Biomedical ontology tutorial_atlanta_june2011_part2

Basic Building Blocks for
Biomedical Ontologies
Barry Smith

1

Problems with UMLS-style
approaches
• let a million ontologies bloom, each one close
to the terminological habits of its authors
• in concordance with the “not invented here”
syndrome
• then map these ontologies, and use these
mappings to integrate your different pots of
data
2

Mappings are hard
They create an N2 problem; are fragile, and
expensive to maintain
Need new authorities to maintain(one for each
pair of mapped ontologies), yielding new risk
of forking – who will police the mappings?
The goal should be to minimize the need for
mappings, by avoiding redundancy in the first
place – one ontology for each domain
Invest resources in disjoint ontology modules
which work well together – reduce need for
mappings to minimum possible 8

Why should you care?
• you need to create systems for data mining
and text processing which will yield useful
digitally coded output
• if the codes you use are constantly in need of
ad hoc repair huge, resources will be wasted
• serious investment in annotation will be
defeated from the start
• relevant data will not be found, because it will
be lost in multiple semantic cemeteries
9

How to do it right?
• how create an incremental, evolutionary
process, where what is good survives, and what
is bad fails
• where the number of ontologies needing to be
used together is small – integration = addition
• where these ontologies are stable
• by creating a scenario in which people will find it
profitable to reuse ontologies, terminologies and
coding systems which have been tried and tested
10

Reasons why GO has been
successful
It is a system for prospective standardization
built with coherent top level but with content
contributed and monitored by domain specialists
Based on community consensus
Updated every night
Clear versioning principles ensure backwards
compatibility; prior annotations do not lose their
value
Initially low-tech to encourage users, with
movement to more powerful formal approaches
(including OWL-DL – though still proceeding
caution)
11

GO has learned the lessons of
successful cooperation

• Clear documentation
• The terms chosen are already familiar
• Fully open source (allows thorough testing in
manifold combinations with other ontologies)
• Subjected to considerable third-party critique
• Tracker for user input and help desk with rapid
turnaround

12

GO has been amazingly successful in
overcoming the data balkanization
problem
but it covers only generic biological entities of
three sorts:
– cellular components
– molecular functions
– biological processes
no diseases, symptoms, disease
biomarkers, protein interactions,
experimental processes … 13

CONTINUANT OCCURRENT
RELATION
TO TIME

INDEPENDENT DEPENDENT
GRANULARITY

Anatomical
Organism Organ
ORGAN AND Entity
(NCBI Function
ORGANISM (FMA,
Taxonomy) (FMP, CPRO) Phenotypic Biological
CARO) Quality Process
(PaTO) (GO)
CELL AND Cellular Cellular
Cell
CELLULAR Component Function
(CL)
COMPONENT (FMA, GO) (GO)
Molecule
Molecular Function Molecular Process
MOLECULE (ChEBI, SO,
(GO) (GO)
RnaO, PrO)

OBO (Open Biomedical Ontology) Foundry proposal
(Gene Ontology in yellow) 14

RELATION
TO TIME


GRANULARITY

Environment Ontology
Anatomical
Organism Organ
ORGAN AND Entity
(NCBI Function
ORGANISM (FMA,
CARO)

(ENVO)
Quality Process
(PaTO) (GO)
Cell
(CL)

Molecule
(GO) (GO)
RnaO, PrO)

15

RELATION
TO TIME


GRANULARITY

COMPLEX OF Family, Community, Population Population
ORGANISMS Deme, Population Phenotype Process
Anatomical Organ
ORGAN AND Organism Entity Function
ORGANISM (NCBI (FMA, (FMP, CPRO) Phenotypic
Taxonomy) Biological
CARO) Quality
Process
(PaTO)
(GO)
Cell
(CL)
Molecule
(GO) (GO)
RnaO, PrO)

Population-level ontologies 16

The OBO Foundry: a step-by-step,
evidence-based approach to
expanding the GO
 Developers commit to working to ensure
that, for each domain, there is community
convergence on a single ontology
 and agree in advance to collaborate with
developers of ontologies in adjacent
domains.

http://obofoundry.org 17

OBO Foundry Principles
 Common governance (coordinating editors)
 Common training
 Common architecture:
• simple shared top level ontology (BFO)
• shared Relation Ontology:
www.obofoundry.org/ro

