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Uses Java Webstart

Noble Coder

Named Entity Recognition (NER) engine for biomedical text

NOBLE Coder is a generic tool and API that auto codes free text with concepts from controlled terminology. Its algorithm is similar to IndexFinder or ConceptMapper, but unlike these systems, NOBLE Coder uses NoSQL for storage which enables it to code with huge terminologies while keeping its in-memory footprint small.

Noble Coder is part of the Noble Tools Suite, a set of Natural Language Processing (NLP) tools and Application Programming Interfaces (API) written in Java for interfacing with ontologies, auto coding text and extracting information. The Noble Tools suite also includes a generic ontology API for interfacing with Web Ontology Language (OWL) files, OBO and BioPortal ontologies and a number of support utilities and methods useful for NLP (e.g. string normalization, ngram and stemming)


Noble Tools was developed by Eugene Tseytlin in the Crowley-Jacobson Lab at the Department of Biomedical Informatics, University of Pittsburgh. NOBLE was originally developed for the SlideTutor Project, but is now a key component of the TIES system. Other projects have used NOBLE tool as well, including EDDA

Work on NOBLE Coder was supported by the following grants:

  • NCI - 1U24CA180921 (PI Crowley-Jacobson)
  • NCI - R01 CA132672 (PI Crowley-Jacobson)
  • NCI - R25 CA101959 (PI Crowley-Jacobson)
  • NLM - R00 LM010943 (PI Bekhuis)

Try It

Enter text with medical terms:

Noble Coder Annotated Text:

Use It


From the Browser

The Noble Coder Tool can be used to run Noble Coder on a set of documents using either pre-built terminologies or your own custom built terminology.



Uses Java Webstart. You can also download an executable JAR file here
Help Documentation: http://noble-tools.dbmi.pitt.edu/help.html


In Your Code

If you are interested in using Noble Coder from within your Java code, a library jar file is available for you to download.

DOWNLOAD JAR

Javadoc API Documentation: http://noble-tools.dbmi.pitt.edu/doc/api


Use pre-built terminologies

We have pre-built some terminologies for you to use. Download and install them by simply unzipping the directory into the $USER_DIR/.noble/terminologies folder.

  • NCI Thesaurus (15.03e) - NCI Thesaurus (NCIt) provides reference terminology for many NCI systems. It covers vocabulary for clinical care, translational and basic research, and public information and administrative activities.
  • NCI Metathesaurus (201502) - NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities.
  • SNOMED CT (2014_09) - SNOMED Clinical Terms (SNOMED CT) is the most comprehensive, multilingual clinical healthcare terminology in the world.
  • MeSH (2014_02) - MeSH (Medical Subject Headings) is the NLM controlled vocabulary thesaurus used to index articles for PubMed.
  • RxNORM (13AB_140303F) - RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, MediSpan, Gold Standard Drug Database, and Multum. By providing links between these vocabularies, RxNorm can mediate messages between systems that are not using the same software and vocabulary.
  • FMA (4.2.0) - The Foundational Model of Anatomy Ontology (FMA) is a project of the Structural Informatics Group from the Department of Biological Structure at the University of Washington (UW) School of Medicine. The FMA is an intellectual property of the University of Washington. The FMA is a reference ontology for the domain of human anatomy.

Licensing

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If you are an individual user or an educational institution, you can redistribute it and/or modify it under the terms of the BSD 3-Clause License.

Copyright (c) 2015, University of Pittsburgh
All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

  • Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
  • Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
  • Neither the name of [project] nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

For all other users, licensing is decided on a case by case basis through Nexi Inc.

If you have any questions about licensing, please Nexi at: http://nexihub.com/contact

GitHub Project:
https://github.com/dbmi-pitt/nobletools