data-raw/combine_drug_data.R
In nf-osi/kairos: kairos: NF Analysis Explorer
## code to prepare `combine_drug_data` dataset goes here
library(reticulate)
use_condaenv("synapse250", required = T)
synapseclient <- reticulate::import('synapseclient')
syn <- synapseclient$Synapse()
library(tidyverse)
syn$login()
ids <- c(#"syn20555550", ##Field Lab NF Drug Screens
"syn12292394", ##NF2 Synodos low-throughput screen
"syn12292393", ##NTAP pNF NCATS single agent
# "syn12292585", ##NTAP pNF 6x6 NCATS combination
#"syn12292601", ##NF2 Synodos 10x10 NCATS combination
"syn12292395", ##NF1 Synodos MN secondary screen
#"syn12293222", ##NF2 Synodos 6x6 NCATS combination
"syn12296219", ##NF2 Synodos NCATS single agent MIPE 4.0
"syn12297785") ##NF2 Synodos NCATS single agent MIPE 1.0 Syn5,Syn1 only
foo <- map(ids, function(x){
readr::read_csv(syn$get(x)$path, col_types = "c")
}) %>% set_names(ids)
data <- dplyr::bind_rows(foo)
cmpd_names <- data %>%
select(compoundName) %>%
distinct() %>%
filter(!is.na(compoundName))
##DTEX v4 name map
# name_map <- readr::read_csv(syn$get("syn25388380")$path)
# name_map_2 <- left_join(cmpd_names %>% mutate(join_col = tolower(compoundName)),
# name_map %>% mutate(join_col = tolower(synonym))) %>%
# select(-join_col)
#
# unmapped_cmpds <- filter(name_map_2, is.na(inchikey)) %>%
# select(compoundName) %>%
# distinct()
##to avoid Error in the HTTP2 framing layer issue
httr::set_config(httr::config(http_version = 0))
inchikeys <- sapply(cmpd_names$compoundName, function(x){
httr::set_config(httr::config(http_version = 0))
foo <- dtexbuilder::.convert_id_to_structure_pubchem(x, id_type = 'name', output_type = 'InChIKey')
})
cmpd_names$inchikey <- inchikeys
##retrieve prebaked compound maps for missing ids
synodos_nf1 <- syn$get("syn26532681")$path %>% readr::read_csv()
synodos_nf2 <- syn$get("syn26532683")$path %>% readr::read_csv()
synodos_nf2_extra <- syn$get("syn26532686")$path %>% readr::read_csv()
curated_cmpd_structures <- bind_rows(synodos_nf1, synodos_nf2, synodos_nf2_extra)
cmpd_structures <- filter(cmpd_names, !is.na(inchikey)) %>%
rename(screen_id = compoundName) %>%
bind_rows(curated_cmpd_structures)
unknown_structures <- cmpd_names %>%
rename(screen_id = compoundName) %>%
filter(!screen_id %in% cmpd_structures$screen_id)
structure_map <- cmpd_structures %>%
bind_rows(unknown_structures)
##this is the standardized model name map
map <- syn$tableQuery("SELECT distinct * FROM syn16979992", includeRowIdAndRowVersion = FALSE)$filepath %>%
read_csv
map_2 <- tribble(
~modelSystemName, ~synonym,
"ipnNF95.11C", "ipnNF95.11c",
"ST8814", "ST88-14",
"sNF02.2", "SNF02.2",
"ST88-3", "st88-3",
"MEF", "MEF WT",
"MEF CAP2KO", "MEF CAP2KO"
)
map <- bind_rows(map, map_2)
cellosaurus <- syn$tableQuery("SELECT distinct name AS \"modelSystemName\", cellosaurus_id FROM syn18506933", includeRowIdAndRowVersion = F)$filepath %>%
read_csv
cellosaurus_2 <- tribble(
~modelSystemName, ~cellosaurus_id,
"HCT116 p53-", "CVCL_HD97",
"HCT116 p53+", "CVCL_0291",
"HT1080", "CVCL_0317",
"HFF", NA,
"MTC", NA
)
cellosaurus <- bind_rows(cellosaurus, cellosaurus_2)
