1 a general introduction to biomedical ontology barry smith
Post on 21-Dec-2015
215 views
TRANSCRIPT
![Page 1: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/1.jpg)
1
A General Introduction to Biomedical Ontology
Barry Smith
http://ontology.buffalo.edu/smith
![Page 2: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/2.jpg)
2
How to create the conditions for a step-by-step evolution towards high quality ontologies in the biomedical domain
which will serve as stable attractors for clinical and biomedical researchers in the future?
Problem
![Page 3: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/3.jpg)
3
Answer:
Ontology development should cease to be an art, and become a science
= embrace the scientific method
If two scientists have a dispute, then they resolve it
![Page 4: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/4.jpg)
4
Scientific ontologies have special features
Computational concerns are not considerations relevant to the truth of an assertion in the ontology
Myth, fiction, folklore are not considerations relevant to the truth of an assertion in the ontology
Every entity referred to by a term in a scientific ontology must exist
![Page 5: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/5.jpg)
5
A problem of terminologies
Concept representations
Conceptual data models
Semantic knowledge models
...Information consists in representations of entities in a given domain what, then, is an information representation?
![Page 6: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/6.jpg)
6
Problem of ensuring sensible cooperation in a massively interdisciplinary community
concepttypeinstancemodelrepresentationdata
![Page 7: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/7.jpg)
7
A basic distinction
universal vs. instance
science text vs. clinical document
man vs. Musen
![Page 8: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/8.jpg)
8
Instances are not represented in an ontology built for scientific
purposes
It is the generalizations that are important
(but instances must still be taken into account)
![Page 9: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/9.jpg)
9
A 515287 DC3300 Dust Collector Fan
B 521683 Gilmer Belt
C 521682 Motor Drive Belt
Catalog vs. inventory
![Page 10: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/10.jpg)
10
Ontology universals Instances
![Page 11: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/11.jpg)
11
Ontology = A Representation of universals
![Page 12: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/12.jpg)
12
Ontology = A Representation of universals
Each node of an ontology consists of:
• preferred term (aka term)
• term identifier (TUI, aka CUI)
• synonyms
• definition, glosses, comments
![Page 13: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/13.jpg)
13
Each term in an ontology represents exactly one universal
It is for this reason that ontology terms should be singular nouns
National Socialism is_a Political Systems
![Page 14: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/14.jpg)
14
An ontology is a representation of universals
We learn about universals in reality from looking at the results of scientific experiments in the form of scientific theories – which describe not what is particular in reality but rather what is general
Ontologies need to exploit the evolutionary path to convergence created by science
![Page 15: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/15.jpg)
siamese
mammal
cat
organism
substanceuniversals
animal
instances
frogleaf class
![Page 16: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/16.jpg)
16
Rules for formating terms• Terms should be in the singular• Terms should be lower case• Avoid abbreviations even when it is clear in
context what they mean (‘breast’ for ‘breast tumor’)
• Avoid acronyms• Avoid mass terms (‘tissue’, ‘brain mapping’,
‘clinical research’ ...)• Treat each term ‘A’ in an ontology is shorthand
for a term of the form ‘the universal A’
![Page 17: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/17.jpg)
17
Problem of ensuring sensible cooperation in a massively interdisciplinary community
concepttypeinstancemodelrepresentationdata
![Page 18: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/18.jpg)
18
Problem of ensuring sensible cooperation in a massively interdisciplinary community
concept representation
data type
data instance
conceptual knowledge model
![Page 19: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/19.jpg)
19
Three Levels to Keep Straight
Level 1: the reality on the side of the organism (patient)
Level 2: cognitive representations of this reality on the part of clinicians
Level 3: publicly accessible concretisations of these cognitive representations in textual, graphical and digital artifacts
We are all interested primarily in Level 1
![Page 20: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/20.jpg)
20
Three Levels to Keep Straight
Level 1: the reality on the side of the organism (patient)
Level 2: cognitive representations of this reality on the part of clinicians
Level 3: publicly accessible concretisations of these cognitive representations in textual, graphical and digital artifacts
We (scientists) are all interested primarily in Level 1
![Page 21: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/21.jpg)
