JCoRe OpenNLP Constituency Parser · UIMA wrapper for the OpenNLP Parser. 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.
JULIE Lab Xerces · A slightly adapted version of Xerces to allow the XMLStringBuffer responsible for XML attribute scanning to start larger and thus avoid extended appending times. The initial buffer size is controlled by settting the system property julielab.xerces.attributebuffersize (also available as constant XMLScanner#ATTRIBUTE_BUFFER_SIZE).
LINNAEUS Species Tagger · This is a mavenized version of the LINNAEUS Species Tagger by Martin Gerner with minor modifications. Refer to the README.md file for an overview of the changes.
BioPortal Ontology Tools · This project contains some utilities to process ontologies and related data as retrieved from BioPortal. The tools include the download of ontologies from BioPortal, download of mappings from BioPortal and the extraction of names, synonyms, descriptions and superclasses of ontology concepts from downloaded ontologies.
JCoRe XMI Collection Reader · Reads in XMI representions of CAS objects from files and converts them to CAS objects. Is able to read (g)zipped files and can recursively search subdirectories for XMI files to read.
JCoRe PubMed Central Reader · A UIMA reader for the Pubmed Central NXML format.
JCoRe BioNLP Format Reader · This reader generates CAS' from data that adheres to the BioNLP-ST format.
JCoRe BioNLP Format Consumer · This consumer is used to generate BioNLP-ST (2009) compliant data from a CAS.
JCoRe BioLemmatizer · Lemmatization tool for morphological analysis of biomedical literature downloaded from SourceForge
JCoRe Banner · Banner gene tagging tool. Bases on version 0.0.12-SNAPSHOT from scm:git:[email protected]:oaqa/banner.git.
Dragontool · Copy of the dragontools from http://dragon.ischool.drexel.edu with very limited functionality due to the lack of publicly available Maven dependencies. Used in JULIELab JCoRe as dependency for the BANNER gene tagger.
JCoRe Linnaeus Species AE Proxies Dictionary · This project is a resource for the JULES Linnaeus Annotator. The dictionary contained herein is used for the recognition of concrete species names in text, e.g. "human", "mouse", "n. furzeri", "c. elegans" etc as well as species hints, i.e. indirect clues to a species like the word "patient" which most likely refers to a human. For the task of only finding concrete species names in text, there is the project jcore-linnaeus-species-ae-species-dict.
This is a copy of the SecondString library from https://sourceforge.net/projects/secondstring/ to obtain a usable Maven artifact.
JCoRe Lingscope AE · This component marks spans of biomedical text to lie in the scope of a negation or hedge. The Lingscope (https://sourceforge.net/projects/lingscope/) algorithm is used to do this.
JCoRe Database Checkpoint AE · This is a JeDIS component. It can be used to set the 'last component' column in a subset table. This help to keep track of the pipeline status.
JCoRe Annotation Adder · Adds annotations from external sources, e.g. files, into the CAS.
Learning to Rank · This is a copy of the original RankLib from the Lemur project (https://sourceforge.net/p/lemur/wiki/RankLib/). The copy serves as a possibility to create a Maven artifact uploaded to Maven central since the Lemur project doesn't provide Maven artifacts on central. Additionally, changes have been made to use RankLib more easily as a library from the code of another program. Also, for thread-safety, the static, global feature number counter is not used any more.
JULIE Lab Concept Creation for BioPortal · This project uses the JULIE Lab BioPortal Tools to create database concepts for ontology classes.
Gene Mapping · Mapper to find database entries of gene entity mentions
JCoRe XMI Writer · JULES XMI Writer. A CAS consumer that writes converts CAS objects to XMI files.
