrents

Continuants

Distinguishing criterion (differentia): Time


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Basic Formal Ontology

Entities

Occurrents- SPAN entities

Dependent entities which do not endure through time;

unfold themselves in successive temporal phases

(e.g., processes, actions)

have temporal parts


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Basic Formal Ontology

Entities

Occurrents- SPAN entities

Dependent entities which do not endure through time;

unfold themselves in successive temporal phases

(e.g., processes, actions)

have temporal parts

Continuants- SNAP entities

Entities which endurein toto

in every instant of time at which they exist

have spatial parts

Independent continuants

objects, components

Dependent continuants

attributes, roles, qualities, functions


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

END OF DIVERSION


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

A theory of biomedical reality

Biological entity

Biological continuant

Biological occurrent

is-a


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Biological entity

Biological continuant

Biological occurrent

is-a

Extra-organismal

biological continuant

Organismal

continuant


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Biological entity

Biological continuant

Biological occurrent

is-a

Extra-organismal

biological continuant

Organismal

continuant

Independent

organismal

continuant

Dependent

organismal

continuant


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Biological entity

Biological continuant

Biological occurrent

is-a

Extra-organismal

biological continuant

Organismal

continuant

Independent

organismal

continuant

Dependent

organismal

continuant

Material

anatomical

entity

Material

pathological

entity

Anatomical structure

Canonical

anatomical structure

Variant

anatomical structure

Portion of canonical

body substance

Portion of blood

Portion of cytosol

Pathological structure

Neoplasm

Inflammatory structure

Degenerated structure

Portion of pathological

body substance

Portion of pus

Portion of amyloid


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Biological entity

Biological continuant

Biological occurrent

is-a

Extra-organismal

biological continuant

Organismal

continuant

Independent

organismal

continuant

Dependent

organismal

continuant

Material

anatomical

entity

Material

pathological

entity

Immaterial

anatomical

continuant

Physiological

continuant

Immaterial

pathological

continuant

Anatomical structure

Canonical

anatomical structure

Variant

anatomical structure

Portion of canonical

body substance

Portion of blood

Portion of cytosol

Pathological structure

Neoplasm

Inflammatory structure

Degenerated structure

Portion of pathological

body substance

Portion of pus

Portion of amyloid

Anatomical space

Cavity of lysosome

Anatomical surface

E-face of plasma

membrane

Anatomical line

Anatomical point

Function

Secrete

Flex; Extend

Physiological state

Relaxed state

Contracted state

Physiological role

Antagonist

Pathological space

Cavity of abscess

Pathological surface

Boundary of tumor

Malfunction

Atrial fibrillation

Pathological state

Malnutrition

Pathological role


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Biological entity

Biological continuant

Biological occurrent

is-a

Extra-organismal

biological continuant

Organismal

continuant

Extra-organismal

biological occurrent

Organismal

occurrent

Independent

organismal

continuant

Dependent

organismal

continuant

Material

anatomical

entity

Material

pathological

entity

Immaterial

anatomical

continuant

Physiological

continuant

Immaterial

pathological

continuant

Anatomical structure

Canonical

anatomical structure

Variant

anatomical structure

Portion of canonical

body substance

Portion of blood

Portion of cytosol

Pathological structure

Neoplasm

Inflammatory structure

Degenerated structure

Portion of pathological

body substance

Portion of pus

Portion of amyloid

Anatomical space

Cavity of lysosome

Anatomical surface

E-face of plasma

membrane

Anatomical line

Anatomical point

Function

Secrete

Flex; Extend

Physiological state

Systole

Physiological role

Antagonist

Pathological space

Cavity of abscess

Pathological surface

Boundary of tumor

Malfunction

Atrial fibrillation

Pathological state

Malnutrition

Pathological role


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Biological entity

Biological continuant

Biological occurrent

is-a

Extra-organismal

biological continuant

Organismal

continuant

Extra-organismal

biological occurrent

Organismal

occurrent

Independent

organismal

continuant

Dependent

organismal

continuant

Physiological

process

Pathological