18

Open Biomedical Ontologies Foundry
Seeks to create high quality, validated terminology
modules across all of the life sciences which will be
• one ontology for each domain, so no need for
mappings
• close to language use of experts
• evidence-based
• incorporate a strategy for motivating potential
developers and users
• revisable as science advances 19

Principles
http://obofoundry.org/wiki/index.php/OBO_FoundryPrincip

20

RELATION TO CONTINUANT OCCURRENT
TIME

GRANULARITY INDEPENDENT DEPENDENT

Anatomical
Organism Organ Organism-Level
ORGAN AND Entity
(NCBI Function Process
ORGANISM (FMA,
Taxonomy) (FMP, CPRO) Phenotypic (GO)
CARO) Quality
(PaTO)
Cell Cellular Process
(CL) (GO)

Molecule Molecular
Molecular Function
MOLECULE (ChEBI, SO, Process
(GO)
RnaO, PrO) (GO)

OBO Foundry coverage
21

ORTHOGONALITY

modularity ensures
• annotations can be additive
• division of labor amongst domain experts
• high value of training in any given module
• lessons learned in one module can benefit
work on other modules
• incentivization of those responsible for
individual modules

22

Benefits of coordination

• Can more easily reuse what is made by others
• Can more easily inspect and criticize what is
made by others
• Leads to innovations (e.g. Mireot strategy for
importing terms into ontologies)

23

RELATION
TO TIME


GRANULARITY

Anatomical
Organism Entity Organ
ORGAN AND
(NCBI (FMA, Function
ORGANISM
Taxonomy) CARO) (FMP, CPRO) Phenotypic Biological
Quality Process
XAO ZFA
(PaTO) (GO)
Cell
(CL)
Molecule (SO, RnaO) Molecular
Molecular Function
MOLECULE Process
ChEBI PRO (GO)
(GO)

Current Foundry members in yellow
24

Foundry ontologies currently under
review

Plant Ontology (PO)
Ontology for Biomedical Investigations (OBI)
Ontology for General Medical Science (OBMS)
Infectious Disease Ontology (IDO)

25

top level Basic Formal Ontology (BFO)

Information Artifact Ontology for Biomedical Ontology of General
mid-level Ontology Investigations Medical Science
(IAO) (OBI) (OGMS)

Anatomy Ontology
(FMA*, CARO) Infectious
Disease
Cellular
Cell Ontology (IDO*)
Component
Ontology (EnvO)
Ontology
domain level (CL)
(FMA*, GO*)
Phenotypic Biological
Quality Process
Ontology Ontology (GO*)
Subcellular Anatomy Ontology (SAO) (PaTO)
Sequence Ontology
(SO*) Molecular
Function
Protein Ontology
(GO*)
(PRO*)
OBO Foundry Modular Organization 26

OBI

The Ontology for Biomedical Investigations

hfp://purl.org/obo/OBI_0000225

27

Purpose of OBI

To provide a resource for the unambiguous
description of the components of
biomedical investigations such as the
design, protocols and instrumentation,
material, data and types of analysis and
statistical tools applied to the data

 NOT designed to model biology

28

OBI Collaborating Communities
Crop sciences Generation Challenge Programme (GCP),
Environmental genomics MGED RSBI Group,
www.mged.org/Workgroups/rsbi
Genomic Standards Consortium (GSC),
www.genomics.ceh.ac.uk/genomecatalogue
HUPO Proteomics Standards Initiative (PSI), psidev.sourceforge.net
Immunology Database and Analysis Portal, www.immport.org
Immune Epitope Database and Analysis Resource (IEDB),
http://www.immuneepitope.org/home.do
International Society for Analytical Cytology, http://www.isac-net.org/
Metabolomics Standards Initiative (MSI),
Neurogenetics, Biomedical Informatics Research Network (BIRN),
Nutrigenomics MGED RSBI Group, www.mged.org/Workgroups/rsbi
Polymorphism
Toxicogenomics MGED RSBI Group, www.mged.org/Workgroups/rsbi
Transcriptomics MGED Ontology Group
29

Ontology for General Medical
Science
http://code.google.com/p/ogms/

(OBO) http://purl.obolibrary.org/obo/ogms.obo
(OWL) http://purl.obolibrary.org/obo/ogms.owl

