README.md

BioNER Progress

Introduction

Named entity recognition (NER) is the problem of finding references to entities (mentions) in natural language text, and labeling them with their location and type. In biomedical domain, biomedical NER (BioNER) focuses on the biomedical entities like gene, protein, chemical, disease, mutation, etc.

This repository aims to track the progress in BioNER and give a related paper list and an overview of the state-of-the-art (SOTA).

Contents

• Papers

  • Survey Papers
  • Dictionary-based Methods
  • Rule-based Methods
  • Machine Learning-based Methods
    • SVM-based Methods
    • HMM-based Methods
    • MEMM-based Mehtods
    • CRF-based Methods
    • Neural Network-based Methods
    • Others

• SOTA

  • Chemical NER
    • CHEMDNER
    • CDR-Chemical
  • Disease NER
    • NCBI-Disease
    • CDR-Disease
  • Gene/Protein NER
    • BC2GM
    • JNLPBA
  • Mutation NER
    • MutationFinder
    • tmVar
  • Species NER
    • LINNAEUS