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John Fox (Director, OpenClinical)
As a user and teacher of ontological methods in medicine and engineering I have for years warned my students that the design of domain ontologies is a black art with no theoretical foundations and few practical principles.
4
Ontology success stories, and some reasons for failure
Linked Open Data, from Musicbrainz to Mouse Genome Informatics
5
John Fox, OpenClinicalAs a user and teacher of ontological methods in medicine and engineering I have for years warned my students that the design of domain ontologies is a black art with no theoretical foundations and few practical principles. … I now have a much more positive story for my students. …
6
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)Original OBO Foundry ontologies
(Gene Ontology in yellow) 7
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)
rationale of OBO Foundry coverage
GRANULARITY
RELATION TO TIME
8
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 Component(FMA, GO)
Cellular Function
(GO)
MOLECULEMolecule
(ChEBI, SO,RnaO, PrO)
Molecular Function(GO)
Molecular Process
(GO)Environment Ontology (EnvO)
En
viro
nm
ents
9
RELATION TO TIME
CONTINUANT
OCCURRENTGRANULARITY
INDEPENDENTCONTINUANT
DEPENDENT CONTINUANT
ORGAN ANDORGANISM
Organism
NCBITaxonom
y
Anatomical Entity(FMA, CARO)
OrganFunction
(FMP, CPRO)
Biological Process
(GO)Ontology for Biomedical Investigatio
ns(OBI)
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)
Env
iron
men
t Ont
olog
y (E
NV
O)
10
Phe
noty
pic
Qua
lity
(PA
TO
)
Recognizing a new family of protocol-driven processes (investigation, assay, clinical trial …)
RELATION TO TIME
CONTINUANTOCCURRENT
GRANULARITY
INDEPENDENTCONTINUANT
DEPENDENT CONTINUANT
INFORMATION ARTIFACT
ORGAN ANDORGANISM
Organism
NCBITaxonom
y
Anatomical Entity(FMA, CARO)
OrganFunction
(FMP, CPRO)
IAOSoftware,
Algorithms,…
Sequence Data,
EHR Data …
Biological
Process(GO)
OBICELL AND CELLULAR
COMPONENT
Cell(CL)
Cellular Componen
t(FMA, GO)
Cellular Function
(GO)
MOLECULEMolecule
(ChEBI, SO,RnaO, PrO)
Molecular Function
(GO)
Images,Image Data,
Flow Cytometry
Data, …
Molecular Process
(GO)OBI:
Imaging
Env
iron
men
t Ont
olog
y (E
NV
O)
11
Phe
noty
pic
Qua
lity
(PA
TO
)
Recognizing a new family of information entities: data, publications, images, algorithms …
examples of BFO/OBO Foundry approach extended into other domains
12
NIF Standard Neuroscience Information Framework
UNEP Ontology Framework
United Nations Environment Program Ontologies
IDO Consortium Infectious Disease Ontology Suite
MilPortal Intelligence and Information Warfare Directorate, US Army
cROP Common Reference Ontologies for Plants
Introduction to Biomedical Ontology for Imaging Informatics
Barry Smith, PhD, FACMIUniversity at Buffalo
May 11, 2015
RELATION TO TIME
CONTINUANT
OCCURRENT
GRANULARITY
INDEPENDENTCONTINUANT
DEPENDENT CONTINUANT
ORGAN ANDORGANISM
Organism
NCBITaxonom
y
Anatomical Entity(FMA, CARO)
OrganFunction
(FMP, CPRO)
Biological Process
(GO)
Ontology for
Biomedical Investigatio
ns(OBI)
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)
OBI: Imaging Ontology Branch
Env
iron
men
t Ont
olog
y (E
NV
O)
15
Phe
noty
pic
Qua
lity
(PA
TO
)
Recognizing a new family of processes (investigation, assay, protocol-driven process)
Anatomy Ontology(FMA*, CARO) Disease Ontology
(OGMS, IDO, HDO, HPO)
Biological
Processes
Assays (Protocol-
driven processes)
Cell Ontology(CL)
Subcellular Anatomy Ontology
(SAO)
Phenotypic QualityOntology(PATO)
Sequence Ontology
(SO)Molecular
Function Ontology(GO)Protein Ontology
(PRO) Extension Strategy + Modular Organization
INDEPENDENT
CONTINUANT(~THING))
DEPENDENT CONTINUANT(~ATTRIBUTE)
OCCURRENT(~PROCESS)
Basic Formal Ontology (BFO)
16
Structure of a typical investigation as viewed by OBI (from http://obi-ontology.org/page/Investigation)
The Ontology for Biomedical Investigations
RELATION TO TIME
CONTINUANTOCCURRENT
GRANULARITY
INDEPENDENTCONTINUANT
DEPENDENT CONTINUANT
INFORMATION ARTIFACT
ORGAN ANDORGANISM
Organism
NCBITaxonom
y
Anatomical Entity(FMA, CARO)
OrganFunction
(FMP, CPRO)
Software, Algorithms
…
Patient Demographic
Data,EHR Data,
Public Health Data,
…
Biological
Process(GO)
OBI
CELL AND CELLULAR
