BASIC FORMAL BASIC FORMAL ONTOLOGYONTOLOGY

Robert Arp, Ph.D.Ontology Research Group (ORG)

www.org.buffalo.edu

National Center for Biomedical Ontology (NCBO)www.bioontology.org

I: Meanings of‘Ontology’

II: Basic Formal Ontology

III: 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

PORPHYRIAN TREE

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:

kindstypes

categoriesgeneraspecies

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)

siamese

mammal

cat

organism

substance

animal

instances

frog

universals

Example Domain Ontology

Mechanism

Doorbell Ther-mometer Clock Trap

Animal Trap

Rodent Trap

Mouse Trap

Spring-Loaded Bar Mouse Trap

Electric Mouse Trap

Glue Mouse Trap

Rat Trap

Insect Trap Bear Trap Fish Trap

Human TrapMouse Trap

Beverage

Alcoholic Beverage

Beer

Ale

Bitter Ale Mild Ale Sweet Ale

Lager Lambic Beer

Wine Whisk(e)y

Non-Alcoholic Beverage

Soda Coffee

Example Domain Ontology

Beer

BORROWED FROM: http://www.bio.davidson.edu/courses/genomics/2006/martens... 3DN

A Gene Ontology Example:

Glutathione

A Gene Ontology Example:

Cytokinesis

is_a

part_of

A Gene Ontology Example

Scientific Experiment Ontologyhttp://technology.newscientist.com/article/dn9288-translator-lets-

computers-understand-experiments-.html

is_a

p/o = part_of

Entity

Polyatomic Entity

Biological Entity

Biomol-ecules

Small Molecules

Lipid

LC Fatty Acyls

LC Docos-anoids

LC Eicos-anoids

LC Lipoxins

LC Hepoxilins

LC Cluvalones

Part of a Lipid

Ontology

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.

ONTOLOGY SCOPE URL CUSTODIANSCell Ontology (CL) cell types from prokaryotes to mammals obo.sourceforge.net/cgi-

bin/detail.cgi?cellJonathan Bard, Michael Ashburner,

Oliver Hofmann

Chemical Entities of Biological Interest

(ChEBI)

molecular entities which are products of nature or synthetic products used to intervene in the

processes of living organismsebi.ac.uk/chebi Paula Dematos, Rafael Alcantara

Common Anatomy Reference Ontology

(CARO)

anatomical structures in human and model organisms (initially mouse, fly, zebrafish) (under development) Melissa Haendel, David Sutherland

Disease Ontology (DO)

(Candidate member)human diseases and associated conditions diseaseontology.source

forge.netRex Chisholm, Warren Kibbe, John

Osborne, Wendy Wolf

Foundational Model of Anatomy (FMA) structure of the human body fma.biostr.

washington.edu JLV Mejino Jr., Cornelius Rosse

Gene Ontology (GO)attributes of gene products (divided into: cellular component, molecular function,

biological process) in all organismswww.geneontology.org Gene Ontology Consortium

Ontology for Biomedical

Investigations (OBI)

design, protocol, instrumentation, data and analysis applied in functional genomics

investigationsfugo.sf.net OBI/FuGO Working Group

Phenotypic Quality Ontology (PATO) qualities of anatomical structures

obo.sourceforge.net/cgi-bin/ detail.cgi?

attribute_and_value

Michael Ashburner, Suzanna Lewis, Georgios Gkoutos

Protein Ontology (PrO) protein types and modifications classified on the basis of evolutionary relationships pir.georgetown.edu/pro Cathy Wu, Darren Natale

Relation Ontology (RO) relations between universals and instances in biomedical ontologies obofoundry.org/ro Chris Mungall

Ontology (RnaO)three-dimensional structures and homologous sequence alignments and associated attributes

and processes(under development) Ontology Consortium

Sequence Ontology (SO) features and properties of nucleic sequences www.sequenceontology.

Org 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…)

How do you find your data?1

THE SILO EFFECT2

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?

1

CHAOS

Part of the solution seems to involve consensus-based- standardized terminologies - coding schemes

THE SILO EFFECT2

Many domains that arenon-interoperable,

non-communicative, isolated, insolated, encapsulated

“silos” of data

Data

Data

Data

Data

Data Data

Data

THE SILO EFFECT

Data

Data

Data

Data

Data Data

Data

THE SILO EFFECT

Informatics problems that contribute to 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

THE SILO EFFECT

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

** Human Error: Incorrect Thinking

Cognitive representationsRepresentational artifacts

Reality

Three Levels to Keep Straight

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

Data

Data

Data

Data

Data

Data

Data

Formal Ontology E.G., Basic Formal Ontology

From this…

To this…

Data

Data

Data

Data

Data Data

Data

Data

Data

Data

Data

Data

Data

Data

Formal Ontology E.G., Basic Formal Ontology

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 tosupport 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

Taxonomy with Formal Rules =

Ontology

Philosophical Ontology

E.G., Porphyrian Tree

Domain Ontology

Domain Reference OntologyE.G., Table of the Elements, Linnean, GO, FMA

Domain Application OntologyE.G., Amazon.com, Library of Congress catalogue

Formal Ontology

Formal Reference OntologyE.G., SUMO, DOLCE, BFO

Formal Application OntologyE.G., Friend of a Friend (FOAF)

Simple Taxonomy

E.G., Thesaurus

An Ontology of Ontologies

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 ONTOLOGYUniversals

(1) real objects, substances, endurants, or continuants- SNAP shots of reality

(2) real processes, activities,perdurants, or occurrents- SPAN of time

Relationsis_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

In classifying parts of reality, we keep track of these two different kinds of

entities in two different ways

continuant (substance, object)

t i m

e

occurrent (process)

