uima-uimaj: A Java repository from sark245

Welcome to the Apache UIMA Java SDK

Apache UIMA helps you managing unstructured data (such as texts) that is enriched useful information. For example, if you want to identify a mention of an entity in a text or possible link that entity to a reference dataset, then Apache UIMA provides:

a convenient data structure --the Common Analysis Structure (CAS)-- to represent that data
a type system concept service as a schema for the enriched data that is stored in the CAS
a component model consisting of reader, analysis engines (processors) and consumers (writers) to process that data
a model for aggregating multiple analysis engines into pipelines and executing them (optionally parallelized)
various options for (de)serializing the CAS from/to different formats
any many additional features!

Note the Apache UIMA Java SDK only provides a framework for building analytics but it does not provide any analytics. However, there are various third-parties that build on Apache UIMA and that provide collections of analysis components or ready-made solutions.

Using Apache UIMA Java SDK

You can add the Apache UIMA Java SDK to your project easily in most build tools by importing it from Maven Central. For example if you use Maven, you can add the following dependency to your project:

<dependency>
  <groupId>org.apache.uima</groupId>
  <artifactId>uimaj-core</artifactId>
  <version>3.2.0</version>
</dependency>

Next, we give a few brief examples of how to use the Apache UIMA Java SDK and the Apache uimaFIT library. Apache uimaFIT is a separate dependency that you can add:

<dependency>
  <groupId>org.apache.uima</groupId>
  <artifactId>uimafit-core</artifactId>
  <version>3.2.0</version>
</dependency>

Creating a type system

The type system defines the type of information that we want to attach to the unstructured information (here a text document). In our example, we want to identify mentions of entities, so we define a type my.Entity with a feature category which can be used to store the category the entity belongs to.

To illustrate the information UIMA internally maintains about the annotation schema, we write the generated schema as XML to screen.

String TYPE_NAME_ENTITY = "my.Entity";
String TYPE_NAME_TOKEN = "my.Token";
String FEAT_NAME_CATEGORY = "category";

var tsd = UIMAFramework.getResourceSpecifierFactory().createTypeSystemDescription();
tsd.addType(TYPE_NAME_TOKEN, "", CAS.TYPE_NAME_ANNOTATION);
var entityTypeDesc = tsd.addType(TYPE_NAME_ENTITY, "", CAS.TYPE_NAME_ANNOTATION);
entityTypeDesc.addFeature(FEAT_NAME_CATEGORY, "", CAS.TYPE_NAME_STRING);

tsd.toXML(System.out);

Creating a Common Analaysis Structure object

Now we create a Common Analysis Structure (CAS) object into which we store the text that we want to analyse.

Again, to illustrate the information that UIMA internally stores in the CAS object, we write an XML representation of the object to screen.

var cas = CasFactory.createCas(tsd);
cas.setDocumentText("Welcome to Apache UIMA.");
cas.setDocumentLanguage("en");

CasIOUtils.save(cas, System.out, SerialFormat.XMI_PRETTY);

Adding and retrieving annotations

Now, we create an annotation of the type my.Entity to identify the mention of Apache UIMA in the example text.

Finally, we iterate over all annotations in the CAS and print them to screen. This includes the default DocumentAnnotation that is always created by UIMA as well as the my.Entity annotation that we created ourselves.

var entityType = cas.getTypeSystem().getType(TYPE_NAME_ENTITY);
var entity = cas.createAnnotation(entityType, 11, 22);
cas.addFsToIndexes(entity);

for (var anno : cas.<Annotation>select(entityType)) {
   System.out.printf("%s: [%s]%n", anno.getType().getName(), anno.getCoveredText());
}

Working with analysis components

In order to organize different types of analysis into steps, we usually package them into individual analysis engines. We illustrate now how such components can be built and how they can be put executed as an analysis pipeline.

class TokenAnnotator extends CasAnnotator_ImplBase {
  public void process(CAS cas) throws AnalysisEngineProcessException {
    var tokenType = cas.getTypeSystem().getType(TYPE_NAME_TOKEN);
    var bi = BreakIterator.getWordInstance();
    bi.setText(cas.getDocumentText());
    int begin = bi.first();
    int end;
    for (end = bi.next(); end != BreakIterator.DONE; end = bi.next()) {
      var token = cas.createAnnotation(tokenType, begin, end);
      cas.addFsToIndexes(token);
      begin = end;
    }
  }
}

class EntityAnnotator extends CasAnnotator_ImplBase {
  public void process(CAS cas) throws AnalysisEngineProcessException {
    var tokenType = cas.getTypeSystem().getType(TYPE_NAME_TOKEN);
    var entityType = cas.getTypeSystem().getType(TYPE_NAME_ENTITY);
    for (var token : cas.<Annotation>select(tokenType)) {
      if (Character.isUpperCase(token.getCoveredText().charAt(0))) {
        var entity = cas.createAnnotation(entityType, token.getBegin(), token.getEnd());
        cas.addFsToIndexes(entity);
      }
    }
  }
}

cas = CasFactory.createCas(tsd);
cas.setDocumentText("John likes Apache UIMA.");
cas.setDocumentLanguage("en");

var pipeline = AnalysisEngineFactory.createEngineDescription(
  AnalysisEngineFactory.createEngineDescription(TokenAnnotator.class),
  AnalysisEngineFactory.createEngineDescription(EntityAnnotator.class));

SimplePipeline.runPipeline(cas, pipeline);

for (var anno : cas.<Annotation>select(entityType)) {
   System.out.printf("%s: [%s]%n", anno.getType().getName(), anno.getCoveredText());
}

Building

To build Apache UIMA, you need at least a Java 8 JDK and a recent Maven 3 version.

After cloning the repository, change into the repository directory and run the following command:

mvn clean install

UIMA component providers

Here is list of several well-known projects that provide their analysis tools as UIMA components or that wrap third-party analysis tools as UIMA components:

Apache cTAKES - Natural language processing system for extraction of information from electronic medical record clinical free-text.
Apache OpenNLP - Wraps OpenNLP for UIMA. Adaptable to different type systems.
Apache Ruta - Generic rule-based text analytics. Works with any type system.
ClearTK - Wraps several third-party tools (OpenNLP, CoreNLP, etc.) and offers a flexible framework for training own machine learning models. Uses CleartK type system.
DKPro Core - Wraps many third-party tools (OpenNLP, CoreNLP, etc.) and supporting a wide range of data formats. Uses DKPro Core type system.
JULIE Lab Component Repository (JCoRe) Wraps several third-party tools (OpenNLP, CoreNLP, etc.) and supporting a wide range of data formats, in particular from the biomed domain. Uses JCore type system.

This is not an exhaustive list. If you feel any particular project should be listed here, please let us know. You could find additional ones e.g. by:

following the GitHub dependency graph
searching Google Scholar for UIMA

Interoperability

The Apache UIMA Java SDK can be used with any programming language based on the Java Virtual Machine including Java, Groovy, Scala, and many other languages.

Interoperability with Python can for example be achieved via the third-party DKPro Cassis library which can be used to read, manipulate and write CAS data in the XMI format.

sark245/uima-uimaj