Searching by name

[ucb]

Hi,

I am new to the library and am not sure if I could be coing somthing more, but I have experimented with PFOA translation. I get no results:

db_name<-'ctsgetr.sqlite' # local cache
id<-tolower(c("alanine",'lactic acid','Perfluorooctane Acid','PFOA','Perfluorooctanoic acid'))
from<-"Chemical Name"
to<-"CAS"

CTSgetR(id,from,to,db_name=db_name)

Output:

                      id         CAS
1                alanine 115967-49-2
2            lactic acid  10326-41-7
3   perfluorooctane acid        <NA>
4                   pfoa        <NA>
5 perfluorooctanoic acid        <NA>

The last entry in id is verbatim from PubChem. Also, if I turn tables and search by CID, I get a related CAS and not the main CAS for the CID:
PubChem Page

db_name<-'ctsgetr.sqlite' # local cache
id<-tolower(c("9554"))
from<-"PubChem CID"
to<-"CAS"

CTSgetR(id,from,to,db_name=db_name)

Output:

     id       CAS
 1 9554 2395-00-8

Are there some other databases I should be loading in addition to what is recommended as a local cache (db_name<-'ctsgetr.sqlite' # local cache)

[dgrapov]

Hi @ucb, Thanks for the nice example of what you tried. I've tested and am not able to replicate the issue. The db_name object is a local cache for storing results retrived from the primary source (https://cts.fiehnlab.ucdavis.edu/) to speed up redundant queries. Switching it just refreshes the cache in case the primary source changed some of its ID mappings.

library(CTSgetR)

db_name<-'ctsgetr.sqlite' # local cache
id<-tolower(c("alanine",'lactic acid','Perfluorooctane Acid','PFOA','Perfluorooctanoic acid'))
from<-"Chemical Name"
to<-"CAS"

CTSgetR(id,from,to,db_name=db_name)

id         CAS
1                alanine 115967-49-2
2            lactic acid  10326-41-7
3   perfluorooctane acid        <NA>
4                   pfoa   2395-00-8
5 perfluorooctanoic acid   2395-00-8

db_name<-'ctsgetr2.sqlite' # try new cache
init_CTSgetR_db(db_name)
id<-tolower(c("alanine",'lactic acid','Perfluorooctane Acid','PFOA','Perfluorooctanoic acid'))
from<-"Chemical Name"
to<-"CAS"
CTSgetR(id,from,to,db_name=db_name)

id         CAS
1                alanine 115967-49-2
2            lactic acid  10326-41-7
3   perfluorooctane acid        <NA>
  4                   pfoa   2395-00-8
5 perfluorooctanoic acid   2395-00-8

I am not sure why, but maybe the primary source website had some issues when you queried it?