BASIC FORMAL
ONTOLOGY
Robert Arp, Ph.D.
Ontology Research Group (ORG)
www.org.buffalo.edu
National Center for Biomedical Ontology (NCBO)
www.bioontology.org
I:
II:
III:
Meanings of
‘Ontology’
Basic Formal
Ontology
Constructing a
Domain Ontology
Part I:
Meanings of
‘Ontology’
(1) Philosophical Ontology
(2) Domain Ontology
(3) Formal Ontology
(1) Philosophical Ontology
“...I can fit wholesale evolution and a
creating god into my ontology without
contradiction.”
“...just because it has mental existence
doesn’t mean it has ontological
existence.”
- Ontos (being, existence)+ Logos
(word, account, explanation)
- The study of what is, of the
kinds and structures of objects,
properties, events, processes,
and relations in every area of
reality
- “The branch of Metaphysics that
studies the nature of existence.”
Random House College Dictionary
Thing
PORPHYRIAN
TREE
Material
Substance
Animate
(Living) Entity
Living Entity
with Sensation
(Animal)
Rational
Animal
(Human)
NonRational
Animal
Immaterial
Substance
Non-Animate
Entity
Living Entity
without
Sensation
(Vegetation)
Compare:
Linnean Taxonomy
and Periodic Table
To a certain extent,
all of us are
Philosophical
Ontologists in that
we naturally and
automatically
categorize any and
all things in reality
so as to understand,
explain, control,
dominate, and
navigate reality.
(1) Philosophical Ontology
(2) Domain Ontology
(3) Formal Ontology
(2) Domain Ontology
“...I’m working on an ontology
for annelids.”
“...the Gene Ontology has
data on that HOX gene.”
- Representation of the entities and relations
existing within a particular domain of reality
such as medicine, geography, ecology, or law
Gene Ontology (GO)
Foundational Model of Anatomy (FMA)
Environment Ontology (EnvO)
- Opposed to ontology in the philosophical
sense, which has all of reality as its subject
matter
- Ideally, provides a controlled, structured
vocabulary to annotate data in order to make
it more easily searchable by human beings
and processable by computers
ONTOLOGY:
“a representational artifact,
comprising a taxonomy as its main
part, whose representational units
are intended to designate some
combination of universals, defined
classes, and certain relations
between them.” *
* Smith, B., Kusnierczyk, W., Schober, D., & Ceusters, W. (2006). Towards a
reference terminology for ontology research and development in the
biomedical domain. Proceedings of KR-MED 2006, 1, 1-14.
REALISM-BASED ONTOLOGY:
“…built out of representational units
which are intended to refer
exclusively to (real) universals, and
corresponds to that part of the
content of a scientific theory that is
captured by its constituent general
terms and the interrelations between
the universals denoted by these
terms.” (Smith et al., 2006)
Method of Ontological Realism
• Find out what the world is like by
doing science, talking to other
scientists, and working
continuously with them to ensure
that you don’t go wrong
• Build representations adequate to
this world, not to some simplified
model in your laptop
Informatics:
The science of information collection,
categorization, management, storage,
processing, retrieval, and dissemination.
“…the fundamental role of a domain
ontology is to support knowledge
sharing and reuse.” *
* Domingue, J., & Motta, E. (1999). A knowledge-based news server
supporting ontology-driven story enrichment and knowledge retrieval.
In D. Fensel & R. Studer (Eds.), Knowledge acquisition, modeling and
management (pp. 104-112). Berlin: Springer.
