Group: JULIELab

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UIMA wrapper for the OpenNLP Sentence Segmentation. The difference to the official OpenNLP UIMA wrapper is basically the type system. In this project the JCoRe type system is employed and is thus compatible to other JCoRe components.

JULIELab Neo4j Plugins Concepts Representation

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. In this project the JCoRe type system is employed and is thus compatible to other JCoRe components.

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

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

Evaluation package for IOB based annotations.

UIMA Wrapper for the JULIE Token Boundary Detector.

UIMA wrapper for OpenNLP Tokenizer. The difference to the official OpenNLP UIMA wrapper is basically the type system. In this project the JCoRe type system is employed and is thus compatible to other JCoRe components.

A UIMA reader for the Pubmed Central NXML format.

JULIELab RankLib Mallet

This project has a lot of business classes to work with genes and related named entities. Genes are part of a GeneDocument and may have gold IDs as well as mapped/predicted IDs. Another large part are species because most (all?) gene ID databases are species specific. So there are also classes or members to represent species mentions and the assignment of species IDs (taxonomy IDs) to genes. There is little to no business logic herein. This project is only useful as building ...

Gene Candidate Retrieval

A Collection Reader that employs the JCoRe XML mapper to read XML documents. A mapping file must be delivered to determine which XML file elements have to be converted to which CAS annotation types and features. This is the base component for the JCoRe PubMed and Medline readers.

UIMA wrapper for the OpenNLP Chunker. The difference to the official OpenNLP UIMA wrapper is basically the type system. In this project the JCoRe type system is employed and is thus compatible to other JCoRe components.

This project provides common interfaces used by other embedding classes.

JULIELab SMAC Utilities

UIMA Wrapper for the JULIE Sentence Boundary Detector.

Uses the Linnaeus software (http://linnaeus.sourceforge.net/) to detect species mentions and map them to NCBI taxonomy IDs. This project contains the UIMA wrapper around the original Linnaeus software but does not include any dictionaries. Since Linnaeus works with different dictionaries (e.g. concrete species name mention recognition, species proxy/clue recognition, ...) each of the different resource has been stored in a project of its own in jcore-projects. The ...

JULIELab Maven Aether Utilities