Question: Searching NCBI eutils for relevant Papers
0
gravatar for zamanys4
2.5 years ago by
zamanys410
zamanys410 wrote:

Hi,

I have a list of genes identified after a statistical test on a Kidney cancer (Renal cell carcinoma) data. Now, I am going to see how many of these genes have been validated in previous kidney cancer related publications. I am thinking of searching Eutils for the gene names and papers with the keywords like kidney cancer in the abstract. As I have not used Eutils before, I am not sure what is the best way to do that. I appreciate if anyone can help.

rna-seq next-gen genome gene • 534 views
ADD COMMENTlink modified 2.5 years ago by Lars Juhl Jensen11k • written 2.5 years ago by zamanys410
2
gravatar for Lars Juhl Jensen
2.5 years ago by
Copenhagen, Denmark
Lars Juhl Jensen11k wrote:

That should work, but it would require that you first come up with a good search to find the papers, secondly create or find a good method for recognizing gene names in text, and lastly come up with a scoring scheme. That would be reinventing the wheel, though.

A much easier solution would be to go to one of the various databases of disease-gene associations such as DISEASES, DisGeNet, or MalaCards. The DISEASES database is maintained by my group.

You can view genes associated with kidney cancer in the DISEASES database via this URL: http://diseases.jensenlab.org/disease/DOID:263

If you want to retrieve the top-100 genes in JSON format, you can do that via the REST API (not documented yet): http://diseases.jensenlab.org/Textmining?type1=-26&id1=DOID:3908&type2=9606&limit=100&format=json

Lastly, you can download all text-mined disease-gene associations from DISEASES here: http://download.jensenlab.org/human_disease_textmining_full.tsv

ADD COMMENTlink written 2.5 years ago by Lars Juhl Jensen11k

Thank you, Sir. I give it a try and will cite it if it helps.

ADD REPLYlink written 2.5 years ago by zamanys410
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