Building Ontologies
from the Ground Up
When users set out to model their
professional activity
Mark A. Musen
Professor of Medicine and Computer Science
Stanford University
v 1.00
1
“An ontology is a specification of
a conceptualization” (T. Gruber)
• A conceptualization is the way we think
about a domain
• A specification provides a formal way of
writing it down
2
Porphyry’s depiction of Aristotle’s
Categories
Supreme genus:
Differentiae:
SUBSTANCE
material
immaterial
Subordinate genera:
Differentiae:
BODY
animate
inanimate
Subordinate genera:
LIVING
Differentiae:
sensitive
Proximate genera:
ANIMAL
Differentiae:
rational
Species:
Individuals:
SPIRIT
MINERAL
insensitive
PLANT
irrational
HUMAN
Socrates
Plato
BEAST
Aristotle
…
3
4
Creating Ontologies
in Machine-Processable Form
• Provides a mechanism for developers to codify
salient distinctions about the world or some
application area
• Provides a structure for knowledge bases that can
enable
–
–
–
–
Information retrieval
Information integration
Automated translation
Decision support
5
Ontologies are cropping up everywhere!
• Indexing of online information for
access by humans or search
engines
• Product catalogs for e-commerce
• Reference terminologies for
machine translation and data
interchange
• Standard terms for describing
experimental data
6
The New Philosophers
• Categorizing “what exists” in machineunderstandable form
• Providing a structure that enables
– Developers to locate and update relevant
descriptions
– Computers to infer relationships and properties
• Creating new abstractions to facilitate the
creation of this structure
7
8
Part of the CYC Upper Ontology
9
There is a misconception …
• That people building ontologies are all well versed
in metaphysics, computer science, knowledge
representation, and the content domain
• That ontologies in the real world are as “clean” as
SUMO, DOLCE, and other upper-level ontologies
• That most people who are creating ontologies
understand all the ramifications of what they are
doing!
10
Lots of ontology builders are not
very good philosophers
• Nearly always, ontologies are created to address
pressing professional needs
• The people who have the most insight into
professional knowledge may have little
appreciation for metaphysics, principles of
knowledge representation, or computational logic
• There simply aren’t enough good philosophers to
go around
11
A case in point: The International
Classification of Diseases
• An enumeration of diseases that forms the basis
for all medical claims and reimbursements in the
United States
• A “legacy” terminology that has its roots in 19th
century epidemiology
• Created initially by biostatisticians with a pressing
need to compare death statistics in different
European countries
• A system that won’t go away—and yet we would
never create anything like it again
12
The notion of disease emerged in
the 17th century
• Thomas Sydenham: “The selfsame phenomena
that you observe in the sickness of a Socrates you
would observe in the sickness of a simpleton”
– Description of a plant applies to its species;
– Description of disease should be similar
• Over the next 100 years, diverse classification
systems for diseases emerged
• Emphasis became to understand disease in terms
of associate pathological findings at autopsy
13
The Origins of the International
Classification of Diseases
• First International Statistical Congress, 1853,
initially commissioned development of a
nomenclature for coding causes of death
• The resulting nomenclature was revised in 1855,
1864, 1874, 1880, 1886, with continued confusion
as to how diseases should be classified
• In 1891, Jacques Bertillon generated a synthesis
organized largely anatomically; adopted by the
International Statistical Institute in 1893 as the
International List of Causes of Death
14
The ICD becomes an
International Standard
• In 1948, the World Health Organization became
responsible for the International List of Causes of
Death
• Nonfatal diseases were then added to the list, in
the course of multiple revisions to what then
became the ICD
• The Ninth revision, ICD-9 was released in 1977
• In 1978, after “clinical modification,” ICD-9-CM
became a source taxonomy “for statistics
concerning the planning, monitoring, and
evaluation of health services”
15
A Small Portion of ICD9-CM
724
724.0
724.00
724.01
724.02
724.09
724.1
724.2
724.3
724.4
724.5
724.6
724.7
724.70
724.71
724.71
724.8
724.9
Unspecified disorders of the back
Spinal stenosis, other than cervical
Spinal stenosis, unspecified region
Spinal stenosis, thoracic region
Spinal stenosis, lumbar region
Spinal stenosis, other
Pain in thoracic spine
Lumbago
Sciatica
Thoracic or lumbosacral neuritis
Backache, unspecified
Disorders of sacrum
Disorders of coccyx
Unspecified disorder of coccyx
Hypermobility of coccyx
Coccygodynia
Other symptoms referable to back
Other unspecified back disorders
Enumerative schemes
are finite and fixed
Hard to add terms
Hard to find terms
Definitions of terms
are informal at best
16
ICD9 (1977): A Handful of Codes for
Traffic Accidents
17
ICD10 (1999):
587 codes for such accidents
topClass
I Certain infectious and parasitic diseases
II Neoplasms
III Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism
IV Endocrine, nutritional and metabolic diseases
V Mental and behavioural disorders
VI Diseases of the nervous system
VII Diseases of the eye and adnexa
VIII Diseases of the ear and mastoid process
IX Diseases of the circulatory systems
X Diseases of the respiratory system
XI Diseases of the digestive system
XII Diseases of the skin and subcutaneous tissue
XIII Diseases of the musculoskeletal system and connective tissue
XIV Diseases of the genitourinary system
XV Pregnancy, childbirth and the puerperium
XVI Certain conditions originating in the perinatal period
XVII Congenital malformations, deformations and chromosomal abnormalities
XVIII Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified
XIX Injury, poisoning and certain other consequences of external causes
XX External causes of morbidity and mortality
V01-V99 Transport accidents
V01-V09 Pedestrian injured in transport accident
V10-V19 Pedal cyclist injured in transport accident
V10 Pedal cyclist injured in collision with pedestrian or animal
V10.0 Pedal cyclist injured in collision with pedestrian or animal, driver, nontraffic accident
V10.00 Pedal cyclist injured in collision with pedestrian or animal, driver, nontraffic accident, while engaged in sports activity
V10.01 Pedal cyclist injured in collision with pedestrian or animal, driver, nontraffic accident, while engaged in leisure activity
V10.02 Pedal cyclist injured in collision with pedestrian or animal, driver, nontraffic accident, while working for an income
V10.03 Pedal cyclist injured in collision with pedestrian or animal, driver, nontraffic accident, while engaged in other types of work
V10.04 Pedal cyclist injured in collision with pedestrian or animal, driver, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V10.08 Pedal cyclist injured in collision with pedestrian or animal, driver, nontraffic accident, while engaged in other specified activities
V10.09 Pedal cyclist injured in collision with pedestrian or animal, driver, nontraffic accident, during unspecified activity
V10.1 Pedal cyclist injured in collision with pedestrian or animal, passenger, nontraffic accident
V10.10 Pedal cyclist injured in collision with pedestrian or animal, passenger, nontraffic accident, while engaged in sports activity
V13 Pedal cyclist injured in collision with car, pick-up truck or van
V10.11 Pedal cyclist injured in collision with pedestrian or animal, passenger, nontraffic accident, while engaged in leisure activity
V13.0 Pedal cyclist injured in collision with car, pick-up truck or van, driver, nontraffic accident
V10.12 Pedal cyclist injured in collision with pedestrian or animal, passenger, nontraffic accident, while working for an income
