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Creates globi interaction dataset #18

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Creates globi interaction dataset #18

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527755c
ref key for Evans 2013
arw36 Apr 17, 2020
0ac4b0d
add year to Hamblin
arw36 Apr 17, 2020
90bad56
Replaced Anderson 1998 with Davies & Walker 1974
arw36 Apr 17, 2020
1bf644b
add ref key for Bujaru P. guyannensis association
arw36 Apr 17, 2020
1b26478
update Bujaru ref
arw36 Apr 17, 2020
c4b4c9d
for globi database
arw36 Apr 17, 2020
5334ec5
clean up df
arw36 Apr 19, 2020
948f9ca
add columns ref
arw36 Apr 19, 2020
144553e
add dois
arw36 Apr 19, 2020
6e23568
add dois
arw36 Apr 19, 2020
ac9f183
adjust taxon levels, change to pathogen
arw36 Apr 28, 2020
dfa757d
add Pinheiro ref
arw36 May 7, 2020
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55 changes: 55 additions & 0 deletions R/create-globi-interactions.R
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Original file line number Diff line number Diff line change
@@ -0,0 +1,55 @@
# Merge into GloBi format
library(dplyr)
# read in datasheets
asc <- read.csv(file = "data/associations.csv")
ref <- read.csv(file = "data/references.csv")
host <- read.csv(file = "data/hosts.csv")
virus <- read.csv(file = "data/viruses.csv")

# merge sheets
asc <- left_join(asc, ref, by = "referencekey") # merge in the references
asc <- left_join(asc, host, by = "hHostNameFinal") # merge in the host taxonomy
asc <- left_join(asc, virus, by = "vVirusNameCorrected") # merge in the virus taxonomy

# select columns for interactions sheet
asc <- dplyr::select(asc, vVirusNameCorrected, vOrder, vFamily, vGenus, hHostNameFinal, hOrder, hFamily, hGenus, Reference)


# create globi interactions sheet
globi_df = data.frame("sourceOccurrenceId" = rep("", nrow(asc)),
"sourceTaxonId" = rep("", nrow(asc)),
"sourceTaxonName" = asc$vVirusNameCorrected,
"sourceTaxonOrder" = asc$vOrder,
"sourceTaxonFamily" = asc$vFamily,
"sourceTaxonGenus" = asc$vGenus,
"sourceBodyPartId" = rep("", nrow(asc)),
"sourceBodyPartName" = rep("", nrow(asc)),
"sourceLifeStageId" = rep("", nrow(asc)),
"sourceLifeStageName" = rep("", nrow(asc)),
"interactionTypeId" = rep("http://purl.obolibrary.org/obo/RO_0002556", nrow(asc)),
"interactionTypeName" = rep("pathogen of", nrow(asc)),
"targetOccurrenceId" = rep("", nrow(asc)),
"targetTaxonId" = rep("", nrow(asc)),
"targetTaxonName" = asc$hHostNameFinal,
"targetTaxonOrder" = asc$hOrder,
"targetTaxonFamily" = asc$hFamily,
"targetTaxonGenus" = asc$hGenus,
"targetBodyPartId" = rep("", nrow(asc)),
"targetBodyPartName" = rep("", nrow(asc)),
"targetLifeStageId" = rep("", nrow(asc)),
"targetLifeStageName" = rep("", nrow(asc)),
"localityId" = rep("", nrow(asc)),
"localityName" = rep("", nrow(asc)),
"decimalLatitude" = rep("", nrow(asc)),
"decimalLongitude" = rep("", nrow(asc)),
"observationDateTime" = rep("", nrow(asc)),
"referenceDoi" = rep("", nrow(asc)),
"referenceUrl" = rep("", nrow(asc)),
"referenceCitation" = asc$Reference )

# remove underscore from host name and virus name
globi_df$sourceTaxonName <- gsub("_"," ",globi_df$sourceTaxonName)
globi_df$targetTaxonName <- gsub("_"," ",globi_df$targetTaxonName)

# save merged file
write.csv(globi_df, file = "data/globi_interactions.csv")
6 changes: 3 additions & 3 deletions data/associations.csv
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Expand Up @@ -30,7 +30,7 @@ Laguna_Negra_virus,Akodon_simulator,wild,PCR,2,Levis et al. 2004
Andes_virus,Akodon_varius,wild,Antibodies,0,Sosa-Estani et al. 2002
Akabane_virus,Alcelaphus_buselaphus,wild,Antibodies,0,Davies & Jessett 1985
Alcelaphine_herpesvirus_2,Alcelaphus_buselaphus,wild,Isolation,2,Reid & Rowe 1973
Bluetongue_virus,Alcelaphus_buselaphus,wild,Antibodies,0,Hamblin et al.
Bluetongue_virus,Alcelaphus_buselaphus,wild,Antibodies,0,Hamblin et al. 1990
Bovine_viral_diarrhea_virus_1,Alcelaphus_buselaphus,wild,SNT,1,Hamblin & Hedger 1979
Crimean-Congo_hemorrhagic_fever_virus,Alcelaphus_buselaphus,wild,Antibodies,0,Shepherd et al. 1987
Foot-and-mouth_disease_virus,Alcelaphus_buselaphus,wild,Antibodies,0,Ayebazibwe et al. 2010
Expand Down Expand Up @@ -877,7 +877,7 @@ Yellow_fever_virus,Erythrocebus_patas,wild,Isolation,2,Deubel et al. 1985
Vesicular_exanthema_of_swine_virus,Eschrichtius_robustus,wild,Antibodies,0,Smith & Latham 1978
Rabies_virus,Euderma_maculatum,wild,Isolation,2,Nadin-Davis et al. 2001
Akabane_virus,Eudorcas_thomsonii,wild,Antibodies,0,Davies & Jessett 1985
Bluetongue_virus,Eudorcas_thomsonii,wild,Antibodies,0,Anderson et al. 1998
Bluetongue_virus,Eudorcas_thomsonii,wild,Antibodies,0,Davies & Walker 1974
Equid_herpesvirus_1,Eudorcas_thomsonii,captive,PCR,2,Wohlsein et al. 2011
Equid_herpesvirus_9,Eudorcas_thomsonii,wild,Isolation,2,Fukushi et al. 1997
Foot-and-mouth_disease_virus,Eudorcas_thomsonii,wild,Antibodies,0,Anderson 1981
Expand Down Expand Up @@ -2215,7 +2215,7 @@ Western_equine_encephalitis_virus,Procyon_lotor,wild,hemmaglutination,0,Hardy 19
Venezuelan_equine_encephalitis_virus,Proechimys_guairae,wild,Antibodies,0,Navarro et al. 2005
Aroa_virus,Proechimys_guyannensis,wild,isolation,2,Shope 2003
Bimiti_virus,Proechimys_guyannensis,wild,Isolation,2,Shope et al. 1988
Bujaru_virus,Proechimys_guyannensis,wild,Isolation,2,NA
Bujaru_virus,Proechimys_guyannensis,wild,Isolation,2,Woodall 1967
Caraparu_virus,Proechimys_guyannensis,wild,Isolation,2,Shope et al. 1988
Catu_virus,Proechimys_guyannensis,wild,Isolation,2,Shope et al. 1988
Encephalomyocarditis_virus,Proechimys_guyannensis,wild,Isolation,2,Tesh & Wallace 1978
Expand Down
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