Domain ontology contrasted with:
- Database
- Rule-Based Language
- Thesaurus
- Glossary
- Catalogue
- Inventory
- Axiomatic Theory
- Simple Taxonomy
Ontology
characterized
as a hybrid of:
- Taxonomy
- Axiomatic
Theory
Domain Ontologies are
representations of
universals in reality:
kinds
types
categories
genera
species
The Central Distinction
universal vs. instance
(catalogue vs. inventory)
(science text vs. diary)
(human being vs. George Bush)
(mouse brain vs. Mickey Mouse’s brain)
(cytoplasm vs. this cytoplasm under the scope)
substance
universals
organism
animal
mammal
cat
siamese
instances
frog
Example Domain
Ontology
Mechanism
Doorbell
Thermometer
Clock
Animal
Trap
Mouse Trap
Rodent
Trap
SpringLoaded Bar
Mouse Trap
Trap
Insect Trap
Mouse Trap
Rat Trap
Electric
Mouse Trap
Glue
Mouse Trap
Human
Trap
Bear Trap
Fish Trap
Example Domain
Ontology
Beverage
NonAlcoholic
Beverage
Alcoholic
Beverage
Ale
Beer
Wine
Lager
Lambic
Beer
Whisk(e)y
Soda
Beer
Bitter Ale
Mild Ale
Sweet Ale
Coffee
BORROWED FROM:
http://www.bio.davidson
.edu/courses/genomics/2
006/martens... 3DN
A Gene Ontology
Example:
Glutathione
A Gene Ontology
Example:
Cytokinesis
is_a
part_of
A Gene Ontology
Example
Scientific Experiment Ontology
http://technology.newscientist.com/article/dn9288-translator-letscomputers-understand-experiments-.html
p/o =
part_of
is_a
Entity
Part of a
Lipid
Ontology
Polyatomic
Entity
Biological
Entity
Biomolecules
Small
Molecules
Being developed by:
Low, H-S., Alexander, G., Baker, C., &
Wenk, M. (2008). Lipid ontology
Lipid
LC Fatty
Acyls
LC Docosanoids
LC Eicosanoids
LC
Lipoxins
LC
Hepoxilins
Available at:
http://MUS.12R.lipidontology.biochem
.nus.edu.sg/lipidversion3.owl.
LC
Cluvalones
ONTOLOGY
SCOPE
Cell Ontology (CL)
cell types from prokaryotes to mammals
Chemical Entities of
Biological Interest
(ChEBI)
molecular entities which are products of nature
or synthetic products used to intervene in the
processes of living organisms
ebi.ac.uk/chebi
Paula Dematos, Rafael Alcantara
anatomical structures in human and model
organisms (initially mouse, fly, zebrafish)
(under development)
Melissa Haendel, David Sutherland
human diseases and associated conditions
diseaseontology.source
forge.net
Rex Chisholm, Warren Kibbe, John
Osborne, Wendy Wolf
structure of the human body
fma.biostr.
washington.edu
JLV Mejino Jr., Cornelius Rosse
www.geneontology.org
Gene Ontology Consortium
fugo.sf.net
OBI/FuGO Working Group
obo.sourceforge.net/
cgi-bin/ detail.cgi?
attribute_and_value
Michael Ashburner, Suzanna Lewis,
Georgios Gkoutos
Common Anatomy
Reference Ontology
(CARO)
Disease Ontology (DO)
(Candidate member)
Foundational Model of
Anatomy (FMA)
Gene Ontology (GO)
Ontology for Biomedical
Investigations (OBI)
Phenotypic Quality
Ontology (PATO)
attributes of gene products (divided into:
cellular component, molecular function,
biological process) in all organisms
design, protocol, instrumentation, data and
analysis applied in functional genomics
investigations
qualities of anatomical structures
URL
obo.sourceforge.net/cgi- Jonathan Bard, Michael Ashburner,
bin/detail.cgi?cell
Oliver Hofmann
protein types and modifications classified on
pir.georgetown.edu/pro
the basis of evolutionary relationships
relations between universals and instances in
Relation Ontology (RO)
obofoundry.org/ro
biomedical ontologies
three-dimensional structures and homologous
Ontology (RnaO)
sequence alignments and associated attributes
(under development)
and processes
Sequence Ontology
www.sequenceontology.
features and properties of nucleic sequences
(SO)
Org
Protein Ontology (PrO)
CUSTODIANS
Cathy Wu, Darren Natale
Chris Mungall
Ontology Consortium
Karen Eilbeck
Because of:
- Varying perspectives, methodologies, ideas, and
Data
- Extraordinary depth, magnitude of data…
- Overwhelmed with data and information…
- More information than humans can handle…
A couple of problems result
(there are more…)
A Couple of Problems
(there are more…)
1
How do you find your data?
2
THE SILO EFFECT
1
How do you find your data?
- How do you understand the
significance of the data you
collected 3 years earlier?
- How do you reason with the data
when you find it?
- How do you integrate your data with
other people’s data?