21
Entity =def
anything which exists, including things and processes, functions and qualities, beliefs and actions, documents and software (Levels 1, 2 and 3)
![Page 22: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/22.jpg)
22
Three Levels to Keep Straight
Level 1: the reality on the side of the organism (patient)
Level 2: cognitive representations of this reality on the part of clinicians
Level 3: publicly accessible concretisations of these cognitive representations in textual, graphical and digital artifacts
![Page 23: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/23.jpg)
23
A scientific ontology
is about reality (Level 1)
= the benchmark of correctness
![Page 24: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/24.jpg)
24
Ontology development
starts with Level 2 = the cognitive representations of clinicians or researchers as embodied in their theoretical and practical knowledge of the reality on the side of the patient
![Page 25: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/25.jpg)
25
Ontology development
results in Level 3 representational artifacts
comparable to
clinical texts
basic science texts
biomedical terminologies
![Page 26: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/26.jpg)
26
Domain =def
a portion of reality that forms the subject-matter of a single science or technology or mode of study;
proteomics
radiology
viral infections in mouse
![Page 27: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/27.jpg)
27
Representation =def
an image, idea, map, picture, name or description ... of some entity or entities.
![Page 28: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/28.jpg)
28
Analogue representations
![Page 29: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/29.jpg)
29
Representational units =def
terms, icons, alphanumeric identifiers ... which refer, or are intended to refer, to entities
![Page 30: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/30.jpg)
30
Composite representation =defrepresentation
(1) built out of representational units
which
(2) form a structure that mirrors, or is intended to mirror, the entities in some domain
![Page 31: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/31.jpg)
31
Periodic Table
The Periodic Table
![Page 32: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/32.jpg)
32
Two kinds of composite representations
Cognitive representations (Level 2)
Representational artefacts (Level 3)
The reality on the side of the patient (Level 1)
![Page 33: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/33.jpg)
33
Ontologies are here
![Page 34: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/34.jpg)
34
or here
![Page 35: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/35.jpg)
35
Ontologies are representational artifacts
![Page 36: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/36.jpg)
36
What do ontologies represent?
![Page 37: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/37.jpg)
A 515287 DC3300 Dust Collector Fan
B 521683 Gilmer Belt
C 521682 Motor Drive Belt
![Page 38: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/38.jpg)
A 515287 DC3300 Dust Collector Fan
B 521683 Gilmer Belt
C 521682 Motor Drive Belt
instances
universals
![Page 39: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/39.jpg)
39
Two kinds of composite representational artifacts
Databases, inventories: represent what is particular in reality = instances
Ontologies, terminologies, catalogs: represent what is general in reality = universals
![Page 40: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/40.jpg)
40
Ontologies do not represent concepts in people’s heads
![Page 41: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/41.jpg)
41
Ontologies represent universals in reality
![Page 42: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/42.jpg)
42
“lung” is not the name of a concept
concepts do not stand in
part_of
connectedness
causes
treats ...
relations to each other
![Page 43: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/43.jpg)
43
Ontology is a tool of science
Scientists do not describe the concepts in scientists’ heads
They describe the universals in reality, as a step towards finding ways to reason about (and treat) instances of these universals
![Page 44: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/44.jpg)
44
people who think ontologies are representations of concepts make
mistakes
congenital absent nipple is_a nipple
failure to introduce or to remove other tube or instrument is_a disease
bacteria causes experimental model of disease
![Page 45: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/45.jpg)
45
An ontology is like a scientific text; it is a representation of universals in reality
![Page 46: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/46.jpg)
46
The clinician has a cognitive representation which involves theoretical knowledge
derived from textbooks
![Page 47: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/47.jpg)
47
Two kinds of composite representational artifacts
Databases represent instances
Ontologies represent universals
![Page 48: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/48.jpg)
48
Instances stand in similarity relations
Frank and Bill are similar as humans, mammals, animals, etc.
