|Developer(s)||Apache Software Foundation|
4.0.0 / April 25, 2017
|Type||Natural language processing, Bioinformatics, Text mining, Information Extraction|
Apache cTAKES: clinical Text Analysis and Knowledge Extraction System is an open-source natural language processing system for information extraction from electronic health record clinical free-text. It processes clinical notes, identifying types of clinical named entities — drugs, diseases/disorders, signs/symptoms, anatomical sites and procedures. Each named entity has attributes for the text span, the ontology mapping code, context (family history of, current, unrelated to patient), and negated/not negated.
cTAKES was built using the UIMA Unstructured Information Management Architecture framework and OpenNLP natural language processing toolkit.
Components of cTAKES are specifically trained for the clinical domain, and create rich linguistic and semantic annotations that can be utilized by clinical decision support systems and clinical research.
These components include:
- Named Section identifier
- Sentence boundary detector
- Rule-based tokenizer
- Formatted list identifier
- Context dependent tokenizer
- Part-of-speech tagger
- Phrasal chunker
- Dictionary lookup annotator
- Context annotator
- Negation detector
- Uncertainty detector
- Subject detector
- Dependency parser
- patient smoking status identifier
- Drug mention annotator
Development of cTAKES began at the Mayo Clinic in 2006. The development team, led by Dr. Guergana Savova and Dr. Christopher Chute, included physicians, computer scientists and software engineers. After its deployment, cTAKES became an integral part of Mayo's clinical data management infrastructure, processing more than 80 million clinical notes.
- University of Colorado
- Brandeis University
- University of Pittsburgh
- University of California at San Diego
Such collaborations have extended cTAKES' capabilities into other areas such as Temporal Reasoning, Clinical Question Answering, and coreference resolution for the clinical domain.
In 2013, cTAKES released their first release as an Apache incubator project: cTAKES 3.0.
In March 2013, cTAKES became an Apache Top Level Project (TLP).
- Denecke, Kerstin (2015-08-31). "Tools and Resources for Information Extraction". Health Web Science: Social Media Data for Healthcare. Springer. p. 67. ISBN 978-3-319-20582-3 – via Google Books.
- Khalifa, Abdulrahman; Meystre, Stéphane (2015-12-01). "Adapting existing natural language processing resources for cardiovascular risk factors identification in clinical notes". Journal of Biomedical Informatics. Proceedings of the 2014 i2b2/UTHealth Shared-Tasks and Workshop on Challenges in Natural Language Processing for Clinical Data. 58 (Supplement): S128–S132. doi:10.1016/j.jbi.2015.08.002.
- Khudairi, Sally (2017-04-25). "The Apache Software Foundation Announces Apache® cTAKES™ v4.0" (Press release). Forest Hill, MD: The Apache Software Foundation. Globe Newswire. Retrieved 2017-09-20.
- Savova, Guergana K; Masanz, James J; Ogren, Philip V; Zheng, Jiaping; Sohn, Sunghwan; Kipper-Schuler, Karin C; Chute, Christopher G (2010). "Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications". Journal of the American Medical Informatics Association : JAMIA. 17 (5): 507–513. doi:10.1136/jamia.2009.001560. ISSN 1067-5027. PMC . PMID 20819853.
- "History". Apache cTAKES™ - clinical Text Analysis Knowledge Extraction System. 2015-06-22. Retrieved 2018-01-11.
- cTAKES Official Website
- Apache cTAKES Project Information page from ASF
- Abstract (JAMIA)
- Open Health Natural Language Processing (OHNLP) Consortium
- Strategic Health IT Advanced Research Projects (SHARP) Program
- SHARP Area 4 - Secondary Use of EHR Data
- The Automated Retrieval Console (ARC)
- Informatics for Integrating Biology and the Bedside