Building Ontologies with Basic Formal Ontology

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Building Ontologies with Basic Formal Ontology

•   Barry Smith
• May 27, 2015

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• http//ontology.buffalo.edu/BOBFO

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(No Transcript)
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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.

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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, 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. I now have a much
  more positive story for my students.

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RELATION TO TIME GRANULARITY CONTINUANT CONTINUANT CONTINUANT CONTINUANT OCCURRENT
RELATION TO TIME GRANULARITY INDEPENDENT INDEPENDENT DEPENDENT DEPENDENT
ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality(PaTO) Biological Process (GO)
CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) Phenotypic Quality(PaTO) Biological Process (GO)
MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Function (GO) Molecular Process (GO)
Original OBO Foundry ontologies (Gene Ontology
in yellow)
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CONTINUANT CONTINUANT CONTINUANT CONTINUANT OCCURRENT
INDEPENDENT INDEPENDENT DEPENDENT DEPENDENT
ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality(PaTO) Organism-Level Process (GO)
CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) Phenotypic Quality(PaTO) Cellular Process (GO)
MOLECULE Molecule (ChEBI, SO, RNAO, PRO) Molecule (ChEBI, SO, RNAO, PRO) Molecular Function (GO) Molecular Function (GO) Molecular Process (GO)
rationale of OBO Foundry coverage
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RELATION TO TIME GRANULARITY CONTINUANT CONTINUANT CONTINUANT CONTINUANT CONTINUANT OCCURRENT
RELATION TO TIME GRANULARITY INDEPENDENT INDEPENDENT INDEPENDENT DEPENDENT DEPENDENT
ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality(PaTO) Biological Process (GO)
CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) Phenotypic Quality(PaTO) Biological Process (GO)
MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Function (GO) Molecular Process (GO)
Environments
Environment Ontology (EnvO)
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RELATION TO TIME CONTINUANT CONTINUANT CONTINUANT CONTINUANT CONTINUANT OCCURRENT OCCURRENT
GRANULARITY INDEPENDENT CONTINUANT INDEPENDENT CONTINUANT INDEPENDENT CONTINUANT DEPENDENT CONTINUANT DEPENDENT CONTINUANT OCCURRENT OCCURRENT
ORGAN AND ORGANISM Organism NCBI Taxonomy Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Biological Process (GO) Ontology for Biomedical Investigations (OBI)
CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) Biological Process (GO) Ontology for Biomedical Investigations (OBI)
MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Function (GO) Molecular Process (GO) Ontology for Biomedical Investigations (OBI)
Phenotypic Quality (PATO)
Environment Ontology (ENVO)
Recognizing a new family of protocol-driven
processes (investigation, assay, clinical trial )
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RELATION TO TIME CONTINUANT CONTINUANT CONTINUANT CONTINUANT CONTINUANT CONTINUANT OCCURRENT OCCURRENT
GRANULARITY INDEPENDENT CONTINUANT INDEPENDENT CONTINUANT INDEPENDENT CONTINUANT DEPENDENT CONTINUANT DEPENDENT CONTINUANT INFORMATION ARTIFACT OCCURRENT OCCURRENT
ORGAN AND ORGANISM Organism NCBI Taxonomy Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) IAO Software, Algorithms, Sequence Data, EHR Data Biological Process (GO) OBI
CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) IAO Software, Algorithms, Sequence Data, EHR Data Biological Process (GO) OBI
MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Function (GO) Images, Image Data, Flow Cytometry Data, Molecular Process (GO) OBI Imaging
Phenotypic Quality (PATO)
Environment Ontology (ENVO)
Recognizing a new family of information entities
data, publications, images, algorithms
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examples of BFO/OBO Foundry approach extended
into other domains
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
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• Common Reference Ontologies for Plants (cROP)

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 Introduction to Biomedical Ontology for Imaging
Informatics

