In tidymass/tinytools: All the usefull tools for MS data processing and analysis

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(tinytools)

Compound ID converter

Two web tools are used for compound compound convert.

1. cts.fiehnlab

cts.fiehnlab is http://cts.fiehnlab.ucdavis.edu/service/convert. It support a lot of databases.

library(tinytools)

We can use the trans_id_database() to get the databases that cts.fiehnlab.

database_name = trans_id_database(server = "cts.fiehnlab")

head(database_name$From$From)

head(database_name$To$From)

We can see that it support a lot of (> 200) databases.

We can try the most common convert, from KEGG to HMDB.

trans_ID(
  query = "C00001",
  from = "KEGG",
  to = "Human Metabolome Database",
  top = 1,
  server = "cts.fiehnlab"
)

Now, trans_ID doesn't support verctor query. So you can use the purrr::map() to achive this.

c("C00001", "C00001", "C00001") %>%
  purrr::map(
    .f = function(x) {
      trans_ID(
        query = x,
        from = "KEGG",
        to = "Human Metabolome Database",
        top = 1,
        server = "cts.fiehnlab"
      )
    }
  ) %>%
  do.call(rbind, .) %>%
  as.data.frame()

2. chemspider

This is from https://www.chemspider.com/InChI.asmx.

We can use the trans_id_database() to get the databases that chemspider

database_name2 = trans_id_database(server = "chemspider")

database_name2$From

database_name2$To

This is very useful if you want to get the inchikey, inchi or smiles for one compound. But this web only support "ChemSpider ID" (csid), so we need use cts.fiehnlab convert to csid first.

trans_ID(
  query = "C00001",
  from = "KEGG",
  to = "ChemSpider",
  top = 1,
  server = "cts.fiehnlab"
)

trans_ID(
  query = "140526",
  from = "csid",
  to = "mol",
  top = 1,
  server = "chemspider"
)

tidymass/tinytools documentation built on Jan. 2, 2022, 5:18 p.m.