34

OGMS-based initiatives
Vital Signs Ontology (VSO) (Welch Allyn)
EHR / Demographics Ontology
Infectious Disease Ontology
Mental Health Ontology
Emotion Ontology

35

Science
Jobst Landgrebe (then Co-Chair of the HL7
Vocabulary Group):
“the best ontology effort in the whole
biomedical domain by far”

36

EXPERIMENTAL
ARTIFACTS
Ontology for Biomedical Investigations (OBI)
CLINICAL
MEDICINE
Ontology of General Medical Science (OGMS)
INFORMATION
ARTIFACTS
Information Artifact Ontology (IAO)

How to keep clear about the distinction
• processes of observation,
• results of such processes (measurement
data)
• the entities observed

37

How is the OBO Foundry organized?

• Top-Level: Basic Formal Ontology (BFO)
• Mid-Level: IAO, OBI, OGMS ...
• Domain-Level: Foundry Bio-Ontologies

38

top level Basic Formal Ontology (BFO)

Information Artifact Ontology for Biomedical Ontology of General
mid-level Ontology Investigations Medical Science
(IAO) (OBI) (OGMS)

Anatomy Ontology
(FMA*, CARO) Infectious
Disease
Cellular
Cell Ontology (IDO*)
Component
Ontology (EnvO)
Ontology
domain level (CL)
(FMA*, GO*)
Phenotypic Biological
Quality Process
Ontology Ontology (GO*)
Subcellular Anatomy Ontology (SAO) (PaTO)
Sequence Ontology
(SO*) Molecular
Function
Protein Ontology
(GO*)
(PRO*)
OBO Foundry Modular Organization 39

BFO: the very top

Continuant Occurrent
(Process, Event)

Independent Dependent
Continuant Continuant

40

RELATION
TO TIME

GRANULARITY

Anatomical
Organism Organ
ORGAN AND Entity
(NCBI Function
ORGANISM (FMA,
CARO) Quality Process
(PaTO) (GO)
Cell
(CL)
Molecule
(GO) (GO)
RnaO, PrO)

41

RELATION CONTINUANT OCCURRENT
TO TIME

GRANULARITY INDEPENDENT DEPENDENT

Anatomical
Organism Organ Organism-Level
ORGAN AND Entity
(NCBI Function Process
ORGANISM (FMA,
Taxonomy) (FMP, CPRO) Phenotypic (GO)
CARO) Quality
(PaTO)
Cell Cellular Process
(CL) (GO)

Molecule Molecular
Molecular Function
MOLECULE (ChEBI, SO, Process
(GO)
RnaO, PrO) (GO)

obofoundry.org 42

BFO & GO

continuant occurrent

independent dependent
continuant continuant

cellular molecular biological
component function processes

43

Basic Formal Ontology
types

Continuant Occurrent

process, event
Independent Dependent
Continuant Continuant

thing quality

.... ..... .......
instances
44

Experience with BFO in
building ontologies provides
• a community of skilled ontology developers
and users (user group has 120 members)
• associated logical tools
• documentation for different types of users
• a methodology for building conformant
ontologies by starting with BFO and populating
downwards

45

How to build an ontology
import BFO into ontology editor such as Protégé
work with domain experts to create an initial mid-
level classification
find ~50 most commonly used terms corresponding
to types in reality
arrange these terms into an informal is_a hierarchy
according to this universality principle
A is_a B ≡ every instance of A is an instance of B
fill in missing terms to give a complete hierarchy
(leave it to domain experts to populate the lower
levels of the hierarchy)
47

Users of BFO
PharmaOntology (W3C HCLS SIG)
MediCognos / Microsoft Healthvault
Cleveland Clinic Semantic Database in Cardiothoracic
Surgery
Major Histocompatibility Complex (MHC) Ontology (NIAID)
Neuroscience Information Framework Standard (NIFSTD)
and Constituent Ontologies
Interdisciplinary Prostate Ontology (IPO)
Nanoparticle Ontology (NPO): Ontology for Cancer
Nanotechnology Research
Neural Electromagnetic Ontologies (NEMO)
ChemAxiom – Ontology for Chemistry 49
:.