•   Barry Smith, PhD, FACMI
• University at Buffalo
• May 11, 2015

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RELATION TO TIME CONTINUANT CONTINUANT CONTINUANT CONTINUANT CONTINUANT OCCURRENT OCCURRENT
GRANULARITY INDEPENDENT CONTINUANT INDEPENDENT CONTINUANT INDEPENDENT CONTINUANT DEPENDENT CONTINUANT DEPENDENT CONTINUANT OCCURRENT OCCURRENT
ORGAN AND ORGANISM Organism NCBI Taxonomy Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Biological Process (GO) Ontology for Biomedical Investigations (OBI)
CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) Biological Process (GO) Ontology for Biomedical Investigations (OBI)
MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Function (GO) Molecular Process (GO) OBI Imaging Ontology Branch
Phenotypic Quality (PATO)
Environment Ontology (ENVO)
Recognizing a new family of processes
(investigation, assay, protocol-driven process)
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Basic Formal Ontology (BFO)
Independent Continuant (Thing)) Dependent Continuant (Attribute) Occurrent (Process)
Anatomy Ontology (FMA, CARO) Disease Ontology (OGMS, IDO, HDO, HPO) Biological Processes Assays (Protocol-driven processes)
Cell Ontology (CL) Disease Ontology (OGMS, IDO, HDO, HPO) Biological Processes Assays (Protocol-driven processes)
Subcellular Anatomy Ontology (SAO) Phenotypic Quality Ontology(PATO) Biological Processes Assays (Protocol-driven processes)
Sequence Ontology (SO) Molecular Function Ontology (GO) Biological Processes Assays (Protocol-driven processes)
Protein Ontology (PRO) Molecular Function Ontology (GO) Biological Processes Assays (Protocol-driven processes)
Extension Strategy Modular
Organization
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The Ontology for Biomedical Investigations
Structure of a typical investigation as viewed by
OBI (from http//obi-ontology.org/page/Investigat
ion)
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RELATION TO TIME CONTINUANT CONTINUANT CONTINUANT CONTINUANT CONTINUANT CONTINUANT OCCURRENT OCCURRENT
GRANULARITY INDEPENDENT CONTINUANT INDEPENDENT CONTINUANT INDEPENDENT CONTINUANT DEPENDENT CONTINUANT DEPENDENT CONTINUANT INFORMATION ARTIFACT OCCURRENT OCCURRENT
ORGAN AND ORGANISM Organism NCBI Taxonomy Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Software, Algorithms Patient Demographic Data, EHR Data, Public Health Data, Biological Process (GO) OBI
CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) Software, Algorithms Patient Demographic Data, EHR Data, Public Health Data, Biological Process (GO) OBI
MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Function (GO) Images, Image Data, Flow Cytometry Data, Molecular Process (GO) OBI Imaging
Phenotypic Quality (PATO)
Environment Ontology (ENVO)
Recognizing a new family of attributes (data,
information artifacts, including images)
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Basic Formal Ontology (BFO)
Independent Continuant (Thing)) Dependent Continuant (Attribute) information Artifact (Data) Occurrent (Process)
Anatomy Ontology (FMA, CARO) Disease Ontology (OGMS, IDO, HDO, HPO) Images, Image Data, Image Metadata Biological Process Ontology (GO) Assays
Cell Ontology (CL) Disease Ontology (OGMS, IDO, HDO, HPO) Images, Image Data, Image Metadata Biological Process Ontology (GO) Assays
Subcellular Anatomy Ontology (SAO) Phenotypic Quality Ontology(PATO) Images, Image Data, Image Metadata Biological Process Ontology (GO) Assays
Sequence Ontology (SO) Molecular Function Ontology (GO) Images, Image Data, Image Metadata Biological Process Ontology (GO) Assays
Protein Ontology (PRO) Molecular Function Ontology (GO) Images, Image Data, Image Metadata Biological Process Ontology (GO) Assays
Extension Strategy Modular
Organization
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The Ontology for Biomedical Investigations
Structure of a typical investigation as viewed by
OBI (from http//obi-ontology.org/page/Investigat
ion)
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OBI Pipeline applied to Imaging Assays
specimen extraction
purification imaging
data collection
assay
transformation
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need to extend this pipeline also to clinical
diagnosis and treatment (from OGMS)
Ontology for General Medical Science
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need to extend this pipeline also to clinical
diagnosis and treatment
specimen extraction
purification imaging
data collection
assay
transformation
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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
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IAO Information Artifact Ontology

