vectorbase invertebrate vectors of human pathogens
Post on 19-Dec-2015
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VectorBaseInvertebrate Vectors of Human Pathogens
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.
Intelligent Databases
Open access
Intelligent Databases
Open access
The answer, is...
InteroperabilityInteroperability Efficient searchesEfficient searches
Decision Support SystemsDecision Support Systems
3610 (2392 unique)3610 (2392 unique)
IRBase
The example of Insecticide Resistance:
Aedes aegypti, 2098 records
The example of Insecticide Resistance:
Aedes aegypti, 2098 records
The example of Insecticide Resistance:
Aedes aegypti - DDT, 133 records
The example of Insecticide Resistance:
Anopheles gambiae, 771 records
The example of Insecticide Resistance:
A. gambiae - DDT, 198 records
The example of Insecticide Resistance:
A. gambiae - permethrin, 190 records
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
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
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
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.
UO GAZ PATO IDOMAL
VBCV
IDOMAL
IDOMAL
Linking PopGen and ontologies; Phenotypes, IR, transmission and popu- lation/ecology data
Soon to come in VectorBase!
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.
LOGICAL THOUGHT IS NOT A PRIVILEGE OF A FEW
IT’S AN OBLIGATION FOR EVERYONE !!!
Thank you!Thank you!