V10.13 Pedal cyclist injured in collision with pedestrian or animal, passenger, nontraffic accident, while engaged in other types of work
V13.00 Pedal cyclist injured in collision with car, pick-up truck or van, driver, nontraffic accident, while engaged in sports activity
V10.14 Pedal cyclist injured in collision with pedestrian or animal, passenger, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V13.01 Pedal cyclist injured in collision with car, pick-up truck or van, driver, nontraffic accident, while engaged in leisure activity
V10.18 Pedal cyclist injured in collision with pedestrian or animal, passenger, nontraffic accident, while engaged in other specified activities
V13.02 Pedal cyclist injured in collision with car, pick-up truck or van, driver, nontraffic accident, while working for an income
V10.19 Pedal cyclist injured in collision with pedestrian or animal, passenger, nontraffic accident, during unspecified activity
V13.03 Pedal cyclist injured in collision with car, pick-up truck or van, driver, nontraffic accident, while engaged in other types of work
V10.2 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, nontraffic accident
V10.20 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, nontraffic accident, while engaged in sports activity
V13.04 Pedal cyclist injured in collision with car, pick-up truck or van, driver, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V10.21 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, nontraffic accident, while engaged in leisure activity
V13.08 Pedal cyclist injured in collision with car, pick-up truck or van, driver, nontraffic accident, while engaged in other specified activities
V10.22 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, nontraffic accident, while working for an income
V13.09 Pedal cyclist injured in collision with car, pick-up truck or van, driver, nontraffic accident, during unspecified activity
V10.23 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, nontraffic accident, while engaged in other types of work
V13.1 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, nontraffic accident
V10.24 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V10.28 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, nontraffic accident, while engaged in other specified activities
V13.10 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, nontraffic accident, while engaged in sports activity
V10.29 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, nontraffic accident, during unspecified activity
V13.11 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, nontraffic accident, while engaged in leisure activity
V10.3 Pedal cyclist injured in collision with pedestrian or animal, while boarding or alighting
V13.12 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, nontraffic accident, while working for an income
V10.30 Pedal cyclist injured in collision with pedestrian or animal, while boarding or alighting, while engaged in sports activity
V15.2 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, nontraffic accident
V15.20 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, nontraffic accident, while engaged in sports activity
V15.21 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, nontraffic accident, while engaged in leisure activity
V15.22 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, nontraffic accident, while working for an income
V15.23 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, nontraffic accident, while engaged in other types of work
V15.24 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V15.28 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, nontraffic accident, while engaged in other specified activities
V15.29 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, nontraffic accident, during unspecified activity
V15.3 Pedal cyclist injured in collision with railway train or railway vehicle, while boarding or alighting
V15.30 Pedal cyclist injured in collision with railway train or railway vehicle, while boarding or alighting, while engaged in sports activity
V15.31 Pedal cyclist injured in collision with railway train or railway vehicle, while boarding or alighting, while engaged in leisure activity
V15.32 Pedal cyclist injured in collision with railway train or railway vehicle, while boarding or alighting, while working for an income, while working for an income
V15.33 Pedal cyclist injured in collision with railway train or railway vehicle, while boarding or alighting, while engaged in other types of work
V10.31 Pedal cyclist injured in collision with pedestrian or animal, while boarding or alighting, while engaged in leisure activity
V13.13 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, nontraffic accident, while engaged in other types of work
V10.32 Pedal cyclist injured in collision with pedestrian or animal, while boarding or alighting, while working for an income
V15.34 Pedal cyclist injured in collision with railway train or railway vehicle, while boarding or alighting, while resting, sleeping, eating or engaging in other vital activities
V13.14 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V10.33 Pedal cyclist injured in collision with pedestrian or animal, while boarding or alighting, while engaged in other types of work
V15.38 Pedal cyclist injured in collision with railway train or railway vehicle, while boarding or alighting, while engaged in other specified activities
V13.18 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, nontraffic accident, while engaged in other specified activities
V10.34 Pedal cyclist injured in collision with pedestrian or animal, while boarding or alighting, while resting, sleeping, eating or engaging in other vital activities
V15.39 Pedal cyclist injured in collision with railway train or railway vehicle, while boarding or alighting, during unspecified activity
V13.19 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, nontraffic accident, during unspecified activity
V10.38 Pedal cyclist injured in collision with pedestrian or animal, while boarding or alighting, while engaged in other specified activities
V15.4 Pedal cyclist injured in collision with railway train or railway vehicle, driver, traffic accident
V10.39 Pedal cyclist injured in collision with pedestrian or animal, while boarding or alighting, during unspecified activity
V13.2 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, nontraffic accident
V10.4 Pedal cyclist injured in collision with pedestrian or animal, driver, traffic accident
V15.40 Pedal cyclist injured in collision with railway train or railway vehicle, driver, traffic accident, while engaged in sports activity
V13.20 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, nontraffic accident, while engaged in sports activity
V10.40 Pedal cyclist injured in collision with pedestrian or animal, driver, traffic accident, while engaged in sports activity
V15.41 Pedal cyclist injured in collision with railway train or railway vehicle, driver, traffic accident, while engaged in leisure activity
V13.21 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, nontraffic accident, while engaged in leisure activity
V10.41 Pedal cyclist injured in collision with pedestrian or animal, driver, traffic accident, while engaged in leisure activity
V15.42 Pedal cyclist injured in collision with railway train or railway vehicle, driver, traffic accident, while working for an income
V13.22 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, nontraffic accident, while working for an income
V10.42 Pedal cyclist injured in collision with pedestrian or animal, driver, traffic accident, while working for an income
V10.43 Pedal cyclist injured in collision with pedestrian or animal, driver, traffic accident, while engaged in other types of work
V15.43 Pedal cyclist injured in collision with railway train or railway vehicle, driver, traffic accident, while engaged in other types of work
V13.23 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, nontraffic accident, while engaged in other types of work
