NegBio documentation

Contents:

• Getting Started with NegBio
  • Installing
    • Prerequisites
    • Installing from source (recommended)
    • Installing from pip
  • Using NegBio
    • Prepare the dataset
    • Run the script
      • Using CheXpert algorithm
      • Using MetaMap
  • Next Steps
• NegBio User Guide
  • Run the pipeline step-by-step
    • 1. Convert text files to BioC format
    • 2. Normalize reports
    • 3. Split each report into sections
    • 4. Splits each report into sentences
    • 5. Named entity recognition
    • 6. Parse the sentence
    • 7. Convert the parse tree to UD
    • 8. Detect negative and uncertain findings
    • 9. Cleans intermediate information
• NegBio Developer Guide
  • Create the documentation
• License
• Contributing
• Acknowledgments
• Disclaimer
• Reference

Indices and tables

• Index
• Module Index
• Search Page