Jake Lever

Get a nicely-chunked local copy of the biomedical literature (to use for other projects)!

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Text mining for pharmacogenomic associations for PharmGKB

Biomedical wordlists (of drugs, genes, etc) for several text mining projects

Machine learning to text-mine coronavirus research for CoronaCentral.ai

Tool for extracting MeSH tags from PubMed documents

Text mining cancer biomarkers for the CIVIC database

Text-mined knowledgebase for drivers, oncogenes and tumor suppressors in cancer

A Python biomedical relation extraction package that uses a supervised approach (i.e. needs training data).

Testing framework for online labs

Bug bounty programme for Text As Data course

A deployment repo for a Shiny server

Tools to work with Global Network of Biomedical Relationships data

Nutrigenomics example text mining project using PubRunner

Vancouver Event and Relation System for Extraction

A framework for keeping biomedical text mining result up-to-date

Analysis code for knowledge discovery project

Abbreviation definition dection library trained on PubMed abstracts

Personal webpage

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Website for viewing database of Coronavirus research at CoronaCentral.ai

Python tool for doing big uploads to Zenodo

Basic test case for stressing a GPU

Job submitter for OpenShift cluster

Demonstration of some text classification methods in R

Data structures and code to read/write BioC XML and Json.

Tool for scanning a website for broken links

A Open Information Extraction tool for extracting relations from text

Scripts to run word2vec on PubMed corpus files