process

Secreting

Secreting insulin

Transcribing RNA

Mutating

Metastasizing

Necrosing

Material

anatomical

entity

Material

pathological

entity

Immaterial

anatomical

continuant

Physiological

continuant

Immaterial

pathological

continuant

Anatomical structure

Canonical

anatomical structure

Variant

anatomical structure

Portion of canonical

body substance

Portion of blood

Portion of cytosol

Pathological structure

Neoplasm

Inflammatory structure

Degenerated structure

Portion of pathological

body substance

Portion of pus

Portion of amyloid

Anatomical space

Cavity of lysosome

Anatomical surface

E-face of plasma

membrane

Anatomical line

Anatomical point

Function

Secrete

Flex; Extend

Physiological state

Systole

Physiological role

Antagonist

Pathological space

Cavity of abscess

Pathological surface

Boundary of tumor

Malfunction

Atrial fibrillation

Pathological state

Malnutrition

Pathological role


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Ontology of

Biomedical Reality (OBR)

Biological entity

Biological continuant

Biological occurrent

is-a

Extra-organismal

biological continuant

Organismal

continuant

Extra-organismal

biological occurrent

Organismal

occurrent

Independent

organismal

continuant

Dependent

organismal

continuant

Physiological

process

Pathological

process

Secreting

Secreting insulin

Transcribing RNA

Mutating

Metastasizing

Necrosing

Material

anatomical

entity

Material

pathological

entity

Immaterial

anatomical

continuant

Physiological

continuant

Immaterial

pathological

continuant

Anatomical structure

Canonical

anatomical structure

Variant

anatomical structure

Portion of canonical

body substance

Portion of blood

Portion of cytosol

Pathological structure

Neoplasm

Inflammatory structure

Degenerated structure

Portion of pathological

body substance

Portion of pus

Portion of amyloid

Anatomical space

Cavity of lysosome

Anatomical surface

E-face of plasma

membrane

Anatomical line

Anatomical point

Function

Secrete

Flex; Extend

Physiological state

Systole

Physiological role

Antagonist

Pathological space

Cavity of abscess

Pathological surface

Boundary of tumor

Malfunction

Atrial fibrillation

Pathological state

Malnutrition

Pathological role


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Theory of biological continuants

Organismal

continuant

Independent

organismal

continuant

Material

anatomical

entity

Material

pathological

entity

Anatomical structure

Definition:

Material physical anatomical entity which has inherent 3D shape; generated by coordinated expression of the organism's own structural genes;


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Theory of biological continuants

Anatomical

Structure

Human

Body

Biological

Macromolecule

Body

Part

Acellular

Anatomical

Structure

Cell

Part

Cell

Portion

of tissue

Organ

Part

Organ

Organ

System


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Theory of biological continuants

Material Physical

Anatomical Entity

Portion of

body substance

Anatomical

Structure

Human

Body

Biological

Macromolecule

Body

Part

Acellular

Anatomical

Structure

Cell

Part

Cell

Portion

of tissue

Organ

Part

Organ

Organ

System


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Theory of biological continuants

Independent

organismal

continuant

Material Physical

Anatomical Entity

Portion of

body substance

Anatomical

Structure

Human

Body

Biological

Macromolecule

Body

Part

Acellular

Anatomical

Structure

Cell

Part

Cell

Portion

of tissue

Organ

Part

Organ

Organ

System


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Theory of biological continuants

Independent

organismal

continuant

Dependent

organismal

continuant

Material Physical

Anatomical Entity

Non-material Physical

Anatomical Entity

Portion of

body substance

Anatomical

Structure

Space

Surface

Line

Human

Body

Biological

Macromolecule

Body

Part

Acellular

Anatomical

Structure

Cell

Part

Cell

Portion

of tissue

Organ

Part

Organ

Organ

System


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

FMA: created with ontological methods

Independent

organismal

continuant

Dependent

organismal

continuant

Material Physical

Anatomical Entity

Non-material Physical

Anatomical Entity

Portion of

body substance

Anatomical

Structure

Space

Surface

Line

Human

Body

Biological

Macromolecule

Body

Part

Acellular

Anatomical

Structure

Cell

Part

Cell

Portion

of tissue

Organ

Part

Organ

Organ

System


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Ontological methods


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Somatic cell which has as direct parts of its cytoplasm myofibrils organized in various patterns.