• https//code.google.com/p/information-artifact-ont
  ology/

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http//bioportal.bioontology.org/ontologies/IAO
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A list of ontologies using IAO
Adverse Event Reporting Ontology (AERO) Bioinformatics Web Service Ontology Biological Collections Ontology (BCO) Chemical Methods Ontology (CHMO) Cognitive Paradigm Ontology (COGPO) Comparative Data Analysis Ontology Computational Neuroscience Ontology Core Clinical Protocol Ontology (C2PO) Document Act Ontology Eagle-I Research Resource Ontology (ERO) The Email Ontology Emotion Ontology (MFOEM) Experimental Factor Ontology (EFO) Exposé Ontology IAO-Intel Infectious Disease Ontology (IDO) Influenza Research Database (IRD) Information Entity Ontology Mental Functioning Ontology (MF) Ontology for Biomedical Investigations Ontology 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 Ontology Proper Name Ontology Semanticscience Integrated Ontology Software Ontology (SWO) Translational Medicine Ontology (TMO) Twitter Ontology Vaccine Ontology (VO)
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The Ontology for Biomedical Investigations
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The Ontology for Biomedical Investigations
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OBI and IAO
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Basic Formal Ontology (BFO)
Independent Continuant (Thing)) Dependent Continuant (Attribute) Occurrent (Process) IAO OBI
Patient Demographics Phenotype (Disease, ) Disease processes Data about all of these things including image data Algorithms, software, protocols, Instruments, Biomaterials, Functions Parameters, Assay types, Statistics
Anatomy Phenotype (Disease, ) Disease processes Data about all of these things including image data Algorithms, software, protocols, Instruments, Biomaterials, Functions Parameters, Assay types, Statistics
Histology Genotype (GO) Biological processes (GO) Data about all of these things including image data Algorithms, software, protocols, Instruments, Biomaterials, Functions Parameters, Assay types, Statistics
Chemistry Genotype (GO) Biological processes (GO) Data about all of these things including image data Algorithms, software, protocols, Instruments, Biomaterials, Functions Parameters, Assay types, Statistics
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Basic Formal Ontology (BFO)
Independent Continuant (Thing)) Dependent Continuant (Attribute) Occurrent (Process) IAO OBI
Patient Demographics Phenotype (Disease, ) Disease processes Data about all of these things including image data Algorithms, software, protocols, Instruments, Biomaterials, Functions Parameters, Assay types, Statistics
Anatomy Phenotype (Disease, ) Disease processes Data about all of these things including image data Algorithms, software, protocols, Instruments, Biomaterials, Functions Parameters, Assay types, Statistics
Histology Genotype (GO) Biological processes (GO) Data about all of these things including image data Algorithms, software, protocols, Instruments, Biomaterials, Functions Parameters, Assay types, Statistics
Chemistry Genotype (GO) Biological processes (GO) Data about all of these things including image data Algorithms, software, protocols, Instruments, Biomaterials, Functions Parameters, Assay types, Statistics
CMPO
OBI-Imaging
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• BFO

Ontology for General Medical Science
Cardiovascular Disease Ontology Genetic Disease
Ontology Cancer Disease Ontology Genetic Disease
Ontology Immune Disease Ontology Environmental
Disease Ontology Oral Disease Ontology Infectious
Disease Ontology
IDO Staph Aureus IDO MRSA IDO
Australian MRSA IDO Australian
Hospital MRSA
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Pathology Image Workflow
output
agent
patient OBI0000093
pathologist PIO0000004
histology assay OBI0600020
annotations various
specimen collection
part of
input
pathology specimen PIO0000002
pathology slide PIO0000003
pathology image PIO0000001
RDF database
part of
slide preparation
slide imaging
input
part of
output
agent
software pipeline OBI0001943
automated histology assay PIO0000005
annotations various