Question: How to programmatically query NCBI Gene database
1
gravatar for ishengomae
5.0 years ago by
ishengomae100
Tanzania, United Republic Of
ishengomae100 wrote:

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.

 

R biopython database gene ncbi • 4.0k views
ADD COMMENTlink modified 3.3 years ago by govardhanks20 • written 5.0 years ago by ishengomae100

Check this post. Its pretty fresh:  edirect: Entrez Unix Command line . Also check this link: http://people.duke.edu/~ccc14/pcfb/biopython/BiopythonEntrez.html

ADD REPLYlink written 5.0 years ago by Ashutosh Pandey11k
1

Thanks to all for the help.

ADD REPLYlink written 5.0 years ago by ishengomae100
3
gravatar for Cytosine
5.0 years ago by
Cytosine440
Ljubljana, Slovenia
Cytosine440 wrote:

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

 

ADD COMMENTlink written 5.0 years ago by Cytosine440
1
gravatar for jeremy S
5.0 years ago by
jeremy S30
Thailand
jeremy S30 wrote:

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

ADD COMMENTlink written 5.0 years ago by jeremy S30
1

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

ADD REPLYlink written 5.0 years ago by Neilfws48k
1
gravatar for govardhanks
3.3 years ago by
govardhanks20
govardhanks20 wrote:

(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

ADD COMMENTlink written 3.3 years ago by govardhanks20
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