Biomedical Literature Mining- Steps and Resources

Question

[Manu Madhavan]

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.

Answer 1

[jared.andrews07]

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.

[Jean-Karim Heriche]

A link or reference to the book is missing.

[jared.andrews07]

Totally thought I put it in there, nice catch.

[Manu Madhavan]

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?

[jared.andrews07]

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.