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Enabling Knowledge Creation and Sharing on the Web

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Title: Enabling Knowledge Creation and Sharing on the Web


1
BASIC FORMAL ONTOLOGY
Robert Arp, Ph.D. Ontology Research Group
(ORG) www.org.buffalo.edu National Center for
Biomedical Ontology (NCBO) www.bioontology.org
2
I Meanings of OntologyII Basic Formal
OntologyIII Constructing a Domain
Ontology
3
Part IMeanings of Ontology
4
(1) Philosophical Ontology (2) Domain
Ontology (3) Formal Ontology
5
  • Philosophical Ontology
  • ...I can fit wholesale evolution and a creating
    god into my ontology without contradiction.
  • ...just because it has mental existence doesnt
    mean it has ontological existence.

6
  • - 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

7
PORPHYRIAN TREE
Compare Linnean Taxonomy and Periodic Table
8
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.
9
(1) Philosophical Ontology (2) Domain
Ontology (3) Formal Ontology
10
(2) Domain Ontology ...Im working on an
ontology for annelids. ...the Gene Ontology
has data on that HOX gene.
11
  • 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

12
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.
13
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)
14
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 dont
    go wrong
  • Build representations adequate to this world, not
    to some simplified model in your laptop

15
InformaticsThe 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.
16
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

17
Domain Ontologies are representations
ofuniversals in reality kindstypescategories
generaspecies
18
The Central Distinction
universal vs. instance (catalogue vs.
inventory) (science text vs. diary) (human being
vs. George Bush) (mouse brain vs. Mickey Mouses
brain) (cytoplasm vs. this cytoplasm under the
scope)
19
universals
mammal
frog
20
Example Domain Ontology
Mouse Trap
21
Example Domain Ontology
Beer
22

BORROWED FROM http//www.bio.davidson.edu/courses
/genomics/2006/martens... 3DN
A Gene Ontology Example Glutathione
23
A Gene Ontology Example Cytokinesis
24
is_a part_of
A Gene Ontology Example
25
Scientific Experiment Ontology http//technology.n
ewscientist.com/article/dn9288-translator-lets-com
puters-understand-experiments-.html
26
p/o part_of
is_a
27
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.lipidontolo
gy.biochem.nus.edu.sg/lipidversion3.owl.
28
Ontology Scope URL Custodians
Cell Ontology (CL) cell types from prokaryotes to mammals obo.sourceforge.net/cgi-bin/detail.cgi?cell Jonathan 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 organisms ebi.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.net Rex 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 organisms www.geneontology.org Gene Ontology Consortium
Ontology for Biomedical Investigations (OBI) design, protocol, instrumentation, data and analysis applied in functional genomics investigations fugo.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
29
  • 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)
30
A Couple of Problems(there are more)
1
How do you find your data?
2
THE SILO EFFECT
31
How do you find your data?
1
  • - 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
    peoples data?

32
CHAOS
33
Part of the solution seems to involve
consensus-based- standardized terminologies -
coding schemes
34
THE SILO EFFECT
2
Many domains that are non-interoperable, non-commu
nicative, isolated, insolated, encapsulated
silos of data
35
THE SILO EFFECT
36
THE SILO EFFECT
37
  • 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
38
Three Levels to Keep Straight
Human Error Incorrect Thinking
  • 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

