SlideShare une entreprise Scribd logo
1  sur  36
1
Ontology and the NCI
Thesaurus
Barry Smith
with thanks to Werner Ceusters and Louis Goldberg
2
Ontology developments in Buffalo
Department of Philosophy: 8 full-time
ontologists
National Center for Ontological Research
(http://ncor.us)
NYS Center of Excellence in Bioinformatics &
Life Sciences
Werner Ceusters Referent Tracking Pilot EHR
3
GO +
OBO
National Center for Biomedical Ontology
Berkeley Drosophila Genome Project
Cambridge University Department of Genetics
Mayo Clinic
University of Oregon Institute of Neuroscience
University of California San Francisco Medical
Center
University at Buffalo Department of Philosophy
http://ncbo.us
4
A methodology for quality
assurance of ontologies
rules for ontology building based on two millennia of
philosophical research on classification and categorization
targets thus far in the biomedical domain:
– FMA
– SNOMED
– GALEN
– Gene Ontology
– UMLS Semantic Network
– ICF (International Classification of Functioning,
Disability and Health)
– ISO Terminology Standards
– HL7-RIM
5
–FMA
• SNOMED
• GALEN
– Gene Ontology
» UMLS-SN
» ICF
» HL7-RIM
6
Ontologies of Reality vs.
Information Models
Data:
sequence, expression, genotype, structure
Data structures:
patterns, clusters, alignments, ...
UMLS-SN: amino acid sequence is_a idea or
concept
Swimming is healthy and has 8 letters
7
New criteria for admission to OBO
(Open Biomedical Ontologies)
Library
Satisfaction of basic principles of ontology
design
Goal: to move beyond information retrieval
and statistical clustering to automatic
reasoning
8
First Rule: Univocity
Terms should have the same meanings on
every occasion of use.
They should refer to the same kinds of
entities in reality
9
Second Rule: Positivity
Complements of kinds are not themselves
kinds.
Terms such as ‘non-mammal’ or ‘non-
membrane’ or ‘other metalworker in New
Zealand’ do not designate genuine kinds
in reality.
10
Third Rule: Objectivity
Which kinds exist is not a function of our
knowledge.
Terms such as ‘unknown’ or ‘unclassified’ or
‘unlocalized’ do not designate biological
natural kinds.
11
Fourth Rule: Single Inheritance
No kind in a classificatory hierarchy
should have more than one is_a
parent on the immediate higher
level
12
Basic ontological relations such as is_a and
part_of should be shared by all ontologies
thing
carblue thing
blue car
is_a1 is_a2
13
Fifth Rule
Use common upper-level categories and
relations (is_a, part_of ...)
• with precise formal definitions for machine
purposes
• with equivalent natural language
definitions for human beings
14
Sixth Rule: Intelligibility of
Definitions
The terms used in a definition should be simpler
(more intelligible) than the term to be defined
otherwise the definition provides no assistance
– to human understanding
– to machine processing
Definitions should be intuitively
meaningful (should not contradict
common sense)
15
The National Cancer Institute
Thesaurus (NCIT)
part of OBO
but does not (yet) satisfy these principles
16
NCIT
“a biomedical vocabulary that provides
consistent, unambiguous codes and
definitions for concepts used in cancer
research”
“exhibits ontology-like properties in its
construction and use”.
17
Goals
to make use of current terminology “best practices”
to relate relevant concepts to one another in a
formal structure, so that computers as well as
humans can use the Thesaurus for a variety of
purposes, including the support of automatic
reasoning;
to speed the introduction of new concepts and
new relationships in response to the emerging
needs of basic researchers, clinical trials,
information services and other users.
18
Formal Definitions
of 37,261 nodes, 33,720 were stipulated to
be primitive in the DL sense
Thus only a small portion of the NCIT
ontology can be used for purposes of
automatic classification and error-
checking.
19
Verbal Definitions
About half the NCIT terms are assigned
verbal definitions
Unfortunately some are assigned more than
one
20
Disease Progression
Definition1
Cancer that continues to grow or spread.
Definition2
Increase in the size of a tumor or spread of
cancer in the body.
Definition3
The worsening of a disease over time. This
concept is most often used for chronic and
incurable diseases where the stage of the
disease is an important determinant of therapy
and prognosis.
21
To make matters worse Disease
Progression has subclass:
Cancer Progression
Definition:
The worsening of a cancer over time. This
concept is most often used for incurable
cancers where the stage of the cancer is
an important determinant of therapy and
prognosis.
22
Cancer
an object (which can grow and spread)
a process (of getting better or worse)
23
Confuses definitions with
descriptions
Tuberculosis
Definition
A chronic, recurrent infection caused by the bacterium
Mycobacterium tuberculosis. Tuberculosis (TB) may affect almost
any tissue or organ of the body with the lungs being the most
common site of infection. The clinical stages of TB are primary or
initial infection, latent or dormant infection, and recrudescent or
adult-type TB. Ninety to 95% of primary TB infections may go
unrecognized. Histopathologically, tissue lesions consist of
granulomas which usually undergo central caseation necrosis. Local
symptoms of TB vary according to the part affected; acute
symptoms include hectic fever, sweats, and emaciation; serious
complications include granulomatous erosion of pulmonary bronchi
associated with hemoptysis. If untreated, progressive TB may be
associated with a high degree of mortality. This infection is
frequently observed in immunocompromised individuals with AIDS
or a history of illicit IV drug use.
24
A better solution
Tuberculosis
Definition:
A chronic, recurrent infection caused by the
bacterium Mycobacterium tuberculosis.
25
Inherits ontological and terminological incoherence
from source vocabularies such as UMLS-SN
Conceptual Entities
Definition
An organizational header for concepts
representing mostly abstract entities.
Confuses use and mention (swimming is healthy
and has eight letters)
Includes as subtypes:
action, change, color, death, event, fluid,
injection, temperature
26
and imprecision
Duratec, Lactobutyrin, Stilbene Aldehyde
classified as Unclassified Drugs and
Chemicals
27
and problematic synonyms
Anatomic Structure, System, or Substance ~ Anatomic
Structures and Systems
Does ‘anatomic’ apply only to structure or also to system
and substance?
Biological Function ~ Biological Process
some biological processes are the exercises of biological
functions
others (e.g. pathological processes) not
Genetic Abnormality ~ Molecular Abnormality (with
subtype: Molecular Genetic Abnormality) (definitions
not supplied)
28
more problematic synonyms
Diseases and Disorders ~ Disease ~ Disorder
Definition1 for Disease:
A disease is any abnormal condition of the body or mind
that causes discomfort, dysfunction, or distress to the
person affected or those in contact with the person. ...
Definition2 for Disease
A definite pathologic process with a characteristic set of
signs and symptoms. ...
Condition ≠ Process
Definition2 contradicts NCIT’s own classification hierarchy
29
Ontological problems
Three disjoint classes of plants:
Vascular Plant
Non-vascular Plant
Other Plant
30
Ontological problems
Abnormal Cell is a top-level class (thus not
subsumed by Cell
Cell is a subclass of Other Anatomic
Concept (so that cells themselves are
concepts)
Normal Cell is a subclass of Microanatomy.
31
Next step
Alignment of OBO ontologies through a common
system of top-level categories in the OBO-UBO
(Upper Biomedical Ontology)
and through a common system of formally
defined relations in the OBO-RO (Relation
Ontology)
see “Relations in Biomedical Ontologies”, Genome
Biology Apr. 2005
Donnelly, M., Bittner, T. and Rosse, C. 2005. 'A
Formal Theory for Spatial Representation and
Reasoning in Biomedical Ontologies'. Artificial
Intelligence in Medicine
32
is_a
A is_a B
Definition
For all x, t if x instance_of A at t then x
instance_of B at t
allows reliable cross-ontology inferences
from ‘abnormal cell’ to ‘cell’
33
part_of
A part_of B
Definition
For all x, t if x instance_of A at t then there is some y, y
instance_of B at t and x part_of y
‘part_of’ is the instance-level part relation, e.g. between
this nucleus and this cell
The all-some structure of such definitions allows
cascading of inferences
(i) within ontologies
(ii) between ontologies
(iii) between ontologies and EHR repositories of
instance-data
34
Cascading inferences
Whichever A you choose, its including B will be
included in some C, which will include as part
also the A with which you begin
The same principle applies to the other relations
located_at, transformation_of, derived_from
etc. in the OBO-RO
(UML treatment here very poor)
35
NCIT as now constituted will block
such automatic reasoning
Neither Normal Cell nor Abnormal Cells are
Cells within the context of the NCIT
36
Some consolations
NCIT is open source
NCIT has broad coverage
NCIT has some formal structure (DL)
NCIT has realized the errors of its ways
NCIT is much, much better than (for
example) the HL7-RIM

