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

Review of existing image ontologies B. Smith, et al., “Biomedical Imaging Ontologies: A Survey and Proposal for Future Work”, Journal of Pathology Informatics, 2015Biomedical Imaging Ontologies: A Survey and Proposal for Future Work 2

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RadLex 4

5 QIBO

DICOM

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14 Definition: Reaching a decision through the application of an algorithm designed to weigh the different factors involved.

15 Definition: Reaching a decision through the application of an algorithm designed to weigh the different factors involved. Confuses an algorith with an act of reaching a decision Defines ‘algorithm’ as a special kind of application of an algorithm. (This is worse than circular.)

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) 16 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) 17

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) 19 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) 20

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

23 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

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

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

IAO = Information Artifact Ontology: on-artifact-ontology/ 30

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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 33

The Ontology for Biomedical Investigations 34

OBI and IAO 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

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) 37 CMPO OBI- Imaging