Users of BFO
GO Gene Ontology
CL Cell Ontology
SO Sequence Ontology
ChEBI Chemical Ontology
PATO Phenotype (Quality) Ontology
FMA Foundational Model of Anatomy Ontology
ChEBI Chemical Entities of Biological Interest
PRO Protein Ontology
Plant Ontology
Ontology for Biomedical Investigations
RNA Ontology 50
:.

Users of BFO
Ontology for Risks Against Patient Safety (RAPS/REMINE)
eagle-i an VIVO (NCRR)
IDO Infectious Disease Ontology (NIAID)
National Cancer Institute Biomedical Grid Terminology
(BiomedGT)
US Army Biometrics Ontology
US Army Command and Control Ontology
Sleep Domain Ontology
Subcellular Anatomy Ontology (SAO)
Translaftional Medicine On (VO)
Yeast Ontology (yOWL)
Zebrafish Anatomical Ontology (ZAO) 51
:.

Basic Formal Ontology



organism

54

Continuants

• continue to exist through time,
preserving their identity while
undergoing different sorts of changes
• independent continuants – objects,
things, ...
• dependent continuants – qualities,
attributes, shapes, potentialities ...

55

Occurrents
• processes, events, happenings
– your life
– this process of accelerated cell division

56

Qualities
temperature
blood pressure
mass
...
are continuants
they exist through time while
undergoing changes

57

Qualities
temperature / blood pressure / mass ...

are dimensions of variation within the
structure of the entity
a quality is something which can
change while its bearer remains one
and the same

58

A Chart representing how
John’s temperature changes

59

A Chart representing how
John’s temperature changes

60

BFO: The Very Top



quality

temperature 62

Blinding Flash of the Obvious

quality

organism
temperature types
John’s
John
temperature
instances
63


quality

organism
temperature types
John’s
John
temperature
instances
64

inheres_in
.

organism
temperature types
John’s
John
temperature
instances

65

temperature types

37ºC 37.1ºC 37.2ºC 37.3ºC 37.4ºC 37.5ºC

instantiates instantiates instantiates instantiates instantiates instantiates
at t1 at t2 at t3 at t4 at t5 at t6

John’s temperature

instances 66

human types

embryo fetus neonate infant child adult

instantiates instantiates instantiates instantiates instantiates instantiates
at t1 at t2 at t3 at t4 at t5 at t6

John

instances 67

Temperature subtypes
Development-stage subtypes

are threshold divisions (hence we do
not have sharp boundaries, and we
have a certain degree of choice, e.g. in
how many subtypes to distinguish,
though not in their ordering)

68


quality

organism
temperature types
John’s
John
temperature
instances

69

occurrent

quality process

organism course of
temperature temperature
changes

John’s John’s
John
temperature temperature history
70

occurrent

quality process

organism
temperature life of an
organism

John’s John’s
John
temperature life
71

BFO: The Very Top



quality disposition

72

BFO: The Very Top



quality
function
role
disposition
73

disposition
- of a glass vase, to shatter if dropped
- of a human, to eat
- of a banana, to ripen
- of John, to lose hair

74

disposition
if it ceases to exist, then its bearer
and/or its immediate surrounding
environment is physically changed
its realization occurs when its bearer is in
some special physical circumstances
its realization is what it is in virtue of the
bearer’s physical make-up

75

occurrent

function process
eye
to see process of
seeing

John’s eye function of John’s John seeing
eye: to see
80

OGMS
Science

http://code.google.com/p/ogms

88

R T U New York State
Center of Excellence in
Bioinformatics & Life
Sciences
Ontology of General Medical Science (OGMS)
• ontology for the representation of
– diseases, signs, symptoms
– clinical processes
– diagnosis, treatment and outcomes
• fundamental idea:
– a disease is a disposition rooted in some
(physical) disorder in the organism
89

R T U New York State
Center of Excellence in
Bioinformatics & Life
Sciences
Motivation
• Clarity about:
– disease etiology and progression
– disease and the diagnostic process
– phenotype and signs/symptoms
– entities in reality and observations of sucn
entities

90

Physical Disorder

91

Physical Disorder
– independent
continuant
fiat object part

A causally linked
combination of physical
components of the
extended organism that
is clinically abnormal. 92
:.

Clinically abnormal

– (1) not part of the life plan for an organism
of the relevant type (unlike aging or
pregnancy),
– (2) causally linked to an elevated risk
either of pain or other feelings of illness,
or of death or dysfunction, and
– (3) such that the elevated risk exceeds a
certain threshold level.*

*Compare: baldness
93

Pathological Process
=def. A bodily process that is a
manifestation of a disorder and is clinically
abnormal.