Contenu connexe

Tendances

Poli CV SHORT_11-02-2015
Poli CV SHORT_11-02-2015Poli CV SHORT_11-02-2015
Poli CV SHORT_11-02-2015
Valeria Poli
 
JournalofCancerEpidemiologyandTreatment3
JournalofCancerEpidemiologyandTreatment3JournalofCancerEpidemiologyandTreatment3
JournalofCancerEpidemiologyandTreatment3
Christian Schmidt
 
Ontology and the Austrian tradition
Ontology and the Austrian traditionOntology and the Austrian tradition
Ontology and the Austrian tradition
Barry Smith
 

Tendances (14)

Researchers Study the Cells of Origin for Medulloblastoma Subtypes
Researchers Study the Cells of Origin for Medulloblastoma SubtypesResearchers Study the Cells of Origin for Medulloblastoma Subtypes
Researchers Study the Cells of Origin for Medulloblastoma Subtypes
 
Missouri China Programme: Science Communication
Missouri China Programme: Science CommunicationMissouri China Programme: Science Communication
Missouri China Programme: Science Communication
 
Resume_JWS
Resume_JWSResume_JWS
Resume_JWS
 
Poli CV SHORT_11-02-2015
Poli CV SHORT_11-02-2015Poli CV SHORT_11-02-2015
Poli CV SHORT_11-02-2015
 
Molecular.biology.of.the.cell.alberts.6th.ed
Molecular.biology.of.the.cell.alberts.6th.edMolecular.biology.of.the.cell.alberts.6th.ed
Molecular.biology.of.the.cell.alberts.6th.ed
 
JournalofCancerEpidemiologyandTreatment3
JournalofCancerEpidemiologyandTreatment3JournalofCancerEpidemiologyandTreatment3
JournalofCancerEpidemiologyandTreatment3
 
OMIM Integration in Human Disease Ontology
OMIM Integration in Human Disease OntologyOMIM Integration in Human Disease Ontology
OMIM Integration in Human Disease Ontology
 
carcinogenesis mutagenesis
carcinogenesis   mutagenesiscarcinogenesis   mutagenesis
carcinogenesis mutagenesis
 
Ontology and the Austrian tradition
Ontology and the Austrian traditionOntology and the Austrian tradition
Ontology and the Austrian tradition
 
The TDR Targets Database, an introduction.
The TDR Targets Database, an introduction.The TDR Targets Database, an introduction.
The TDR Targets Database, an introduction.
 
