This is a test version of Biostars. For the public version, visit https://www.biostars.org.
taxonomy information based on SRA id

I would like to get taxonomy information (species, family, class, and so on) based on SRA id using rentrez package. I was trying to build a query but was not sure if approaching it correctly.

The taxonomy information are directly included in sra database, as: entrez_db_searchable("sra") --> [ORGN] - Scientific and common names of organism, and all higher levels of taxonomy.

So if I understand correctly, I don't need to link any other database (e.g taxonomy) to get all I need. When I tried:

test <- entrez_search(db="sra", term="ERR5883998[ACCN]", rettype="xml", parsed=TRUE)
test
Entrez search result with 1 hits (object contains 1 IDs and no web_history object)
Search term (as translated):  ERR5883998[ACCN]

But when I want to extract XML to extract taxonomy, I got error:

info <- XML::xmlToList(test)
Error in UseMethod("xmlSApply") : 
no applicable method for 'xmlSApply' applied to an object of class "c('esearch', 'list')"
rentrez r
• 1,793 views • link
written by agata • agata

2 answers

I found a way how to use the rentrez package to obtain the ScienticName based on SRAid (here more info: manual). Maybe someone else will also find it useful.

test <- entrez_search(db="sra", term=sraid)
tax_rec <- entrez_fetch(db="sra", id=test$ids, rettype="xml", parsed=TRUE)
tax_list <- XML::xmlToList(tax_rec)
info <- tax_list$EXPERIMENT_PACKAGE$RUN_SET$RUN$Pool$Member$.attrs
organism <- as.vector(info["organism"])
• 0 views • link
written by agata • agata

Using EntrezDirect:

$ esearch -db sra -query ERR5883998 | efetch -format runinfo | awk -F "," '{print $28,$29}'
TaxID ScientificName
39272 Allacma fusca

OR

$ efetch -db sra -id ERR5883998 -format runinfo | awk -F "," '{print $28,$29}'
TaxID ScientificName
39272 Allacma fusca
• 0 views • link
written by GenoMax GenoMax

Thank you for your help, but I need a solution specifically in the R environment - rentrez package

• 0 views • link
written by agata • agata

Log in to answer this question.

More posts like this