CHAOS
Part of the solution seems to
involve consensus-based
- standardized terminologies
- coding schemes
2
THE SILO EFFECT
Many domains that are
non-interoperable,
non-communicative, isolated,
insolated, encapsulated
“silos” of data
THE SILO EFFECT
Data
Data
Data
Data
Data
Data
Data
THE SILO EFFECT
Data
Data
Data
Data
Data
Data
Data
Informatics problems that
contribute to SILO
EFFECT:
THE SILO
EFFECT
- Dumb Beast
- Nonsense-In-Nonsense-Out
- Computer Solipsism
- Human Idiosyncrasy
- Tower of Babel
- Pressures from Insurance Companies
- Legal Pressures
** Human Error: Incorrect Thinking
** Human Error: Incorrect Thinking
Three Levels to Keep Straight
• Level 1: The entities in reality, both instances
and universals
• Level 2: Cognitive representations of this reality
on the part of scientists
• Level 3: Publicly accessible concretizations of
these cognitive representations in textual,
graphical, or computational representational
artifacts
Three Levels to Keep Straight
Cognitive representations
Representational artifacts
Reality
PROBLEM:
DE-SILOING all of this
domain data so that it may be
found (!), queried effectively,
shared, and re-used…
PROBLEM:
DE-SILOING all of this
domain data so that it may be
found (!), queried effectively,
shared, and re-used…
SOLUTION:
Formal Ontology
(1) Philosophical Ontology
(2) Domain Ontology
(3) Formal Ontology
(3) Formal Ontology
“...This upper-level ontology
should help organize these
domains.”
“...IEEE just came out with the
latest version of SUMO that
may solve some of these
problems.”
Assists in making communication
between and among domain
ontologies possible by providing:
-Common language
-Common formal framework
for reasoning
Concerns, at least:
- Adoption of a set of basic
categories of objects
- Discerning what kinds of entities
fall within each of these categories
of objects
- Determining what relationships
hold between the different
categories in the domain ontology
Formal Ontology is like a “backbone” or “spine”
making communication, interoperability, and
optimal dissemination of information possible
between and among domain ontologies
Formal Ontology
E.G., Basic Formal Ontology
Data
Data
Data
Data
Data
Data
Data
Data
Data
Data
Data
From this…
Data
Data
Data
To this…
Formal Ontology
E.G., Basic Formal Ontology
Data
Data
Data
Data
Data
Data
Data
From this…
To this…
Program Announcement Number: PAR-07-425
Title: Data Ontologies for Biomedical
Research (R01)
NIH Blueprint for Neuroscience Research, (http://neuroscienceblueprint.nih.gov/)
National Cancer Institute (NCI), (http://www.cancer.gov)
National Center for Research Resources (NCRR), (http://www.ncrr.nih.gov/)
National Eye Institute (NEI), (http://www.nei.nih.gov/)
National Heart Lung and Blood Institute (NHLBI), (http://http.nhlbi.nih.gov )
National Human Genome Research Institute (NHGRI), (http://www.genome.gov)
National Institute on Alcohol Abuse and Alcoholism (NIAAA), (http://www.niaaa.nih.gov/)
National Institute of Biomedical Imaging and Bioengineering (NIBIB), (http://www.nibib.nih.gov/)
National Institute of Child Health and Human Development (NICHD), (http://www.nich.nih.gov/)
National Institute on Drug Abuse (NIDA), (http://www.nida.nih.gov/)
National Institute of Environmental Health Sciences (NIEHS), (http://www.niehs.nih.gov/)
National Institute of General Medical Sciences (NIGMS), (http://www.nigms.nih.gov/)
National Institute of Mental Health (NIMH), (http://www.nimh.nih.gov/)
National Institute of Neurological Disorders and Stroke (NINDS), (http://www.ninds.nih.gov/)
National Institute of Nursing Research (NINR), (http://www.ninr.nih.gov)
PAR-07-425 Purpose
“Optimal use of informatics tools… and
(data) resources depends upon explicit
understandings of concepts related to the
data upon which they compute.”
“This is typically accomplished by a tool
or resource adopting a formal controlled
vocabulary and ontology.”
