basic building blocks for biomedical ontologies
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Basic Building Blocks for Biomedical Ontologies. Barry Smith. 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 - PowerPoint PPT PresentationTRANSCRIPT
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 hardThey create an N2 problem; are fragile, and expensive to
maintainNeed 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 consensusUpdated every nightClear 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
problembut 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
RELATION TO TIME
GRANULARITY
CONTINUANT OCCURRENT
INDEPENDENT DEPENDENT
ORGAN ANDORGANISM
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO)
OrganFunction
(FMP, CPRO) Phenotypic
Quality(PaTO)
Biological Process
(GO)CELL AND CELLULAR
COMPONENT
Cell(CL)
Cellular Compone
nt(FMA, GO)
Cellular Function
(GO)
MOLECULEMolecule
(ChEBI, SO,RnaO, PrO)
Molecular Function(GO)
Molecular Process
(GO)
OBO (Open Biomedical Ontology) Foundry proposal(Gene Ontology in yellow) 14
RELATION TO TIME
GRANULARITY
CONTINUANT OCCURRENT
INDEPENDENT DEPENDENT
ORGAN ANDORGANISM
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO)
OrganFunction
(FMP, CPRO) Phenotypic
Quality(PaTO)
Biological Process
(GO)CELL AND CELLULAR
COMPONENT
Cell(CL)
Cellular Compone
nt(FMA, GO)
Cellular Function
(GO)
MOLECULEMolecule
(ChEBI, SO,RnaO, PrO)
Molecular Function(GO)
Molecular Process
(GO)
Environment Ontology
En
viro
nm
ent
On
tolo
gy
(EN
VO
)
15
RELATION TO TIME
GRANULARITY
CONTINUANT OCCURRENT
INDEPENDENT DEPENDENT
COMPLEX OFORGANISMS
Family, Community, Deme, Population
OrganFunction
(FMP, CPRO)
Population Phenotype
PopulationProcess
ORGAN ANDORGANISM
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO) Phenotypic
Quality(PaTO)
Biological Process
(GO)CELL AND CELLULAR
COMPONENT
Cell(CL)
Cellular Componen
t(FMA, GO)
Cellular Function
(GO)
MOLECULEMolecule
(ChEBI, SO,RnaO, PrO)
Molecular Function(GO)
Molecular Process
(GO)
Population-level ontologies 16
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
The OBO Foundry: a step-by-step, evidence-based approach to
expanding the GO
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_FoundryPrinciples
20
CONTINUANT OCCURRENT
INDEPENDENT DEPENDENT
ORGAN ANDORGANISM
Organism(NCBI
Taxonomy)
Anatomical Entity
(FMA, CARO)
OrganFunction
(FMP, CPRO) Phenotypic
Quality(PaTO)
Organism-Level Process
(GO)
CELL AND CELLULAR
COMPONENT
Cell(CL)
Cellular Compone
nt(FMA, GO)
Cellular Function
(GO)
Cellular Process
(GO)
MOLECULEMolecule
(ChEBI, SO,RnaO, PrO)
Molecular Function(GO)
Molecular Process
(GO)
OBO Foundry coverage
GRANULARITY
RELATION TO TIME
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
CONTINUANT OCCURRENT
INDEPENDENT DEPENDENT
ORGAN ANDORGANISM
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO)
OrganFunction
(FMP, CPRO) Phenotypic
Quality(PaTO)
Biological Process
(GO)XAO ZFA
CELL AND CELLULAR
COMPONENT
Cell(CL)
Cellular Compone
nt(FMA, GO)
Cellular Function
(GO)
MOLECULEMolecule (SO, RnaO)
Molecular Function(GO)
Molecular Process
(GO)ChEBI PRO
Current Foundry members in yellow24
Foundry ontologies currently under review
Plant Ontology (PO)Ontology for Biomedical Investigations (OBI)Ontology for General Medical Science (OBMS)Infectious Disease Ontology (IDO)
25
Anatomy Ontology(FMA*, CARO)
Environment
Ontology(EnvO)
Infectious Disease
Ontology(IDO*)
Biological Process
Ontology (GO*)
Cell Ontology
(CL)
CellularComponentOntology
(FMA*, GO*) Phenotypic Quality
Ontology(PaTO)
Subcellular Anatomy Ontology (SAO)Sequence Ontology
(SO*) Molecular Function
(GO*)Protein Ontology(PRO*) OBO Foundry Modular Organization
top level
mid-level
domain level
Information Artifact Ontology
(IAO)
Ontology for Biomedical Investigations
(OBI)
Ontology of General Medical Science
(OGMS)
Basic Formal Ontology (BFO)
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 CommunitiesCrop sciences Generation Challenge Programme (GCP),Environmental genomics MGED RSBI Group, www.mged.org/Workgroups/rsbiGenomic Standards Consortium (GSC),
www.genomics.ceh.ac.uk/genomecatalogueHUPO Proteomics Standards Initiative (PSI), psidev.sourceforge.netImmunology Database and Analysis Portal, www.immport.orgImmune Epitope Database and Analysis Resource (IEDB),
http://www.immuneepitope.org/home.doInternational 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/rsbiPolymorphismToxicogenomics MGED RSBI Group, www.mged.org/Workgroups/rsbiTranscriptomics MGED Ontology Group
29
30
31
32
33
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
Ontology for General Medical 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
Anatomy Ontology(FMA*, CARO)
Environment
Ontology(EnvO)
Infectious Disease
Ontology(IDO*)
Biological Process
Ontology (GO*)
Cell Ontology
(CL)
CellularComponentOntology
(FMA*, GO*) Phenotypic Quality
Ontology(PaTO)
Subcellular Anatomy Ontology (SAO)Sequence Ontology
(SO*) Molecular Function