Disease =def. – A disposition to undergo
pathological processes that exists in an
organism because of one or more
disorders in that organism.
95

Cirrhosis - environmental exposure
• Etiological process - phenobarbitol-induced hepatic cell death
– produces
• Disorder - necrotic liver
– bears
• Disposition (disease) - cirrhosis
– realized_in
• Pathological process - abnormal tissue repair with cell proliferation
and fibrosis that exceed a certain threshold; hypoxia-induced cell
death
– produces
• Abnormal bodily features
– recognized_as
• Symptoms - fatigue, anorexia
• Signs - jaundice, enlarged spleen
96

Dispositions and Predispositions
All diseases are dispositions; not all
dispositions are diseases.

Predisposition to Disease
=def. – A disposition in an organism that
constitutes an increased risk of the
organism’s subsequently developing some
disease.

97

HNPCC - genetic pre-disposition
• Etiological process - inheritance of a mutant mismatch repair gene
– produces
• Disorder - chromosome 3 with abnormal hMLH1
– bears
• Disposition (disease) - Lynch syndrome
– realized_in
• Pathological process - abnormal repair of DNA mismatches
– produces
• Disorder - mutations in proto-oncogenes and tumor suppressor genes
with microsatellite repeats (e.g. TGF-beta R2)
– bears
• Disposition (disease) - non-polyposis colon cancer
– realized in
• Symptoms (including pain)

98

Huntington’s Disease - genetic
• Etiological process - inheritance of  Symptoms & Signs
>39 CAG repeats in the HTT gene  used_in
– produces  Interpretive process
• Disorder - chromosome 4 with
 produces
abnormal mHTT
– bears  Hypothesis - rule out Huntington’s
• Disposition (disease) - Huntington’s  suggests
disease  Laboratory tests
– realized_in  produces
• Pathological process - accumulation of
mHTT protein fragments, abnormal
 Test results - molecular detection of
transcription regulation, neuronal cell the HTT gene with >39CAG repeats
death in striatum  used_in
• Abnormal bodily features  produces
– recognized_as  Result - diagnosis that patient X has a
• Symptoms - anxiety, depression disorder that bears the disease
• Signs - difficulties in speaking and Huntington’s disease
swallowing
99

HNPCC - genetic pre-disposition
• Etiological process - inheritance of a mutant mismatch repair
gene
– produces
• Disorder - chromosome 3 with abnormal hMLH1
– bears
• Disposition (disease) - Lynch syndrome
– realized_in
• Pathological process - abnormal repair of DNA mismatches
– produces
• Disorder - mutations in proto-oncogenes and tumor
suppressor genes with microsatellite repeats (e.g. TGF-beta
R2)
– bears
• Disposition (disease) - non-polyposis colon cancer 100

Cirrhosis - environmental exposure
• Etiological process - phenobarbitol-  Symptoms & Signs
induced hepatic cell death  used_in

 produces
• Disorder - necrotic liver
– bears  Hypothesis - rule out cirrhosis
 suggests
• Disposition (disease) - cirrhosis
 Laboratory tests
– realized_in
 produces
• Pathological process - abnormal tissue  Test results - elevated liver enzymes
repair with cell proliferation and in serum
fibrosis that exceed a certain  used_in
threshold; hypoxia-induced cell death
 Interpretive process
– produces  produces
• Abnormal bodily features  Result - diagnosis that patient X has a
– recognized_as disorder that bears the disease
• Symptoms - fatigue, anorexia cirrhosis
• Signs - jaundice, splenomegaly
101

Systemic arterial hypertension
• Etiological process – abnormal  Symptoms & Signs
reabsorption of NaCl by the kidney  used_in

 produces
• Disorder – abnormally large scattered
molecular aggregate of salt in the  Hypothesis - rule out hypertension
blood  suggests

– bears  Laboratory tests
 produces
• Disposition (disease) - hypertension
– realized_in  Test results -
 used_in
• Pathological process – exertion of
abnormal pressure against arterial wall
 produces
– produces
 Result - diagnosis that patient X has a
disorder that bears the disease hypertension
– recognized_as
• Symptoms - headaches, dizziness
• Signs – elevated blood pressure
102