Destructive impact of t-lymphocytes, NK and mast cells on basal cell layers:...
Destructive impact of t-lymphocytes, NK and mast  cells on basal cell layers:...Destructive impact of t-lymphocytes, NK and mast  cells on basal cell layers:...
Destructive impact of t-lymphocytes, NK and mast cells on basal cell layers:...
 
ICT for a Global Infrastructure for Health Research
ICT for a Global Infrastructure for Health ResearchICT for a Global Infrastructure for Health Research
ICT for a Global Infrastructure for Health Research
 
Curriculum vita
Curriculum vitaCurriculum vita
Curriculum vita
 
How to design and conduct a complex literature search
How to design and conduct a complex literature searchHow to design and conduct a complex literature search
How to design and conduct a complex literature search
 

Similaire à Ontology and the National Cancer Institute Thesaurus (2005)

0953946809106235.pdf
0953946809106235.pdf0953946809106235.pdf
0953946809106235.pdf
BkesNar
 
Chapter 1. Introduction
Chapter 1. IntroductionChapter 1. Introduction
Chapter 1. Introduction
butest
 
A N NA L S O F FA M I LY M E D I C I N E ✦ W W W. A N N FA.docx
A N NA L S  O F  FA M I LY  M E D I C I N E  ✦ W W W. A N N FA.docxA N NA L S  O F  FA M I LY  M E D I C I N E  ✦ W W W. A N N FA.docx
A N NA L S O F FA M I LY M E D I C I N E ✦ W W W. A N N FA.docx
sleeperharwell
 
A N NA L S O F FA M I LY M E D I C I N E ✦ W W W. A N N FA.docx
A N NA L S  O F  FA M I LY  M E D I C I N E  ✦ W W W. A N N FA.docxA N NA L S  O F  FA M I LY  M E D I C I N E  ✦ W W W. A N N FA.docx
A N NA L S O F FA M I LY M E D I C I N E ✦ W W W. A N N FA.docx
blondellchancy
 
A N NA L S O F FA M I LY M E D I C I N E ✦ W W W. A N N FA.docx
A N NA L S  O F  FA M I LY  M E D I C I N E  ✦ W W W. A N N FA.docxA N NA L S  O F  FA M I LY  M E D I C I N E  ✦ W W W. A N N FA.docx
A N NA L S O F FA M I LY M E D I C I N E ✦ W W W. A N N FA.docx
ronak56
 
Revolutionizing medicine in the 21st century through systems approaches
Revolutionizing medicine in the 21st century through systems approachesRevolutionizing medicine in the 21st century through systems approaches
Revolutionizing medicine in the 21st century through systems approaches
Institute for Systems Biology
 
Running head SOCIAL AND ETHICAL IMPLICATION OF BIOTECHNOLOGY .docx
Running head SOCIAL AND ETHICAL IMPLICATION OF BIOTECHNOLOGY     .docxRunning head SOCIAL AND ETHICAL IMPLICATION OF BIOTECHNOLOGY     .docx
Running head SOCIAL AND ETHICAL IMPLICATION OF BIOTECHNOLOGY .docx
todd521
 
application_of_bioinformatics_in_various_fields.ppt
application_of_bioinformatics_in_various_fields.pptapplication_of_bioinformatics_in_various_fields.ppt
application_of_bioinformatics_in_various_fields.ppt
shankjunk
 
application_of_bioinformatics_in_various_fields.ppt
application_of_bioinformatics_in_various_fields.pptapplication_of_bioinformatics_in_various_fields.ppt
application_of_bioinformatics_in_various_fields.ppt
shankjunk
 
Week 1 Flow And Error 10
Week 1 Flow And Error 10Week 1 Flow And Error 10
Week 1 Flow And Error 10
mtfinn
 

Similaire à Ontology and the National Cancer Institute Thesaurus (2005) (20)

Bio ontology drtc-seminar_anwesha
Bio ontology drtc-seminar_anweshaBio ontology drtc-seminar_anwesha
Bio ontology drtc-seminar_anwesha
 
0953946809106235.pdf
0953946809106235.pdf0953946809106235.pdf
0953946809106235.pdf
 
Human Disease and Genomics
Human Disease and GenomicsHuman Disease and Genomics
Human Disease and Genomics
 
Chapter 1. Introduction
Chapter 1. IntroductionChapter 1. Introduction
Chapter 1. Introduction
 
Spectral analysis for tumour diagnosis and classification in surgical patholo...
Spectral analysis for tumour diagnosis and classification in surgical patholo...Spectral analysis for tumour diagnosis and classification in surgical patholo...
Spectral analysis for tumour diagnosis and classification in surgical patholo...
 
A N NA L S O F FA M I LY M E D I C I N E ✦ W W W. A N N FA.docx
A N NA L S  O F  FA M I LY  M E D I C I N E  ✦ W W W. A N N FA.docxA N NA L S  O F  FA M I LY  M E D I C I N E  ✦ W W W. A N N FA.docx
A N NA L S O F FA M I LY M E D I C I N E ✦ W W W. A N N FA.docx
 
A N NA L S O F FA M I LY M E D I C I N E ✦ W W W. A N N FA.docx
A N NA L S  O F  FA M I LY  M E D I C I N E  ✦ W W W. A N N FA.docxA N NA L S  O F  FA M I LY  M E D I C I N E  ✦ W W W. A N N FA.docx
A N NA L S O F FA M I LY M E D I C I N E ✦ W W W. A N N FA.docx
 
