How to retrieve proteins and find associated genes using Batch Entrez?

Question

[caioraposo94]

The search works perfectly if I select the protein database, because I'm working with protein's accession numbers, but at the results It doesn't show the associated gene of the respective proteins, It might be normal, so to simplify the data manipulation I am using both site and the following script: https://biopython.org/wiki/Annotate_Entrez_Gene_IDs which is doing a great job retrieving the proteins but I still can't find the respective genes, that's why I tried to do a double search, one for the proteins and the other to find the genes using the accession numbers that the results return to me which is without the .1 or .2 in the final. No success. Is there another tool that can solve my problem? Or am I doing It the wrong way?

Answer 1

[vkkodali_ncbi]

Is something like this not working out for you?

elink -db protein -target gene -id NP_002817 -name protein_gene | efetch -db gene

Could you give me a few example protein accessions for which you were unable to retrieve a gene id?

[caioraposo94]

Searching for NP_001342354.1 returns:

Name: olfactory receptor 1F12 [Homo sapiens] Id: 1243057630 Caption: NP_001342354 Extra: gi|1243057630|ref|NP_001342354.1|[1243057630]

Along with other things like, create data, update date, TaxId, Flags. But no gene reference. Since I'm using the script provided by Biopython's toolkit with little changes like, db='protein', maybe the report was built to work comparing gene to gene, not protein to gene. This terminal way might be a better idea.

[vkkodali_ncbi]

I am not sure why the Biopython way is not working for you. From my end, the Entrez Direct method works fine.

$ elink -db protein -id NP_001342354.1 -target gene -name protein_gene | efetch -db gene 
1. OR1F12
Official Symbol: OR1F12 and Name: olfactory receptor family 1 subfamily F member 12 [Homo sapiens (human)]
Other Aliases: OR1F12PQ, OR6-12, hs6M1-35P, OR1F12
Other Designations: olfactory receptor 1F12; olfactory receptor OR6-12; seven transmembrane helix receptor
Chromosome: 6; Location: 6p22.1
Annotation: Chromosome 6 NC_000006.12 (28073316..28074329)
ID: 442179

[caioraposo94]

I'll definitely try it out, many thanks.