EXAMPLES:
Basic Formal Ontology (BFO)
Standard Upper Merged
Ontology (SUMO)
Descriptive Ontology for
Linguistic and Cognitive
Engineering (DOLCE)
BFO is an ontology to
support integration of
scientific research data
SUMO contains many portions which
are more properly conceived of as
domain ontologies (airports, bacteria)
DOLCE is tilted towards objects of
general thought and communication
(fiction, mythology)
Taxonomy
An Ontology
of Ontologies
Philosophical
Ontology
E.G., Porphyrian Tree
Taxonomy with
Formal Rules =
Simple
Taxonomy
Ontology
E.G., Thesaurus
Domain
Ontology
Domain
Reference
Ontology
Domain
Application
Ontology
E.G., Table of the
Elements, Linnean,
GO, FMA
E.G., Amazon.com,
Library of Congress
catalogue
Formal
Ontology
Formal
Reference
Ontology
Formal
Application
Ontology
E.G., SUMO,
DOLCE, BFO
E.G., Friend of a
Friend (FOAF)
Part II:
Basic Formal
Ontology (BFO)
BFO: General Preliminaries
- Upper-Level, Top-Level, Formal...
“...applicable to all domains of objects”*
* Barry Smith and David Woodruff Smith, The Cambridge
Companion to Husserl, ed. Barry Smith and David Woodruff
Smith (Cambridge: Cambridge University Press, 1995), 28.
EMBRACES
- Perspectivalism
- Granularity
- Fallibility
REALISM-BASED ONTOLOGY
Universals
(1) real objects, substances,
endurants, or continuants
- SNAP shots of reality
(2) real processes, activities,
perdurants, or occurrents
- SPAN of time
Relations
is_a, part_of, has_participant
Universals
(1) real objects, substances,
endurants, or continuants
- SNAP shots of reality
(2) real processes, activities,
perdurants, or occurrents
- SPAN of time
continuants vs. occurrents
continuant (substance, object)
occurrent (process)
In classifying parts of reality, we keep
track of these two different kinds of
entities in two different ways
continuant entities
- have continuous existence in time
- preserve their identity through change
- exist in toto, if they exist at all
occurrent entities
- have temporal parts
- unfold themselves phase by phase
- exist only in their phases/stages
Two Orthogonal, Independent,
Complementary Perspectives
stocks and flows
commodities and services
product and process
anatomy and physiology
The tumor developed in the lung over 25 years.
The tumor developed in the lung over 25 years.
substances
things
objects
continuants
The tumor developed in the lung over 25 years.
substances
things
objects
continuants
processes
activities
occurrents
BFO: The Very Top
continuant
independent
continuant
dependent
continuant
occurrent
(always
dependent
on one or more
independent
continuants)
BFO: The Very Top
continuant
independent
continuant
dependent
continuant
objects
fiat objects
sites
qualities
functions
roles
dispositions
occurrent
(always
dependent
on one or more
independent
continuants)
processes
fiat process parts
process contexts
BFO: The Very Top
Example:
continuant
independent
continuant
object:
mice
dependent
continuant
occurrent
(always
dependent
on one or more
independent
continuants)
quality:
process:
that are black
have drugs
injected in them
BFO: The Very Top
Example:
continuant
independent
continuant
object:
LSD
dependent
continuant
quality:
that is
hallucinogenic
occurrent
(always
dependent
on one or more
independent
continuants)
process:
is digested in the
blood stream
BFO: The Very Top
Example:
continuant
independent
continuant
object:
kidney
dependent
continuant
function:
whose
function is to
filter urine
occurrent
(always
dependent
on one or more
independent
continuants)
process:
filters urine
BFO: The Very Top
Example:
continuant
independent
continuant
dependent
continuant
object:
disposition:
conjuctiva
which is affected
with conjunctivitis
occurrent
(always
dependent
on one or more
independent
continuants)
process:
engages in edema
Example:
BFO: The Very Top
continuant
independent
continuant
site:
inner area,
spare tire
dependent
continuant
role:
acts as
reservoir
occurrent
(always
dependent
on one or more
independent
continuants)
process:
colonization of
mosquitoes
Three Dichotomies
• continuant vs. occurrent
• dependent vs. independent
• instance vs. universal
universals exist in reality
through their instances
occurrent
(process)
continuant
(object)
independent
continuant
(molecule,
cell, organ,
organism)
dependent
continuant
(quality,
functioning
function,
disease)
side-effect,
stochastic
process, ...
