Chapter 6 Small tools

This chapter consists of:

Among compound name, if you have any one as identifier (PubChem id (cid), KEEG id, HMDB, CAS), you will get the rest of them and corresponding chemical properties related to this compound

Copy excel file under the folder of utils_DBs_api, replace the context of identifier as yours. e.g. If your identifier is PubChem_CID, choose the sheet name as PubChem_CID, replace the context of PubChem_CID numbers as yours

6.1 Play with various ids

The script DBs_ids_properties.R is available under the folder of J:\CBMR\SUN-CBMR-Metabolomics\Workflow\Script\modules

6.1.1 Source paths on the server

source("H:/From_SUND/Scripts/utils/utils_MS2_set_up/set_up_paths.R")

6.1.2 Provide identifier for grabbing other information 🕵

You have to choose one from these 5 options (“PubChem_CID”, “Compound_Name”, “KEGG”, “CAS”, “HMDB”)

identifier <- "PubChem_CID" 

6.1.3 Provide filename and sheetname for searching other information 🕵

absolute path

filename_xlsx <- "H:/From_SUND/Scripts/test/test_DB_ids.xlsx"

6.1.4 What properties you would like to get 🕵

You could find other options from function get_info_based_cid_to_xlsx.R under the folder of containing functions

properties <- c("IUPACName", "InChIKey", "CanonicalSMILES", "MonoisotopicMass")

6.1.5 Provide the path for containing output 🕵

path_output <- "H:/From_SUND/Scripts/outputs"

6.1.6 Conduct

source(paste0(path_utils_DBs_api, "/DBs_api.R"))