Species-Neutral vs. Multi-Species Ontologies

Barry Smith

New York Times response

US DoD Civil Affairs strategy for non-classified information sharing

7

• DoD annual budget $800 billion• IT budget for HR alone: $6 billion• http://goo.gl/znpWk

RELATION TO TIME

GRANULARITY

CONTINUANT OCCURRENT

INDEPENDENT DEPENDENT

COMPLEX OFORGANISMS

Family, Community, Deme, Population

OrganFunction

(FMP, CPRO)

Population Phenotype

PopulationProcess

ORGAN ANDORGANISM

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)

MOLECULEMolecule

(CHEBI, SO,RNAO, PRO)

Molecular Function

(GO)

Molecular Process

(GO)Population-level ontologies 11

Environm

ent (EnvO

, EO

)

OBO Foundry approach extended into other domains

12

NIF Standard Neuroscience Information Framework

ISF Ontologies Integrated Semantic Framework for Clinical and Translational Science

OGMS and Extensions Ontology for General Medical Science

IDO Consortium Infectious Disease OntologycROP Common Reference

Ontologies for Plants

Anatomy Ontology(FMA*, CARO)

Environment

Ontology(EnvO)

Disease, Disorder and

Treatment (OGMS)

Biological Process

Ontology (GO*)

Cell Ontology

(CL)

CellularComponentOntology

(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 OntologyGenetic Disease OntologyCancer Disease OntologyGenetic Disease OntologyImmune Disease OntologyEnvironmental Disease OntologyOral Disease OntologyInfectious Disease Ontology…

OGMS

Cardiovascular Disease OntologyGenetic Disease OntologyCancer Disease OntologyGenetic Disease OntologyImmune Disease OntologyEnvironmental Disease OntologyOral Disease OntologyInfectious Disease Ontology…

BFO, OGMS, and IDO

• Material Entity• Disposition• Process

• Disorder• Disease• Disease Course

• Infection• Infectious Disease• Infectious Disease Course

OGMS

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 …

How IDO evolvesIDOCore

IDOSa

IDOHumanSa

IDORatSa

IDOStrep

IDORatStrep

IDOHumanStrep

IDOMRSA

IDOHumanBacterial

IDOAntibioticResistant

IDOMAL IDOHIVCORE 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: 10.1016/j.jbi.2007.07.007.

• PRO: sub-typing within the ontology– species neutral label

• mouse label• arabidopsis label• …

• IDO: Hasse diagram