organism <- syn$tableQuery("select distinct name as \"modelSystemName\", organism as \"organism_name\" from syn18506936",includeRowIdAndRowVersion = FALSE)$filepath %>%
read_csv
organism_2 <- tribble(
~modelSystemName, ~organism_name,
"HCT116 p53-", "human",
"HCT116 p53+", "human",
"HT1080", "human",
"HFF", "human",
"MTC", "mouse",
"MEF", "mouse",
"MEF CAP2KO", "mouse",
"N5", "human",
"N10", "human"
)
organism <- bind_rows(organism, organism_2)
disease <- tribble(
~model_name, ~disease_name, ~disease_efo_id,
"ST8814", "NF1", NA,
"90-8", "NF1", NA,
"STS26T", "NF1", NA,
"T265", "NF1", NA,
"HCT116 p53+", "cancer", 0000311,
"HCT116 p53-", "cancer", 0000311,
"HEI193", "NF2", NA,
"HT1080", "cancer", 0000311,
"RT4", "NF2", NA,
"S462TY", "NF1", NA,
"ST88-3", "NF1", NA,
"Syn1", "no disease", NA,
"Syn10", "NF2", NA,
"Syn12", "NF2", NA,
"Syn2", "no disease", NA,
"Syn3", "NF2", NA,
"Syn4", "NF2", NA,
"Syn5", "NF2", NA,
"Ben-Men-1", "NF2", NA,
"Syn7", "NF2", NA,
"HS01", "NF2", NA,
"HS11", "no disease", NA,
"MS01", "NF2", NA,
"MS02", "NF2", NA,
"MS03", "NF2", NA,
"MS12", "no disease", NA,
"MS11", "no disease", NA,
"ipn02.3", "no disease", NA,
"ipn02.8", "no disease", NA,
"ipNF05.5 (mixed clone)", "NF1", NA,
"ipNF05.5 (single clone)", "NF1", NA,
"ipNF06.2A", "NF1", NA,
"ipNF95.11b C/T", "NF1", NA,
"ipnNF95.11C", "NF1", NA,
"ipNF95.6", "NF1", NA,
"HFF", "no disease", NA,
"MTC", "no disease", NA,
"ipNF95.11b C", "NF1", NA,
"N5", "NF1", NA,
"N10", "no disease", NA)
symptom <- tribble(
~model_name, ~symptom_name, ~symptom_efo_id,
"ST8814", "MPNST", 0000760,
"90-8", "MPNST", 0000760,
"STS26T", "MPNST", 0000760,
"T265", "MPNST", 0000760,
"HCT116 p53+", "colorectal carcinoma", 1001951,
"HCT116 p53-", "colorectal carcinoma", 1001951,
"HEI193", "schwannoma", 0000693,
"HT1080", "fibrosarcoma", 0002087,
"RT4", "schwannoma", 0000693,
"S462TY", "MPNST", 0000760,
"ST88-3", "MPNST", 0000760,
"Syn1", "no symptom", NA,
"Syn10", "meningioma", NA,
"Syn12", "meningioma", NA,
"Syn2", "no symptom", NA,
"Syn3", "no symptom", NA,
"Syn4", "no symptom", NA,
"Syn5", "no symptom", NA,
"Ben-Men-1", "meningioma", NA,
"Syn7", "meningioma", NA,
"HS01", "no symptom", 0000693,
"HS11", "no symptom", NA,
"MS01", "schwannoma", 0000693,
"MS02", "schwannoma", 0000693,
"MS03", "schwannoma", 0000693,
"MS12", "no symptom", NA,
"MS11", "no symptom", NA,
"ipn02.3", "no symptom", NA,
"ipn02.8", "no symptom", NA,
"ipNF05.5 (mixed clone)", "pNF", 0000658,
"ipNF05.5 (single clone)", "pNF", 0000658,
"ipNF06.2A", "pNF", 0000658,
"ipNF95.11b C/T", "pNF", 0000658,
"ipnNF95.11C", "pNF", 0000658,
"ipNF95.6", "pNF", 0000658,
"HFF", "no symptom", NA,
"MTC", "no symptom", NA,
"ipNF95.11b C", "pNF", 0000658,
"N5", "no symptom", NA,
"N10", "no symptom", NA)
data <- bind_rows(foo) %>%
group_by(experimentSynapseId,compoundName,individualId) %>%
add_column("drug_screen_id" = group_indices(.)) %>%
ungroup() %>%
rename(screen_id = compoundName) %>%
filter(stdCompoundConcentration != 0) %>%
group_by(drug_screen_id, individualId, experimentSynapseId, studySynapseId, funder, recordId, percentViability, screen_id, stdCompoundConcentrationUnit) %>%
summarize(stdCompoundConcentration=sum(as.numeric(stdCompoundConcentration))) %>%
ungroup() %>%
filter(stdCompoundConcentration != 0) %>%