V10.44 Pedal cyclist injured in collision with pedestrian or animal, driver, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V15.44 Pedal cyclist injured in collision with railway train or railway vehicle, driver, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V13.24 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V10.48 Pedal cyclist injured in collision with pedestrian or animal, driver, traffic accident, while engaged in other specified activities
V15.48 Pedal cyclist injured in collision with railway train or railway vehicle, driver, traffic accident, while engaged in other specified activities
V13.28
Pedal
cyclist
injured
in
collision
with
car,
pick-up
truck
or
van,
unspecified
pedal
cyclist,
nontraffic
accident,
while
engaged
in
other
specified
activities
V10.49 Pedal cyclist injured in collision with pedestrian or animal, driver, traffic accident, during unspecified activity
V15.49 Pedal cyclist injured in collision with railway train or railway vehicle, driver, traffic accident, during unspecified activity
V10.5 Pedal cyclist injured in collision with pedestrian or animal, passenger, traffic accident
V13.29 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, nontraffic accident, during unspecified activity
V10.50 Pedal cyclist injured in collision with pedestrian or animal, passenger, traffic accident, while engaged in sports activity
V15.5 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, traffic accident
V13.3 Pedal cyclist injured in collision with car, pick-up truck or van, while boarding or alighting
V10.51 Pedal cyclist injured in collision with pedestrian or animal, passenger, traffic accident, while engaged in leisure activity
V15.50 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, traffic accident, while engaged in sports activity
V13.30 Pedal cyclist injured in collision with car, pick-up truck or van, while boarding or alighting, while engaged in sports activity
V10.52 Pedal cyclist injured in collision with pedestrian or animal, passenger, traffic accident, while working for an income
V15.51 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, traffic accident, while engaged in leisure activity
V13.31 Pedal cyclist injured in collision with car, pick-up truck or van, while boarding or alighting, while engaged in leisure activity
V10.53 Pedal cyclist injured in collision with pedestrian or animal, passenger, traffic accident, while engaged in other types of work
V15.52 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, traffic accident, while working for an income
V10.54 Pedal cyclist injured in collision with pedestrian or animal, passenger, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V13.32 Pedal cyclist injured in collision with car, pick-up truck or van, while boarding or alighting, while working for an income
V10.58 Pedal cyclist injured in collision with pedestrian or animal, passenger, traffic accident, while engaged in other specified activities
V15.53 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, traffic accident, while engaged in other types of work
V13.33 Pedal cyclist injured in collision with car, pick-up truck or van, while boarding or alighting, while engaged in other types of work
V10.59 Pedal cyclist injured in collision with pedestrian or animal, passenger, traffic accident, during unspecified activity
V15.54 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V13.34
Pedal
cyclist
injured
in
collision
with
car,
pick-up
truck
or
van,
while
boarding
or
alighting,
while
resting,
sleeping,
eating
or
engaging
in
other
vital
activities
V10.9 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, traffic accident
V15.58 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, traffic accident, while engaged in other specified activities
V13.38 Pedal cyclist injured in collision with car, pick-up truck or van, while boarding or alighting, while engaged in other specified activities
V10.90 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, traffic accident, while engaged in sports activity
V10.91 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, traffic accident, while engaged in leisure activity
V15.59 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, traffic accident, during unspecified activity
V13.39 Pedal cyclist injured in collision with car, pick-up truck or van, while boarding or alighting, during unspecified activity
V10.92 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, traffic accident, while working for an income
V15.9 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, traffic accident
V13.4 Pedal cyclist injured in collision with car, pick-up truck or van, driver, traffic accident
V10.93 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, traffic accident, while engaged in other types of work
V15.90 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, traffic accident, while engaged in sports activity
V13.40 Pedal cyclist injured in collision with car, pick-up truck or van, driver, traffic accident, while engaged in sports activity
V10.94 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V15.91 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, traffic accident, while engaged in leisure activity
V10.98 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, traffic accident, while engaged in other specified activities
V13.41 Pedal cyclist injured in collision with car, pick-up truck or van, driver, traffic accident, while engaged in leisure activity
V10.99 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, traffic accident, during unspecified activity
V15.92 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, traffic accident, while working for an income
V13.42 Pedal cyclist injured in collision with car, pick-up truck or van, driver, traffic accident, while working for an income
V11 Pedal cyclist injured in collision with other pedal cycle
V15.93 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, traffic accident, while engaged in other types of work
V13.43 Pedal cyclist injured in collision with car, pick-up truck or van, driver, traffic accident, while engaged in other types of work
V11.0 Pedal cyclist injured in collision with other pedal cycle, driver, nontraffic accident
V15.94 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V13.44 Pedal cyclist injured in collision with car, pick-up truck or van, driver, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V11.00 Pedal cyclist injured in collision with other pedal cycle, driver, nontraffic accident, while engaged in sports activity
V15.98 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, traffic accident, while engaged in other specified activities
V11.01 Pedal cyclist injured in collision with other pedal cycle, driver, nontraffic accident, while engaged in leisure activity
V13.48 Pedal cyclist injured in collision with car, pick-up truck or van, driver, traffic accident, while engaged in other specified activities
V11.02 Pedal cyclist injured in collision with other pedal cycle, driver, nontraffic accident, while working for an income
V15.99 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, traffic accident, during unspecified activity
V13.49 Pedal cyclist injured in collision with car, pick-up truck or van, driver, traffic accident, during unspecified activity
V11.03 Pedal cyclist injured in collision with other pedal cycle, driver, nontraffic accident, while engaged in other types of work
V16
Pedal
cyclist
injured
in collision with other nonmotor vehicle
V13.5 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, traffic accident
V11.04 Pedal cyclist injured in collision with other pedal cycle, driver, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V16.0 Pedal cyclist injured in collision with other nonmotor vehicle, driver, nontraffic accident
V13.50 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, traffic accident, while engaged in sports activity
V11.08 Pedal cyclist injured in collision with other pedal cycle, driver, nontraffic accident, while engaged in other specified activities
