Group: JULIELab

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The JCoRe type system.

A simple project for the automatic creation of descriptors for UIMAfit-enabled components.

Utilities for UIMA compliant components.

JULIELab Java Utilities

Reads XML using the VTD parser.

A utility for managing documents stored in a PostgreSQL database. The documents are imported into a PostgreSQL DB as full texts with the goal to be able to retrieve the documents by their PubMedID efficiently.

The central interfaces and services for the concept database manager.

A Collection Reader that converts XML, stored in a database, to CAS objects. The conversion is the same employed by the jcore-xml-reader, making use of the jcore-xml-mapper.

This is a JeDIS component. It can be used to set the 'last component' column in a subset table.

Abstract database reader for database driven processing

JCoRe Pipeline Builder Base

Reads CAS XMI data from a relational database (Postgres). Thus, the stored CASes may then be processed further.

A UIMA wrapper around the BioSem Event Extractor from the University of Amsterdam. http://www.ncbi.nlm.nih.gov/pubmed/22859502

UIMA wrapper for the OpenNLP POS Tagger. The difference to the official OpenNLP UIMA wrapper is basically the type system.

UIMA wrapper for the OpenNLP Sentence Segmentation. The difference to the official OpenNLP UIMA wrapper is basically the type system.

Writes CAS data in XMI format into a relational (PostgreSQL) database. It is possible to write the whole XMI for each document into the database.

A generic XML mapper to create CAS instances reflecting contents of XML documents. Especially created to read PubMed/Medline XML.

JULIELab Neo4j Plugins Concepts Representation

This project contains various utilities used for the Neo4j server plugins developed at the JULIE lab.

Gene Candidate Retrieval