..... ..... .... .....
instances
continuant
Relation: is_a
Note:
Similarity to
Porphyrian
Tree
HUMAN
HEART
continuant
human
heart
surface of
the heart
pink,
smooth
all hearts in
this room
stops if no
circulation
a biopsy of
the heart
pumps
blood
chest
cavity
prop in a
display
occurrent
Relation: is_a
Note: Similarity to
Porphyrian Tree
occurrent
ECG/EKG
TEST
ECG (EKG)
test
start/end
of ECG
all ECGs in
clinic
2nd lead
attached
activities
in clinic
s/t ECG
began
moment
ECG began
s/t region
of ECG
time
occupied
REALISM-BASED ONTOLOGY
Universals
(1) real objects, substances,
endurants, or continuants
- SNAP shots of reality
(2) real processes, activities,
perdurants, or occurrents
- SPAN of time
Relations
is_a, part_of, has_participant
REALISM-BASED ONTOLOGY
Relations
is_a
part_of
has_participant, ...
- Instance Level
- Universal Level
is_a
part_of
located_in
part_of
adjacent_to
instance_of …
inheres_in
derives_from
participates_in
contained_in…
INSTANCE LEVEL RELATIONS
INSTANCE LEVEL RELATIONS
UNIVERSAL RELATIONS
UNIVERSAL RELATIONS
Multiple Sclerosis Ontology
(being developed by Barry Smith and others)
The Relations Ontology
http://www.obofoundry.org/ro/
Based on:
Smith, B., Ceusters, W., Klagges, B., Köhler, J., Kumar,
A., Lomax, J., et al. (2005). Relations in biomedical
ontologies. Genome Biology, 6, R46.
Groups and Organizations Using BFO:
AstraZeneca - Clinical Information Science
BioPAX-OBO
BIRN Ontology Task Force (BIRN OTF)
Computer Task Group Inc.
Duke University Laboratory of Computational Immunology
Dumontier Lab
INRIA Lorraine Research Unit
Kobe University Graduate School of Medicine
Language and Computing
National Center for Multi-Source Information Fusion
Ontology Works
University of Texas Southwestern Medical Center Science
Science Commons: Neurocommons
Neurocommons team is working to:
- Release, improve, and extend an open
knowledge base of annotations to the
biomedical abstracts (in RDF)
- Debug and tailor an open-source
codebase for computational biology
- Gradually integrate major neuroscience
databases into the annotation graph…
From:
http://sciencecommons.org/projects/data/
“All the while using these efforts to further
bring together the community within
neuroscience around open approaches to
systems biology…”
Alan Ruttenberg
http://sciencecommons.org/about/whoweare/ruttenberg/
…currently involved in a number of open biomedical
ontology efforts, including:
BioPAX: representing molecular and cellular pathways…
Ontology for Biomedical Investigations (OBI)…
Basic Formal Ontology (BFO) that will form the upperlevel ontology for the OBO foundry …
A Few Ontologies Using BFO
BioTop: A Biomedical Top-Domain Ontology
Common Anatomy Reference Ontology (CARO)
Foundational Model of Anatomy (FMA)
Gene Ontology (GO)
Infectious Disease Ontology (IDO)
Ontology for Biomedical Investigations (OBI)
Ontology for Clinical Investigations (OCI)
Phenotypic Quality Ontology (PaTO)
Protein Ontology (PRO)
RNA Ontology (RnaO)
Senselab Ontology
Sequence Ontology (SO)
Subcellular Anatomy Ontology (SAO)
Vaccine Ontology (VO)
http://obofoundry.org
Researchers use Protégé,
OBO-Edit, Microsoft Excel,
or any number of other
media (chalk boards) to
classify entities using BFO
http://www.ifomis.org/bfo/
BFO Protégé
96
Microsoft Excel
MS Excel
Lipid Ontology using BFO Protégé being developed by:
Low, H-S., Alexander, G., Baker, C., & Wenk, M. (2008). Lipid ontology.
Available at:
http://MUS.12R.lipidontology.biochem.nus.edu.sg/lipidversion3.owl.
