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Species-Neutral vs. Multi-Species Ontologies

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).

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Species-Neutral vs. Multi-Species Ontologies

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

  2. New York Times response

  3. US DoD Civil Affairs strategy for non-classified information sharing

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

  5. Environment (EnvO, EO) Population-level ontologies

  6. OBO Foundry approach extended into other domains

  7. top level mid-level domain level Basic Formal Ontology (BFO) Extension Strategy – Downward Population

  8. OGMS Downward Population Hub-Spokes Strategy

  9. 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 …

  10. 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 …

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

  12. 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 …

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

  14. 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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