V11.09 Pedal cyclist injured in collision with other pedal cycle, driver, nontraffic accident, during unspecified activity
V16.00 Pedal cyclist injured in collision with other nonmotor vehicle, driver, nontraffic accident, while engaged in sports activity
V13.51 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, traffic accident, while engaged in leisure activity
V11.1 Pedal cyclist injured in collision with other pedal cycle, passenger, nontraffic accident
V16.01 Pedal cyclist injured in collision with other nonmotor vehicle, driver, nontraffic accident, while engaged in leisure activity
V13.52 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, traffic accident, while working for an income
V11.10 Pedal cyclist injured in collision with other pedal cycle, passenger, nontraffic accident, while engaged in sports activity
V16.02 Pedal cyclist injured in collision with other nonmotor vehicle, driver, nontraffic accident, while working for an income
V13.53 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, traffic accident, while engaged in other types of work
V11.11 Pedal cyclist injured in collision with other pedal cycle, passenger, nontraffic accident, while engaged in leisure activity
V16.03 Pedal cyclist injured in collision with other nonmotor vehicle, driver, nontraffic accident, while engaged in other types of work
V11.12 Pedal cyclist injured in collision with other pedal cycle, passenger, nontraffic accident, while working for an income
V13.54 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V11.13 Pedal cyclist injured in collision with other pedal cycle, passenger, nontraffic accident, while engaged in other types of work
V16.04 Pedal cyclist injured in collision with other nonmotor vehicle, driver, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V13.58 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, traffic accident, while engaged in other specified activities
V11.14 Pedal cyclist injured in collision with other pedal cycle, passenger, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V16.08 Pedal cyclist injured in collision with other nonmotor vehicle, driver, nontraffic accident, while engaged in other specified activities
V13.59 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, traffic accident, during unspecified activity
V11.18 Pedal cyclist injured in collision with other pedal cycle, passenger, nontraffic accident, while engaged in other specified activities
V16.09 Pedal cyclist injured in collision with other nonmotor vehicle, driver, nontraffic accident, during unspecified activity
V13.9 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, traffic accident
V11.19 Pedal cyclist injured in collision with other pedal cycle, passenger, nontraffic accident, during unspecified activity
V16.1 Pedal cyc
V11.2 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, nontraffic accident
V13.90 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, traffic accident, while engaged in sports activity
V11.20 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, nontraffic accident, while engaged in sports activity
V13.91 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, traffic accident, while engaged in leisure activity
V11.21 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, nontraffic accident, while engaged in leisure activity
V13.92 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, traffic accident, while working for an income
V11.22 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, nontraffic accident, while working for an income
V13.93 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, traffic accident, while engaged in other types of work
V11.23 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, nontraffic accident, while engaged in other types of work
V11.24 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V13.94 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V11.28 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, nontraffic accident, while engaged in other specified activities
V13.98 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, traffic accident, while engaged in other specified activities
V11.29 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, nontraffic accident, during unspecified activity
V13.99 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, traffic accident, during unspecified activity
V11.3 Pedal cyclist injured in collision with other pedal cycle, while boarding or alighting
V11.30 Pedal cyclist injured in collision with other pedal cycle, while boarding or alighting, while engaged in sports activity
V14 Pedal cyclist injured in collision with heavy transport vehicle or bus
V11.31 Pedal cyclist injured in collision with other pedal cycle, while boarding or alighting, while engaged in leisure activity
V14.0 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, nontraffic accident
V11.32 Pedal cyclist injured in collision with other pedal cycle, while boarding or alighting, while working for an income
V14.00 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, nontraffic accident, while engaged in sports activity
V11.33 Pedal cyclist injured in collision with other pedal cycle, while boarding or alighting, while engaged in other types of work
•V31.22 Occupant of three-wheeled motor vehicle injured in
collision with pedal cycle, person on outside of vehicle, nontraffic
accident, while working for income
•W65.40 Drowning and submersion while in bath-tub, street and
highway, while engaged in sports activity
•X35.44 Victim of volcanic eruption, street and highway, while
resting, sleeping, eating or engaging in other vital activities
V14.01 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, nontraffic accident, while engaged in leisure activity
V11.34 Pedal cyclist injured in collision with other pedal cycle, while boarding or alighting, while resting, sleeping, eating or engaging in other vital activities
V11.38 Pedal cyclist injured in collision with other pedal cycle, while boarding or alighting, while engaged in other specified activities
V14.02 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, nontraffic accident, while working for an income
V11.39 Pedal cyclist injured in collision with other pedal cycle, while boarding or alighting, during unspecified activity
V14.03 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, nontraffic accident, while engaged in other types of work
V11.4 Pedal cyclist injured in collision with other pedal cycle, driver, traffic accident
V14.04 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V11.40 Pedal cyclist injured in collision with other pedal cycle, driver, traffic accident, while engaged in sports activity
V14.08 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, nontraffic accident, while engaged in other specified activities
V11.41 Pedal cyclist injured in collision with other pedal cycle, driver, traffic accident, while engaged in leisure activity
V11.42 Pedal cyclist injured in collision with other pedal cycle, driver, traffic accident, while working for an income
V14.09 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, nontraffic accident, during unspecified activity
V11.43 Pedal cyclist injured in collision with other pedal cycle, driver, traffic accident, while engaged in other types of work
V14.1 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, nontraffic accident
V11.44 Pedal cyclist injured in collision with other pedal cycle, driver, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V14.10 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, nontraffic accident, while engaged in sports activity
V11.48 Pedal cyclist injured in collision with other pedal cycle, driver, traffic accident, while engaged in other specified activities
V11.49 Pedal cyclist injured in collision with other pedal cycle, driver, traffic accident, during unspecified activity
