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Introduction to Biomedical Ontology for Imaging Informatics

Barry Smith, PhD, FACMIUniversity at BuffaloMay 11, 2015National Center for Biomedical Ontology (NCBO)NIH Roadmap Center 2005-2015

Stanford University School of MedicineMayo ClinicUniversity at Buffalo23

Old biology data4/

MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDVDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDV

New biology data5http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=116006492sequence of X chromosome in bakers yeast

5How to do biology across the genome?MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDVMKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDVMKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDVMKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDV

6http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=116006492sequence of X chromosome in bakers yeast

6how to link the kinds of phenomena represented here7

http://ehealthadvice.info/what-is-crohns-disease/7or here8

https://meded.ucsd.edu/isp/2002/desai/adenocarcinoma.html8MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPIPSKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDSFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDVVAGEAASSNHHQKISRVTRKRPREPKSTNDILVAGQKLFGSSFEFRDLHQLRLCYEIYMADTPSVAVQAPPGYGKTELFHLPLIALASKGDVEYVSFLFVPYTVLLANCMIRLGRRGCLNVAPVRNFIEEGYDGVTDLYVGIYDDLASTNFTDRIAAWENIVECTFRTNNVKLGYLIVDEFHNFETEVYRQSQFGGITNLDFDAFEKAIFLSGTAPEAVADAALQRIGLTGLAKKSMDINELKRSEDLSRGLSSYPTRMFNLIKEKSEVPLGHVHKIRKKVESQPEEALKLLLALFESEPESKAIVVASTTNEVEELACSWRKYFRVVWIHGKLGAAEKVSRTKEFVTDGSMQVLIGTKLVTEGIDIKQLMMVIMLDNRLNIIELIQGVGRLRDGGLCYLLSRKNSWAARNRKGELPPKEGCITEQVREFYGLESKKGKKGQHVGCCGSRTDLSADTVELIERMDRLAEKQATASMSIVALPSSFQESNSSDRYRKYCSSDEDSNTCIHGSANASTNASTNAITTASTNVRTNATTNASTNATTNASTNASTNATTNASTNATTNSSTNATTTASTNVRTSATTTASINVRTSATTTESTNSSTNATTTESTNSSTNATTTESTNSNTSATTTASINVRTSATTTESTNSSTSATTTASINVRTSATTTKSINSSTNATTTESTNSNTNATTTESTNSSTNATTTESTNSSTNATTTESTNSNTSAATTESTNSNTSATTTESTNASAKEDANKDGNAEDNRFHPVTDINKESYKRKGSQMVLLERKKLKAQFPNTSENMNVLQFLGFRSDEIKHLFLYGIDIYFCPEGVFTQYGLCKGCQKMFELCVCWAGQKVSYRRIAWEALAVERMLRNDEEYKEYLEDIEPYHGDPVGYLKYFSVKRREIYSQIQRNYAWYLAITRRRETISVLDSTRGKQGSQVFRMSGRQIKELYFKVWSNLRESKTEVLQYFLNWDEKKCQEEWEAKDDTVVVEALEKGGVFQRLRSMTSAGLQGPQYVKLQFSRHHRQLRSRYELSLGMHLRDQIALGVTPSKVPHWTAFLSMLIGLFYNKTFRQKLEYLLEQISEVWLLPHWLDLANVEVLAADDTRVPLYMLMVAVHKELDSDDVPDGRFDILLCRDSSREVGELIGLFYNKTFRQKLEYLLEQISEVWLLPHWLDLANVEVLAADDTRVPLYMLMVAVHKELDSDDVPDGRFDILLCRDSSREVGELIGLFYNKTFRQKLEYLLEQISEVWLLPHWLDLANVEVLAADDTRVPLYMLMVAVHKELDSDDVPDGRFDILLCRDSSREVGE

9to data like this?http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=1160064929AnswerSemantic enhancement(Annotation, labeling, tagging )

An ontology is a controlled structured vocabulary to support annotation of data10QuestionsHow to build an ontology?

How to bring it about that all scientists in a domain use the same ontology aggressively to annotate their data?

How to bring it about that scientists in neighboring domains use ontologies for this purpose that are interoperable?

11Precursor: International System of Units (SI)

1212

By far the most successful: GO (Gene Ontology)

15GO provides a controlled vocabulary of terms for use in annotating (describing, tagging) datamulti-species, multi-disciplinary, open source

contributing to the cumulativity of scientific results obtained by distinct research communities

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Gene products involved in cardiac muscle development in humans1717Prerequisites for ontology successAggressive use in tagging data across multiple communitiesFeedback cycle between ontology editors and ontology users to ensure continuous updateLogically and biologically coherent definitions logical = to allow computational reasoning and quality assurance

18> $100 mill. invested in literature curation using GOover 200 million annotations relating gene products described in the UniProt, Ensembl and other databases to terms in the GO (Gigascience 3/1/4)experimental results reported in 52,000 scientific journal articles manually annotated by expert biologists using GO19GO is amazingly successful in overcoming problems of balkanizationbut it covers only generic biological entities of three sorts:cellular componentsmolecular functionsbiological processes

and it does not provide representations of diseases, symptoms, anatomy, pathways, 2020Ontology success stories, and some reasons for failure

