Building Ontologies with Basic Formal Ontology Barry Smith May 27, 2015.

Building Ontologies with Basic Formal Ontology

Barry SmithMay 27, 2015

http://ontology.buffalo.edu/BOBFO 2

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.

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Ontology success stories, and some reasons for failure

Linked Open Data, from Musicbrainz to Mouse Genome Informatics

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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. …

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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



ORGAN ANDORGANISM

Organism(NCBI

Taxonomy)

Anatomical Entity

(FMA, CARO)

OrganFunction


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 Process

(GO)

rationale of OBO Foundry coverage

GRANULARITY

RELATION TO TIME

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RELATION TO TIME

GRANULARITY



ORGAN ANDORGANISM

Organism(NCBI

Taxonomy)


OrganFunction


Quality(PaTO)

Biological Process

(GO)

CELL AND CELLULAR

COMPONENT

Cell(CL)

Cellular Component(FMA, GO)

Cellular Function

(GO)

MOLECULEMolecule



Molecular Process

(GO)Environment Ontology (EnvO)

En

viro

nm

ents

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RELATION TO TIME

CONTINUANT

OCCURRENTGRANULARITY

INDEPENDENTCONTINUANT

DEPENDENT CONTINUANT

ORGAN ANDORGANISM

Organism

NCBITaxonom

y


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


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



INFORMATION ARTIFACT

ORGAN ANDORGANISM

Organism

NCBITaxonom

y


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


Molecular Function

(GO)

Images,Image Data,

Flow Cytometry

Data, …

Molecular Process

(GO)OBI:

Imaging

Env

iron

men

t Ont

olog

y (E

NV

O)

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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

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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

Common Reference Ontologies for Plants (cROP)

Introduction to Biomedical Ontology for Imaging Informatics

Barry Smith, PhD, FACMIUniversity at Buffalo

May 11, 2015

RELATION TO TIME

CONTINUANT

OCCURRENT

GRANULARITY



ORGAN ANDORGANISM

Organism

NCBITaxonom

y


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


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)

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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



INFORMATION ARTIFACT

ORGAN ANDORGANISM

Organism

NCBITaxonom

y


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


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)


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Structure of a typical investigation as viewed by OBI (from http://obi-ontology.org/page/Investigation)


specimen extraction purification imaging datacollection assay transformation

OBI Pipeline applied to Imaging Assays

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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

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Even here, things are not as bad as they seem

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http://purl.obolibrary.org/obo/IAO_0000064: algorithm

http://purl.obolibrary.org/obo/IAO_0000064



IAO = Information Artifact Ontology:

https://code.google.com/p/information-artifact-ontology/

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http://bioportal.bioontology.org/ontologies/IAO

http://bioportal.bioontology.org/ontologies/IAO

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)


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OBI and IAO

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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


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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


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CMPO

OBI-Imaging

BFO

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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

Building Ontologies with Basic Formal Ontology Barry Smith May 27, 2015.

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