V14.11 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, nontraffic accident, while engaged in leisure activity
V11.5 Pedal cyclist injured in collision with other pedal cycle, passenger, traffic accident
V14.12 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, nontraffic accident, while working for an income
V11.50 Pedal cyclist injured in collision with other pedal cycle, passenger, traffic accident, while engaged in sports activity
V14.13 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, nontraffic accident, while engaged in other types of work
V11.51 Pedal cyclist injured in collision with other pedal cycle, passenger, traffic accident, while engaged in leisure activity
V14.14 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V11.52 Pedal cyclist injured in collision with other pedal cycle, passenger, traffic accident, while working for an income
V11.53 Pedal cyclist injured in collision with other pedal cycle, passenger, traffic accident, while engaged in other types of work
V14.18 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, nontraffic, while engaged in other specified activities accident
V11.54 Pedal cyclist injured in collision with other pedal cycle, passenger, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V14.19 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, nontraffic, during unspecified activity accident
V11.58 Pedal cyclist injured in collision with other pedal cycle, passenger, traffic accident, while engaged in other specified activities
V14.2
Pedal
cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, nontraffic accident
V11.59 Pedal cyclist injured in collision with other pedal cycle, passenger, traffic accident, during unspecified activity
V14.20 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, nontraffic accident, while engaged in sports activity
V11.9 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, traffic accident
V11.90 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, traffic accident, while engaged in sports activity
V14.21 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, nontraffic accident, while engaged in leisure activity
V11.91 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, traffic accident, while engaged in leisure activity
V14.22 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, nontraffic accident, while working for an income
V11.92 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, traffic accident, while working for an income
V14.23 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, nontraffic accident, while engaged in other types of work
V11.93 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, traffic accident, while engaged in other types of work
V11.94 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V14.24 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V11.98 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, traffic accident, while engaged in other specified activities
V14.28 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, nontraffic accident, while engaged in other specified activities
V11.99 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, traffic accident, during unspecified activity
V14.29 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, nontraffic accident, during unspecified activity
V12 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle
V14.3 Pedal cyclist injured in collision with heavy transport vehicle or bus, while boarding or alighting
V12.0 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, nontraffic accident
V12.00 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, nontraffic accident, while engaged in sports activity
V14.30 Pedal cyclist injured in collision with heavy transport vehicle or bus, while boarding or alighting, while engaged in sports activity
V12.01 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, nontraffic accident, while engaged in leisure activity
V14.31 Pedal cyclist injured in collision with heavy transport vehicle or bus, while boarding or alighting, while engaged in leisure activity
V12.02 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, nontraffic accident, while working for an income
V14.32 Pedal cyclist injured in collision with heavy transport vehicle or bus, while boarding or alighting, while working for an income
V12.03 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, nontraffic accident, while engaged in other types of work
V14.33 Pedal cyclist injured in collision with heavy transport vehicle or bus, while boarding or alighting, while engaged in other types of work
V12.04 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V12.08 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, nontraffic accident, while engaged in other specified activities
V14.34 Pedal cyclist injured in collision with heavy transport vehicle or bus, while boarding or alighting, while resting, sleeping, eating or engaging in other vital activities
V12.09 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, nontraffic accident, during unspecified activity
V14.38 Pedal cyclist injured in collision with heavy transport vehicle or bus, while boarding or alighting, while engaged in other specified activities
V12.1 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, nontraffic accident
V14.39 Pedal cyclist injured in collision with heavy transport vehicle or bus, while boarding or alighting, during unspecified activity
V12.10 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, nontraffic accident, while engaged in sports activity
V12.11 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, nontraffic accident, while engaged in leisure activity
V14.4 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, traffic accident
V12.12 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, nontraffic accident, while working for an income
V14.40 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, traffic accident, while engaged in sports activity
V12.13 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, nontraffic accident, while engaged in other types of work
V14.41 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, traffic accident, while engaged in leisure activity
V12.14 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V14.42 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, traffic accident, while working for an income
V12.18 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, nontraffic accident, while engaged in other specified activities
V12.19 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, nontraffic accident, during unspecified activity
V14.43 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, traffic accident, while engaged in other types of work
V12.2 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, nontraffic accident
V14.44 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V12.20 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, nontraffic accident, while engaged in sports activity
V14.48 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, traffic accident, while engaged in other specified activities
V12.21 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, nontraffic accident, while engaged in leisure activity
V14.49 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, traffic accident, during unspecified activity
V12.22 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, nontraffic accident, while working for an income
V12.23 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, nontraffic accident, while engaged in other types of work
V14.5 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, traffic accident
V12.24 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V14.50 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, traffic accident, while engaged in sports activity
V12.28 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, nontraffic accident, while engaged in other specified activities
V14.51 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, traffic accident, while engaged in leisure activity
