New to NLP
Topaz is an application, which extracts relevant medical concepts and modifiers, such as negation and temporality, from clinical documents.
When Topaz is run, clinical reports in a folder designated as "input_directory" in startup.properties are analyzed and results are stored in XML format to corresponding files in a folder designated as "output_directory".
Topaz is a UIMA collection processing engine (CPE), which extract relevant medical concepts and modifiers, such as negation and temporality, from clinical documents.
A single distribution folder is provided, which contains information and configuration files. UIMA description files are located in the /desc directory. The main CPE description file is /desc/UTopazCPE.xml.
Java SE 6 JRE or JDK
Dual core processor
4 GB of RAM
1 GB of storage for program
10+ GB of storage recommended for large datasets
To download Topaz, please go to the University of Pittsburgh's website to request access.
NLP Task PerformedInformation Extraction
Topaz User Documentation
Learn how to install and configure Topaz startup properties.
Learn how to edit and extend Topaz's Knowledge Base to make the tool fit your domain and information extraction needs.
A step by step walkthrough on how to enhance Topaz's knowledge base.
Learn how to run Topaz on your machine.
If you are familiar with UIMA, learn how you can integrate Topaz into other UIMA analysis engines. In addition, the primitive analysis engines contained in Topaz are described further.
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Pineda AL, Tsui FC, Visweswaran S, Cooper GF. Detection of Patients with Influenza Syndrome Using Machine-Learning Models Learned from Emergency Department Reports. ISDS 2012 Conference. Online Journal of Public Health Informatics. 5(1):e41, 2013
Samore MH. Natural Language Processing: Can it Help Detect Cases and Characterize Outbreaks? Advances in Disease Surveillance 2008;5:59