Species-Neutral vs. Multi-Species Ontologies Barry Smith.

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Presentation transcript:

Species-Neutral vs. Multi-Species Ontologies Barry Smith

New York Times response

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RELATION TO TIME GRANULARITY CONTINUANT OCCURRE NT INDEPENDENTDEPENDENT COMPLEX OF ORGANISMS Family, Community, Deme, Population Organ Function (FMP, CPRO) Population Phenotype Population Process ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) 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) Population-level ontologies 11 Environment (EnvO, EO)

OBO Foundry approach extended into other domains 12 NIF StandardNeuroscience Information Framework ISF OntologiesIntegrated Semantic Framework for Clinical and Translational Science OGMS and ExtensionsOntology for General Medical Science IDO ConsortiumInfectious Disease Ontology cROPCommon Reference Ontologies for Plants

Anatomy Ontology (FMA*, CARO) Environment Ontology (EnvO) Disease, Disorder and Treatment (OGMS) Biological Process Ontology (GO*) Cell Ontology (CL) Cellular Component Ontology (FMA*, GO*) Phenotypic Quality Ontology (PaTO) CHEBI Sequence Ontology (SO*) Molecular Function (GO*) Protein Ontology (PRO*) Extension Strategy – Downward Population 14 top level mid-level domain level Information Artifact Ontology (IAO) Ontology for Biomedical Investigations (OBI) Spatial Ontology (BSPO) Basic Formal Ontology (BFO)

OGMS Downward Population Hub-Spokes Strategy

OGMS Cardiovascular Disease Ontology Genetic Disease Ontology Cancer Disease Ontology Genetic Disease Ontology Immune Disease Ontology Environmental Disease Ontology Oral Disease Ontology Infectious Disease Ontology …

OGMS Cardiovascular Disease Ontology Genetic Disease Ontology Cancer Disease Ontology Genetic Disease Ontology Immune Disease Ontology Environmental Disease Ontology Oral Disease Ontology Infectious Disease Ontology …

BFO, OGMS, and IDO Material Entity Disposition Process Disorder Disease Disease Course Infection Infectious Disease Infectious Disease Course

OGMS 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 …

How IDO evolves IDOCore IDOSa IDOHumanSa IDORatSa IDOStrep IDORatStrep IDOHumanStrep IDOMRSA IDOHumanBacterial IDOAntibioticResistant IDOMALIDOHIV CORE and SPOKES: Domain ontologies SEMI-LATTICE: By subject matter experts in different communities of interest. IDOFLU 20

Options for multi-species GO: scrambled up Kuśnierczyk W. Taxonomy-based partitioning of the Gene Ontology. Journal of Biomedical Informatics. 2008;41:282–292. doi: /j.jbi PRO: sub-typing within the ontology – species neutral label mouse label arabidopsis label … IDO: Hasse diagram