V12.29 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, nontraffic accident, during unspecified activity
V14.52 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, traffic accident, while working for an income
V12.3 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, while boarding or alighting
V14.53 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, traffic accident, while engaged in other types of work
V12.30 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, while boarding or alighting, while engaged in sports activity
V14.54 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V12.31 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, while boarding or alighting, while engaged in leisure activity
V14.58 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, traffic accident, while engaged in other specified activities
V12.32 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, while boarding or alighting, while working for an income
V14.59 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, traffic accident, during unspecified activity
V12.33 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, while boarding or alighting, while engaged in other types of work
V12.34 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, while boarding or alighting, while resting, sleeping, eating or engaging in other vital activities
V14.9 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, traffic accident
V12.38 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, while boarding or alighting, while engaged in other specified activities
V14.90 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, traffic accident, while engaged in sports activity
V12.39 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, while boarding or alighting, during unspecified activity
V14.91 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, traffic accident, while engaged in leisure activity
V14.92 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, traffic accident, while working for an income
V12.4 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, traffic accident
V14.93 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, traffic accident, while engaged in other types of work
V12.40 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, traffic accident, while engaged in sports activity
V14.94 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V12.41 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, traffic accident, while engaged in leisure activity
V14.98 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, traffic accident, while engaged in other specified activities
V12.42 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, traffic accident, while working for an income
V14.99 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, traffic accident, during unspecified activity
V12.43 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, traffic accident, while engaged in other types of work
V12.44 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V15 Pedal cyclist injured in collision with railway train or railway vehicle
V12.48 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, traffic accident, while engaged in other specified activities
V12.49 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, traffic accident, during unspecified activity
V12.5 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, traffic accident
V12.50 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, traffic accident, while engaged in sports activity
V12.51 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, traffic accident, while engaged in leisure activity
V12.52 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, traffic accident, while working for an income
V12.53 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, traffic accident, while engaged in other types of work
V12.54 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V12.58 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, traffic accident, while engaged in other specified activities
V12.59 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, traffic accident, during unspecified activity
V12.9 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, traffic accident
V15.0 Pedal cyclist injured in collision with railway train or railway vehicle, driver, nontraffic accident
V15.00 Pedal cyclist injured in collision with railway train or railway vehicle, driver, nontraffic accident, while engaged in sports activity
V15.01 Pedal cyclist injured in collision with railway train or railway vehicle, driver, nontraffic accident, while engaged in leisure activity
V15.02 Pedal cyclist injured in collision with railway train or railway vehicle, driver, nontraffic accident, while working for an income
V15.03 Pedal cyclist injured in collision with railway train or railway vehicle, driver, nontraffic accident, while engaged in other types of work
V15.04 Pedal cyclist injured in collision with railway train or railway vehicle, driver, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V15.08 Pedal cyclist injured in collision with railway train or railway vehicle, driver, nontraffic accident, while engaged in other specified activities
V15.09 Pedal cyclist injured in collision with railway train or railway vehicle, driver, nontraffic accident, during unspecified activity
V15.1 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, nontraffic accident
V15.10 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, nontraffic accident, while engaged in sports activity
V15.11 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, nontraffic accident, while engaged in leisure activity
V12.90 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, traffic accident, while engaged in sports activity
V15.12 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, nontraffic accident, while working for an income
V12.91 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, traffic accident, while engaged in leisure activity
V15.13 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, nontraffic accident, while engaged in other types of work
V12.92 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, traffic accident, while working for an income
V15.14 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V12.93 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, traffic accident, while engaged in other types of work
V15.18 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, nontraffic accident, while engaged in other specified activities
V15.19 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, nontraffic accident, during unspecified activity
18
ICD is used for lots of
(too many?) things!
• ICD is used to code all patient encounters with the
health-care system for purposes of
–
–
–
–
–
Billing and reimbursement
Institutional planning
Disease surveillance and public health
Quality assurance
Economic modeling by third-party payors
• ICD was never intended to make the distinctions
relevant to all these tasks!
• When patient encounters are encoded with ICD, it
is impossible to keep all these uses in mind
19
If real ontologists could build
the ICD from scratch …
• Diseases would be organized with well-defined
relationships
• Diseases would be associated with computerunderstandable definitions
• There would be well-defined rules to enable
aggregation of primitive concepts into complex
descriptions—and for ensuring that those
descriptions were sensible
• There would be well-defined mechanisms for
creating use-specific views of the ICD
20
The pressing need to standardize
the names of human genes
21
But the human genome is only
part of the problem …
• Scientist maintain huge databases of gene
sequences and gene expression for a wide range of
“model organisms” (e.g., mouse, rat, yeast, fruit
fly, round worm, slime mold)
• Database entries are annotated with the entries
such as the name of a gene, the function of the
gene, and so on
• How do you ensure uniformity in the nature of
these annotations?
