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Biomedical Literature Mining- Steps and Resources

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.

bionlp literature mining
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updated by jared.andrews07 jared.andrews07 • written by Manu Madhavan • Manu Madhavan

1 answer

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.

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written by jared.andrews07 jared.andrews07

Totally thought I put it in there, nice catch.

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written by jared.andrews07 jared.andrews07

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?

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written by Manu Madhavan • Manu Madhavan

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.

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written by jared.andrews07 jared.andrews07

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