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

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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, 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. … 6

RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT 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) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO) Original OBO Foundry ontologies (Gene Ontology in yellow) 7

CONTINUANTOCCURRENT INDEPENDENTDEPENDENT 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) Cellular Process (GO) MOLECULE Molecule (ChEBI, SO, RNAO, PRO) Molecular Function (GO) Molecular Process (GO) rationale of OBO Foundry coverage GRANULARITY RELATION TO TIME 8

RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT 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) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO) Environment Ontology (EnvO) Environments 9

RELATION TO TIME CONTINUANT OCCURRENT GRANULARITY INDEPENDENT CONTINUANT DEPENDENT CONTINUANT 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) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO) Environment Ontology (ENVO) 10 Phenotypic Quality (PATO) Recognizing a new family of protocol-driven processes (investigation, assay, clinical trial …)

RELATION TO TIME CONTINUANT OCCURRENT GRANULARITY INDEPENDENT CONTINUANT DEPENDENT CONTINUANT INFORMATION ARTIFACT 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) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Images, Image Data, Flow Cytometry Data, … Molecular Process (GO) OBI: Imaging Environment Ontology (ENVO) 11 Phenotypic Quality (PATO) Recognizing a new family of information entities: data, publications, images, algorithms …

examples of BFO/OBO Foundry approach extended into other domains 12 NIF StandardNeuroscience Information Framework UNEP Ontology Framework United Nations Environment Program Ontologies IDO ConsortiumInfectious Disease Ontology Suite MilPortalIntelligence and Information Warfare Directorate, US Army cROPCommon Reference Ontologies for Plants

Common Reference Ontologies for Plants (cROP)

Introduction to Biomedical Ontology for Imaging Informatics Barry Smith, PhD, FACMI University at Buffalo May 11, 2015

RELATION TO TIME CONTINUANT OCCURRENT GRANULARITY INDEPENDENT CONTINUANT DEPENDENT CONTINUANT 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) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO) OBI: Imaging Ontology Branch Environment Ontology (ENVO) 15 Phenotypic Quality (PATO) 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 Quality Ontology (PATO) Sequence Ontology (SO) Molecular Function Ontology (GO) Protein Ontology (PRO) Extension Strategy + Modular Organization I NDEPENDENT C ONTINUANT (~T HING )) D EPENDENT C ONTINUANT (~A TTRIBUTE ) O CCURRENT (~P ROCESS ) Basic Formal Ontology (BFO) 16

Structure of a typical investigation as viewed by OBI (from The Ontology for Biomedical Investigations

RELATION TO TIME CONTINUANT OCCURRENT GRANULARITY INDEPENDENT CONTINUANT DEPENDENT CONTINUANT INFORMATION ARTIFACT 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) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Images, Image Data, Flow Cytometry Data, … Molecular Process (GO) OBI: Imaging Environment Ontology (ENVO) 18 Phenotypic Quality (PATO) 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 Quality Ontology (PATO) Sequence Ontology (SO) Molecular Function Ontology (GO) Protein Ontology (PRO) Extension Strategy + Modular Organization I NDEPENDENT C ONTINUANT (~T HING )) D EPENDENT C ONTINUANT (~A TTRIBUTE ) INFORMATION A RTIFACT (~D ATA ) O CCURRENT (~P ROCESS ) Basic Formal Ontology (BFO) 19

Structure of a typical investigation as viewed by OBI (from The Ontology for Biomedical Investigations

specimen extraction purification imaging data collection 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 data collection assay transformation need to extend this pipeline also to clinical diagnosis and treatment

24 Even here, things are not as bad as they seem

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28 obo/IAO_ http://purl.obolibrary.org/ obo/IAO_ : algorithm

IAO = Information Artifact Ontology: on-artifact-ontology/ 29

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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 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)

The Ontology for Biomedical Investigations 32

The Ontology for Biomedical Investigations 33

OBI and IAO 34

Patient Demograp hics Phenotype (Disease, …) Disease processes Data about all of these things including image data … Algorithms, software, protocols, … Instruments, Biomaterials, Functions Parameters, Assay types, Statistics … Anatomy Histology Genotype (GO) Biological processes (GO) Chemistry I NDEPENDENT C ONTINUANT (~T HING )) D EPENDENT C ONTINUANT (~A TTRIBUTE ) O CCURRENT (~P ROCESS ) IAOOBI Basic Formal Ontology (BFO) 35

Patient Demograp hics Phenotype (Disease, …) Disease processes Data about all of these things including image data … Algorithms, software, protocols, … Instruments, Biomaterials, Functions Parameters, Assay types, Statistics … Anatomy Histology Genotype (GO) Biological processes (GO) Chemistry I NDEPENDENT C ONTINUANT (~T HING )) D EPENDENT C ONTINUANT (~A TTRIBUTE ) O CCURRENT (~P ROCESS ) IAOOBI Basic Formal Ontology (BFO) 36 CMPO OBI- Imaging

BFO 37 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 …

patient OBI: pathology specimen PIO: pathology slide PIO: pathology image PIO: pathologist PIO: software pipeline OBI: histology assay OBI: annotations various automated histology assay PIO: annotations various RDF database slide preparation part of output input agent slide imaging specimen collection Pathology Image Workflow