mirror of
https://github.com/johrpan/ubigen.git
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104 lines
2.8 KiB
R
104 lines
2.8 KiB
R
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library(data.table)
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library(here)
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i_am("scripts/drugs_input.R")
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# Source: PubChem ID exchange based on CMap drug identifiers.
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drugs_cmap_pubchem <- fread(here("scripts/input/drugs_cmap_pubchem.tsv"))
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drugs_cmap_pubchem <- na.omit(drugs_cmap_pubchem)
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# Source: UniChem ID mapping
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drugs_chembl_pubchem <- fread(here("scripts/input/drugs_chembl_pubchem.tsv"))
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# Source: ChEMBL SQLite database
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# SELECT DISTINCT
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# chembl_id,
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# synonyms AS name,
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# mesh_heading AS indication,
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# mechanism_of_action
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# FROM molecule_dictionary
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# LEFT JOIN drug_indication
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# ON molecule_dictionary.molregno = drug_indication.molregno
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# LEFT JOIN drug_mechanism
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# ON molecule_dictionary.molregno = drug_mechanism.molregno
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# LEFT JOIN (
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# SELECT molregno, synonyms FROM molecule_synonyms WHERE syn_type == 'INN'
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# ) AS molecule_synonyms
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# ON molecule_dictionary.molregno = molecule_synonyms.molregno
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# WHERE name IS NOT NULL
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# OR indication IS NOT NULL
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# OR mechanism_of_action IS NOT NULL;
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drugs_chembl <- fread(here("scripts/input/drugs_chembl.csv"))
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# Source: PubChem ID list upload based on identifiers converted from CMap
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# drug names using the PubChem ID exchange.
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drugs_pubchem <- fread(here("scripts/input/drugs_pubchem.csv"))
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drugs_pubchem <- drugs_pubchem[, .(cid, cmpdname, annotation)]
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drugs_pubchem <- unique(drugs_pubchem, by = "cid")
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drugs_pubchem <- drugs_pubchem[,
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.(
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cmpdname,
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annotation = strsplit(annotation, "|", fixed = TRUE) |> unlist()
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),
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by = cid
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]
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# Filter for WHO ATC annotations
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drugs_pubchem <- drugs_pubchem[stringr::str_detect(annotation, "^[A-Z] - ")]
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# Extract ATC levels
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drugs_pubchem[, atc_1 := stringr::str_match(
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annotation,
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"^[A-Z] - ([^>]*)"
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)[, 2] |> stringr::str_trim()]
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drugs_pubchem[, atc_2 := stringr::str_match(
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annotation,
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"> [A-Z][0-9][0-9] - ([^>]*)"
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)[, 2] |> stringr::str_trim()]
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drugs_pubchem[, atc_3 := stringr::str_match(
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annotation,
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"> [A-Z][0-9][0-9][A-Z] - ([^>]*)"
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)[, 2] |> stringr::str_trim()]
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drugs_pubchem <- drugs_pubchem[, .(cid, cmpdname, atc_1, atc_2, atc_3)]
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setnames(drugs_pubchem, c("cid", "cmpdname"), c("pubchem_cid", "pubchem_name"))
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drugs <- merge(
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drugs_cmap_pubchem,
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drugs_chembl_pubchem,
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by = "pubchem_cid",
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all.x = TRUE
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)
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drugs <- merge(
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drugs,
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drugs_chembl,
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by = "chembl_id",
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all.x = TRUE
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)
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drugs <- merge(
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drugs,
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drugs_pubchem,
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by = "pubchem_cid",
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all.x = TRUE,
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allow.cartesian = TRUE
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)
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# Prefer INN name, then PubChem, then CMap:
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drugs[name == "", name := NA]
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drugs[is.na(name), name := pubchem_name]
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drugs[name == "", name := NA]
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drugs[is.na(name), name := stringr::str_to_sentence(drug)]
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drugs[, pubchem_name := NULL]
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# Clean up empty values:
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drugs[indication == "", indication := NA]
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drugs[mechanism_of_action == "", mechanism_of_action := NA]
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fwrite(drugs, file = here("scripts/output/drugs.csv"))
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