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Muscle cell which has as its direct parts myofilaments organized into sarcomeres.


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Muscle cell which has as its direct parts myofilaments organized into sarcomeres.

Striated muscle cell which has as its direct parts one or two centrally placed nuclei.


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Continuants in Cardiac Cycle

Participants

Biatrial part

of heart

Biventricular part

of heart


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

How do we represent pathological continuants?

Fibrous

pericardium

Pericardial cavity


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

How do we represent pathological continuants?


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

How do we represent pathological continuants?


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

How do we represent pathological continuants?

Will the processes remain

normal?


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Can we propose a theory of

biological processes?

Rationale for theory of continuants:

based on gene expression of dependent continuants

compatible with theory of OBR

Rationale for theory of processes:

need to formulate a hypothesis

evaluate it through instantiation of

physiological and pathological processes


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Can we propose a theory of

biological processes?

Start with a hypothesis:

A process is an occurrent which is realized through the conversion of physical energy of one kind to another or to a change in structural order.


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Theory of biological processes

Hypothesis:

A process is an occurrent which is realized through the conversion of physical energy of one kind to another or to a change in structural order.

Rationale:

processes involve

movement of their participants

caused by some force

generated by dissipation of energy


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Where is energy generated?


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Sarcomere


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Movie


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Sarcomere

Ca++


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Movie


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Conversion of energy from one kind to another

Conversion of chemical

to mechanical energy

Molecular conformational

change

Liberated energy


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Macromolecule

Transmission of force by participants in cardiac cycle


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Movie


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

OPERATORS

Movie


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

How do we classify processes?

Definition

  • Process is

  • - an occurrent which is realized through the conversion of physical energy of one kind to another or to a change in structural order

  • - a transformation of one state of an occurrent into another state.

    • - a change in the values of the set of attributes that define a state.


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

How do we classify processes?

Definition

  • Process is

  • - an occurrent which is realized through the conversion of physical energy of one kind to another or to a change in structural order.

  • - a transformation of one state of an occurrent into another state.

    • - a change in the values of the set of attributes that define a state

  • State is

  • a dependent continuant specified by the values of a set of attributes.


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

How do we classify processes?

Definition

  • Process is

  • - an occurrent which is realized through the conversion of physical energy of one kind to another or to a change in structural order.

  • - a transformation of one state of an occurrent into another state.

    • - a change in the values of the set of attributes that define a state

  • State is

  • a dependent continuant specified by the values of a set of attributes

  • A biological process is

  • a process the direct participants of which are one or more anatomical entities


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Can OBR accommodate constituents of cardiac cycle?

Biological occurrent

Extra-organismal

biological occurrent

Organismal

occurrent

Physiological

process

Pathological

process

Need to deal with

non-biological participants

Ca++

non-biological processes

chemical bonding and bond breaking

attributes and operators

generalize to non-biological domains Laws of physics and chemistry operate in

biological and non-biological domains of reality


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Conflict with OBR

Biological occurrent

OBR hypothesis

must be modified

Extra-organismal

biological occurrent

Organismal

occurrent

Physiological

process

Pathological

process

Need to deal with

non-biological participants

Ca++

non-biological processes

chemical bonding and bond breaking

attributes and operators

generalize to non-biological domains Laws of physics and chemistry operate in

biological and non-biological domains of reality


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

How do we classify processes?

Process

Acyclic process

Cyclic process


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

How do we classify processes?

