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Searching NCBI eutils for relevant Papers

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.

gene rna-seq next-gen genome
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updated by Lars Juhl Jensen Lars Juhl Jensen • written by zamanys4 • zamanys4

1 answer

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

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written by Lars Juhl Jensen Lars Juhl Jensen

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

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written by zamanys4 • zamanys4

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