(GO*)Protein Ontology(PRO*) OBO Foundry Modular Organization
top level
mid-level
domain level
Information Artifact Ontology
(IAO)
Ontology for Biomedical Investigations
(OBI)
Ontology of General Medical Science
(OGMS)
Basic Formal Ontology (BFO)
39
BFO: the very top
Continuant Occurrent(Process, Event)
IndependentContinuant
DependentContinuant
40
RELATION TO TIME
GRANULARITY
CONTINUANT OCCURRENT
INDEPENDENT DEPENDENT
ORGAN ANDORGANISM
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO)
OrganFunction
(FMP, CPRO) Phenotypic
Quality(PaTO)
Biological Process
(GO)CELL AND CELLULAR
COMPONENT
Cell(CL)
Cellular Compone
nt(FMA, GO)
Cellular Function
(GO)
MOLECULEMolecule
(ChEBI, SO,RnaO, PrO)
Molecular Function(GO)
Molecular Process
(GO)
41
CONTINUANT OCCURRENT
INDEPENDENT DEPENDENT
ORGAN ANDORGANISM
Organism(NCBI
Taxonomy)
Anatomical Entity
(FMA, CARO)
OrganFunction
(FMP, CPRO) Phenotypic
Quality(PaTO)
Organism-Level Process
(GO)
CELL AND CELLULAR
COMPONENT
Cell(CL)
Cellular Compone
nt(FMA, GO)
Cellular Function
(GO)
Cellular Process
(GO)
MOLECULEMolecule
(ChEBI, SO,RnaO, PrO)
Molecular Function(GO)
Molecular Process
(GO)
obofoundry.org
GRANULARITY
RELATION TO TIME
42
BFO & GO
continuant occurrent
biological processes
independentcontinuant
cellular component
dependentcontinuant
molecular function
43
Basic Formal Ontology
Continuant Occurrent
process, eventIndependentContinuant
thing
DependentContinuant
quality
.... ..... .......
types
instances44
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
Example: The Cell Ontology
How to build an ontologyimport 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 BFOPharmaOntology (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 BFOGO 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
Environment Ontology
Ontology for Biomedical Investigations
RNA Ontology
50
:.
Users of BFOOntology 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
continuant occurrent
independentcontinuant
dependentcontinuant
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
Qualitiestemperatureblood pressuremass...
are continuantsthey exist through time while undergoing changes
57
Qualitiestemperature / blood pressure /
mass ...are dimensions of variation within the structure of the entitya 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
continuant
independentcontinuant
dependentcontinuant
quality
occurrent
temperature 62
Blinding Flash of the Obvious
independentcontinuant
dependentcontinuant
quality
temperature types
instances
organism
John John’s
temperature 63
Blinding Flash of the Obvious
independentcontinuant
dependentcontinuant
quality
temperature types
instances
organism
John John’s
temperature 64
Blinding Flash of the Obvious
temperature types
instances
organism
John John’s
temperature .inheres_in
65
temperature types
instances
John’s temperature
37ºC37.1º
C37.5º
C37.2º
C37.3º
C37.4º
C
instantiates at t1
instantiates at t2
instantiates at t3
instantiates at t4
instantiates at t5
instantiates at t6
66
human types
instances
John
embryo
fetus adultneonat
einfant child
instantiates at t1
instantiates at t2
instantiates at t3
instantiates at t4
instantiates at t5
instantiates at t6
67
Temperature subtypesDevelopment-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
independentcontinuant
dependentcontinuant
quality
temperature types
instances
organism
John John’s
temperature
69
independentcontinuant
dependentcontinuant
quality
temperature
organism
John John’s
temperature
occurrent
process
course of temperature
changes
John’s temperature history
70
independentcontinuant
dependentcontinuant
quality
temperature
organism
John John’s
temperature
occurrent
process
life of an organism
John’s life
71
BFO: The Very Top
continuant occurrent
independentcontinuant
dependentcontinuant
quality disposition
72
BFO: The Very Top
continuant
independentcontinuant
dependentcontinuant
qualityfunctionroledisposition
occurrent
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
dispositionif it ceases to exist, then its bearer and/or its immediate surrounding environment is physically changedits realization occurs when its bearer is in some special physical circumstancesits realization is what it is in virtue of the bearer’s physical make-up
75
independentcontinuant
dependentcontinuant
function
to seeeye
John’s eye function of John’s eye: to see
occurrent
process
process of seeing
John seeing
80
OGMSOntology for General Medical
Science
http://code.google.com/p/ogms
88
New York State Center of Excellence in Bioinformatics & Life Sciences
R T U New York State Center of Excellence in Bioinformatics & Life Sciences
R T U
• 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
Ontology of General Medical Science (OGMS)
89
New York State Center of Excellence in Bioinformatics & Life Sciences
R T U New York State Center of Excellence in Bioinformatics & Life Sciences
R T U
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 continuantfiat 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: baldness93