COMPONENT
Cell(CL)
Cellular Componen
t(FMA, GO)
Cellular Function
(GO)
MOLECULEMolecule
(ChEBI, SO,RnaO, PrO)
Molecular Function
(GO)
Images,Image Data,
Flow Cytometry
Data, …
Molecular Process
(GO)OBI:
Imaging
Env
iron
men
t Ont
olog
y (E
NV
O)
18
Phe
noty
pic
Qua
lity
(PA
TO
)
Recognizing a new family of attributes (data, information artifacts, including images)
Anatomy Ontology(FMA*, CARO) Disease Ontology
(OGMS, IDO, HDO, HPO)
Images,Image Data, Image
Metadata …
Biological Process
Ontology (GO)
Assays
Cell Ontology(CL)
Subcellular Anatomy Ontology
(SAO)
Phenotypic QualityOntology(PATO)
Sequence Ontology
(SO)
Molecular Function Ontology
(GO)Protein Ontology(PRO)
Extension Strategy + Modular Organization
INDEPENDENT
CONTINUANT(~THING))
DEPENDENT CONTINUANT(~ATTRIBUTE)
INFORMATION
ARTIFACT (~DATA)
OCCURRENT(~PROCESS)
Basic Formal Ontology (BFO)
19
Structure of a typical investigation as viewed by OBI (from http://obi-ontology.org/page/Investigation)
The Ontology for Biomedical Investigations
specimen extraction purification imaging datacollection assay transformation
OBI Pipeline applied to Imaging Assays
22
need to extend this pipeline also to clinical diagnosis and treatment (from OGMS*)
*Ontology for General Medical Science
specimen extraction purification imaging datacollection assay transformation
need to extend this pipeline also to clinical diagnosis and treatment
28
http://purl.obolibrary.org/obo/IAO_0000064: algorithm
A list of ontologies using IAOAdverse Event Reporting Ontology (AERO)Bioinformatics Web Service OntologyBiological Collections Ontology (BCO)Chemical Methods Ontology (CHMO)Cognitive Paradigm Ontology (COGPO)Comparative Data Analysis Ontology Computational Neuroscience OntologyCore Clinical Protocol Ontology (C2PO)Document Act OntologyEagle-I Research Resource Ontology (ERO)The Email OntologyEmotion Ontology (MFOEM)Experimental Factor Ontology (EFO)Exposé OntologyIAO-IntelInfectious Disease Ontology (IDO)Influenza Research Database (IRD)Information Entity OntologyMental Functioning Ontology (MF)
Ontology for Biomedical InvestigationsOntology for Drug Discovery Investigations Ontology for General Medical Science (OGMS)Ontology for Newborn Screening Follow-up and Translational Research (ONSTR)Ontology of Clinical Research (OCRE)Ontology of Data Mining (OntoDM) Ontology of Medically Related Social Entities (OMRSE)Ontology of Vaccine Adverse Events Oral Health and Disease Ontology (OHDO)Population and Community OntologyProper Name OntologySemanticscience Integrated OntologySoftware Ontology (SWO)Translational Medicine Ontology (TMO)Twitter OntologyVaccine Ontology (VO)
Patient Demogra
phics Phenotype
(Disease, …)
Disease process
esData about all of
these things including
image data …Algorithms,
software,protocols, …
Instruments, Biomaterials,
FunctionsParameters, Assay types,
Statistics…
Anatomy
Histology
Genotype (GO)
Biological
processes (GO)
Chemistry
INDEPENDENT
CONTINUANT
(~THING))
DEPENDENT
CONTINUANT
(~ATTRIBUTE)
OCCURRENT
(~PROCESS)
IAO OBI
Basic Formal Ontology (BFO)
35
Patient Demogra
phics Phenotype
(Disease, …)
Disease process
esData about all of
these things including
image data …Algorithms,
software,protocols, …
Instruments, Biomaterials,
FunctionsParameters, Assay types,
Statistics…
Anatomy
Histology
Genotype (GO)
Biological
processes (GO)
Chemistry
INDEPENDENT
CONTINUANT
(~THING))
DEPENDENT
CONTINUANT
(~ATTRIBUTE)
OCCURRENT
(~PROCESS)
IAO OBI
Basic Formal Ontology (BFO)
36
CMPO
OBI-Imaging
BFO
37
Ontology for General Medical Science Cardiovascular Disease OntologyGenetic Disease OntologyCancer Disease OntologyGenetic Disease OntologyImmune Disease OntologyEnvironmental Disease OntologyOral Disease Ontology
Infectious Disease Ontology IDO Staph Aureus IDO MRSA IDO Australian MRSA IDO Australian Hospital MRSA …
patientOBI:0000093
pathology specimen
PIO:0000002
pathology slide
PIO:0000003
pathologyimage
PIO:0000001
pathologistPIO:0000004
softwarepipeline
OBI:0001943
histology assayOBI:0600020
annotationsvarious
automatedhistology assayPIO:0000005
annotationsvarious
RDFdatabase
slidepreparation
part of
part of
part of
output
output
input
input
agent
agent
slideimaging
specimencollection
Pathology Image Workflow