## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", # cache = TRUE, class.output="scroll-100", cache.path = "cached/" ) library(PubChemR) ## ----eval=FALSE--------------------------------------------------------------- # get_pug_rest( # identifier = NULL, # namespace = "cid", # domain = "compound", # operation = NULL, # output = "JSON", # searchtype = NULL, # property = NULL, # options = NULL, # save = FALSE, # dpi = 300, # path = NULL, # file_name = NULL, # ... # ) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "2244", namespace = "cid", domain = "compound", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemDataResult <- pubChemData(result) ## ----------------------------------------------------------------------------- pubChemDataResult$PC_Compounds[[1]]$id ## ----------------------------------------------------------------------------- pubChemDataResult$PC_Compounds[[1]]$atoms ## ----------------------------------------------------------------------------- pubChemDataResult$PC_Compounds[[1]]$bonds ## ----------------------------------------------------------------------------- pubChemDataResult$PC_Compounds[[1]]$coords ## ----------------------------------------------------------------------------- pubChemDataResult$PC_Compounds[[1]]$charge ## ----------------------------------------------------------------------------- pubChemDataResult$PC_Compounds[[1]]$props[[2]] ## ----------------------------------------------------------------------------- pubChemDataResult$PC_Compounds[[1]]$props[[3]] ## ----------------------------------------------------------------------------- pubChemDataResult$PC_Compounds[[1]]$props[[4]] ## ----------------------------------------------------------------------------- pubChemDataResult$PC_Compounds[[1]]$props[[5]] ## ----------------------------------------------------------------------------- pubChemDataResult$PC_Compounds[[1]]$props[[7]] ## ----------------------------------------------------------------------------- pubChemDataResult$PC_Compounds[[1]]$props[[13]] ## ----------------------------------------------------------------------------- pubChemDataResult$PC_Compounds[[1]]$props[[14]] ## ----------------------------------------------------------------------------- pubChemDataResult$PC_Compounds[[1]]$props[[15]] ## ----------------------------------------------------------------------------- pubChemDataResult$PC_Compounds[[1]]$props[[17]] ## ----------------------------------------------------------------------------- pubChemDataResult$PC_Compounds[[1]]$props[[18]] ## ----------------------------------------------------------------------------- pubChemDataResult$PC_Compounds[[1]]$props[[19]] ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = c("1","2","3","4","5"), namespace = "cid", domain = "compound", property = c("MolecularFormula","MolecularWeight","CanonicalSMILES"), output = "CSV") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "glucose", namespace = "name", domain = "compound", operation = "cids", output = "TXT") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "CCCC", namespace = "smiles", domain = "compound", operation = "cids", output = "TXT") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "5793", namespace = "cid", domain = "compound", operation = "cids", output = "TXT", searchtype = "fastidentity", options = list(identity_type = "same_connectivity")) result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "US20050159403A1", namespace = "xref/PatentID", domain = "substance", operation = "sids", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----eval=FALSE--------------------------------------------------------------- # result <- get_pug_rest(identifier = "2244", namespace = "cid", domain = "compound", output = "SDF") ## ----------------------------------------------------------------------------- get_pug_rest(identifier = "lipitor", namespace = "name", domain = "compound", output = "PNG") ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "2244", namespace = "cid", domain = "compound", property = "MolecularWeight", output = "TXT") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = c("1","2","3","4","5"), namespace = "cid", domain = "compound", property = c("MolecularWeight", "MolecularFormula", "HBondDonorCount", "HBondAcceptorCount", "InChIKey", "InChI"), output = "CSV") ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "vioxx", namespace = "name", domain = "compound", operation = "synonyms", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "2244", namespace = "cid", domain = "compound", operation = c("xrefs","MMDBID"), output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "137349406", namespace = "sid", domain = "substance", operation = c("xrefs","PatentID"), output = "TXT") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "504526", namespace = "aid", domain = "assay", operation = "description", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "1000", namespace = "aid", domain = "assay", operation = "summary", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "504526", namespace = "aid", domain = "assay", output = "CSV") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "504526", namespace = "aid", domain = "assay", operation = "JSON?sid=104169547,109967232", output = "JSON") result ## ----------------------------------------------------------------------------- result <- pubChemData(result) result$PC_AssaySubmit$assay ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "504526", namespace = "aid", domain = "assay", operation = "concise", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "504526", namespace = "aid", domain = "assay", operation = "doseresponse/CSV?sid=104169547,109967232", output = "CSV") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = c("490","1000"), namespace = "aid", domain = "assay", operation = "targets/ProteinGI,ProteinName,GeneID,GeneSymbol", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "USP2", namespace = "target/genesymbol", domain = "assay", operation = "aids", output = "TXT") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "EC50", namespace = "activity", domain = "assay", operation = "aids", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "1956,13649", namespace = "geneid", domain = "gene", operation = "summary", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "EGFR", namespace = "genesymbol", domain = "gene", operation = "summary", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "ERBB1", namespace = "synonym", domain = "gene", operation = "summary", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "1956,13649", namespace = "geneid", domain = "gene", operation = "summary", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "13649", namespace = "geneid", domain = "gene", operation = "aids", output = "TXT") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "13649", namespace = "geneid", domain = "gene", operation = "concise", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "13649", namespace = "geneid", domain = "gene", operation = "pwaccs", output = "TXT") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "P00533,P01422", namespace = "accession", domain = "protein", operation = "summary", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "ChEMBL:CHEMBL203", namespace = "synonym", domain = "protein", operation = "summary", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "P00533,P01422", namespace = "accession", domain = "protein", operation = "summary", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "P00533", namespace = "accession", domain = "protein", operation = "aids", output = "TXT") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "Q01279", namespace = "accession", domain = "protein", operation = "concise", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "P00533", namespace = "accession", domain = "protein", operation = "pwaccs", output = "TXT") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "Reactome:R-HSA-70171", namespace = "pwacc", domain = "pathway", operation = "summary", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "Reactome:R-HSA-70171,BioCyc:HUMAN_PWY-4983", namespace = "pwacc", domain = "pathway", operation = "summary", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "Reactome:R-HSA-70171", namespace = "pwacc", domain = "pathway", operation = "cids", output = "TXT") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "Reactome:R-HSA-70171", namespace = "pwacc", domain = "pathway", operation = "geneids", output = "TXT") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "Reactome:R-HSA-70171", namespace = "pwacc", domain = "pathway", operation = "accessions", output = "TXT") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "9606,2697049", namespace = "taxid", domain = "taxonomy", operation = "summary", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "Homo sapiens", namespace = "synonym", domain = "taxonomy", operation = "summary", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "9606,10090,10116", namespace = "taxid", domain = "taxonomy", operation = "summary", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "2697049", namespace = "taxid", domain = "taxonomy", operation = "aids", output = "TXT") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "1409578", namespace = "aid", domain = "assay", operation = "concise", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "CHEMBL3308376,CVCL_0045", namespace = "cellacc", domain = "cell", operation = "summary", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "HeLa", namespace = "synonym", domain = "cell", operation = "summary", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "CVCL_0030,CVCL_0045", namespace = "cellacc", domain = "cell", operation = "summary", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "HeLa", namespace = "synonym", domain = "cell", operation = "aids", output = "TXT") result ## ----------------------------------------------------------------------------- pubChemData(result) ## ----------------------------------------------------------------------------- result <- get_pug_rest(identifier = "79900", namespace = "aid", domain = "assay", operation = "concise", output = "JSON") result ## ----------------------------------------------------------------------------- pubChemData(result)