Vaccine Ontology
http://www.violinet.org/wiki/index.php/Vaccine_Ontology
BFO RESOURCES
Institute for Formal Ontology and
Medical Information Science (IFOMIS)
http://www.ifomis.uni-saarland.de/bfo/
Ontology Research Group (ORG)
http://org.buffalo.edu/
Part III:
Constructing a
Domain
Ontology
13 Basic Steps
Steps #1 - #13
Step #1: Determine the purpose of the
domain ontology:
reference or application?
Step #2: Determine and demarcate the
relevant subject-matter of the domain.
Step #3: Determine the level of granularity
of the domain.
Step #4: Provide explicit statement of the
intended subject-matter of the domain.
Taxonomy
An Ontology
of Ontologies
Philosophical
Ontology
E.G., Porphyrian Tree
Taxonomy with
Formal Rules =
Simple
Taxonomy
Ontology
E.G., Thesaurus
Domain
Ontology
Domain
Reference
Ontology
Domain
Application
Ontology
E.G., Table of the
Elements, Linnean,
GO, FMA
E.G., Amazon.com,
Library of Congress
catalogue
Formal
Ontology
Formal
Reference
Ontology
Formal
Application
Ontology
E.G., SUMO,
DOLCE, BFO
E.G., Friend of a
Friend (FOAF)
relation to
time
granularity
continuant
occurrent
independent
Organism
organ and
(Species
organism
Taxonomy)
cell and
cellular
component
molecule
Cell
(CL)
dependent
Anatomical
Entity
(FMA,
CARO)
Organ
Function
(GO+)
Cellular
Component
(FMA,GO)
Cellular
Function
(GO+)
Molecule
(ChEBI, SO,
RnaO, PrO)
OrganismLevel
Process
Phenotypic
(GO)
Quality
(PaTO)
Cellular
Process
(GO)
Molecular Function
(GO)
Molecular
Process
(GO)
Demarcation and Determining Granularity
The Foundational Model of Anatomy (FMA)
http://sig.biostr.washington.edu/projects/fm/AboutFM.html
“…the FMA is a domain ontology that represents a
coherent body of explicit declarative knowledge about
human anatomy.”
The Gene Ontology (GO)
http://www.geneontology.org/GO.doc.shtml
“…The Gene Ontology Project has developed three
structured controlled vocabularies (ontologies) that
describe gene products in terms of their associated
biological processes, cellular components, and
molecular functions in a species-independent manner.”
Step #5: Determine the most basic
(a) universals
(b) relations
dealt with in the domain.
Step #6: Construct a list of terms for the
domain.
Step #7: Seek precision in categorizing,
but go for the simpler, “low hanging
fruit” first.
INFECTIOUS DISEASE ONTOLOGY
http://www.bioontology.org/wiki/index.php/ Infectious_Disease_Ontology
•
•
•
•
•
•
•
•
•
•
•
•
•
reservoir
host reservoir
end reservoir
colonization
oral-fecal transmission
transmission
incubation period
infectious disease progression
contagious
quality of pathogen
epidemic
symptom
vehicle
• “end reservoir is_a reservoir”
• “oral-fecal transmission is_a
transmission”
• “contagious is_a quality of
pathogen”
• “incubation period part_of
infectious disease progression”
• “colonization part_of infectious
disease progression”
• vehicle located_in reservoir
• symptom preceded_by incubation
period
• epidemic has_participant
colonization
High-Hanging Low-Hanging
Fruit:
Fruit:
Life
What is “Right”
Meaning
Gene?
Neuropathy?
Cancer?
Cell
Minimal Risk
Quality of Life
Homeotic Gene
Cauda Equina Syndrome
Leukemia
Step #8: Regiment the
information in order to
ensure logical and scientific
coherence:
Avoid the Pitfalls of
Incorrect Thinking (IT)
Some Pitfalls of
Incorrect
Thinking (IT)
IT: Simply Getting the Facts Wrong *
FROM GO, SNOMED, BRIDG, and UMLS
(1) “extracellular region is_a cellular component”
(2) “extrinsic to membrane part_of membrane”
(3) ‘derives from’ confused with ‘develops from’
(4) “both testes is_a testis”
(5) Animal =Def. “A non-person living entity…”
(6) “An ontology is the same thing as a database…”
(7) “An ontology is just a taxonomy…”
* N.B. It may be the case that the examples of IT used
in this presentation have been resolved.
