vectorbase invertebrate vectors of human pathogens
Post on 19-Dec-2015
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VectorBaseInvertebrate Vectors of Human Pathogens
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Lots of data out there…Data on: Distribution of vectors and their ecology Insecticide resistance Transmission capacity
For diseases:Malaria, Chagas, Dengue, Lymph. filariasis, etc.
Projects funded by: Innovative Vector Control Consortium - IVCC The WHO/Gates Foundation Vector Biology and Control Project - VBC African Network on Vector Research - ANVR Marathon Oil (and other private investors) And several more, including national programmes
Problems:Fragmentation of data; Secrecy; Independence; “Dialects” and syntax; etc.
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Intelligent Databases
Open access
Intelligent Databases
Open access
The answer, is...
InteroperabilityInteroperability Efficient searchesEfficient searches
Decision Support SystemsDecision Support Systems
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3610 (2392 unique)3610 (2392 unique)
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IRBase
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The example of Insecticide Resistance:
Aedes aegypti, 2098 records
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The example of Insecticide Resistance:
Aedes aegypti, 2098 records
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The example of Insecticide Resistance:
Aedes aegypti - DDT, 133 records
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The example of Insecticide Resistance:
Anopheles gambiae, 771 records
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The example of Insecticide Resistance:
A. gambiae - DDT, 198 records
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The example of Insecticide Resistance:
A. gambiae - permethrin, 190 records
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OBI/MIRO: assay MIRO: resistance assay
CHEBI: insecticideis_a participates_in
MIRO: Organism
MIRO: resistance
VB_CV: genotype
PATO: Phenotype
VB_CV/MIRO: Mosquito population
GAZ: Geolocation
IDOMAL: Human population
IDOMAL: Transmission
detection assay
IDOMAL:Human biting rate
Sporozoite rateParous rate
Vectorial capacity
ENVO : Environmental conditionse.g.
Rice field,Irrigation scheme,
swamp,altitude,
av. temperature,annual rainfall,
av. humidity
GAZ:Country,Province,District,
GPS coordinates
OBI/MIRO: collection assay
IDOMAL:Season
Season +
Geolocation +
Human population +
Mosq. population
is_ahas_input
has_output is_a
has_output
has_outputis_a
has_input
has_member
has_quality
is_a
has_qualityis_about
located_in
IDOMAL: Malaria control measures
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OBI/MIRO: assay MIRO: resistance assay
CHEBI: insecticideis_a participates_in
MIRO: Organism
MIRO: resistance
VB_CV: genotype
PATO: Phenotype
VB_CV/MIRO: Mosquito population
GAZ: Geolocation
IDOMAL: Human population
IDOMAL: Transmission
detection assay
IDOMAL:Human biting rate
Sporozoite rateParous rate
Vectorial capacity
ENVO : Environmental conditionse.g.
Rice field,Irrigation scheme,
swamp,altitude,
av. temperature,annual rainfall,
av. humidity
GAZ:Country,Province,District,
GPS coordinates
OBI/MIRO: collection assay
IDOMAL:Season
Season +
Geolocation +
Human population +
Mosq. population
is_ahas_input
has_output is_a
has_output
has_outputis_a
has_input
has_member
has_quality
is_a
has_qualityis_about
located_in
IDOMAL: Malaria control measures
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OBI/"VIRO": assay "VIRO": resistance assay
CHEBI: insecticideis_a participates_in
"VIRO": Organism
"VIRO": resistance
VB_CV: genotype
PATO: Phenotype
VB_CV/"VIRO": Vectorpopulation
GAZ: Geolocation
"VIRO": Human population
"IDOVBD": Transmission
detection assay
"IDOVBD":Transmission data
relating to vectors of other vector-borne
diseases
ENVO : Environmental conditionse.g.
Rice field,Irrigation scheme,
swamp,altitude,
av. temperature,annual rainfall,
av. humidity
GAZ:Country,Province,District,
GPS coordinates
OBI/"VIRO": collection assay
"IDOVBD": Disease control measures
"IDOVBD":Season
Season +
Geolocation +
Human population +
Vector population
is_ahas_input
has_output is_a
has_output
has_outputis_a
has_input
has_member
has_quality
is_a
has_qualityis_about
located_in
“VBDbase”
"IDOVBD":Additional data
models
“Oth_Ont2”:Additional data
models
“Oth_Ont1”:Additional data
models
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PopGen in VectorBasePopGen in VectorBase
George Christophides, with Bob MacCallum and Seth Redmont
Kitsos Louis, with Emmanuel Dialynas and Pantelis Topalis
A new section of VB being developed that will house data on the population biology of anophelines, as well as data on malaria transmission and IR.
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UO GAZ PATO IDOMAL
VBCV
IDOMAL
IDOMAL
Linking PopGen and ontologies; Phenotypes, IR, transmission and popu- lation/ecology data
Soon to come in VectorBase!
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TGMA – Mosquito Anatomy Ontology; CARO/BFO
TADS – Tick Anatomy Ontology; CARO/BFO
MIRO – Ontology of Insecticide Resistance; (move) to IDOMAL
IDOMAL – Malaria Ontology; IDO/BFO
VBCV – Ontology/CV for “completion” of PopGen
IDOMAL extension, “IDOChagas”, PLO (Parasite Lifecycle) with Priti Parykh, Chris Stoeckert et al.
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LOGICAL THOUGHT IS NOT A PRIVILEGE OF A FEW
IT’S AN OBLIGATION FOR EVERYONE !!!
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Thank you!Thank you!