how to get entrez IDs from wormbase gene IDs

Question

[leranwangcs]

Hi,

I'm trying to get the gene functions for a list of wormbase genes. But I only have the wormbase gene IDs looks like this: "WBGene00001237" "WBGene00001239" "WBGene00001240". I need to get the entrez IDs so that I can map them to the GeneRIF database to fetch the functions.

Does anybody know how to convert Wormbase ID to Entrez IDs?

Thanks!

[Ram]

How is this question different from Annotate wormbase genes ?

[leranwangcs]

Hi Ram, so in that question you have provided me with a table in which it has the gene names in it and it worked well. But in my next step of analysis, in order to get the gene functions, I must have the Entrez ID to map to the geneRIP database. I didn't find that column in the table that you pointed me to.

Answer 1

[GenoMax]

I must have the Entrez ID

Entrezdirect command line equivalent for @Ram's answer is

$ esearch -db gene -query "aat-1 [GENE] AND 6239 [taxID]" | efetch -format docsum | xtract -pattern DocumentSummary -element Id 
177793

[leranwangcs]

Thank you! I'll try this!

Answer 2

[Ram]

I'm not conversant with eutils but you should be able to use that to search NCBI using the Gene Name and Tax ID like so:

https://www.ncbi.nlm.nih.gov/gene/?term=(aat-1%5BGene+Name%5D)+AND+6239%5BTaxonomy+ID%5D

This takes you to the page with Entrez ID 177793

Or you could search for CELE_<Locus Name>[Gene Name] (example: CELE_F52H2.2[Gene Name]) to get to the result. Maybe GenoMax can help with writing an entrez search for this

[leranwangcs]

Thanks for the suggestion!