A N NA L S O F FA M I LY M E D I C I N E ✦ W W W. A N N FA.docx
A N NA L S  O F  FA M I LY  M E D I C I N E  ✦ W W W. A N N FA.docxA N NA L S  O F  FA M I LY  M E D I C I N E  ✦ W W W. A N N FA.docx
A N NA L S O F FA M I LY M E D I C I N E ✦ W W W. A N N FA.docx
 
Specific Aims NIH Sample Grant Proposal
Specific Aims NIH Sample Grant ProposalSpecific Aims NIH Sample Grant Proposal
Specific Aims NIH Sample Grant Proposal
 
Mechanism of action of the Body Wave
Mechanism of action of the Body WaveMechanism of action of the Body Wave
Mechanism of action of the Body Wave
 
Revolutionizing medicine in the 21st century through systems approaches
Revolutionizing medicine in the 21st century through systems approachesRevolutionizing medicine in the 21st century through systems approaches
Revolutionizing medicine in the 21st century through systems approaches
 
Running head SOCIAL AND ETHICAL IMPLICATION OF BIOTECHNOLOGY .docx
Running head SOCIAL AND ETHICAL IMPLICATION OF BIOTECHNOLOGY     .docxRunning head SOCIAL AND ETHICAL IMPLICATION OF BIOTECHNOLOGY     .docx
Running head SOCIAL AND ETHICAL IMPLICATION OF BIOTECHNOLOGY .docx
 
Searching for phenotypes of sepsis an application of machine learning to elec...
Searching for phenotypes of sepsis an application of machine learning to elec...Searching for phenotypes of sepsis an application of machine learning to elec...
Searching for phenotypes of sepsis an application of machine learning to elec...
 
Brn jm anto-11062014
Brn jm anto-11062014Brn jm anto-11062014
Brn jm anto-11062014
 
Organoid culture in cancer
Organoid culture in cancerOrganoid culture in cancer
Organoid culture in cancer
 
Genetic variation and evolution and their importance to medicine
Genetic variation and evolution and their importance to medicineGenetic variation and evolution and their importance to medicine
Genetic variation and evolution and their importance to medicine
 
Isaac Kohane, "A Data Perspective on Autonomy, Human Rights, and the End of N...
Isaac Kohane, "A Data Perspective on Autonomy, Human Rights, and the End of N...Isaac Kohane, "A Data Perspective on Autonomy, Human Rights, and the End of N...
Isaac Kohane, "A Data Perspective on Autonomy, Human Rights, and the End of N...
 
application_of_bioinformatics_in_various_fields.ppt
application_of_bioinformatics_in_various_fields.pptapplication_of_bioinformatics_in_various_fields.ppt
application_of_bioinformatics_in_various_fields.ppt
 
application_of_bioinformatics_in_various_fields.ppt
application_of_bioinformatics_in_various_fields.pptapplication_of_bioinformatics_in_various_fields.ppt
application_of_bioinformatics_in_various_fields.ppt
 
Week 1 Flow And Error 10
Week 1 Flow And Error 10Week 1 Flow And Error 10
Week 1 Flow And Error 10
 

Plus de Barry Smith

The Division of Deontic Labor
The Division of Deontic LaborThe Division of Deontic Labor
The Division of Deontic Labor
Barry Smith
 
e‐Human Beings: The contribution of internet ranking systems to the developme...
e‐Human Beings: The contribution of internet ranking systems to the developme...e‐Human Beings: The contribution of internet ranking systems to the developme...
e‐Human Beings: The contribution of internet ranking systems to the developme...
Barry Smith
 
Ontology in Buffalo -- Big Data 2013
Ontology in Buffalo -- Big Data 2013Ontology in Buffalo -- Big Data 2013
Ontology in Buffalo -- Big Data 2013
Barry Smith
 

Plus de Barry Smith (20)

An application of Basic Formal Ontology to the Ontology of Services and Commo...
An application of Basic Formal Ontology to the Ontology of Services and Commo...An application of Basic Formal Ontology to the Ontology of Services and Commo...
An application of Basic Formal Ontology to the Ontology of Services and Commo...
 
Ways of Worldmarking: The Ontology of the Eruv
Ways of Worldmarking: The Ontology of the EruvWays of Worldmarking: The Ontology of the Eruv
Ways of Worldmarking: The Ontology of the Eruv
 
The Division of Deontic Labor
The Division of Deontic LaborThe Division of Deontic Labor
The Division of Deontic Labor
 
Ontology of Aging (August 2014)
Ontology of Aging (August 2014)Ontology of Aging (August 2014)
Ontology of Aging (August 2014)
 
Meaningful Use
Meaningful UseMeaningful Use
Meaningful Use
 
The Fifth Cycle of Philosophy
The Fifth Cycle of PhilosophyThe Fifth Cycle of Philosophy
The Fifth Cycle of Philosophy
 
Ontology of Poker
Ontology of PokerOntology of Poker
Ontology of Poker
 
Clinical trial data wants to be free: Lessons from the ImmPort Immunology Dat...
Clinical trial data wants to be free: Lessons from the ImmPort Immunology Dat...Clinical trial data wants to be free: Lessons from the ImmPort Immunology Dat...
Clinical trial data wants to be free: Lessons from the ImmPort Immunology Dat...
 