Human, mammal and animal are universals at different levels of granularity
![Page 49: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/49.jpg)
49
How do we know which general terms designate universals?
Roughly: terms used in a plurality of sciences to designate entities about which we have a plurality of different kinds of testable proposition
(compare: cell, electron ...)
![Page 50: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/50.jpg)
siamese
mammal
cat
organism
substanceuniversals
animal
instances
frog
“leaf node”
![Page 51: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/51.jpg)
51
Class =def
a maximal collection of particulars determined by a general term (‘cell’, ‘oophorectomy’ ‘VA Hospital’, ‘breast cancer patient in Buffalo VA Hospital’)
the class A
= the collection of all particulars x for which ‘x is A’ is true
![Page 52: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/52.jpg)
52
Defined class =def
a class defined by a general term which does not designate a universal
the class of all diabetic patients in Leipzig on 4 June 1952
![Page 53: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/53.jpg)
53
terminology
a representational artifact whose representational units are natural language terms (with IDs, synonyms, comments, etc.) which are intended to designate defined classes.
![Page 54: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/54.jpg)
54
universals < defined classes < ‘concepts’
Not all of those things which people like to call ‘concepts’ correspond to defined classes
“Surgical or other procedure not carried out because of patient's decision”
![Page 55: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/55.jpg)
55
‘Concepts’INTRODUCER, GUIDING, FAST-CATH TWO-PIECE GUIDING INTRODUCER (MODELS 406869, 406892, 406893, 406904), ACCUSTICK II WITH RO MARKER INTRODUCER SYSTEM, COOK EXTRA LARGE CHECK-FLO INTRODUCER, COOK KELLER-TIMMERMANS INTRODUCER, FAST-CATH HEMOSTASIS INTRODUCER, MAXIMUM HEMOSTASIS INTRODUCER, FAST-CATH DUO SL1 GUIDING INTRODUCER FAST-CATH DUO SL2 GUIDING INTRODUCER
is_a HCFA Common Procedure Coding System
![Page 56: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/56.jpg)
56
SynonymsINTRODUCER, GUIDING, FAST-CATH TWO-PIECE GUIDING INTRODUCER (MODELS 406869, 406892, 406893, 406904), ACCUSTICK II WITH RO MARKER INTRODUCER SYSTEM, COOK EXTRA LARGE CHECK-FLO INTRODUCER, COOK KELLER-TIMMERMANS INTRODUCER, FAST-CATH HEMOSTASIS INTRODUCER, MAXIMUM HEMOSTASIS INTRODUCER, FAST-CATH DUO SL1 GUIDING INTRODUCER FAST-CATH DUO SL2 GUIDING INTRODUCER
![Page 57: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/57.jpg)
57
OWL is a good representation of defined classes
• soft tissue tumor AND/OR sarcoma
• cell differentiation or development pathway
• other accidental submersion or drowning in water transport accident injuring other specified person
• other suture of other tendon of hand
![Page 58: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/58.jpg)
58
Definition of ‘ontology’
ontology =def. a representational artifact whose representational units (which may be drawn from a natural or from some formalized language) are intended to represent
1. universals in reality
2. those relations between these universals which obtain universally (= for all instances)
lung is_a anatomical structure
lobe of lung part_of lung
![Page 59: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/59.jpg)
59
The OBO Relation OntologyGenome Biology 2005, 6:R46
![Page 60: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/60.jpg)
60
In every ontology
some terms and some relations are primitive = they cannot be defined (on pain of infinite regress)
Examples of primitive relations:
identity
instantiation
instance-level part_of
![Page 61: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/61.jpg)
61
is_aA is_a B =def
For all x, if x instance_of A then x instance_of B
cell division is_a biological process
Here A and B are universals
![Page 62: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/62.jpg)
62
Part_of as a relation between universals is more problematic than is standardly supposed
heart part_of human being ?
human heart part_of human being ?
human being has_part human testis ?
testis part_of human being ?