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 Perspectivesstocks and flows

commodities and servicesproduct 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 processes objects activities continuants occurrents

BFO: The Very Top

continuant occurrent

(always dependent

on one or more independent continuants)

independentcontinuant

dependentcontinuant

BFO: The Very Top

continuant occurrent

(always dependent

on one or more independent continuants)

independentcontinuant

dependentcontinuant

objectsfiat objectssites

qualitiesfunctionsrolesdispositions

processesfiat process partsprocess contexts

BFO: The Very Top

continuant occurrent

(always dependent

on one or more independent continuants)

independentcontinuant

dependentcontinuant

object:mice

quality:that are black

process:have drugs injected in them

Example:

BFO: The Very Top

continuant occurrent

(always dependent

on one or more independent continuants)

independentcontinuant

dependentcontinuant

object:LSD

quality:that is hallucinogenic

process:is digested in the blood stream

Example:

BFO: The Very Top

continuant occurrent

(always dependent

on one or more independent continuants)

independentcontinuant

dependentcontinuant

object:kidney

function:whose function is to filter urine

process:filters urine

Example:

BFO: The Very Top

continuant occurrent

(always dependent

on one or more independent continuants)

independentcontinuant

dependentcontinuant

object:conjuctiva

disposition:which is affected with conjunctivitis

process:engages in edema

Example:

BFO: The Very Top

continuant occurrent

(always dependent

on one or more independent continuants)

independentcontinuant

dependentcontinuant

site:inner area, spare tire

role:acts as reservoir

process:colonization of mosquitoes

Example:

Three Dichotomies• continuant vs. occurrent• dependent vs. independent• instance vs. universal

universals exist in reality through their instances

continuant(object)

occurrent(process)

independentcontinuant

(molecule, cell, organ,organism)

dependentcontinuant

(quality, function,disease)

functioning side-effect, stochastic process, ...

..... ..... .... .....instances

continuant Relation: is_a

Note: Similarity to Porphyrian

Tree

continuant

human heart

surface of the heart

all hearts in this room

a biopsy of the heart

chest cavity

pink, smooth

stops if no circulation

pumps blood

prop in a display

HUMAN HEART

occurrent Relation: is_a

Note: Similarity to Porphyrian Tree

occurrent

ECG (EKG) test

start/end of ECG

all ECGs in clinic

2nd lead attached

activities in clinic

s/t ECG began

s/t region of ECG

moment ECG began

time occupied

ECG/EKG TEST

REALISM-BASED ONTOLOGYUniversals

(1) real objects, substances, endurants, or continuants- SNAP shots of reality

(2) real processes, activities,perdurants, or occurrents- SPAN of time

Relationsis_a, part_of, has_participant

REALISM-BASED ONTOLOGY

Relationsis_apart_ofhas_participant, ...

- Instance Level - Universal Level

is_a

part_of

located_in adjacent_to part_of instance_of …

inheres_in participates_in

derives_from 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 Ruttenberghttp://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 upper- level 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 OntologySequence 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 Ontologyhttp://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 StepsSteps #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

Taxonomy with Formal Rules =

Ontology

Philosophical Ontology

E.G., Porphyrian Tree

Domain Ontology

Domain Reference OntologyE.G., Table of the Elements, Linnean, GO, FMA

Domain Application OntologyE.G., Amazon.com, Library of Congress catalogue

Formal Ontology

Formal Reference OntologyE.G., SUMO, DOLCE, BFO

Formal Application OntologyE.G., Friend of a Friend (FOAF)

Simple Taxonomy

E.G., Thesaurus

An Ontology of Ontologies

relation to time

granularity

continuant

occurrentindependent dependent

organ andorganism

Organism(Species

Taxonomy)

Anatomical Entity(FMA, CARO)

OrganFunction

(GO+) Phenotypic Quality(PaTO)

Organism-Level

Process(GO)

cell and cellular compo-

nent

Cell(CL)

Cellular Compo-

nent(FMA,GO)

Cellular Function

(GO+)

Cellular Process

(GO)

moleculeMolecule

(ChEBI, SO,RnaO, PrO)

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-HangingFruit:

LifeWhat is “Right”MeaningGene?Neuropathy?Cancer?

Low-HangingFruit:

CellMinimal RiskQuality of LifeHomeotic GeneCauda Equina SyndromeLeukemia

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 DefinitionsFROM 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 DefinitionsFROM 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 unintendedreaction, 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 ConfusionFROM 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 ConfusionFROM 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 particulars2) Representing concepts rather than real entities3) Blurring the use/mention distinction4) Blurring the perception/reality distinction5) Giving examples instead of definitions6) Giving circular definitions7) Not ensuring necessary and specific conditions8) Equivocation9) Using categories of non-existent entities10) 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).

Data

Data

Data

Data

Data

Data

Data

Formal Ontology E.G., Basic Formal Ontology

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 CountlessCs of Computational

Categorization:

FROM

CognizanceTO

CoordinationTO

Comfort

Cognizance of Informatics ProblemsCooperation of Researchers, Doctors…Conferences, Colloquia, Meetings…Clarity of Terms and RelationsCogency: Counter-Example Free?Coherency of Domain OntologiesCoordination of Domain OntologiesComputational TractabilityCommunicability of InformationCoding of Information CorrectlyConvenience of Accessibility to InformationCare of Humans/Animals (First, Do No Harm)Comfort of Humans/Animals

Thank YouThis 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.