Enhancing the Quality of ImmPort Data
Enhancing the Quality of ImmPort DataEnhancing the Quality of ImmPort Data
Enhancing the Quality of ImmPort Data
 
The Philosophome: An Exercise in the Ontology of the Humanities
The Philosophome: An Exercise in the Ontology of the HumanitiesThe Philosophome: An Exercise in the Ontology of the Humanities
The Philosophome: An Exercise in the Ontology of the Humanities
 
IAO-Intel: An Ontology of Information Artifacts in the Intelligence Domain
IAO-Intel: An Ontology of Information Artifacts in the Intelligence DomainIAO-Intel: An Ontology of Information Artifacts in the Intelligence Domain
IAO-Intel: An Ontology of Information Artifacts in the Intelligence Domain
 
Science of Emerging Social Media
Science of Emerging Social MediaScience of Emerging Social Media
Science of Emerging Social Media
 
Ethics, Informatics and Obamacare
Ethics, Informatics and ObamacareEthics, Informatics and Obamacare
Ethics, Informatics and Obamacare
 
e‐Human Beings: The contribution of internet ranking systems to the developme...
e‐Human Beings: The contribution of internet ranking systems to the developme...e‐Human Beings: The contribution of internet ranking systems to the developme...
e‐Human Beings: The contribution of internet ranking systems to the developme...
 
Ontology of aging and death
Ontology of aging and deathOntology of aging and death
Ontology of aging and death
 
ImmPort strategies to enhance discoverability of clinical trial data
ImmPort strategies to enhance discoverability of clinical trial dataImmPort strategies to enhance discoverability of clinical trial data
ImmPort strategies to enhance discoverability of clinical trial data
 
Ontology of Documents (2005)
Ontology of Documents (2005)Ontology of Documents (2005)
Ontology of Documents (2005)
 
Introduction to the Logic of Definitions
Introduction to the Logic of DefinitionsIntroduction to the Logic of Definitions
Introduction to the Logic of Definitions
 
Ontology in Buffalo -- Big Data 2013
Ontology in Buffalo -- Big Data 2013Ontology in Buffalo -- Big Data 2013
Ontology in Buffalo -- Big Data 2013
 
How to Do Things With Documents
How to Do Things With DocumentsHow to Do Things With Documents
How to Do Things With Documents
 

Dernier

Gorgeous Call Girls Dehradun {8854095900} ❤️VVIP ROCKY Call Girls in Dehradun...
Gorgeous Call Girls Dehradun {8854095900} ❤️VVIP ROCKY Call Girls in Dehradun...Gorgeous Call Girls Dehradun {8854095900} ❤️VVIP ROCKY Call Girls in Dehradun...
Gorgeous Call Girls Dehradun {8854095900} ❤️VVIP ROCKY Call Girls in Dehradun...
Sheetaleventcompany
 
Cara Menggugurkan Kandungan Dengan Cepat Selesai Dalam 24 Jam Secara Alami Bu...
Cara Menggugurkan Kandungan Dengan Cepat Selesai Dalam 24 Jam Secara Alami Bu...Cara Menggugurkan Kandungan Dengan Cepat Selesai Dalam 24 Jam Secara Alami Bu...
Cara Menggugurkan Kandungan Dengan Cepat Selesai Dalam 24 Jam Secara Alami Bu...
Cara Menggugurkan Kandungan 087776558899
 
Goa Call Girl Service 📞9xx000xx09📞Just Call Divya📲 Call Girl In Goa No💰Advanc...
Goa Call Girl Service 📞9xx000xx09📞Just Call Divya📲 Call Girl In Goa No💰Advanc...Goa Call Girl Service 📞9xx000xx09📞Just Call Divya📲 Call Girl In Goa No💰Advanc...
Goa Call Girl Service 📞9xx000xx09📞Just Call Divya📲 Call Girl In Goa No💰Advanc...
Sheetaleventcompany
 
💚Chandigarh Call Girls Service 💯Piya 📲🔝8868886958🔝Call Girls In Chandigarh No...
💚Chandigarh Call Girls Service 💯Piya 📲🔝8868886958🔝Call Girls In Chandigarh No...💚Chandigarh Call Girls Service 💯Piya 📲🔝8868886958🔝Call Girls In Chandigarh No...
💚Chandigarh Call Girls Service 💯Piya 📲🔝8868886958🔝Call Girls In Chandigarh No...
Sheetaleventcompany
 
Call Girl In Indore 📞9235973566📞 Just📲 Call Inaaya Indore Call Girls Service ...
Call Girl In Indore 📞9235973566📞 Just📲 Call Inaaya Indore Call Girls Service ...Call Girl In Indore 📞9235973566📞 Just📲 Call Inaaya Indore Call Girls Service ...
Call Girl In Indore 📞9235973566📞 Just📲 Call Inaaya Indore Call Girls Service ...
Sheetaleventcompany
 
💚Call Girls In Amritsar 💯Anvi 📲🔝8725944379🔝Amritsar Call Girl No💰Advance Cash...
💚Call Girls In Amritsar 💯Anvi 📲🔝8725944379🔝Amritsar Call Girl No💰Advance Cash...💚Call Girls In Amritsar 💯Anvi 📲🔝8725944379🔝Amritsar Call Girl No💰Advance Cash...
💚Call Girls In Amritsar 💯Anvi 📲🔝8725944379🔝Amritsar Call Girl No💰Advance Cash...
Sheetaleventcompany
 

Dernier (20)

Gorgeous Call Girls Dehradun {8854095900} ❤️VVIP ROCKY Call Girls in Dehradun...
Gorgeous Call Girls Dehradun {8854095900} ❤️VVIP ROCKY Call Girls in Dehradun...Gorgeous Call Girls Dehradun {8854095900} ❤️VVIP ROCKY Call Girls in Dehradun...
Gorgeous Call Girls Dehradun {8854095900} ❤️VVIP ROCKY Call Girls in Dehradun...
 