left_join(structure_map %>% select(screen_id, inchikey))
data <- data %>%
mutate(synonym = individualId) %>%
left_join(distinct(map)) %>%
left_join(distinct(cellosaurus)) %>%
left_join(distinct(organism)) %>%
select(drug_screen_id, recordId, experimentSynapseId, studySynapseId, funder, modelSystemName, cellosaurus_id, organism_name, screen_id, inchikey, stdCompoundConcentration, stdCompoundConcentrationUnit, percentViability) %>%
set_names(c("drug_screen_id", "drug_assay_id", "experiment_synapse_id", "study_synapse_id", "funder", "model_name", "cellosaurus_id", "organism_name", "screen_id", "inchikey", "dosage", "dosage_unit", "response")) %>%
mutate(response_type = "percent viability", response_unit = "%", model_type = "cell line") %>%
left_join(distinct(disease)) %>%
left_join(distinct(symptom))
write.csv(data, "combined_NF_screening_data_December_2021_release.csv", row.names = F, na = "")
syn$store(synapseclient$File("combined_NF_screening_data_December_2021_release.csv", parentId = "syn12292355",
"resourceType" = "experimentalData",
"dataType" = "drugScreen",
"drugScreenType" = "smallMoleculeLibraryScreen",
"assay" = "cellViabilityAssay"),
used = c(ids,"syn17090820","syn16979992","syn26532681","syn26532683", "syn26532686"))
##remove old outdated data
tableId <- "syn20556247"
results <- synTableQuery(sprintf("select * from %s", tableId))
deleted <- synDelete(results)
##add new data
table <- Table(tableId, data)
table <- synStore(table)
#
usethis::use_data(combine_drug_data, overwrite = TRUE)
nf-osi/kairos documentation built on Dec. 30, 2022, 9:39 p.m.
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## code to prepare `combine_drug_data` dataset goes here
library(reticulate)
use_condaenv("synapse250", required = T)
synapseclient <- reticulate::import('synapseclient')
syn <- synapseclient$Synapse()
library(tidyverse)
syn$login()
ids <- c(#"syn20555550", ##Field Lab NF Drug Screens
"syn12292394", ##NF2 Synodos low-throughput screen
"syn12292393", ##NTAP pNF NCATS single agent
# "syn12292585", ##NTAP pNF 6x6 NCATS combination
#"syn12292601", ##NF2 Synodos 10x10 NCATS combination
"syn12292395", ##NF1 Synodos MN secondary screen
#"syn12293222", ##NF2 Synodos 6x6 NCATS combination
"syn12296219", ##NF2 Synodos NCATS single agent MIPE 4.0
"syn12297785") ##NF2 Synodos NCATS single agent MIPE 1.0 Syn5,Syn1 only
foo <- map(ids, function(x){
readr::read_csv(syn$get(x)$path, col_types = "c")
}) %>% set_names(ids)
data <- dplyr::bind_rows(foo)
cmpd_names <- data %>%
select(compoundName) %>%
distinct() %>%
filter(!is.na(compoundName))
##DTEX v4 name map
# name_map <- readr::read_csv(syn$get("syn25388380")$path)
# name_map_2 <- left_join(cmpd_names %>% mutate(join_col = tolower(compoundName)),
# name_map %>% mutate(join_col = tolower(synonym))) %>%
# select(-join_col)
#
# unmapped_cmpds <- filter(name_map_2, is.na(inchikey)) %>%
# select(compoundName) %>%
# distinct()
##to avoid Error in the HTTP2 framing layer issue
httr::set_config(httr::config(http_version = 0))
inchikeys <- sapply(cmpd_names$compoundName, function(x){
httr::set_config(httr::config(http_version = 0))