39
Three Levels to Keep Straight
  • Cognitive representations
  • Representational artifacts
  • Reality

40
PROBLEMDE-SILOING all of this domain data so
that it may be found (!), queried effectively,
shared, and re-used
41
PROBLEMDE-SILOING all of this domain data so
that it may be found (!), queried effectively,
shared, and re-used
SOLUTIONFormal Ontology
42
(1) Philosophical Ontology (2) Domain
Ontology (3) Formal Ontology
43
(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.
44
Assists in making communication between and among
domain ontologies possible by providing
-Common language -Common formal framework for
reasoning
45
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
46
Formal Ontology is like a backbone or spine
making communication, interoperability, and
optimal dissemination of information possible
between and among domain ontologies
47
From this To this
48
From this To this
49
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)Na
tional 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/)Nati
onal 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/)N
ational Institute of Neurological Disorders and
Stroke (NINDS), (http//www.ninds.nih.gov/)Nation
al Institute of Nursing Research (NINR),
(http//www.ninr.nih.gov)
50
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.
51
EXAMPLES Basic Formal Ontology (BFO)
Standard Upper Merged Ontology (SUMO)
Descriptive Ontology for Linguistic and
Cognitive Engineering (DOLCE)
52
BFO is an ontology tosupport integration
ofscientific 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)

53
An Ontology of Ontologies
54
Part IIBasic Formal Ontology (BFO)
55
  • 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

56
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
57
Universals (1) real objects, substances,
endurants, or continuants - SNAP shots of
reality (2) real processes, activities,
perdurants, or occurrents - SPAN of time
58
continuants vs. occurrents
continuant (substance, object)
  • In classifying parts of reality, we keep track
    of these two different kinds of entities in two
    different ways

59
  • 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

60
Two Orthogonal, Independent, Complementary
Perspectives
  • stocks and flows
  • commodities and services
  • product and process
  • anatomy and physiology

61
  • The tumor developed in the lung over 25 years.

62
  • The tumor developed in the lung over 25 years.
  • substances
  • things
  • objects
  • continuants

63
  • The tumor developed in the lung over 25 years.
  • substances
  • things processes
  • objects activities
  • continuants occurrents

64
BFO The Very Top
continuant
occurrent (always dependent on one or more
independent continuants)
independent continuant
dependent continuant
65
BFO The Very Top
continuant
occurrent (always dependent on one or more
independent continuants)
independent continuant
dependent continuant
objects fiat objects sites
qualities functions roles dispositions
processes fiat process parts process contexts
66
BFO The Very Top
Example
continuant
occurrent (always dependent on one or more
independent continuants)
independent continuant
dependent continuant
object mice
quality that are black
process have drugs injected in them
67
BFO The Very Top
Example
continuant
occurrent (always dependent on one or more
independent continuants)
independent continuant
dependent continuant
object LSD
quality that is hallucinogenic
process is digested in the blood stream
68
BFO The Very Top
Example
continuant
occurrent (always dependent on one or more
independent continuants)
independent continuant
dependent continuant
object kidney
function whose function is to filter urine
process filters urine
69
BFO The Very Top
Example
continuant
occurrent (always dependent on one or more
independent continuants)
independent continuant
dependent continuant
object conjuctiva
disposition which is affected with conjunctivitis
process engages in edema
70
BFO The Very Top
Example
continuant
occurrent (always dependent on one or more
independent continuants)
independent continuant
dependent continuant
site inner area, spare tire
role acts as reservoir
process colonization of mosquitoes
71
Three Dichotomies
  • continuant vs. occurrent
  • dependent vs. independent
  • instance vs. universal

