Species-Neutral vs. Multi-Species Ontologies - PowerPoint PPT Presentation

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Species-Neutral vs. Multi-Species Ontologies

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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 ... arabidopsis label ... – PowerPoint PPT presentation

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Title: Species-Neutral vs. Multi-Species Ontologies


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

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New York Times response
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  • US DoD Civil Affairs strategy for non-classified
    information sharing

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

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RELATION TO TIME GRANULARITY CONTINUANT CONTINUANT CONTINUANT CONTINUANT CONTINUANT OCCURRENT
RELATION TO TIME GRANULARITY INDEPENDENT INDEPENDENT INDEPENDENT DEPENDENT DEPENDENT
COMPLEX OF ORGANISMS Family, Community, Deme, Population Family, Community, Deme, Population Organ Function (FMP, CPRO) Population Phenotype Population Process
ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality(PaTO) Biological Process (GO)
CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) Phenotypic Quality(PaTO) Biological Process (GO)
MOLECULE Molecule (CHEBI, SO, RNAO, PRO) Molecule (CHEBI, SO, RNAO, PRO) Molecule (CHEBI, SO, RNAO, PRO) Molecular Function (GO) Molecular Function (GO) Molecular Process (GO)
Environment (EnvO, EO)
Population-level ontologies
12
OBO Foundry approach extended into other domains
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 Ontology
cROP Common Reference Ontologies for Plants
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top level mid-level domain level
Basic Formal Ontology (BFO)
Information Artifact Ontology (IAO) Ontology for Biomedical Investigations (OBI) Spatial Ontology (BSPO)
Anatomy Ontology (FMA, CARO) Anatomy Ontology (FMA, CARO) Environment Ontology (EnvO) Disease, Disorder and Treatment (OGMS) Biological Process Ontology (GO)
Cell Ontology (CL) Cellular Component Ontology (FMA, GO) Environment Ontology (EnvO) Disease, Disorder and Treatment (OGMS) Biological Process Ontology (GO)
Cell Ontology (CL) Cellular Component Ontology (FMA, GO) Environment Ontology (EnvO) Phenotypic Quality Ontology(PaTO) Biological Process Ontology (GO)
CHEBI CHEBI CHEBI Phenotypic Quality Ontology(PaTO) Biological Process Ontology (GO)
Sequence Ontology (SO) Sequence Ontology (SO) Sequence Ontology (SO) Molecular Function (GO) Biological Process Ontology (GO)
Protein Ontology (PRO) Protein Ontology (PRO) Protein Ontology (PRO) Molecular Function (GO) Biological Process Ontology (GO)
Extension Strategy Downward
Population
15
OGMS
Downward Population Hub-Spokes Strategy
16
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
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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
18
BFO, OGMS, and IDO
  • Material Entity
  • Disposition
  • Process
  • Disorder
  • Disease
  • Disease Course
  • Infection
  • Infectious Disease
  • Infectious Disease Course

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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
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How IDO evolves
IDOCore
IDOMAL
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
21
  • Options for multi-species
  • GO scrambled up
  • Kusnierczyk W. Taxonomy-based partitioning of the
    Gene Ontology. Journal of Biomedical
    Informatics. 200841282292. 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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