ccp nlp

a library of NLP-related code with a trend towards the biomedical domain. Much of this code takes advantage of the Apache UIMA infrastructure and complies with the CCP UIMA Type System, a meta-model type system that eschews explicitly represented types in favor of a generic structure capable of referencing an external data model that containing the full semantic complexity of the types required for a particular application. The philosophy behind this approach to a type system is further described here, and an old, but still applicable document describing its major components is included as part of this project, here.

History

This project represents an evolution of the original bionlp-uima code base which still exists here, for historical purposes only.

Development

This project follows the Git-Flow approach to branching as originally described here. To facilitate the Git-Flow branching approach, this project makes use of the jgitflow-maven-plugin as described here.

Code in the master branch reflects the latest release of this library. Code in the development branch contains the most up-to-date version of this project.

Module descriptions

The ccp-nlp project is a multi-module Maven project. Below is a brief description of the contents of each module.

• ccp-nlp
  • the parent module
• ccp-nlp-core
  • contains utility code for working with text annotations
• ccp-nlp-doc2txt
  • contains code for converting documents from the PubMed Central XML format to plain text
• ccp-nlp-uima
  • includes the CCP type system and some utility code supporting UIMA component construction
• ccp-nlp-annotators
  • contains various utility annotators for such tasks as:
    • filtering annotations from the CAS
    • modifying metadata of annotations in the CAS
    • comparing groups of annotations to each other
• ccp-nlp-uima-collections
  • contains UIMA collection reader component implementations capable of reading documents from:
    • the file system
    • individual lines in a single file
    • a collection of Medline or PubMed XML files
• ccp-nlp-uima-serialization
  • contains analysis engines for annotation serialization in various formats (XMI, Inline XML, BioNLP)
• ccp-nlp-uima-shims
  • a library of simple interfaces designed to facilitate the development of type-system-independent UIMA components
  • contains implementations specific to the CCP type system
• ccp-nlp-wrapper-banner
  • a wrapper of the BANNER annotation tool for use with the CCP type system
• ccp-nlp-wrapper-conceptmapper
  • a wrapper of the UIMA Sandbox ConceptMapper tool
  • provides descriptor-free configuration via UIMAFit, dictionary construction from arbitrary OBO/OWL formatted ontology files, and integration with the CCP Type System

Maven signature

<dependency>
  <groupId>edu.ucdenver.ccp</groupId>
  <artifactId>ccp-nlp-core</artifactId>
  <version>3.3.2</version>
</dependency>

<dependency>
  <groupId>edu.ucdenver.ccp</groupId>
  <artifactId>ccp-nlp-doc2txt</artifactId>
  <version>3.3.2</version>
</dependency>

<dependency>
  <groupId>edu.ucdenver.ccp</groupId>
  <artifactId>ccp-nlp-uima</artifactId>
  <version>3.3.2</version>
</dependency>

<dependency>
  <groupId>edu.ucdenver.ccp</groupId>
  <artifactId>ccp-nlp-uima</artifactId>
  <version>3.3.2</version>
  <type>test-jar</type>
  <scope>test</scope>
</dependency>

<dependency>
  <groupId>edu.ucdenver.ccp</groupId>
  <artifactId>ccp-nlp-uima-annotators</artifactId>
  <version>3.3.2</version>
</dependency>

<dependency>
  <groupId>edu.ucdenver.ccp</groupId>
  <artifactId>ccp-nlp-uima-collections</artifactId>
  <version>3.3.2</version>
</dependency>

<dependency>
  <groupId>edu.ucdenver.ccp</groupId>
  <artifactId>ccp-nlp-uima-serialization</artifactId>
  <version>3.3.2</version>
</dependency>

<dependency>
  <groupId>edu.ucdenver.ccp</groupId>
  <artifactId>ccp-nlp-uima-shims</artifactId>
  <version>3.3.2</version>
</dependency>

<dependency>
  <groupId>edu.ucdenver.ccp</groupId>
  <artifactId>ccp-nlp-wrapper-banner</artifactId>
  <version>3.3.2</version>
</dependency>

<dependency>
  <groupId>edu.ucdenver.ccp</groupId>
  <artifactId>ccp-nlp-wrapper-conceptmapper</artifactId>
  <version>3.3.2</version>
</dependency>

<repository>
	<id>bionlp-sourceforge</id>
	<url>http://svn.code.sf.net/p/bionlp/code/repo/</url>
</repository>