Apache cTAKES

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Apache cTAKES
Developer(s) Apache Software Foundation
Stable release
4.0.0 / April 25, 2017 (2017-04-25)
Written in Java
Operating system Cross-platform
Type Natural language processing, Bioinformatics, Text mining, Information Extraction
License Apache 2.0
Website ctakes.apache.org

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.[1]

cTAKES was built using the UIMA Unstructured Information Management Architecture framework and OpenNLP natural language processing toolkit.[2][3]

Components[edit]

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.[4]

These components include:

  • Named Section identifier
  • Sentence boundary detector
  • Rule-based tokenizer
  • Formatted list identifier
  • Normalizer
  • 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

History[edit]

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.[5]

When Dr. Savova's moved to Boston Children's Hospital in early 2010, the core development team grew to include members there. Further external collaborations include:[5]

  • 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.[5]

In 2010, cTAKES was adopted by the i2b2 program and is a central component of the SHARP Area 4.[5]

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).[5]

See also[edit]

References[edit]

  1. ^ 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. 
  2. ^ 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. 
  3. ^ 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. 
  4. ^ 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 2995668Freely accessible. PMID 20819853. 
  5. ^ a b c d e "History". Apache cTAKES™ - clinical Text Analysis Knowledge Extraction System. 2015-06-22. Retrieved 2018-01-11. 

External links[edit]