datamining

Biomedical text natural language processing (BioNLP) using scispaCy

Here we are going to see how to use scispaCy named entity recognition (NER) models to identify drug and disease names mentioned in a medical transcription dataset. Moreover, we are going to combine NER and rule-based matching to extract the drug names and dosages reported in each transcription.

Automated miRDB custom target search

Command-line tool to automate the search for microRNA targets in the miRDB base and extract the number of binding sites

PMdataX - PubMed data eXtraction

A command-line tool to fetch data from articles available on PubMed

Word2Vec on ASD papers

Word2Vec word embedding analysis on Autism Spectrum Disorder (ASD) articles abstracts available on PubMed