1. UIMA Introduction SHARPn Summit June 11, 2012
Hi, I’m James Masanz from Mayo Clinic.
Welcome.

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

3. UIMA Terminology CAS XCAS JCAS View Analysis Engine (AE) / Annotator
XML output: XCAS XMI
Type System JCasGen
CAS Visual Debugger (CVD)
CPE (Collection Processing Engine)
We will not have time to cover all these today.
Note, those terms in italics are UIMA-specific.

4. UIMA Framework Tooling Defining data types
Passing data from one component to another
Tooling
Viewing results
Debugging
Editing XML visually
UIMA is both a framework and tooling built around the framework.
UIMA = Unstructured Information Management Architecture

5. Data Through a Pipeline
Type System
Defines the data types passed along
CAS (Common Analysis Structure)
Container for the data passed along
Created by UIMA from the Type System
Type System defines what data types will be allowed in the CAS.
A CAS is a runtime datastructure.

6. Parts of a UIMA Pipeline
Collection Reader
Read input document
Analysis Engine(s) / Annotator(s)
Process document
CAS Consumer
Output data

7. Tying a Pipeline Together
CPE descriptor (Collection Processing Engine)
Collection Reader
Analysis Engine(s)
CAS Consumer
Aggregate analysis engine
Multiple Analysis Engines and their order

8. Pipeline Example UIMA term Collection Reader Example
Analysis Engine
CAS Consumer
Example
Read files from a dir
Sentence detector
Tokenizer annotator
Part of Speech tagger
Output tokens to DB

9. UIMA plugin for Eclipse
Provides visual editors for descriptors
Mini GUI for selecting options
Rather than editing XML directly
An “Update site” exists for installing plugin

10. UIMA Tooling Options Tools: Options: CPE Configurator
CVD (CAS Visual Debugger)
Options:
Command line scripts/.bat files
Run within Eclipse

11. Running a Pipeline - CPE
cTAKES provides a script and a bat file
runctakesCPE
Choose a CPE descriptor, such as
test_plaintext.xml
from
cTAKESdesc/cdpdesc/collection_processing_engine

12. Viewing Annotations - CVD
Viewing annotations using the CVD
Load the Type System
Load the XCAS or XMI

13. Annotation Viewers UIMA tools Viewing XML output
CVD (CAS Visual Debugger)
Annotation viewer
Viewing XML output
Any XML viewer
Any text editor

14. Questions?

15. Supplemental slides follow

16. Options to Run a Pipeline
CPE GUI
CVD GUI
Single Aggregate Analysis Engine
No Collection Reader
Instantiate a CpeDescription and invoke
the process() method
uimaFIT– removes dependency on XML

17. Creating a New Annotator
Within Eclipse
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!

18. 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
Load an Analysis Engine
Paste/type in text to process
Family history of hyperlipidemia.

19. 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 UIMA Update site for use in Eclipse
UIMA Update site for use in Eclipse

21. address