22
Gene Ontology Consortium
• Founded in 1998 as a collaboration among
scientists responsible for developing different
databases of genomic data for model organisms
(fruit fly, yeast, mouse)
• Now, essentially all developers of all modelorganism databases participate
• Goal: To produce a dynamic, controlled
vocabulary that can be applied to all organism
databases even as knowledge of gene and protein
roles in cells is accumulating and changing
23
Gene Ontology (GO)
• Comprises three independent “ontologies”
– molecular function of gene products
– cellular component of gene products
– biological process representing the gene product’s
higher order role.
• Uses these terms as attributes of gene products in the
collaborating databases (gene product associations)
• Allows queries across databases using GO terms,
providing linkage of biological information across species
24
GO = Three Ontologies
• Molecular Function
– elemental activity or task
– example: DNA binding
• Cellular Component
– location or complex
– example: cell nucleus
• Biological Process
– goal or objective within cell
– example: secretion
25
26
GO has been wildly successful!!
• Dozens of biologists around the world
contribute to GO on a regular basis
• The ontology is updated every 30 minutes!
• It’s now impossible to work in most areas of
computational biology without making use
of GO terms
27
But GO has real problems …
• Ontologies are represented in an idiosyncratic format that
is not compatible with standard knowledge-representation
systems
• The format is based on directed acyclic graphs of concepts,
without the general ability to specify machine interpretable
properties of concepts or definitions of concepts
• Because of the informal knowledge-representation system,
lots of errors have crept into GO
– Terms that are duplicated in different places
– Terms with no superclasses
– Uncertain relationships between terms
28
29
Tension in the GO Community
• Biologists around the world with pressing needs to
integrate research databases work together to add
terms to GO nearly continuously
– Using an impoverished, nonstandard knowledgerepresentation system
– Using no standards to assure uniform modeling
conventions from one part of GO to another
• Computer scientists bemoan all this
ad-hoc-ery and condemn GO as a hack that will
become increasingly unusable and unmaintainable
30
A wonderful keynote talk
from the recent meeting
on Standards and
Ontologies for Functional
Genomics
The Capulets and Montagues
A plague on both your houses?
Professor Carole Goble
University of Manchester, UK
Warning:
This talk contains sweeping generalisations
31
 Carole Goble
Prologue
Two households, both alike in dignity,
In fair genomics, where we lay our scene,
(One, comforted by its logic’s rigour,
Claims ontology for the realm of pure,
The other, with blessed scientist’s vigour,
Acts hastily on models that endure),
From ancient grudge break to new mutiny,
When “being” drives a fly-man to blaspheme.
From forth the fatal loins of these two foes
Researchers to unlock the book of life;
Whole misadventured piteous overthrows
Can with their work bury their clans’ strife.
The fruitful passage of their GO-mark'd love,
And the continuance of their studies sage,
Which, united, yield ontologies undreamed-of,
Is now the hours' traffic of our stage;
The which if you with patient ears attend,
What here shall miss, our toil shall strive to mend.
32
Based on an idea by Shakespeare
 Carole Goble
The Montagues
One, comforted by its logic’s rigour,
Claims ontology for the realm of pure
Computer Science, Knowledge engineering, AI
Logic and Languages
Theory
Top down, well-behaved neatness
Generic and lots of toys
Methodologies & patterns
Tools and standards
Technology push
Academic pursuit
33
 Carole Goble
The Capulets
The other, with blessed scientist’s vigour,
Acts hastily on models that endure
Life Scientists
Practice
Bottom up, real-world
Specific and many of them
Methodologies, community practice
Tools and standards
Application pull
Practical pursuit – build ‘n’ use it
34
 Carole Goble
The Philosophers
One, comforted by its logic’s rigour,
Claims ontology for the realm of pure
Philosophers
Theory
Truth
Generic – the one true ontology?
Methodologies, patterns & foundational ontologies
Not really into tools
No push or pull
Academic pursuit
35
 Carole Goble
Endurants, Perdurants,
Being, Substance, Event
Philosophers
KR
Montagues
The end
Mechanism providers
Life
Scientists
Capulets
A means to an end
Content providers
36
 Carole Goble
The Princes of Genomics
Rebellious subjects, enemies to peace,
Profaners of this neighbour-stained steel,-Will they not hear? What, ho! you men, you beasts,
That quench the fire of your pernicious rage
With purple fountains issuing from your veins,
On pain of torture, from those bloody hands
Throw your mistemper'd weapons to the ground,
And hear the sentence of your moved prince.
Three civil brawls, bred of an airy word,
By thee, old Capulet, and Montague,
Have thrice disturb'd the quiet of our streets,
And made genomics's ancient citizens
Cast by their grave beseeming ornaments,
To wield old partisans, in hands as old,
Canker'd with peace, to part your canker'd hate:
37
A tragedy?
As in Romeo and Juliette,
the threats are political
and sociological
38
Creating ontologies has become a
widespread cottage industry
• Professional Societies
– MGED: Microarray Gene Expression Data Society
– HUPO: Human Protein Organization
• Government
– NCI Thesaurus
– NIST: Process Specification Language
• Open Biological Ontologies
– GO
– Three dozen (and growing) other ontologies
– Mostly in DAG-Edit, some in Protégé format
39
40
Government Continues to be a
Major Driving Force
• Highly visible intramural initiatives to create
public ontologies at many agencies, including
NIST, NIH, VA, CDC
• Notable variation in these ontologies’
–
–
–
–
Scope
Representational sophistication
“Openness” of content
Opportunities for peer review
41
NCI Enterprise Vocabulary Services
1997: R. Klausner, Director NCI, wanted a “science
management system”
• Know about everything funded by NCI
• Goals and results – “bench to bedside”
- Thereby improve and speed translation of research
Approach:
1. Create integrative terminology
2. Evolve terminology scope from supporting grants
management to supporting science
3. Build Web-accessible infrastructure – caCORE
42
43
More than 37,000
concepts are
represented with
extremely
detailed
granularity in
many areas
44
Definitions may
include
considerable
detail with
respect to
properties that
establish
relationships
with other
concepts
45
NCI Thesaurus is in Active Use
nciterms.nci.nih.gov
ncicb.nci.nih.gov/core/EVS (more info)
Website: 1500-4000 page hits daily, 14K
unique visitors (2004)
• API: NCICB & external applications
• Fulfills NCI and collaborators’ needs
for controlled vocabulary
• Public domain, open content license
46
NCI Thesaurus Guidelines
• Develop content model (based on Ontylog
description logic from Apelon, Inc.)