Process

Acyclic process

Cyclic process

Myosin-actin

binding-unbinding

Sliding of

myofilaments

Increase in LV

blood pressure

Calcium-troponin

binding-unbinding

Shortening of

sarcomere

Flowing of

LV blood to aorta

Myosin head

flexure-unflexure

Contraction

myocyte

myocardial loop

Cardiac cycling


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

How do we classify processes?

Process

Acyclic process

Cyclic process

Chemical-to-

mechanical

energy

Chemical-to-

chemical

energy

Mechanical-to-

mechanical

energy

Mechanical-to-

fluid potential

energy

Fluid potential-to-

fluid kinetic

energy

Chemical-to-

fluid dynamic

energy

Molecular

conformational

change

Myosin-actin

binding-unbinding

Sliding of

myofilaments

Increase in LV

blood pressure

Calcium-troponin

binding-unbinding

Shortening of

sarcomere

Flowing of

LV blood to aorta

Myosin head

flexure-unflexure

Contraction

myocyte

myocardial loop

Cardiac cycling


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

How do we classify processes?


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Testing the ‘Process’ hypothesis

Hypothesis:

A process is an occurrent which is realized through the conversion of physical energy of one kind to another or to a change in structural order.

  • Rationale:

  • processes involve

  • movement of their participants

  • caused by some force

  • generated by dissipation of energy

  • Testing of hypothesis:

    • rooted in non-equilibrium thermodynamics

    • first classification trial yields results

    • intuitive at the operational level

    • conform to single inheritance


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

How do we classify non-biological entities?


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

How do we classify physical attributes?


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

How do we classify operators?


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

How do we represent pathological pathological processes?

Fibrous

pericardium

Pericardial cavity


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Ontology of

Biomedical Reality (OBR)

Biological entity

Biological continuant

Biological occurrent

is-a

Extra-organismal

biological continuant

Organismal

continuant

Extra-organismal

biological occurrent

Organismal

occurrent

Independent

organismal

continuant

Dependent

organismal

continuant

Physiological

process

Pathological

process

Secreting

Secreting insulin

Transcribing RNA

Mutating

Metastasizing

Necrosing

Material

anatomical

entity

Material

pathological

entity

Immaterial

anatomical

continuant

Physiological

continuant

Immaterial

pathological

continuant

Anatomical structure

Canonical

anatomical structure

Variant

anatomical structure

Portion of canonical

body substance

Portion of blood

Portion of cytosol

Pathological structure

Neoplasm

Inflammatory structure

Degenerated structure

Portion of pathological

body substance

Portion of pus

Portion of amyloid

Anatomical space

Cavity of lysosome

Anatomical surface

E-face of plasma

membrane

Anatomical line

Anatomical point

Function

Secrete

Flex; Extend

Physiological state

Systole

Physiological role

Antagonist

Pathological space

Cavity of abscess

Pathological surface

Boundary of tumor

Malfunction

Atrial fibrillation

Pathological state

Malnutrition

Pathological role


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Entity of

Physical Reality

Physical continuant

Physical occurrent

Process

Spatio-

temporal

worm

Non-dimensional

continuant

Dimensional

continuant


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Biological immaterial continuant

Non-biological immaterial continuant

Biological material continuant

Non-biological material continuant

Entity of

Physical Reality

Physical continuant

Physical occurrent

Process

Spatio

temporal

worm

Non-dimensional

continuant

Dimensional

continuant

Material

dimensional continuant

Immaterial

dimensional continuant


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Biological immaterial continuant

Non-biological immaterial continuant

Biological material continuant

Non-biological material continuant

Entity of

Physical Reality

Physical continuant

Physical occurrent

Process

Spatio

temporal

worm

Non-dimensional

continuant

Dimensional

continuant

Spatial attribute

Attribute

Material attribute

Process attribute

Attribute operator

Operator

Structural operator

Biological operator

Material

dimensional continuant

State

Function

Immaterial

dimensional continuant

Role


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Biological immaterial continuant

