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PHAC/CIHR Influenza Research Network

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Presentation made during the Infectious Disease Ontology workshop, December 9th 2010, Baltimore, USA.

Published in: Health & Medicine
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PHAC/CIHR Influenza Research Network

  1. 1. PHAC/CIHR
Influenza
Research
Network
 NCBO/IDO
workshop
 Bal$more
▪
December
9th
2010
 Mélanie
Courtot,
BCCRC,
Vancouver
CA

  2. 2. PCIRN
mission
•  Canadian
na$onal
network
of
key
influenza
 vaccine
researchers.

•  Develops
and
tests
methodologies/methods
 related
to
the
evalua$on
of
pandemic
 influenza
vaccines
as
they
pertain
to
safety,
 immunogenicity
and
effec$veness,
and
 program
implementa$on
and
evalua$on.

•  hJp://www.pcirn.ca/

  3. 3. PCIRN
structure
•  Theme
I:
Rapid
Trials
•  Theme
II:
Rapid
Implementa$on
•  Theme
III:
Vaccine
Coverage
•  Theme
IV:
Vaccine
Safety
•  Theme
V:
Vaccine
Effec$veness
•  +
support
groups
More
than
90
inves$gators
across
30
ins$tu$ons


  4. 4. IT
support
group
•  Aim:
to
standardize
data
(same
variables,
 same
coding)
and
to
assure
the
use
of
 standard
validated
defini$ons
–
if
possible
 from
an
ontological
resource.


•  Objec$ve
is
to
ensure
data
quality
and
 consistency
across
the
network.

  5. 5. Standardiza$on
•  Determine
controlled
vocabulary
•  Minimum
Informa$on:
checklist
to
iden$fy
 gap
•  Iden$fy
exis$ng
ontologies
terms
suppor$ng
 the
network,
and
contribute
to/develop
 resources
as
needed

  6. 6. Ontologies
•  Areas
addressed:
Demographics,
Lab
shipping
 and
results
informa$on,
Vaccine
details,
 Exposure,
Specificity
•  Exis$ng
relevant
resources:
IDO
(Influenza
and
 Vaccine
Ontology),
OBI
(Ontology
for
 Biomedical
Inves$ga$ons),
OGMS
(Ontology
 for
General
Medical
Science)…

  7. 7. Neuraminidase
typing
•  FLU_0000779,
“An
assay
which
aims
at
 determining
the
neuraminidase
type
of
an
 influenza
virus”
assay
(OBI_0000070)and
(has_specified_output
 some

(measurement
datum
(IAO_0000409)
and
(is
 about
some
neuraminidase
(FLU_0000753))))

  8. 8. Influenza
Ontology
•  Influenza
neuraminidase
(FLU_0001034)
is_a
 neuraminidase
(FLU_0000753)
part_of
some
 Influenza
virion
(FLU_0000751)
•  Influenza
virion
is_a
virion
(IDO_0000508)
•  Neuraminidase
is_a
protein
(PRO_000000001)
 which
has_func2on
some
catalyFc
acFvity
 (GO_0003824)

•  Infers
is_a
enzyme
(OBI_0000427)

  9. 9. Viral
RNA
extrac$on
•  viral
RNA
extracFon
(FLU_0000829)
is_a
RNA
 extracFon
(OBI_0666666)
•  has_specified_input
some
Viruses
 (NCBITaxon_10239)
•  has_specified_output
some
ribonucleic
acids
 (ChEBI_33697)
•  [..]
sequencing
assay
(OBI_0600047)
[..]
 GenBank
submission

  10. 10. Vaccine
Ontology
•  Canadian
vaccines
informa$on
 –  Manufacturer
 –  Vaccine
type
(eg
inac$vated)
 –  Adjuvant,
preserva$ves
 –  Poten$al
allergens
 –  Route
of
administra$on
 –  Dose
informa$on
 –  …

  11. 11. Vaxigrip
•  has_part
neomycin
(ChEBI_44577)
and
 (has_role
some
vaccine
allergen
role))
•  has_part
thimerosal
vaccine
preserva$ve
 –  vaccine
addi$ve
and
(has_role
some
vaccine
 preserva$ve
role)
 –  has_part
some
thimerosal
(ChEBI_9546)
•  Intramuscular
injecFon
(OBI_0000934)
 (through
skeletal
muscle
Fssue
(FMA_14069))
•  […]

  12. 12. VO
–
Vaccine
Ontology

  13. 13. Advantages
of
using
IDO
•  Less
work
for
me

•  Common
infrastructure
•  Collabora$ve
plalorm
•  Set
of
resources
following
similar
guidelines
 and
development
principles

  14. 14. Thank
you
•  OBI,
IAO,
OGMS
and
IDO
teams
•  OBO
Foundry
•  PHAC/CIHR
Influenza
Research
Network


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