How to mine a list of papers for overrepresented MeSH terms?
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7.1 years ago
biotech ▴ 540

I've been recently asked to write a review paper. I found that the field of study I'm trying to write is wide, and I would like to give an unbiased overview of what has been published.

Given a list of Pubmed IDs vs MeSH terms, I would like to perform a MeSH (Medical Subject Headings) term enrichment, giving as a result some p-values based on Fisher's exact test, for example.

Maybe this strategy has been already implemented or there is a similar method to achieve the same goal.

Note. This question has also been posted in academia stack forum.

mining bibliometrics reviews bibliography • 1.7k views
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This method has already been implemented but unfortunately its MeSH database is outdated. Maybe worth to build this tool using some R packages. meshop.oicr.on.ca/meshop/index.html

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7.1 years ago
Mary 11k

They've cut back on some of the functions it used to have, but we liked XplorMed: http://xplormed.ogic.ca/info/index.html

You should see PubMatrix too: http://pubmatrix.grc.nia.nih.gov/

iHOP: http://www.ihop-net.org/UniPub/iHOP/

 

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