This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to programmatically query NCBI Gene database

Hi all.

Is there a way by which I can programmatically access the NCBI Gene Database? I have a number of gene names (HGNC gene symbols) of which I want to get a summary of gene function and some literature about those genes. I find the NCBI gene database to be a good place to do this: http://www.ncbi.nlm.nih.gov/gene/?term=LTF ; http://www.ncbi.nlm.nih.gov/gene/4057; But I actually have many genes so I want to know if there is a way I can fetch out to this database via programs (Biopython or R) and for each gene get a summary of gene functions and related publications.

Thanks

biopython database r gene ncbi
• 7,182 views • link
updated by Ram Ram • written by ishengomae ishengomae

Thanks to all for the help.

• 0 views • link
written by ishengomae ishengomae

3 answers

Have a go at Entrez e-utils. Biopython already has libraries that wrap around the e-utils, if you want to use that one.

• 1 views • link
updated by Ram Ram • written by Cytosine Cytosine

There is a package called NCBI2R that has a bunch of API functions for querying NCBI

• 0 views • link
updated by Ram Ram • written by jeremy S • jeremy S

There's also rentrez, which is the best implementation of EUtils for R.

• 0 views • link
updated by Ram Ram • written by Neilfws Neilfws

(not a programtic option though) Would like to suggest UCSC Table browser (https://genome.ucsc.edu/cgi-bin/hgTables) --you might need to enter refseqgene under groups and input your gene's NM_IDS or standard HGNC symbol,output format-selected fields-- try with given examples you can figure out how to get desired output. hope this helps

• 0 views • link
written by govardhanks • govardhanks

Log in to answer this question.

More posts like this