![Page 63: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/63.jpg)
63
two kinds of parthood
1. between instances:
Mary’s heart part_of Mary
this nucleus part_of this cell
2. between universals
human heart part_of human
cell nucleus part_of cell
![Page 64: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/64.jpg)
64
Definition of part_of as a relation between universals
A part_of B =Def. all instances of A are instance-level parts of some instance of B
human testis part_of adult human being
but notadult human being has_part human testis
![Page 65: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/65.jpg)
65
part_of for processes
A part_of B =def.
For all x, if x instance_of A then there is some y, y instance_of B and x part_of y
where ‘part_of’ is the instance-level part relation
EVERY A IS PART OF SOME B
![Page 66: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/66.jpg)
66
part_of for continuants
A part_of B =def.
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 at t
where ‘part_of’ is the instance-level part relation
ALL-SOME STRUCTURE
![Page 67: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/67.jpg)
67
is_a (for processes)
A is_a B =def
For all x, if x instance_of A then x instance_of B
cell division is_a biological process
![Page 68: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/68.jpg)
68
is_a (for continuants)
A is_a B =def
For all x, t if x instance_of A at t then x instance_of B at t
abnormal cell is_a celladult human is_a humanbut not: adult is_a child
![Page 69: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/69.jpg)
69
These definitions allow automatic reasoning across ontologies
Whichever A you choose, the instance of B of which it is a part will be included in some C, which will include as part also the A with which you began
The same principle applies to the other relations in the OBO-RO:
located_at, transformation_of, derived_from, adjacent_to, etc.
![Page 70: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/70.jpg)
70
A part_of B, B part_of C ...
The all-some structure of the definitions in the OBO-RO allows
cascading of inferences
(i) within ontologies
(ii) between ontologies
(iii) between ontologies and EHR repositories of instance-data
![Page 71: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/71.jpg)
71
Instance level
this nucleus is adjacent to this cytoplasm
implies:
this cytoplasm is adjacent to this nucleus
universal level
nucleus adjacent_to cytoplasm
Not: cytoplasm adjacent_to nucleus
![Page 72: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/72.jpg)
72
ApplicationsExpectations of symmetry e.g. for protein-
protein interactions hmay hold only at the instance level
if A interacts with B, it does not follow that B interacts with A
if A is expressed simultaneously with B, it does not follow that B is expressed simultaneously with A
![Page 73: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/73.jpg)
73
OBO Relation Ontology
Foundational is_apart_of
Spatial located_incontained_inadjacent_to
Temporal transformation_ofderives_frompreceded_by
Participation has_participanthas_agent
![Page 74: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/74.jpg)
74
Fiat and bona fide boundaries
![Page 75: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/75.jpg)
75
Continuity
Attachment
Adjacency
![Page 76: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/76.jpg)
76
everything here is an independent continuant
![Page 77: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/77.jpg)
77
structures vs. formations = bona fide vs. fiat boundaries
![Page 78: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/78.jpg)
78
Modes of Connection
The body is a highly connected entity. Exceptions: cells floating free in blood.
![Page 79: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/79.jpg)
79
Modes of Connection
Modes of connection:attached_to (muscle to bone) synapsed_with (nerve to nerve, nerve
to muscle)continuous_with (= share a fiat
boundary)
![Page 80: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/80.jpg)
80
articular eminencearticular (glenoid)fossa
ANTERIOR
Attachment, location, containment
![Page 81: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/81.jpg)
81
Containment involves relation to a hole or cavity
1: cavity2: tunnel, conduit (artery)3: mouth; a snail’s shell
![Page 82: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/82.jpg)
82
Fiat vs. Bona Fide Boundaries
fiat boundary
physical boundary
![Page 83: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/83.jpg)
83
Double Hole Structure
Medium (filling the environing hole)
Tenant (occupying the central hole)
Retainer (a boundary of some surrounding structure)
![Page 84: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/84.jpg)
84
head of condyle
neck of condyle
fossa
fiat boundary
the temporomandibular jointthe temporomandibular joint
![Page 85: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/85.jpg)
85
a continuous_with b= a and b are continuant
instances which share a fiat boundary
This relation is always symmetric:
if x continuous_with y , then y continuous_with x
![Page 86: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/86.jpg)
86
continuous_with(relation between types)
A continuous_with B =Def.