IT: Lack of Clear and Coherent Definitions
FROM NCIT, BRIDG, and SNOMED:
(1) Disease Progression =Def. “Cancer that
continues to grow and spread,” and “Increase
in size of tumor…,” and “The worsening of a
disease over time”
(2) Person =Def. “Human being”
(3) “European is_a ethnic group”
(4) “Other European in New Zealand is_a
ethnic group”
(5) “Mixed ethnic census group is_a ethnic
group”
IT: Circular Definitions
FROM GO and BRIDG
(1) Hemolysis of red blood cells
=Def. “The processes by which an organism effects
hemolysis”
Compare: Filtration of kidneys
=Def. “The processes by which an organism effects
filtration (of kidneys)”
(2) Ingredient =Def. “A substance that acts as an
ingredient within a product. Note that ingredients may
also have ingredients.”
(3) Protection from natural killer cell mediated cytolysis
=Def. “The process of protecting a cell from cytolysis
by natural killer cells”
IT: Examples Instead of Definitions
FROM BRIDG
(1) Adverse Event =Def.
(a) “toxic reaction”…
(b) “…untoward occurrence in a subject
administered a pharmaceutical
product…”
(c) “An unfavorable and unintended
reaction, symptom, syndrome, or
disease encountered by a subject
on a clinical trial…”
(2) Defeasibility =Def. “a line of communication
that is terminated,” “boundaries for software”
IT: Use-Mention Confusion
FROM BIRN, MeSH, NCIT, and HL7
(1) Mouse =Def. “Name for the species Mus musculus”
(2) “National Socialism is_a MeSH Descriptor”
(3) Conceptual Entities =Def. “An organizational
header for concepts representing mostly
abstract entities”
(4) Animal =Def. “a subtype of Living Subject
representing any animal-of-interest to the
Personnel Management domain”
(5) “living subject is_a code system ”
IT: Conception/Perception vs.
Reality Confusion
FROM NCIT and UMLS
(1) Living subject =Def. “An object representing an organism”
(2) Class performed activity =Def. “The description of applying,
dispensing or giving agents or medications to subjects”
(3) Adverse Event =Def. “An observation of a change in the
state of a subject that is assessed as being untoward…”
(4) Objective Result =Def. “An act of monitoring, recognizing
and noting reproducible measurement…”
(5) “Individual allele is_a act of observation ”
(6) “Cancer documentation is_a cancer”
(7) “Bacterium causes experimental model of disease”
Some Pitfalls of Incorrect Thinking to Avoid
1) Representing defined classes or particulars
2) Representing concepts rather than real entities
3) Blurring the use/mention distinction
4) Blurring the perception/reality distinction
5) Giving examples instead of definitions
6) Giving circular definitions
7) Not ensuring necessary and specific conditions
8) Equivocation
9) Using categories of non-existent entities
10) Classifying using multiple inheritance
Step #9: Use basic Aristotelian
structure when formulating
definitions.
- Get at the essential features of an
entity when defining it.
- Use a taxonomy structured by
is_a relations.
Basis for Solid
Classification
Systems
Step #10: Regiment the information in
order to ensure compatibility with other
relevant ontologies (BFO important here).
Formal Ontology
E.G., Basic Formal Ontology
Data
Data
Data
Data
Data
Data
Data
Step #11: Concretize this information
in a representational artifact (on
paper, in Excel, using Protégé…).
Step #12: Formalize the
representational artifact in a
computer tractable language.
Step #13: Implement the artifact in
some specific computing context.
The Countless
Cs of Computational
Categorization:
FROM
Cognizance
TO
Coordination
TO
Comfort
Cognizance of Informatics Problems
Cooperation of Researchers, Doctors…
Conferences, Colloquia, Meetings…
Clarity of Terms and Relations
Cogency: Counter-Example Free?
Coherency of Domain Ontologies
Coordination of Domain Ontologies
Computational Tractability
Communicability of Information
Coding of Information Correctly
Convenience of Accessibility to Information
Care of Humans/Animals (First, Do No Harm)
Comfort of Humans/Animals
Thank You
This work was funded by the National Institutes
of Health through the NIH Roadmap for
Biomedical Research, Grant 1 U 54 HG004028.
Information on the National Centers for
Biomedical Computing can be found at:
http://nihroadmap.nih.gov/bioinformatics.