OBO-Annotator is a natural language processing tool for extracting ontological concepts from text. It uses a text analysis engine based on the Unstructured Information Management Architecture (UIMA) framework and makes use of ontologies that are available in either OBO or OWL format (e.g., at the OBO_Foundry). The application is capable of combining one or more ontologies into a single dictionary. This dictionary is then used by a look-up algorithm to identify terms in text. Users are thus able to combine any number of Web accessible ontologies (using Uniform Resource Identifiers [URIs]). The application is designed to be stateful in that it starts in the state of its last termination. Specifically, OBO-Annotator recalls which ontologies were loaded most recently, as well as which ontologies were updated or added. Currently, the application requires that input documents are in the Medline flat file format. OBO-Annotator returns a pipe-delimited text file, where the fields are:

document_id, term_found, string_in_document, source_ontology, ontology_id, document_starting_character_position

Additional details about how the tool works and documentation can be downloaded from here.

System Requirements
OBO-Annotater is written in Java, and thus designed to be platform independent. The source code and executable jar can be downloaded from the following link:
http://obo-annotator.svn.sourceforge.net/viewvc/obo-annotator/obo-annotator/oboannotator.jar

Installing and Using OBO Annotator

  1. Download the oboannotator.jar file
  2. Uncompress the jar file from the location of download as follows: jar xvf oboannotator.jar
  3. Run the jar file from the command line as follows: java -Xmx1024M -jar oboannotator.jar