for all x, if x instance-of A then there is some y such that y instance_of B and x continuous_with y
![Page 87: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/87.jpg)
87
continuous_with is not always symmetric
Consider lymph node and lymphatic vessel:
Each lymph node is continuous with some lymphatic vessel, but there are lymphatic vessels (e.g. lymphs and lymphatic trunks) which are not continuous with any lymph nodes
![Page 88: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/88.jpg)
88
Adjacent_toas a relation between types
is not symmetric
Consider
seminal vesicle adjacent_to urinary bladder
Not: urinary bladder adjacent_to seminal vesicle
![Page 89: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/89.jpg)
89
instance level
this nucleus is adjacent to this cytoplasm
implies:
this cytoplasm is adjacent to this nucleus
type level
nucleus adjacent_to cytoplasm
Not: cytoplasm adjacent_to nucleus
![Page 90: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/90.jpg)
90
Applications
Expectations of symmetry e.g. for protein-protein interactions may hold only at the instance level
if A interacts with B, it does not follow that B interacts with A
if A is expressed simultaneously with B, it does not follow that B is expressed simultaneously with A
![Page 91: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/91.jpg)
c at t1
C
c at t
C1
time
same instance
transformation_of
pre-RNA mature RNA
adultchild
![Page 92: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/92.jpg)
92
transformation_of
A transformation_of B =Def.
Every instance of A was at some earlier time an instance of B
adult transformation_of child
![Page 93: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/93.jpg)
C
c at t c at t1
C1tumor development
![Page 94: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/94.jpg)
C
c at t
C1
c1 at t1
C'
c' at t
time
instances
zygote derives_fromovumsperm
derives_from
![Page 95: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/95.jpg)
two continuants fuse to form a new continuant
C
c at t
C1
c1 at t1
C'
c' at t fusion
![Page 96: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/96.jpg)
one initial continuant is replaced by two successor continuants
C
c at t
C1
c1 at t1
C2
c1 at t1
fission
![Page 97: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/97.jpg)
one continuant detaches itself from an initial continuant, which itself continues to exist
C
c at t c at t1
C1
c1 at t
budding
![Page 98: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/98.jpg)
one continuant absorbs a second continuant while itself continuing to exist
C
c at t
c at t1
C'
c' at t capture
![Page 99: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/99.jpg)
99
To be added to the Relation Ontology
lacks (between an instance and a type, e.g. this fly lacks wings)
dependent_on (between a dependent entity and its carrier or bearer)
quality_of (between a dependent and an independent continuant)
functioning_of (between a process and an independent continuant)
![Page 100: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/100.jpg)
100
New relations
instance to universal: lacks
continuant to continuant: connected_to
function to process: realized_by
process to function: functioning_of
function to continuant: function_of
continuant to function: has_function
quality to continuant: inheres_in (aka has_bearer)
continuant to quality: has_quality
![Page 101: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/101.jpg)
101
Most important
These relations hold both within and between ontologies
For example the relations between ontologies at different levels of granularity (e.g. molecule and cell) can be captured by relations of part_of between the corresponding types
![Page 102: 1 A General Introduction to Biomedical Ontology Barry Smith](https://reader035.vdocuments.us/reader035/viewer/2022062516/56649d615503460f94a43979/html5/thumbnails/102.jpg)
102
Definition of ‘ontology’
ontology =def. a representational artifact whose representational units (which may be drawn from a natural or from some formalized language) are intended to represent
1. universals in reality
2. those relations between these universals which obtain universally (= for all instances)
lung is_a anatomical structure
lobe of lung part_of lung