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?
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© 2006 The MITRE Corporation. All rights reserved
Starting Ontologies
BVF (Gemina)
TVFac
GO(PAMGO)
Drug Resistance
Toxins
GO
PATO
Sequence Ontology
Taxon IDs
ChemBI
MESH
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© 2006 The MITRE Corporation. All rights reserved
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
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© 2006 The MITRE Corporation. All rights reserved
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
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© 2006 The MITRE Corporation. All rights reserved
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?
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© 2006 The MITRE Corporation. All rights reserved
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 microarraybased 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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© 2006 The MITRE Corporation. All rights reserved