TimeLine API Library

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CNTRO TimeLine API Library

The CNTRO Timeline library is a Java library. This library is intended to be used by developer and analysts who want to integrate this library in their workspace to compute temporal information about clinical events.

Current Release is 1.1.1 (Updated April 24, 2013)

Prerequisites

1. The library reads OWL files as input and these OWL files represents temporal events and relations between them.

The instances of these entities must be of types defined in the CNTRO ontology or extended version of CNTRO ontology for normalized events.
These ontologies are:
  • CNTRO Ontology:
http://informatics.mayo.edu/CNTRO/CNTRO2.0.owl
  • Normalized Event Ontology:
http://informatics.mayo.edu/CNTRO/AE-lst%20(new).owl

2. The OWL files can be either manually edited or can be exported out form annotator tool, which is a Stanford’s Protégé 4.x Editor plugin - ‘Semantator’.

More information on ‘Semantator’ can be found at:
http://informatics.mayo.edu/CNTRO/index.php/Semantator

3. There is no user interface available and should be treated as java library which needs to be used in someone’s workspace.

4. For building and extending the source of this library:

Since this library is written as Maven Project, you may have to import and use it as a Maven Project, otherwise a conversion to a
another type of project might be required.

Download Library Instructions

1. Option 1: Using Jar File

The library is available to be downloaded as a Java archive from the location:
http://informatics.mayo.edu/maven/content/repositories/releases/edu/mayo/bsi/cntro/timeline/cntro-timeline/1.1.1/cntro-timeline-1.1.1.jar

2. Option 2: Using as a Maven Dependency

The timeline library has been developed as a Maven project and is available to be included in user’s pom.xml file using the following information:
Repository location

<repository>
  <id>edu.informatics.maven.Releases</id>
  <name>Informatics Maven Release Repository</name>
  <url>http://informatics.mayo.edu/maven/content/repositories/releases/</url>
  <releases>
    <enabled>true</enabled>
  </releases>
  <snapshots>
    <enabled>false</enabled>
  </snapshots>
</repository>

Dependency

<dependency>
  <groupId>edu.mayo.bsi.cntro.timeline</groupId>
  <artifactId>cntro-timeline</artifactId>
  <version>1.1.1</version>
</dependency>

Download Library Source

The source code for CNTRO TimeLine Library can be downloaded from GitHub at: https://github.com/dksharma/cntro-timeline.git
The project is Java Maven type of project and once you checkout the code, you should be able to build the code and run the test cases.
Sample Code:
The sample code usage is demonstrated in the test case in Java file: SampleEventTest.java
“src/main/java/edu/mayo/informatics/cntro/test/SampleEventTest.java”
There may be other test cases in the same directory as the file above, but they are specially created for particular analysis for files in other resource directories.
You can use those as examples to help you finding various ways to use the API and auxiliary tools included.
Service Interface
The main query service interface (for using the APIs) is defined in: CNTROQuery.java
“src/main/java/edu/mayo/informatics/cntro/queryIF/CNTROQuery.java”

Additional Documentation

This documentation and some additional documentation is included with the project in the file CNTROTimeLineAPILibrary.docx

License

Copyright [2013]

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.