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Presentation made during the Infectious Disease Ontology workshop, December 9th 2010, Baltimore, USA.
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PHAC/CIHRInfluenzaResearchNetwork
MélanieCourtot,BCCRC,VancouverCA
NCBO/IDOworkshopBal$more▪December9th2010
PCIRNmission
• Canadianna$onalnetworkofkeyinfluenzavaccineresearchers.
• Developsandtestsmethodologies/methodsrelatedtotheevalua$onofpandemicinfluenzavaccinesastheypertaintosafety,immunogenicityandeffec$veness,andprogramimplementa$onandevalua$on.
• hJp://www.pcirn.ca/
PCIRNstructure
• ThemeI:RapidTrials• ThemeII:RapidImplementa$on
• ThemeIII:VaccineCoverage
• ThemeIV:VaccineSafety
• ThemeV:VaccineEffec$veness
• +supportgroups
Morethan90inves$gatorsacross30ins$tu$ons
ITsupportgroup
• Aim:tostandardizedata(samevariables,samecoding)andtoassuretheuseofstandardvalidateddefini$ons–ifpossiblefromanontologicalresource.
• Objec$veistoensuredataqualityandconsistencyacrossthenetwork.
Standardiza$on
• Determinecontrolledvocabulary• MinimumInforma$on:checklisttoiden$fygap
• Iden$fyexis$ngontologiestermssuppor$ngthenetwork,andcontributeto/developresourcesasneeded
Ontologies
• Areasaddressed:Demographics,Labshippingandresultsinforma$on,Vaccinedetails,Exposure,Specificity
• Exis$ngrelevantresources:IDO(InfluenzaandVaccineOntology),OBI(OntologyforBiomedicalInves$ga$ons),OGMS(OntologyforGeneralMedicalScience)…
Neuraminidasetyping
• FLU_0000779,“Anassaywhichaimsatdeterminingtheneuraminidasetypeofaninfluenzavirus”
assay(OBI_0000070)and(has_specified_outputsome
('measurementdatum'(IAO_0000409)and('isabout'someneuraminidase(FLU_0000753))))
InfluenzaOntology
• Influenzaneuraminidase(FLU_0001034)is_aneuraminidase(FLU_0000753)part_ofsomeInfluenzavirion(FLU_0000751)
• Influenzavirionis_avirion(IDO_0000508)• Neuraminidaseis_aprotein(PRO_000000001)whichhas_func2onsomecatalyFcacFvity(GO_0003824)
• Infersis_aenzyme(OBI_0000427)
ViralRNAextrac$on
• viralRNAextracFon(FLU_0000829)is_aRNAextracFon(OBI_0666666)
• has_specified_inputsomeViruses(NCBITaxon_10239)
• has_specified_outputsomeribonucleicacids(ChEBI_33697)
• [..]sequencingassay(OBI_0600047)[..]GenBanksubmission
VaccineOntology
• Canadianvaccinesinforma$on– Manufacturer
– Vaccinetype(eginac$vated)– Adjuvant,preserva$ves– Poten$alallergens– Routeofadministra$on– Doseinforma$on– …
Vaxigrip
• has_partneomycin(ChEBI_44577)and(has_rolesome'vaccineallergenrole'))
• has_partthimerosalvaccinepreserva$ve– 'vaccineaddi$ve'and(has_rolesome'vaccinepreserva$verole')
– has_partsomethimerosal(ChEBI_9546)
• IntramuscularinjecFon(OBI_0000934)(throughskeletalmuscleFssue(FMA_14069))
• […]
VO–VaccineOntology
AdvantagesofusingIDO
• Lessworkforme• Commoninfrastructure
• Collabora$veplalorm
• Setofresourcesfollowingsimilarguidelinesanddevelopmentprinciples
Thankyou
• OBI,IAO,OGMSandIDOteams
• OBOFoundry• PHAC/CIHRInfluenzaResearchNetwork