• Leverage existing sources as appropriate
– MeSH, VA NDF-RT, MedDRA …
• Develop unique content where needed
– Cancer genes, gene products, cancer diagnoses, drugs,
chemotherapies, molecular abnormalities etc., and
relationships among them
• Link to other standards using URLs where
possible
– OMIM, Swissprot, GO
47
:
NCI uses an Elaborate Process
for Editing and Maintenance
48
The NCI Thesaurus is not
without its problems
• Upper level concepts are sometimes used
inconsistently or not at all
• Textual definitions of concepts may not always
reflect the meaning implied by the concepts’
position in the ontology
• Reliance on a proprietary knowledgerepresentation system
– Prevents the ability to disseminate the ontology freely
– Adds an unfortunate degree of uncertainty to the
semantics
49
Throughout this cottage industry
• Lots of ontology development, principally by
content experts with little training in conceptual
modeling
• Use of development tools and ontology-definition
languages that may be
– Extremely limited in their expressiveness
– Useless for detecting potential errors and guiding
correction
– Nonadherent to recognized standards
– Proprietary and expensive
50
But the world is beginning to change!
• The Montagues do want to get the modeling
right!
• The Capulets do want to see their work used
by others!
• Useful, open tools and standards are now
available that make it hard to justify closed,
proprietary approaches
51
Some signs the world is changing …
• Developers of several overlapping and incompatible
ontologies of anatomy suddenly are trying to understand
why their models do not agree
• Philosopher Barry Smith suddenly is camping out at
biomedical informatics meetings to get the attention of
ontology developers
• NCI is piloting the use of OWL and Protégé to encode and
manage the NCI thesaurus
• MGED and several other biomedical ontologies are being
authored in OWL and Protégé from the beginning
• Downloads of the Protégé system continue to escalate
52
53
Total Protege Registrations
Month/Year
Oct '04
Jul '04
Apr '04
Jan '04
Oct '03
Jul '03
Apr '03
Jan '03
Oct '02
Jul '02
Apr '02
Jan '02
Oct '01
Jul '01
Apr '01
22000
21000
20000
19000
18000
17000
16000
15000
14000
13000
12000
11000
10000
9000
8000
7000
6000
5000
4000
3000
2000
1000
0
Jan '01
Registrations
Through 10/13/04
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Protégé’s main features
• Simplified editing of ontologies and knowledge bases
• Open-source distribution to encourage development by a
world-wide community of users
• A plug-in architecture that enables developers to add new
features easily
• Support for a wide range of representation formats
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–
–
–
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CLIPS/COOL
XML Schema
UML
RDF
OWL
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Protégé is ecumenical in its support
for formal languages
• Open Knowledge Base Connectivity
Protocol
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–
–
–
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CLIPS/COOL
UML
XML Schema
RDF and RDFS
Topic Maps
• Ontology Web Language (OWL)
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Protégé remains successful
because of its user community
• There are now 89 plug-ins available for use with Protégé
• Collaboration with our users enables rapid debugging and
code fixes
• Some development, such as the creation of extensions to
our basic OWL capabilities, has been a major collaborative
experience
• Annual users groups meetings provide great opportunities
for developers to share strategies, principles, and war
stories
• Members of the international Protégé community are a
huge support base for new users and for fledgling projects
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The NCI Thesaurus
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Bio-Pathway ontologies
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Content Standard for Geospatial Metadata (Federal Geographic Data Committee)
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Egyptian Crop Pests
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Moving from cottage industry
to the industrial age
• There must be widely available tools that
are open-source, that are easy to use, and
that adhere to knowledge representation
standards: Protégé certainly is a candidate
• There must be a large user user community
of developers who use the tools and who
can provide feedback to one another and to
the core team of tool builders
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Moving from cottage industry
to the industrial age II
• Government and professional societies must set
expectations regarding the need for appropriate
standards
• Government and professional societies must invest
in educational programs to teach Montagues to
identify with Capulets, and vice versa
• Demonstration projects must communicate to the
potential developers of future ontologies the
strengths and weaknesses of the guidelines, tools,
and languages that facilitated the development
work
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A thousand flowers are blooming
from every corner of the landscape
• Ontologies are being developed by interested groups from
every sector of academia, industry, and government
• Many of these ontologies have been proven to be
extraordinarily useful to wide communities
• Many of these same ontologies have been shown to be
structurally flawed and of uncertain semantics
• We finally are at the stage where we have tools and
representation languages that can lift us out of the grass
roots to create durable and maintainable ontologies with
rich semantic content
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An infrastructure is now in place
• The need to build new ontologies in
environmental health, phenotypic expression in
model organisms, developmental biology, and
many, many other domains is getting wide
attention
• We finally have the tools and the languages to do
things right
• Now all we need now is the will, the educational
opportunities, and the community feedback to help
developers at the grass roots to reemerge as
philosophers and princes.
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Let’s have a happy ending.
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