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Draft Ontologies

Draft Ontologies. TVFac (Toxin and Virulence Factors) Los Alamos National Laboratory (LANL) Chris Stubben, Murray Wolinsky Antibiotic Ontology LANL Jian Song, Murray Wolinsky Gemina/IDO (Infectious Disease Ontology) Institute of Genome Sciences (IGS) U. Maryland Lynn Schriml

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Draft Ontologies

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  1. Draft Ontologies • TVFac (Toxin and Virulence Factors) • Los Alamos National Laboratory (LANL) • Chris Stubben, Murray Wolinsky • Antibiotic Ontology • LANL • Jian Song, Murray Wolinsky • Gemina/IDO (Infectious Disease Ontology) • Institute of Genome Sciences (IGS) U. Maryland • Lynn Schriml • PAMGO/Pathema • IGS • Michelle Gwinn Giglio • What are the core/shared terms between these ontologies?

  2. Drug Resistance Toxins GOPATOSequence OntologyTaxon IDsChemBIMESH Starting Ontologies BVF (Gemina) TVFac GO(PAMGO)

  3. Virulence or Pathogenesis? • Virulence and pathogenesis are not quite the same thing • Virulence is often viewed from the point of view of the pathogen • Pathogenesis from its effect on the host • Virulence and pathogenicity are not quite the same thing • Pathogenicity is the capacity of the pathogen to cause damage to the host • Virulence is the relative capacity to cause damage • Pathogenicity islands are contiguous clusters of genes that are required for virulence and are not found in closely related bacteria • Virulence factor is a component that permits pathogenicity

  4. VFO Test Case: Vibrio cholerae Toxins • Can we identify and annotate all known cholera toxins from databases and scientific literature them with existing and possible ontology terms? • What is a toxin? • A protein that directly causes disease when introduced to a host • Antibiotics are toxins, just toxins to other bacteria • Need to capture the pathogen-host interaction • The toxin and the host

  5. Vibrio cholerae Toxins • Examples of toxins: • cholera toxin subunit A (ctxA) • accessory cholera enterotoxin (ace) • hemolysin (hlyA) • hemagluttinin protease (hap) • Examples of non-toxins with toxin in their names that are virulence factors: • cholera toxin subunit B (ctxB) - delivery for ctxA • toxin coregulated pilin (tcpA) - adhesion • cholera toxin-positive regulatory protein (toxR) - transcription regulator • antitoxin-encoding gene (higA) - protection to ctxA Is higA a virulence factor?

  6. Minimum Information about Pathogens (MIP) • Minimum information (MI) checklists ensure that descriptions of methods, data and analyses support the unambiguous interpretation, corroboration and reuse of data • Many journals now require that authors reporting microarray-based experiments make available the metadata described by the Minimum Information about a Microarray Experiment (MIAME) checklist • MITRE is currently involved in the Minimum Information about a Genome Sequence/Minimum Information about a Metagenome Sequence (MIGS/MIMS) effort

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