So people started building the needed extra ontologies more or less at random21http://dbpedia.org/fct/images/lod-datasets_2009-03-27_colored.png21Reviewing ontologies which are candidates for the imaging frameworkB. Smith, J. Tomaszewski, and M. Gurcan, Biomedical Imaging Ontologies: A Survey and Proposal for Future Work, Journal of Pathology Informatics, in press2223

RadLex24

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QIBO

DICOM27

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Definition: Reaching a decision through the application of an algorithm designed to weigh the different factors involved.35

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.)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. 36 RELATION TO TIME

GRANULARITYCONTINUANTOCCURRENTINDEPENDENTDEPENDENTORGAN ANDORGANISMOrganism(NCBITaxonomy)Anatomical Entity(FMA, CARO)OrganFunction(FMP, CPRO)Phenotypic Quality(PaTO)Biological Process(GO)CELL AND CELLULAR COMPONENTCell(CL)Cellular Component(FMA, GO)Cellular Function(GO)MOLECULEMolecule(ChEBI, SO,RnaO, PrO)Molecular Function(GO)Molecular Process(GO)Original OBO Foundry ontologies (Gene Ontology in yellow)3838CHEBI: Chemical Entities of Biological InterestCL: Cell OntologyGO: Gene OntologyOBI: Ontology for Biomedical InvestigationsPATO: Phenotypic Quality OntologyPO: Plant OntologyPATO: Phenotypic Quality OntologyPRO: Protein OntologyXAO: Xenopus Anatomy OntologyZFA: Zebrafish Anatomy Ontology http://obofoundry.org3939Anatomy Ontology(FMA*, CARO)Disease Ontology (OGMS, IDO, HDO, HPO)Biological Process Ontology (GO)Cell Ontology(CL)Subcellular Anatomy Ontology (SAO)Phenotypic QualityOntology(PATO)Sequence Ontology (SO)Molecular Function Ontology(GO)Protein Ontology(PRO) Extension Strategy + Modular Organizationtop level

mid-level

domain levelIndependent Continuant(~Thing))Dependent Continuant(~Attribute)Occurrent(~Process)Basic Formal Ontology (BFO)40 40* = dedicated NIH fundingExample: The Cell Ontology

nationalcenter forontologicalresearchnationalcenter forontologicalresearchNCOR

CONTINUANTOCCURRENTINDEPENDENTDEPENDENTORGAN ANDORGANISMOrganism(NCBITaxonomy)Anatomical Entity(FMA, CARO)OrganFunction(FMP, CPRO)Phenotypic Quality(PaTO)Organism-Level Process(GO)CELL AND CELLULAR COMPONENTCell(CL)Cellular Component(FMA, GO)Cellular Function(GO)Cellular Process(GO)MOLECULEMolecule(ChEBI, SO,RNAO, PRO)Molecular Function(GO)Molecular Process(GO)rationale of OBO Foundry coverage GRANULARITYRELATION TO TIME42 RELATION TO TIME

GRANULARITYCONTINUANTOCCURRENTINDEPENDENTDEPENDENTORGAN ANDORGANISMCELL AND CELLULAR COMPONENTMOLECULERationale of OBO Foundry coverage4343 RELATION TO TIME

GRANULARITYCONTINUANTOCCURRENTINDEPENDENTDEPENDENTORGAN ANDORGANISMOrganism(NCBITaxonomy)Anatomical Entity(FMA, CARO)OrganFunction(FMP, CPRO)Phenotypic Quality(PaTO)Biological Process(GO)CELL AND CELLULAR COMPONENTCell(CL)Cellular Component(FMA, GO)Cellular Function(GO)MOLECULEMolecule(ChEBI, SO,RnaO, PrO)Molecular Function(GO)Molecular Process(GO)Environment Ontology (EnvO)Environments 4444OBO Foundry PrinciplesThe ontology is open and able to be integrated freely with other resourcesIt is instantiated in a common formal language.Developers commit to working to ensure that, for each domain, there is community convergence on a single ontology,and agree in advance to collaborate with developers of ontologies in adjacent domains.45OBO Foundry PrinciplesModular development to guarantee additivity of annotationsSingle locus of authority (for editing, error tracking, )Common architecture (BFO)Common governance (coordinating editors)Common training expertise is portable, lessons learned through practice can be pooled

46OBO Foundry approach extended into other domains47NIF Standard

Neuroscience Information Framework IDO ConsortiumInfectious Disease Ontology SuitecROPCommon Reference Ontologies for PlantsUnited Nations Environment ProgramUNEP Ontology Framework47

48IMAGING RELATION TO TIME CONTINUANTOCCURRENTGRANULARITYINDEPENDENTCONTINUANTDEPENDENT CONTINUANTORGAN ANDORGANISMOrganismNCBITaxonomyAnatomical Entity(FMA, CARO)OrganFunction(FMP, CPRO)Biological Process(GO)