❤️Chandigarh Escorts Service☎️9814379184☎️ Call Girl service in Chandigarh☎️ ...
❤️Chandigarh Escorts Service☎️9814379184☎️ Call Girl service in Chandigarh☎️ ...❤️Chandigarh Escorts Service☎️9814379184☎️ Call Girl service in Chandigarh☎️ ...
❤️Chandigarh Escorts Service☎️9814379184☎️ Call Girl service in Chandigarh☎️ ...
 
Call Girls in Lucknow Just Call 👉👉8630512678 Top Class Call Girl Service Avai...
Call Girls in Lucknow Just Call 👉👉8630512678 Top Class Call Girl Service Avai...Call Girls in Lucknow Just Call 👉👉8630512678 Top Class Call Girl Service Avai...
Call Girls in Lucknow Just Call 👉👉8630512678 Top Class Call Girl Service Avai...
 
tongue disease lecture Dr Assadawy legacy
tongue disease lecture Dr Assadawy legacytongue disease lecture Dr Assadawy legacy
tongue disease lecture Dr Assadawy legacy
 
Call Girls Rishikesh Just Call 9667172968 Top Class Call Girl Service Available
Call Girls Rishikesh Just Call 9667172968 Top Class Call Girl Service AvailableCall Girls Rishikesh Just Call 9667172968 Top Class Call Girl Service Available
Call Girls Rishikesh Just Call 9667172968 Top Class Call Girl Service Available
 
Call Girls Bangalore - 450+ Call Girl Cash Payment 💯Call Us 🔝 6378878445 🔝 💃 ...
Call Girls Bangalore - 450+ Call Girl Cash Payment 💯Call Us 🔝 6378878445 🔝 💃 ...Call Girls Bangalore - 450+ Call Girl Cash Payment 💯Call Us 🔝 6378878445 🔝 💃 ...
Call Girls Bangalore - 450+ Call Girl Cash Payment 💯Call Us 🔝 6378878445 🔝 💃 ...
 
Cara Menggugurkan Kandungan Dengan Cepat Selesai Dalam 24 Jam Secara Alami Bu...
Cara Menggugurkan Kandungan Dengan Cepat Selesai Dalam 24 Jam Secara Alami Bu...Cara Menggugurkan Kandungan Dengan Cepat Selesai Dalam 24 Jam Secara Alami Bu...
Cara Menggugurkan Kandungan Dengan Cepat Selesai Dalam 24 Jam Secara Alami Bu...
 
Goa Call Girl Service 📞9xx000xx09📞Just Call Divya📲 Call Girl In Goa No💰Advanc...
Goa Call Girl Service 📞9xx000xx09📞Just Call Divya📲 Call Girl In Goa No💰Advanc...Goa Call Girl Service 📞9xx000xx09📞Just Call Divya📲 Call Girl In Goa No💰Advanc...
Goa Call Girl Service 📞9xx000xx09📞Just Call Divya📲 Call Girl In Goa No💰Advanc...
 
Independent Bangalore Call Girls (Adult Only) 💯Call Us 🔝 7304373326 🔝 💃 Escor...
Independent Bangalore Call Girls (Adult Only) 💯Call Us 🔝 7304373326 🔝 💃 Escor...Independent Bangalore Call Girls (Adult Only) 💯Call Us 🔝 7304373326 🔝 💃 Escor...
Independent Bangalore Call Girls (Adult Only) 💯Call Us 🔝 7304373326 🔝 💃 Escor...
 
💚Chandigarh Call Girls Service 💯Piya 📲🔝8868886958🔝Call Girls In Chandigarh No...
💚Chandigarh Call Girls Service 💯Piya 📲🔝8868886958🔝Call Girls In Chandigarh No...💚Chandigarh Call Girls Service 💯Piya 📲🔝8868886958🔝Call Girls In Chandigarh No...
💚Chandigarh Call Girls Service 💯Piya 📲🔝8868886958🔝Call Girls In Chandigarh No...
 
ANATOMY AND PHYSIOLOGY OF REPRODUCTIVE SYSTEM.pptx
ANATOMY AND PHYSIOLOGY OF REPRODUCTIVE SYSTEM.pptxANATOMY AND PHYSIOLOGY OF REPRODUCTIVE SYSTEM.pptx
ANATOMY AND PHYSIOLOGY OF REPRODUCTIVE SYSTEM.pptx
 
Call Girls Shahdol Just Call 8250077686 Top Class Call Girl Service Available
Call Girls Shahdol Just Call 8250077686 Top Class Call Girl Service AvailableCall Girls Shahdol Just Call 8250077686 Top Class Call Girl Service Available
Call Girls Shahdol Just Call 8250077686 Top Class Call Girl Service Available
 
Call Girl In Indore 📞9235973566📞 Just📲 Call Inaaya Indore Call Girls Service ...
Call Girl In Indore 📞9235973566📞 Just📲 Call Inaaya Indore Call Girls Service ...Call Girl In Indore 📞9235973566📞 Just📲 Call Inaaya Indore Call Girls Service ...
Call Girl In Indore 📞9235973566📞 Just📲 Call Inaaya Indore Call Girls Service ...
 
(RIYA)🎄Airhostess Call Girl Jaipur Call Now 8445551418 Premium Collection Of ...
(RIYA)🎄Airhostess Call Girl Jaipur Call Now 8445551418 Premium Collection Of ...(RIYA)🎄Airhostess Call Girl Jaipur Call Now 8445551418 Premium Collection Of ...
(RIYA)🎄Airhostess Call Girl Jaipur Call Now 8445551418 Premium Collection Of ...
 
