Question: Biomedical Literature Mining- Steps and Resources
0
gravatar for Manu Madhavan
18 months ago by
NIT Calicut
Manu Madhavan20 wrote:

I want to implement NLP pipeline for extracting gene-disease associations from PubMed abstracts. Which are the tools used in various NLP steps such as Tokenisation, POS Tagging, and NER. I would like to implement in Python.

literature mining bionlp • 297 views
ADD COMMENTlink modified 18 months ago by jared.andrews075.5k • written 18 months ago by Manu Madhavan20
1
gravatar for jared.andrews07
18 months ago by
jared.andrews075.5k
St. Louis, MO
jared.andrews075.5k wrote:

This question is definitely too broad, but this book is a decent primer on basic NLP in python. Chapters 3-5 cover your specifically requested tasks. This review on generating gene-disease associations may also be helpful.

ADD COMMENTlink modified 18 months ago • written 18 months ago by jared.andrews075.5k

A link or reference to the book is missing.

ADD REPLYlink written 18 months ago by Jean-Karim Heriche22k

Totally thought I put it in there, nice catch.

ADD REPLYlink written 18 months ago by jared.andrews075.5k

Thanks for the reply. Let me go through the paper.

This question is definitely too broad

Let me focus on the NER in biomedical literature? Could yo please suggests good resources?

ADD REPLYlink modified 18 months ago • written 18 months ago by Manu Madhavan20
1

This book chapter provides good background on text mining in biomedical literature in general, with specific sections on almost all of your topics and names of resources that might be helpful. Without a more specific question, it's hard to do more than point you to links from Google, which I'm sure you can find yourself as well.

ADD REPLYlink written 18 months ago by jared.andrews075.5k
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