foo <- dtexbuilder::.convert_id_to_structure_pubchem(x, id_type = 'name', output_type = 'InChIKey')
})
cmpd_names$inchikey <- inchikeys
##retrieve prebaked compound maps for missing ids
synodos_nf1 <- syn$get("syn26532681")$path %>% readr::read_csv()
synodos_nf2 <- syn$get("syn26532683")$path %>% readr::read_csv()
synodos_nf2_extra <- syn$get("syn26532686")$path %>% readr::read_csv()
curated_cmpd_structures <- bind_rows(synodos_nf1, synodos_nf2, synodos_nf2_extra)
cmpd_structures <- filter(cmpd_names, !is.na(inchikey)) %>%
rename(screen_id = compoundName) %>%
bind_rows(curated_cmpd_structures)
unknown_structures <- cmpd_names %>%
rename(screen_id = compoundName) %>%
filter(!screen_id %in% cmpd_structures$screen_id)
structure_map <- cmpd_structures %>%
bind_rows(unknown_structures)
##this is the standardized model name map
map <- syn$tableQuery("SELECT distinct * FROM syn16979992", includeRowIdAndRowVersion = FALSE)$filepath %>%
read_csv
map_2 <- tribble(
~modelSystemName, ~synonym,
"ipnNF95.11C", "ipnNF95.11c",
"ST8814", "ST88-14",
"sNF02.2", "SNF02.2",
"ST88-3", "st88-3",
"MEF", "MEF WT",
"MEF CAP2KO", "MEF CAP2KO"
)
map <- bind_rows(map, map_2)
cellosaurus <- syn$tableQuery("SELECT distinct name AS \"modelSystemName\", cellosaurus_id FROM syn18506933", includeRowIdAndRowVersion = F)$filepath %>%
read_csv
cellosaurus_2 <- tribble(
~modelSystemName, ~cellosaurus_id,
"HCT116 p53-", "CVCL_HD97",
"HCT116 p53+", "CVCL_0291",
"HT1080", "CVCL_0317",
"HFF", NA,
"MTC", NA
)
cellosaurus <- bind_rows(cellosaurus, cellosaurus_2)
organism <- syn$tableQuery("select distinct name as \"modelSystemName\", organism as \"organism_name\" from syn18506936",includeRowIdAndRowVersion = FALSE)$filepath %>%
read_csv
organism_2 <- tribble(
~modelSystemName, ~organism_name,
"HCT116 p53-", "human",
"HCT116 p53+", "human",
"HT1080", "human",
"HFF", "human",
"MTC", "mouse",
"MEF", "mouse",
"MEF CAP2KO", "mouse",
"N5", "human",
"N10", "human"
)
organism <- bind_rows(organism, organism_2)
disease <- tribble(
~model_name, ~disease_name, ~disease_efo_id,
"ST8814", "NF1", NA,
"90-8", "NF1", NA,
"STS26T", "NF1", NA,
"T265", "NF1", NA,
"HCT116 p53+", "cancer", 0000311,
"HCT116 p53-", "cancer", 0000311,
"HEI193", "NF2", NA,
"HT1080", "cancer", 0000311,
"RT4", "NF2", NA,
"S462TY", "NF1", NA,
"ST88-3", "NF1", NA,
"Syn1", "no disease", NA,
"Syn10", "NF2", NA,
"Syn12", "NF2", NA,
"Syn2", "no disease", NA,
"Syn3", "NF2", NA,
"Syn4", "NF2", NA,
"Syn5", "NF2", NA,
"Ben-Men-1", "NF2", NA,
"Syn7", "NF2", NA,
"HS01", "NF2", NA,
"HS11", "no disease", NA,
"MS01", "NF2", NA,
"MS02", "NF2", NA,
"MS03", "NF2", NA,
"MS12", "no disease", NA,
"MS11", "no disease", NA,
"ipn02.3", "no disease", NA,
"ipn02.8", "no disease", NA,
"ipNF05.5 (mixed clone)", "NF1", NA,
"ipNF05.5 (single clone)", "NF1", NA,
"ipNF06.2A", "NF1", NA,
"ipNF95.11b C/T", "NF1", NA,
"ipnNF95.11C", "NF1", NA,
"ipNF95.6", "NF1", NA,
"HFF", "no disease", NA,
"MTC", "no disease", NA,
"ipNF95.11b C", "NF1", NA,
"N5", "NF1", NA,
"N10", "no disease", NA)
symptom <- tribble(
~model_name, ~symptom_name, ~symptom_efo_id,
"ST8814", "MPNST", 0000760,
"90-8", "MPNST", 0000760,
"STS26T", "MPNST", 0000760,
"T265", "MPNST", 0000760,
