1. UIMA SHARP 4 - NLP May 25, 2010

2. Outline UIMA Terminology (not just TLAs) Parts of a UIMA pipeline Running a pipeline Viewing annotations Creating a new annotator

3. UIMA terminology CAS XCAS JCAS View Analysis Engine (AE) / Annotator –Aggregate Analysis Engine XML output: XCAS XMI Type System JCasGen CAS Visual Debugger (CVD) CPE (Collection Processing Engine)

4. UIMA and Eclipse UIMA plugin for Eclipse requires EMF UIMA plugin provides visual editors for descriptors An “Update site” exists for installing plugin

5. UIMA Pipeline Flow Collection Reader (CAS Initializer - deprecated) Analysis Engine (AE) / Annotator CAS Consumer

6. Pipeline Example Example Read files from a dir Sentence annotator Tokenizer annotator Output tokens to a DB UIMA term Collection Reader Analysis Engine CAS Consumer

7. Options for running UIMA tools Tools: –CPE Configurator –CVD Options: –Command line scripts/.bat files –Run within Eclipse

8. Tying together a UIMA pipeline Type System –Defines the data types passed along CAS (Common Analysis Structure) –Container for the data

9. Tying together a UIMA pipeline CPE descriptor – select the parts –Collection Reader –Analysis Engine(s) –CAS Consumer Aggregate analysis engine –Multiple Analysis Engines and their order

10. Options for running a pipeline CVD GUI –Single Aggregate Analysis Engine –No Collection Reader CPE GUI Instantiate a CpeDescription and invoke the process() method 2.3. Running a CPE from Your Own Java Application

11. Example: Running a pipeline Running cTAKES within Eclipse using a CPE Use run configuration UIMA_CPE_GUI--clinical_documents_pipeline CPE test1.xml from clinical documents pipeline\desc\collection_processing_engine

12. Options for viewing annotations CVD Annotation viewer XML viewer Text editor

13. Example: Viewing annotations Viewing annotations using the CVD Load the Type System Load the XCAS or XMI

14. Example: Running an AE in CVD Using CVD to run an Analysis Engine –No Collection Reader –Single Analysis Engine (can be an aggregate) –No CAS Consumer –Just paste/type in text to process Family history of hyperlipidemia.

15. Creating a New Annotator Create Java project Right click -> Add UIMA Nature Add UIMA jars to.classpath (Build Path) Create Analysis Engine (AE) descriptor Add types to AE descriptor, or optionally create separate Type System descriptor Write code!

16. Questions?

17. Supplemental slides follow

18. Example: Creating a PEAR file Right click -> Add UIMA Nature Right click -> Generate Pear Select Analysis Engine descriptor Select OS and JDK Modify Properties if needed Select what to include

19. Example: Modifying a parameter UIMA’s descriptor editors allow you to modify most parameters without looking at the XML itself.

20. Links Getting started with UIMA http://uima.apache.org/doc-uima-annotator.html UIMA Update site for use in Eclipse http://www.apache.org/dist/incubator/uima/eclipse-update-site/

21. Email address masanz.james@mayo.edu