Biomedical Literature Mining
A (non-free) volume of Methods in Molecular Biology from 2014. Chapters covers introductory principles in text mining, applications in the biological sciences, and potential for use in clinical or medical safety scenarios.
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Getting Started in Text Mining journals.plos.org
A brief introduction to bio-text mining from Cohen and Hunter. More than ten years old but still quite relevant. See also an earlier paper by the same authors.
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BioBERT: a pre-trained biomedical language representation model for biomedical text mining academic.oup.com
Bioinformatics, 2020. [All Versions]. Answering medical questions, identifying relevant clinical trials, and diagnosing diseases based on symptoms, making medical information more accessible to the general public.
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JensenLab text mining exercises jensenlab.org
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Biomedical Informatics on the Cloud: A Treasure Hunt for Advancing Cardiovascular Medicine ahajournals.org
An overview of how BioIE and bioinformatics workflows can be applied to questions in cardiovascular health and medicine research.
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BioInfer corpora.informatik.hu-berlin.de
paper - 1,100 sentences from biomedical research abstracts annotated for relationships (including PPI), named entities, and syntactic dependencies. Additional information and download links are here.
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Clinical information extraction applications: A literature review sciencedirect.com
A review of clinical IE papers published as of September 2016. From Mayo Clinic group (see below).
Biomedical Information Extraction › Tutorials > Pre-LLM Guides, Lectures, and Courses: “A (non-free) volume of Methods in Molecular Biology from 2014. Chapters covers introductory principles in text mining, applications in the biological sciences, and potential for use in clinical or medical safety scenarios.”