Big Picture
94
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 >39 CAG repeats in the HTT gene– produces
• Disorder - chromosome 4 with abnormal mHTT– bears
• Disposition (disease) - Huntington’s disease– realized_in
• Pathological process - accumulation of mHTT protein fragments, abnormal transcription regulation, neuronal cell death in striatum– produces
• Abnormal bodily features– recognized_as
• Symptoms - anxiety, depression• Signs - difficulties in speaking and
swallowing
Symptoms & Signs used_in
Interpretive process produces
Hypothesis - rule out Huntington’s suggests
Laboratory tests produces
Test results - molecular detection of the HTT gene with >39CAG repeats used_in
Interpretive process produces
Result - diagnosis that patient X has a disorder that bears the disease Huntington’s disease
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-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, splenomegaly
Symptoms & Signs used_in
Interpretive process produces
Hypothesis - rule out cirrhosis suggests
Laboratory tests produces
Test results - elevated liver enzymes in serum used_in
Interpretive process produces
Result - diagnosis that patient X has a disorder that bears the disease cirrhosis
101
Systemic arterial hypertension
• Etiological process – abnormal reabsorption of NaCl by the kidney
– produces
• Disorder – abnormally large scattered molecular aggregate of salt in the blood
– bears
• Disposition (disease) - hypertension
– realized_in
• Pathological process – exertion of abnormal pressure against arterial wall
– produces
• Abnormal bodily features
– recognized_as
• Symptoms - headaches, dizziness
• Signs – elevated blood pressure
Symptoms & Signs used_in
Interpretive process produces
Hypothesis - rule out hypertension suggests
Laboratory tests produces
Test results - used_in
Interpretive process produces
Result - diagnosis that patient X has a disorder that bears the disease hypertension
102
Type 2 Diabetes Mellitus• Etiological process –
– produces• Disorder – abnormal pancreatic beta
cells and abnormal muscle/fat cells– bears
• Disposition (disease) – diabetes mellitus– realized_in
• Pathological processes – diminished insulin production , diminished muscle/fat uptake of glucose
– produces• Abnormal bodily features
– recognized_as• Symptoms – polydipsia, polyuria,
polyphagia, blurred vision• Signs – elevated blood glucose and
hemoglobin A1c
Symptoms & Signs used_in
Interpretive process produces
Hypothesis - rule out diabetes mellitus suggests
Laboratory tests – fasting serum blood glucose, oral glucose challenge test, and/or blood hemoglobin A1c produces
Test results - used_in
Interpretive process produces
Result - diagnosis that patient X has a disorder that bears the disease type 2 diabetes mellitus
103
Type 1 hypersensitivity to penicillin• Etiological process – sensitizing of mast
cells and basophils during exposure to penicillin-class substance
– produces• Disorder – mast cells and basophils with
epitope-specific IgE bound to Fc epsilon receptor I
– bears• Disposition (disease) – type I
hypersensitivity– realized_in
• Pathological process – type I hypersensitivity reaction
– produces• Abnormal bodily features
– recognized_as• Symptoms – pruritis, shortness of breath• Signs – rash, urticaria, anaphylaxis
Symptoms & Signs used_in
Interpretive process produces
Hypothesis - suggests
Laboratory tests – produces
Test results – occasionally, skin testing used_in
Interpretive process produces
Result - diagnosis that patient X has a disorder that bears the disease type 1 hypersensitivity to penicillin
104
105
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
John’s coronary heart disease
disease associated
with asymptomatic
(‘silent’) infarction
disease associated with early
lesions and small fibrous
plaques
stable angina
disease associated
with surface disruption of plaque
unstable angina
instantiates at t1
instantiates at t2
instantiates at t3
instantiates at t4
instantiates at t5
time107
independentcontinuant
dependentcontinuant
disposition
diseasedisorder
John’s disordered
heart
John’s coronary heart
disease
occurrent
process
course of disease
course of John’s disease
108
OGMS IDO
Independent Continuant
DisorderInfectious disorder
Dependent Continuant
Disease
Predisposition to disease
Infectious disease
Protective resistance
Occurrent Disease courseInfectious
disease course
Examples of ontology terms
IDO (Infectious Disease Ontology) CoreFollows 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 vectorsProvides 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
• Abnormal bodily features
– 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 - acute inflammation
– produces
• Abnormal bodily features
– recognized_as
• Symptoms - weakness, dizziness
• Signs - fever 113
The disorder also induces normal physiological processes (immune response) that can results in the elimination of the disorder (transient disease course).
Big Picture
114