universals exist in reality through their
instances
72
continuant (object)
occurrent (process)
independent continuant (molecule, cell,
organ, organism)
dependent continuant (quality,
function, disease)
functioning
side-effect, stochastic process, ...
..... ..... .... .....
instances
73
continuant
Relation is_a
Note Similarity to Porphyrian Tree
74
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
75
occurrent
Relation is_a
Note Similarity to Porphyrian Tree
76
occurrent
ECG/EKG TEST
ECG (EKG) test
start/end of ECG
s/t ECG began
moment ECG began
all ECGs in clinic
s/t region of ECG
time occupied
2nd lead attached
activities in clinic
77
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
78
REALISM-BASED ONTOLOGY Relations is_a part_of ha
s_participant, ... - Instance Level -
Universal Level
79
is_a part_of
80
located_in adjacent_to part_of instance_of
81
inheres_in participates_in derives_from
contained_in
82
INSTANCE LEVEL RELATIONS
83
INSTANCE LEVEL RELATIONS
84
UNIVERSAL RELATIONS
85
UNIVERSAL RELATIONS
86
Multiple Sclerosis Ontology (being developed by
Barry Smith and others)
87
The Relations Ontology http//www.obofoundry.org/
ro/Based onSmith, B., Ceusters, W., Klagges,
B., Köhler, J., Kumar, A., Lomax, J., et al.
(2005). Relations in biomedical ontologies.
Genome Biology, 6, R46.
88
Groups and Organizations Using BFOAstraZeneca
- 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
89
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 Fromhttp//sciencecommons.org/projects/
data/
90
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/w
howeare/ruttenberg/ currently involved in a
number of open biomedical ontology efforts,
includingBioPAX representing molecular and
cellular pathwaysOntology for Biomedical
Investigations (OBI)Basic Formal Ontology (BFO)
that will form the upper- level ontology for the
OBO foundry
91
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)
92
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93
Researchers use Protégé, OBO-Edit, Microsoft
Excel, or any number of other media (chalk
boards) to classify entities using BFO
94
http//www.ifomis.org/bfo/
BFO Protégé
95
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96
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97
Microsoft Excel
98
MS Excel
99
Lipid Ontology using BFO Protégé being developed
byLow, H-S., Alexander, G., Baker, C., Wenk,
M. (2008). Lipid ontology.Available at
http//MUS.12R.lipidontology.biochem.nus.edu.sg/li
pidversion3.owl.
100
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101
Vaccine Ontology http//www.violinet.org/wiki/inde
x.php/Vaccine_Ontology
102
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103
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104
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105
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/
106
Part IIIConstructing a Domain Ontology
107
13 Basic StepsSteps 1 - 13
108
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.
109
An Ontology of Ontologies
110
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111
relation to time granularity continuant continuant continuant continuant occurrent
relation to time granularity independent independent dependent dependent occurrent
organ and organism Organism (Species Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (GO) Phenotypic Quality(PaTO) Organism-Level Process (GO)
cell and cellular compo-nent Cell (CL) Cellular Compo-nent (FMA,GO) Cellular Function (GO) Phenotypic Quality(PaTO) Cellular Process (GO)
molecule Molecule (ChEBI, SO, RnaO, PrO) Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Function (GO) Molecular Process (GO)

Demarcation and Determining Granularity
112
The Foundational Model of Anatomy (FMA)
http//sig.biostr.washington.edu/projects/fm/About
FM.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.
113
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.
114
INFECTIOUS DISEASE ONTOLOGY http//www.bioontolog
y.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

115
  • High-Hanging
  • Fruit
  • Life
  • What is Right
  • Meaning
  • Gene?
  • Neuropathy?
  • Cancer?
  • Low-Hanging
  • Fruit
  • Cell
  • Minimal Risk
  • Quality of Life
  • Homeotic Gene
  • Cauda Equina Syndrome
  • Leukemia

116
Step 8 Regiment the information in order to
ensure logical and scientific coherence Avoid
the Pitfalls of Incorrect Thinking (IT)
117
Some Pitfalls of Incorrect Thinking (IT)
118
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.
119
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
120
IT Circular DefinitionsFROM GO and BRIDG(1)
Hemolysis of red blood cellsDef. The processes
by which an organism effects hemolysis
Compare Filtration of kidneysDef. 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
121
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
122
  • IT Use-Mention Confusion
  • FROM BIRN, MeSH, NCIT, and HL7
  • Mouse Def. Name for the species Mus musculus
  • 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

123
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
124
Some Pitfalls of Incorrect Thinking to Avoid1)
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
125
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.
126
Basis for Solid Classification Systems
127
Step 10 Regiment the information in order to
ensure compatibility with other relevant
ontologies (BFO important here).
128
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.
129
The Countless Cs of Computational
Categorization FROM Cognizance TO Coordination
TO Comfort
130
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 Communicabil
ity of Information Coding of Information
Correctly Convenience of Accessibility to
Information Care of Humans/Animals (First, Do No
Harm) Comfort of Humans/Animals
131
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.
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