OHNLP Tool List

From Open Health Natural Language Processing (OHNLP) Consortium
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There are 13 OHNLP Tools listed here.

To add or modify an entry in the list of OHNLP Tools:

  1. Add or modify an OHNLP Tool entry
  2. Update (edit and save) this Tool List page

To download a printable spreadsheet version -> CSV

Click on a Tool name to learn more about the release.

Tool Name License Description
Biomedicus ALv2 The BiomedICUS project is intended to provide a basic platform that can be used for students and researchers interested in biomedical NLP to learn not only how to deploy these applications for processing large collections of text but also how to participate in the development of new biomedical NLP modules and applications.
Clamp Public The CLAMP is a natural language processing tool, based on several award-winning methods and applications developed in University of Texas Health Science Center at Houston, School of Biomedical Informatics.
MedCoref ALv2 MedCoref is an implementation of the multi-pass sieve-based co-reference resolution system for clinical notes.
MedEx ALv2 MedEx-UIMA is an open source tool for extracting medication and signature information from clinical text. It is a Java implementation of the existing (Python) MedEx system, and is based on the UIMA framework. Using the UIMA framework, we re-built the MedEx in Java as a pipeline-based system, where we defined modules including Sentence Boundary Detector, Tokenizer, Section Tagger, Semantic Tagger, Parser and Encoder. The encoder is a new component in MedEx-UIMA, which maps drug name, dose, and form information to most specific RxNorm concepts and normalizes frequency information to TIMEX3 format.
MedKAT/p ALv2 MedKAT/P (Medical Knowledge Analysis Tool) is tailored to the medical/pathology domain, containing components for extracting cancer-specific characteristics from unstructured text.
MedTagger ALv2 MedTagger includes three major components:

MedTagger for indexing based on dictionaries, MedTaggerIE for information extraction based on patterns,

and MedTaggerML for machine learning-based named entity recognition.
MedTime GPLv3 Detect and normalize TIMEX3-based temporal expressions from clinical narrative.
MedXN ALv2 Medication Extraction and Normalization is a medication information extraction system that focuses on assigning the most specific RxNorm RxCUI to medication descriptions. MedXN uses flexible matching, abbreviation expansion, inference, etc. MedXN uses externalized resources to allow end users to customize it simply.
MutD CPL1.0 MutD is a text mining system that extracts relations between protein, mutation and disease from biomedical text.
PEP ALv2 Pathology Extraction Pipeline - an extension to MedKAT/p. Naveen Ashish
UIMATS Ontology ALv2 Transforms a UIMA Type System to an OWL format representation.
V3NLP Public v3NLP is an NLP development framework for VINCI.
Valx ALv2 A system for extracting and structuring numeric comparison statements in text. (This system will be made available TBD.)

List of license abbreviations:

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