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Species-Neutral vs. Multi-Species Ontologies. Barry Smith. New York Times response. US DoD Civil Affairs strategy for non-classified information sharing . DoD annual budget $800 billion IT budget for HR alone: $6 billion http://goo.gl/znpWk. Environment (EnvO, EO). - PowerPoint PPT Presentation
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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
COMPONENTCell(CL)
Cellular Component(FMA, GO)
Cellular Function
(GO)
MOLECULEMolecule
(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 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
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