Ontology for Biomedical Investigations(OBI)CELL AND CELLULAR COMPONENTCell(CL)Cellular Component(FMA, GO)Cellular Function(GO)MOLECULEMolecule(ChEBI, SO,RnaO, PrO)Molecular Function(GO)Molecular Process(GO)OBI: Imaging Ontology BranchEnvironment Ontology (ENVO) 49Phenotypic Quality (PATO)Recognizing a new family of processes (investigation, assay, protocol-driven process)49Anatomy 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 OrganizationIndependent Continuant(~Thing))Dependent Continuant(~Attribute)Occurrent(~Process)Basic Formal Ontology (BFO)50 50* = dedicated NIH funding

Structure of a typical investigation as viewed by OBI (from http://obi-ontology.org/page/Investigation)The Ontology for Biomedical Investigations RELATION TO TIME CONTINUANTOCCURRENTGRANULARITYINDEPENDENTCONTINUANTDEPENDENT CONTINUANTINFORMATION ARTIFACTORGAN ANDORGANISMOrganismNCBITaxonomyAnatomical Entity(FMA, CARO)OrganFunction(FMP, CPRO)Software, Algorithms

Patient Demographic Data,EHR Data, Public Health Data, Biological Process(GO)

OBICELL AND CELLULAR COMPONENTCell(CL)Cellular Component(FMA, GO)Cellular Function(GO)MOLECULEMolecule(ChEBI, SO,RnaO, PrO)Molecular Function(GO)Images,Image Data, Flow Cytometry Data, Molecular Process(GO)

OBI:ImagingEnvironment Ontology (ENVO) 52Phenotypic Quality (PATO)Recognizing a new family of attributes (data, information artifacts, including images)52Anatomy Ontology(FMA*, CARO)Disease Ontology (OGMS, IDO, HDO, HPO)Images,Image Data, Image Metadata Biological Process Ontology (GO)

AssaysCell Ontology(CL)Subcellular Anatomy Ontology (SAO)Phenotypic QualityOntology(PATO)Sequence Ontology (SO)Molecular Function Ontology(GO)Protein Ontology(PRO) Extension Strategy + Modular OrganizationIndependent Continuant(~Thing))Dependent Continuant(~Attribute)information Artifact (~Data)Occurrent(~Process)Basic Formal Ontology (BFO)53 53* = dedicated NIH funding

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 transformationOBI Pipeline applied to Imaging Assayshttp://www.plosone.org/article/info:doi/10.1371/journal.pone.0099979Dugan VG, Emrich SJ, Giraldo-Caldern GI, Harb OS, et al. (2014) Standardized Metadata for Human Pathogen/Vector Genomic Sequences. PLoS ONE 9(6): e99979. doi:10.1371/journal.pone.0099979

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56need to extend this pipeline also to clinical diagnosis and treatment (from OGMS*)*Ontology for General Medical Science56

specimen extraction purification imaging datacollection assay transformationneed to extend this pipeline also to clinical diagnosis and treatment

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099979Dugan VG, Emrich SJ, Giraldo-Caldern GI, Harb OS, et al. (2014) Standardized Metadata for Human Pathogen/Vector Genomic Sequences. PLoS ONE 9(6): e99979. doi:10.1371/journal.pone.0099979

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Even here, things are not as bad as they seem59

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http://purl.obolibrary.org/obo/IAO_0000064: algorithmIAO = Information Artifact Ontology:

https://code.google.com/p/information-artifact-ontology/6364http://bioportal.bioontology.org/ontologies/IAO

http://bioportal.bioontology.org/ontologies/IAO/?p=classes&conceptid=http%3A%2F%2Fwww.ifomis.org%2Fbfo%2F1.1%23Entity64A 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)Expos 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)

The Ontology for Biomedical Investigations

66The Ontology for Biomedical Investigations67

OBI and IAO 68

Patient DemographicsPhenotype(Disease, )Disease processesData about all of these things includingimage data Algorithms, software,protocols, Instruments, Biomaterials, FunctionsParameters, Assay types, Statistics AnatomyHistologyGenotype (GO)Biological processes (GO)ChemistryIndependent Continuant(~Thing))Dependent Continuant(~Attribute)Occurrent(~Process)IAOOBIBasic Formal Ontology (BFO)69 69* = dedicated NIH fundingPatient DemographicsPhenotype(Disease, )Disease processesData about all of these things includingimage data Algorithms, software,protocols, Instruments, Biomaterials, FunctionsParameters, Assay types, Statistics AnatomyHistologyGenotype (GO)Biological processes (GO)ChemistryIndependent Continuant(~Thing))Dependent Continuant(~Attribute)Occurrent(~Process)IAOOBIBasic Formal Ontology (BFO)70 CMPOOBI-Imaging70* = dedicated NIH fundingBFO71Ontology for General Medical Science Cardiovascular Disease OntologyGenetic Disease OntologyCancer Disease OntologyGenetic Disease OntologyImmune Disease OntologyEnvironmental Disease OntologyOral Disease OntologyInfectious Disease Ontology

IDO Staph Aureus IDO MRSA IDO Australian MRSA IDO Australian Hospital MRSA