Cardiac Output, Venous Return, and Their Regulation
Cardiac Output, Venous Return, and Their RegulationCardiac Output, Venous Return, and Their Regulation
Cardiac Output, Venous Return, and Their Regulation
 
ANATOMY AND PHYSIOLOGY OF RESPIRATORY SYSTEM.pptx
ANATOMY AND PHYSIOLOGY OF RESPIRATORY SYSTEM.pptxANATOMY AND PHYSIOLOGY OF RESPIRATORY SYSTEM.pptx
ANATOMY AND PHYSIOLOGY OF RESPIRATORY SYSTEM.pptx
 
Call Girl In Chandigarh 📞9809698092📞 Just📲 Call Inaaya Chandigarh Call Girls ...
Call Girl In Chandigarh 📞9809698092📞 Just📲 Call Inaaya Chandigarh Call Girls ...Call Girl In Chandigarh 📞9809698092📞 Just📲 Call Inaaya Chandigarh Call Girls ...
Call Girl In Chandigarh 📞9809698092📞 Just📲 Call Inaaya Chandigarh Call Girls ...
 
7 steps How to prevent Thalassemia : Dr Sharda Jain & Vandana Gupta
7 steps How to prevent Thalassemia : Dr Sharda Jain & Vandana Gupta7 steps How to prevent Thalassemia : Dr Sharda Jain & Vandana Gupta
7 steps How to prevent Thalassemia : Dr Sharda Jain & Vandana Gupta
 
Call Girls in Lucknow Just Call 👉👉 8875999948 Top Class Call Girl Service Ava...
Call Girls in Lucknow Just Call 👉👉 8875999948 Top Class Call Girl Service Ava...Call Girls in Lucknow Just Call 👉👉 8875999948 Top Class Call Girl Service Ava...
Call Girls in Lucknow Just Call 👉👉 8875999948 Top Class Call Girl Service Ava...
 
💚Call Girls In Amritsar 💯Anvi 📲🔝8725944379🔝Amritsar Call Girl No💰Advance Cash...
💚Call Girls In Amritsar 💯Anvi 📲🔝8725944379🔝Amritsar Call Girl No💰Advance Cash...💚Call Girls In Amritsar 💯Anvi 📲🔝8725944379🔝Amritsar Call Girl No💰Advance Cash...
💚Call Girls In Amritsar 💯Anvi 📲🔝8725944379🔝Amritsar Call Girl No💰Advance Cash...
 

Ontology and the National Cancer Institute Thesaurus (2005)