Type 2 Diabetes Mellitus
• Etiological process –
 Symptoms & Signs
– produces
 used_in
• Disorder – abnormal pancreatic beta  Interpretive process
cells and abnormal muscle/fat cells
 produces
– bears
 Hypothesis - rule out diabetes mellitus
• Disposition (disease) – diabetes  suggests
mellitus  Laboratory tests – fasting serum blood
– realized_in glucose, oral glucose challenge test, and/or
• Pathological processes – diminished blood hemoglobin A1c
insulin production , diminished  produces
muscle/fat uptake of glucose  Test results -
– produces  used_in

• Abnormal bodily features  Interpretive process
– recognized_as  produces

• Symptoms – polydipsia, polyuria,
polyphagia, blurred vision disorder that bears the disease type 2
diabetes mellitus
• Signs – elevated blood glucose and
hemoglobin A1c 103

Type 1 hypersensitivity to penicillin
• Etiological process – sensitizing of mast
cells and basophils during exposure to
 Symptoms & Signs
 used_in
penicillin-class substance
 produces
• Disorder – mast cells and basophils with
epitope-specific IgE bound to Fc epsilon  Hypothesis -
 suggests
receptor I
– bears  Laboratory tests –
 produces
• Disposition (disease) – type I
hypersensitivity  Test results – occasionally, skin testing
 used_in
– realized_in
•
Pathological process – type I
 produces
hypersensitivity reaction
– produces
disorder that bears the disease type 1
• Abnormal bodily features hypersensitivity to penicillin
– recognized_as
• Symptoms – pruritis, shortness of breath
• Signs – rash, urticaria, anaphylaxis 104

Disease vs. Disease course

Disease =def. – A disposition to undergo
pathological processes that exists in an
organism because of one or more
disorders in that organism.
Disease course =def. – The aggregate of
processes in which a disease disposition
is realized.
106

coronary heart
disease
disease
associated disease disease
with early associated with associated
lesions and asymptomatic with surface unstable stable
small fibrous (‘silent’) disruption of angina angina
plaques infarction plaque

instantiates instantiates instantiates instantiates instantiates
at t1 at t2 at t3 at t4 at t5

John’s coronary heart disease

107
time

occurrent

disposition process

disorder course of
disease
disease

John’s John’s
disordered coronary heart course of John’s
heart disease disease

108

Examples of ontology terms
OGMS IDO

Independent Infectious
Disorder
Continuant disorder

Infectious
Disease disease
Dependent
Continuant Predisposition to Protective
disease resistance

Infectious
Occurrent Disease course
disease course

IDO (Infectious Disease Ontology) Core
Follows GO strategy of providing a
canonical ontology of what is involved
in every infectious disease – host,
pathogen, vector, virulence, vaccine,
transmission – accompanied by IDO
Extensions for specific diseases,
pathogens and vectors
Provides common terminology resources
and tested common guidelines for a
vast array of different disease
communities 110

Infectious Disease Ontology Consortium
• MITRE, Mount Sinai, UTSouthwestern –
Influenza
• IMBB/VectorBase – Vector borne diseases (A.
gambiae, A. aegypti, I. scapularis, C. pipiens,
P. humanus)
• Colorado State University – Dengue Fever
• Duke University – Tuberculosis, Staph. aureus
• Cleveland Clinic – Infective Endocarditis
• University of Michigan – Brucellosis
• Duke University, University at Buffalo – HIV
111

Influenza - infectious
• Etiological process - infection of airway epithelial cells with
influenza virus
– produces
• Disorder - viable cells with influenza virus
– bears
• Disposition (disease) - flu
– realized_in
• Pathological process - acute inflammation
– produces
– recognized_as
• Symptoms - weakness, dizziness
• Signs - fever 112

Influenza – disease course
• Etiological process - infection of airway epithelial cells with
influenza virus
– produces
• Disorder - viable cells with influenza virus
– bears
• Disposition (disease) - flu
– realized_in
• Pathological process - The disorder also induces normal
acute inflammation
– produces physiological processes (immune
• Abnormal bodily featuresresponse) that can results in the
– recognized_as elimination of the disorder (transient
• Symptoms - weakness, dizziness
disease course).
• Signs - fever 113

Biomedical ontology tutorial_atlanta_june2011_part2

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