Use Google Docs to identify gene-disease associations in Pubmed

March 3, 2014   

Google Docs allows you to import XML. By using NCBIs esearch service, you can query pubmed for a list of genes. Stick the following code in A2, and a keyword in B2:

=importXML("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=" & B2 ,"(//Count)[1]")

What is more valuable, however, is if given a gene list – you can query pubmed for each gene combined with a second keyword like a disease.

For example, suppose you are studying Cleft lip and Palate and are left with a set of genes identified from a gene expression analysis. Now you want to see if any of those genes have published findings on them related to cleft lip and palate.

You can use the & operator to concatenate two keywords (gene & ” ” & disease). In B2 below you would put the following:

= C2 & " " & D2

The result would look something like this.

Pubmed result counts are in Column A1.Pubmed result counts are in Column A1.

Bioinformatics  Tips  google_doc pubmed