Non-biological immaterial continuant

Biological material continuant

Non-biological material continuant

Ontology of

Physical Reality (OPR)

Entity of

Physical Reality

Physical continuant

Physical occurrent

Process

Spatio-

temporal

worm

Non-dimensional

continuant

Dimensional

continuant

Spatial attribute

Acyclic process

Attribute

Material attribute

Control process

Morphogenetic process

Replication process

Degeneration process

Process attribute

Attribute operator

Cyclic process

Cardiac cycling

Kreb’s cycle

Operator

Structural operator

Biological operator

Material

dimensional continuant

State

Function

Immaterial

dimensional continuant

Role


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Biological immaterial continuant

Non-biological immaterial continuant

Biological material continuant

Non-biological material continuant

Ontology of

Physical Reality (OPR)

Entity of

Physical Reality

Physical continuant

Physical occurrent

Process

Spatio

temporal

worm

Non-dimensional

continuant

Dimensional

continuant

Spatial attribute

Acyclic process

Attribute

Material attribute

Control process

Morphogenetic process

Replication process

Degeneration process

Process attribute

Attribute operator

Cyclic process

Cardiac cycle

Kreb’s cycle

Operator

Structural operator

Biological operator

Material

dimensional continuant

State

Anatomical Structure

Function

Immaterial

dimensional continuant

Role


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

What about our case study: Cardiac Cycle?


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Protégé

a physiological-chemical to fluid kinetic energy change which has as its direct anatomical participants the heart and the portion of blood in the heart


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

What will be the take home message?

What are the problems?

We have established biomedical informatics

Is it a service?

Is it a new biomedical science?

If biomedical informatics is to be a science

What is the theoretical foundation?

What is its methodology?

Are theory and ontological methodology applied in

the practice of biomedical informatics?

How do applications of theory and methodology supportinference about individuals (EHR)?


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Basic Sciences

Characteristics

Taught/learned during

first phase of professional training

Concerned with canonical knowledge

not data pertaining to individuals

Do not target specialties in clinical medicine

Need to be relearned in context of medical specialties

Purpose

Provide general understanding for

reasoning and managing data

pertaining to individuals


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

What kinds of ontologies are there?

  • Formal, top-level ontologies

  • 2. Domain reference ontologies

  • 3. Terminology-based application ontologies


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

What will be the take home message?

What are the solutions?

  • Theoretical solution

    • Propose a theory for biomedical reality

    • derived from top-level ontologies

  • Methodological solution

    • Develop reference ontologies in

    • domains of empirical basic biomedical science

    • using sound methodology

    • Reuse reference ontologies in

    • application ontologies designed for

      • clinical specialties

      • biomedical research

      • education and training


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Continuant

Attribute

Operator

Process

Need for

dynamically defining

disciplinary boundaries

Process

Attribute

Process

Dimensional

continuant

Material or

Spatial

Attribute

Attribute

Operator

Structural

operator

Biological

operator


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Continuant

Attribute

Operator

Process

Process

Attribute

Process

Traditional basic science: anatomy

Dimensional

continuant

Material or

Spatial

Attribute

Attribute

Operator

Structural

operator

Biological

operator


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

Continuant

Attribute

Operator

Process

Traditional basic science:

Physiology and Pathophysiology

Process

Attribute

has attribute

Process

has role-player attributes

has participants

Dimensional

continuant

has attributes

Material or

Spatial

Attribute

Attribute

Operator

Structural

operator

has part

change attribute values

create or

destroy

create or

destroy

Biological

operator


Ambiguity any domain discourse is full with it humans are adapt at dealing with it printed page tolerates it computati

IMIA Working Group 6

Medical Concept Representation

The Foundational Role of Anatomy

for Biomedical Ontologies

Cornelius Rosse M.D., D.Sc.

S t r u c t u r a l I n f o r m a t i c s G r o u p

University of Washington


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