finding the taxonomy ID for C. griseus (Chinese Hamster) for use with Stringdb package

Question

[peter.berry5]

Hi

I am trying to use the StringDB package to map protein interactions. As a first step I need to get the species I am mapping which is C. griseus (Chinese hamster). I got the following info from the String website

Name: Cricetulus griseus Aliases: (Chinese hamster / Chinese hamsters / C. griseus / CHO cell lines / Cricetulus aureus / Cricetulus barabensis griseus / Cricetus griseus) STRING-type: periphery distinct protein-coding genes: 21808 NCBI taxon-Id: 10029

and my code is

BiocManager::install("STRINGdb")
library("STRINGdb")

#read in proteins to be mapped
Attached_DE_Proteins <- read.csv("C:/PETER PROJECT/3d. Mass Spec Processing/Results of R Analysis/DE Gene Lists/Effect of Serum/WCL Analysis/0% Attached v 5% Attached/DE Cutoff equal 1.5/DE 1-5 Attached Cells DE Gene IDs WCL Apr19 Serum Removal.csv")

#call the string database. 
#note if you supply a local input directory the DB will be cached here allowing offline use.
string_db <- STRINGdb$new( version="11", species=10029, score_threshold=400, input_directory="")

#map my DE proteins to the String DB
mapped_proteins <- string_bd$map(Attached_DE_Proteins, "HGNC_Symbol", removeUnmappedRows = TRUE)

However, I get the following error when I run it.

Error: object 'string_bd' not found

Any thoughts on where I am going wrong? I'm still a newbie to the bioinformatics field.

Thanks

[Arup Ghosh]

You have stored the query output in string_db and trying to access information from string_bd.

[peter.berry5]

Hi @ Arup,

If I understand you correctly I have an error in the line

string_db <- STRINGdb$new( version="11", species=10029, score_threshold=400, input_directory="")``

but this code was taken directly from the page 1 of the package vignette. [1]: https://bioconductor.org/packages/release/bioc/vignettes/STRINGdb/inst/doc/STRINGdb.pdf

Could you possibly provide the correct code as an example for me?

Thanks

[WouterDeCoster]

Look carefully. One time you write BD, the other time DB.

[peter.berry5]

Thank you so much. I would have never spotted that.