"HCT116 p53+", "colorectal carcinoma", 1001951,
"HCT116 p53-", "colorectal carcinoma", 1001951,
"HEI193", "schwannoma", 0000693,
"HT1080", "fibrosarcoma", 0002087,
"RT4", "schwannoma", 0000693,
"S462TY", "MPNST", 0000760,
"ST88-3", "MPNST", 0000760,
"Syn1", "no symptom", NA,
"Syn10", "meningioma", NA,
"Syn12", "meningioma", NA,
"Syn2", "no symptom", NA,
"Syn3", "no symptom", NA,
"Syn4", "no symptom", NA,
"Syn5", "no symptom", NA,
"Ben-Men-1", "meningioma", NA,
"Syn7", "meningioma", NA,
"HS01", "no symptom", 0000693,
"HS11", "no symptom", NA,
"MS01", "schwannoma", 0000693,
"MS02", "schwannoma", 0000693,
"MS03", "schwannoma", 0000693,
"MS12", "no symptom", NA,
"MS11", "no symptom", NA,
"ipn02.3", "no symptom", NA,
"ipn02.8", "no symptom", NA,
"ipNF05.5 (mixed clone)", "pNF", 0000658,
"ipNF05.5 (single clone)", "pNF", 0000658,
"ipNF06.2A", "pNF", 0000658,
"ipNF95.11b C/T", "pNF", 0000658,
"ipnNF95.11C", "pNF", 0000658,
"ipNF95.6", "pNF", 0000658,
"HFF", "no symptom", NA,
"MTC", "no symptom", NA,
"ipNF95.11b C", "pNF", 0000658,
"N5", "no symptom", NA,
"N10", "no symptom", NA)
data <- bind_rows(foo) %>%
group_by(experimentSynapseId,compoundName,individualId) %>%
add_column("drug_screen_id" = group_indices(.)) %>%
ungroup() %>%
rename(screen_id = compoundName) %>%
filter(stdCompoundConcentration != 0) %>%
group_by(drug_screen_id, individualId, experimentSynapseId, studySynapseId, funder, recordId, percentViability, screen_id, stdCompoundConcentrationUnit) %>%
summarize(stdCompoundConcentration=sum(as.numeric(stdCompoundConcentration))) %>%
ungroup() %>%
filter(stdCompoundConcentration != 0) %>%
left_join(structure_map %>% select(screen_id, inchikey))
data <- data %>%
mutate(synonym = individualId) %>%
left_join(distinct(map)) %>%
left_join(distinct(cellosaurus)) %>%
left_join(distinct(organism)) %>%
select(drug_screen_id, recordId, experimentSynapseId, studySynapseId, funder, modelSystemName, cellosaurus_id, organism_name, screen_id, inchikey, stdCompoundConcentration, stdCompoundConcentrationUnit, percentViability) %>%
set_names(c("drug_screen_id", "drug_assay_id", "experiment_synapse_id", "study_synapse_id", "funder", "model_name", "cellosaurus_id", "organism_name", "screen_id", "inchikey", "dosage", "dosage_unit", "response")) %>%
mutate(response_type = "percent viability", response_unit = "%", model_type = "cell line") %>%
left_join(distinct(disease)) %>%
left_join(distinct(symptom))
write.csv(data, "combined_NF_screening_data_December_2021_release.csv", row.names = F, na = "")
syn$store(synapseclient$File("combined_NF_screening_data_December_2021_release.csv", parentId = "syn12292355",
"resourceType" = "experimentalData",
"dataType" = "drugScreen",
"drugScreenType" = "smallMoleculeLibraryScreen",
"assay" = "cellViabilityAssay"),
used = c(ids,"syn17090820","syn16979992","syn26532681","syn26532683", "syn26532686"))
##remove old outdated data
tableId <- "syn20556247"
results <- synTableQuery(sprintf("select * from %s", tableId))
deleted <- synDelete(results)
##add new data
table <- Table(tableId, data)
table <- synStore(table)
#
usethis::use_data(combine_drug_data, overwrite = TRUE)
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