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Flexible and powerful platform for biomedical information extraction from text

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Neji is a flexible and powerful platform for biomedical information extraction from scientific texts, such as patents, publications and electronic health records.

Table of contents

What is new in Neji 2?

  • Neji Web Server
    • Management of annotation services and respective dictionaries and machine-learning models
    • Web page with interactive annotation for each service
    • REST API for each service
  • Gimli for machine learning NER training
    • Gimli is now easier to use with faster training and processing times. Its functionalities are now integrated into Neji, providing the same high accuracy previously achieved
  • Multiple linguistic parsers support, for general text and multi-language
  • Support to additional input and output formats, including BioC
  • SDK usability improvements
  • Performance improvements
  • Stability improvements

What you can do with Neji?

With Neji you can build text mining processing pipelines for:

  • Rapidly create REST services and interactive web pages for text mining tasks
  • Concept recognition:
    • Dictionary-based, Machine learning-based and Rule-based
  • Train machine learning models for NER (Named Entity Recognition):
    • Normalization with dictionary matching and Stopword filtering
  • Linguistic parsing:
    • Sentence splitting, Tokenisation, Lemmatisation, Chunking and Dependency parsing
  • Convert between corpora formats:
    • Input formats: BioC, XML, HTML and Text
    • Output formats: JSON, A1, BC2, Base64, BioC, CoNLL, IeXML, Pipe and PipeExtended

Quick start

  1. Download and extract the latest version of Neji
  2. Use to annotate
  3. Use to train new NER models


Neji's documentation is available at

Usage notification

If you are using Neji in your projects, please let us know by sending an e-mail to or

Bugs and features requests

Have a bug or a feature request?

If your problem or idea is not addressed yet, please open a new issue.

Support and consulting

BMD Software

Please contact BMD Software for professional support and consulting services.

Copyright and license

Copyright (C) 2016 BMD Software and University of Aveiro

Neji is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. To view a copy of this license, visit