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cTAKES

cTAKES. Part 1: cTAKES GUI (demo) Part 2: cTAKES Tutorial. Pei J Chen Children’s Hospital Boston / Harvard Medical School. GUI: Key Features. Default Clinical Processing Pipeline Default Central Store of cTAKES output Abstraction from UIMA concepts Dynamic Configuration

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cTAKES

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  1. cTAKES Part 1: cTAKES GUI (demo) Part 2: cTAKES Tutorial Pei J Chen Children’s Hospital Boston /Harvard Medical School

  2. GUI: Key Features • Default Clinical Processing Pipeline • Default Central Store of cTAKES output • Abstraction from UIMA concepts • Dynamic Configuration • Centrally Managed Experiments

  3. Preview Single Doc

  4. Preview Output

  5. Batch Processing

  6. Dynamic Data Sources

  7. Dynamic NLP Pipeline

  8. Dynamic Processors

  9. Centrally Stored Output Sample output on GUI

  10. Centrally Stored Output RDMS (hypersonic DB) Easily export results: select * from ctakes_experiment_result;

  11. Technologies Used Front-End Web GUI • ExtJS • JavaScript Back-End cTAKES • JAVA • UIMA • umiaFIT Middleware Web Services • JAVA • ExtDirect Spring • JSON

  12. Beta release available https://ohnlp.svn.sourceforge.net/svnroot/ohnlp/branches/cTAKES-GUI-0.0.1/ctakes-gui-0.0.1.zip Prerequisite: Java JDK (not JRE) 1.6+ installed Instructions: Unzip and run startup.sh or startup.bat

  13. Thoughts?

  14. Part 2: cTAKES Tutorial • Technical Details • cTAKES components • Where to download cTAKES • Documentation

  15. cTAKES Technical Details • Open source • Apache v2.0 license • Java 1.6 • Dependency on UMLS which requires a UMLS license (free) • Framework • IBM’s Unstructured Information Management Architecture (UIMA) open source framework, Apache project • Methods • Natural Language Processing methods (NLP) • Based on standards and conventions to foster interoperability • Application • High-throughput system

  16. cTAKES: Components • Sentence boundary detection (OpenNLP technology) • Tokenization (rule-based) • Morphologic normalization (NLM’s LVG) • POS tagging (OpenNLP technology) • Shallow parsing (OpenNLP technology) • Named Entity Recognition • Dictionary mapping (lookup algorithm) • types: diseases/disorders, signs/symptoms, anatomical sites, procedures, medications • Assertion module • Dependency parser • Constituency parser • Semantic Role Labeler • Coreference resolver • Drug Profile module • Smoking status classifier

  17. Download cTAKES • cTAKES (currently 2.5): • http://sourceforge.net/projects/ohnlp/files/cTAKES • svn co “https://ohnlp.svn.sourceforge.net/svnroot/ohnlp/branches/SHARPn-cTAKES/” • UIMA Core (2.3.1) • http://uima.apache.org/downloads.cgi • UIMA Eclipse IDE Plugin

  18. Thoughts?

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