  • 1. 1 Ontology and the NCI Thesaurus Barry Smith with thanks to Werner Ceusters and Louis Goldberg
  • 2. 2 Ontology developments in Buffalo Department of Philosophy: 8 full-time ontologists National Center for Ontological Research (http://ncor.us) NYS Center of Excellence in Bioinformatics & Life Sciences Werner Ceusters Referent Tracking Pilot EHR
  • 3. 3 GO + OBO National Center for Biomedical Ontology Berkeley Drosophila Genome Project Cambridge University Department of Genetics Mayo Clinic University of Oregon Institute of Neuroscience University of California San Francisco Medical Center University at Buffalo Department of Philosophy http://ncbo.us
  • 4. 4 A methodology for quality assurance of ontologies rules for ontology building based on two millennia of philosophical research on classification and categorization targets thus far in the biomedical domain: – FMA – SNOMED – GALEN – Gene Ontology – UMLS Semantic Network – ICF (International Classification of Functioning, Disability and Health) – ISO Terminology Standards – HL7-RIM
  • 5. 5 –FMA • SNOMED • GALEN – Gene Ontology » UMLS-SN » ICF » HL7-RIM
  • 6. 6 Ontologies of Reality vs. Information Models Data: sequence, expression, genotype, structure Data structures: patterns, clusters, alignments, ... UMLS-SN: amino acid sequence is_a idea or concept Swimming is healthy and has 8 letters
  • 7. 7 New criteria for admission to OBO (Open Biomedical Ontologies) Library Satisfaction of basic principles of ontology design Goal: to move beyond information retrieval and statistical clustering to automatic reasoning
  • 8. 8 First Rule: Univocity Terms should have the same meanings on every occasion of use. They should refer to the same kinds of entities in reality
  • 9. 9 Second Rule: Positivity Complements of kinds are not themselves kinds. Terms such as ‘non-mammal’ or ‘non- membrane’ or ‘other metalworker in New Zealand’ do not designate genuine kinds in reality.
  • 10. 10 Third Rule: Objectivity Which kinds exist is not a function of our knowledge. Terms such as ‘unknown’ or ‘unclassified’ or ‘unlocalized’ do not designate biological natural kinds.
  • 11. 11 Fourth Rule: Single Inheritance No kind in a classificatory hierarchy should have more than one is_a parent on the immediate higher level
  • 12. 12 Basic ontological relations such as is_a and part_of should be shared by all ontologies thing carblue thing blue car is_a1 is_a2
  • 13. 13 Fifth Rule Use common upper-level categories and relations (is_a, part_of ...) • with precise formal definitions for machine purposes • with equivalent natural language definitions for human beings
  • 14. 14 Sixth Rule: Intelligibility of Definitions The terms used in a definition should be simpler (more intelligible) than the term to be defined otherwise the definition provides no assistance – to human understanding – to machine processing Definitions should be intuitively meaningful (should not contradict common sense)
  • 15. 15 The National Cancer Institute Thesaurus (NCIT) part of OBO but does not (yet) satisfy these principles
  • 16. 16 NCIT “a biomedical vocabulary that provides consistent, unambiguous codes and definitions for concepts used in cancer research” “exhibits ontology-like properties in its construction and use”.
  • 17. 17 Goals to make use of current terminology “best practices” to relate relevant concepts to one another in a formal structure, so that computers as well as humans can use the Thesaurus for a variety of purposes, including the support of automatic reasoning; to speed the introduction of new concepts and new relationships in response to the emerging needs of basic researchers, clinical trials, information services and other users.
  • 18. 18 Formal Definitions of 37,261 nodes, 33,720 were stipulated to be primitive in the DL sense Thus only a small portion of the NCIT ontology can be used for purposes of automatic classification and error- checking.
  • 19. 19 Verbal Definitions About half the NCIT terms are assigned verbal definitions Unfortunately some are assigned more than one
  • 20. 20 Disease Progression Definition1 Cancer that continues to grow or spread. Definition2 Increase in the size of a tumor or spread of cancer in the body. Definition3 The worsening of a disease over time. This concept is most often used for chronic and incurable diseases where the stage of the disease is an important determinant of therapy and prognosis.
  • 21. 21 To make matters worse Disease Progression has subclass: Cancer Progression Definition: The worsening of a cancer over time. This concept is most often used for incurable cancers where the stage of the cancer is an important determinant of therapy and prognosis.
  • 22. 22 Cancer an object (which can grow and spread) a process (of getting better or worse)
  • 23. 23 Confuses definitions with descriptions Tuberculosis Definition A chronic, recurrent infection caused by the bacterium Mycobacterium tuberculosis. Tuberculosis (TB) may affect almost any tissue or organ of the body with the lungs being the most common site of infection. The clinical stages of TB are primary or initial infection, latent or dormant infection, and recrudescent or adult-type TB. Ninety to 95% of primary TB infections may go unrecognized. Histopathologically, tissue lesions consist of granulomas which usually undergo central caseation necrosis. Local symptoms of TB vary according to the part affected; acute symptoms include hectic fever, sweats, and emaciation; serious complications include granulomatous erosion of pulmonary bronchi associated with hemoptysis. If untreated, progressive TB may be associated with a high degree of mortality. This infection is frequently observed in immunocompromised individuals with AIDS or a history of illicit IV drug use.
  • 24. 24 A better solution Tuberculosis Definition: A chronic, recurrent infection caused by the bacterium Mycobacterium tuberculosis.
  • 25. 25 Inherits ontological and terminological incoherence from source vocabularies such as UMLS-SN Conceptual Entities Definition An organizational header for concepts representing mostly abstract entities. Confuses use and mention (swimming is healthy and has eight letters) Includes as subtypes: action, change, color, death, event, fluid, injection, temperature
  • 26. 26 and imprecision Duratec, Lactobutyrin, Stilbene Aldehyde classified as Unclassified Drugs and Chemicals
  • 27. 27 and problematic synonyms Anatomic Structure, System, or Substance ~ Anatomic Structures and Systems Does ‘anatomic’ apply only to structure or also to system and substance? Biological Function ~ Biological Process some biological processes are the exercises of biological functions others (e.g. pathological processes) not Genetic Abnormality ~ Molecular Abnormality (with subtype: Molecular Genetic Abnormality) (definitions not supplied)
  • 28. 28 more problematic synonyms Diseases and Disorders ~ Disease ~ Disorder Definition1 for Disease: A disease is any abnormal condition of the body or mind that causes discomfort, dysfunction, or distress to the person affected or those in contact with the person. ... Definition2 for Disease A definite pathologic process with a characteristic set of signs and symptoms. ... Condition ≠ Process Definition2 contradicts NCIT’s own classification hierarchy
  • 29. 29 Ontological problems Three disjoint classes of plants: Vascular Plant Non-vascular Plant Other Plant
  • 30. 30 Ontological problems Abnormal Cell is a top-level class (thus not subsumed by Cell Cell is a subclass of Other Anatomic Concept (so that cells themselves are concepts) Normal Cell is a subclass of Microanatomy.
  • 31. 31 Next step Alignment of OBO ontologies through a common system of top-level categories in the OBO-UBO (Upper Biomedical Ontology) and through a common system of formally defined relations in the OBO-RO (Relation Ontology) see “Relations in Biomedical Ontologies”, Genome Biology Apr. 2005 Donnelly, M., Bittner, T. and Rosse, C. 2005. 'A Formal Theory for Spatial Representation and Reasoning in Biomedical Ontologies'. Artificial Intelligence in Medicine
  • 32. 32 is_a A is_a B Definition For all x, t if x instance_of A at t then x instance_of B at t allows reliable cross-ontology inferences from ‘abnormal cell’ to ‘cell’
  • 33. 33 part_of A part_of B Definition For all x, t if x instance_of A at t then there is some y, y instance_of B at t and x part_of y ‘part_of’ is the instance-level part relation, e.g. between this nucleus and this cell The all-some structure of such definitions allows cascading of inferences (i) within ontologies (ii) between ontologies (iii) between ontologies and EHR repositories of instance-data
  • 34. 34 Cascading inferences Whichever A you choose, its including B will be included in some C, which will include as part also the A with which you begin The same principle applies to the other relations located_at, transformation_of, derived_from etc. in the OBO-RO (UML treatment here very poor)
  • 35. 35 NCIT as now constituted will block such automatic reasoning Neither Normal Cell nor Abnormal Cells are Cells within the context of the NCIT
  • 36. 36 Some consolations NCIT is open source NCIT has broad coverage NCIT has some formal structure (DL) NCIT has realized the errors of its ways NCIT is much, much better than (for example) the HL7-RIM

Notes de l'éditeur

  1. Problem example: ‘chromosome’ in Sequence Ontology and in Cell Component Ontology means different things Current solution: two distinct terms involved (qualified by respective namespace)
  2. There is no species called ‘non-rabbit’
  3. There is no biological species: unknown rabbit. See discussion below.