Locally Querying Gene Description

Question

[Drio]

I have a list of HUGO and ENS gene ids and I want to associate the ncbi summary to each of them. I want to also account for gene synonyms (also knows as field in the ncbi site) . Finally I'd like to be able to query other species, not only human.

Here is an example for the BRAC1 gene.

So my output should be:

gene_id, summary
BRAC1, This gene encodes a nuclear phosphoprotein that plays a role in maintaining ...
...

I would prefer not having to perform queries over the network so the database should be local.

How would you attack this?

Thanks.

Answer 1

[Sean Davis]

You might just download the NCBI gene data from here:

ftp://ftp.ncbi.nih.gov/gene/DATA/

You can load that into a local RDBMS or NoSQL database for local queries.

Answer 2

[Michael]

This is an old post, but nowadays, we do this with ease using eutils:

esearch -db gene -query '(BRCA1[gene]) AND (homo sapiens[orgn])' | efetch -format docsum | xtract -pattern DocumentSummary  -first Name Summary


BRCA1   This gene encodes a nuclear phosphoprotein that plays a role in maintaining genomic stability, and it also acts as a tumor suppressor....