JarCastingProject Group: de.julielab
JULIE Lab ElasticSearch Query Components
de.julielab : julielab-elastic-query-componentsThis is a Tapestry 5 project that offers a Tapestry-IoC integrated query layer for an ElasticSearch server.
Last Version: 1.5.0
Release Date:
Gene Mapping
de.julielab : gene-name-mapping-aeMapper to find database entries of gene entity mentions
Last Version: 1.0.1
Release Date:
Gene Name Mapping Resource Creation
de.julielab : gene-name-mapping-resource-creationThis project assembles code and files required to build the dictionaries and indexes used by the Gene Mapper.
Last Version: 1.0.1
Release Date:
Gene Name Mapping Parent
de.julielab : gene-name-mappingParent POM for: Mapper to find database entries of gene entity mentions
Last Version: 1.0.1
Release Date:
julielab-maven-aether-utilities
de.julielab : julielab-maven-aether-utilitiesThe Parent POM for all JULIE Lab projects.
Last Version: 1.1.1
Release Date:
JCoRe XMI Splitter Tools
de.julielab : jcore-xmi-splitterParses CAS data in XMI format in order to select specified annotations (XmiSplitter) or or builds a single XMI representation out of the base document and the selected annotations (XmiBuilder). These tools are used by the JCoRe CAS to/from DB Reader/Consumer to store or read portions of XMI files from a PostgrSQL database.
Last Version: 2.3.5
Release Date:
JCoRe Descriptor Creator
de.julielab : jcore-descriptor-creatorA simple project for the automatic creation of descriptors for UIMAfit-enabled components.
Last Version: 2.5.1
Release Date:
Last Version: 2.5.0
Release Date:
Last Version: 2.5.0
Release Date:
JCoRe Database Reader
de.julielab : jcore-db-readerAbstract database reader for database driven processing
Last Version: 2.5.0
Release Date:
JCoRe OpenNLP POS Tagger
de.julielab : jcore-opennlp-postag-aeUIMA 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.
Last Version: 2.5.0
Release Date:
JCoRe BioSem Event Annotator
de.julielab : jcore-biosem-aeA UIMA wrapper around the BioSem Event Extractor from the University of Amsterdam. http://www.ncbi.nlm.nih.gov/pubmed/22859502
Last Version: 2.5.0
Release Date:
JCoRe OpenNLP Sentence Splitter
de.julielab : jcore-opennlp-sentence-aeUIMA 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.
Last Version: 2.5.0
Release Date:
JCoRe Open NLP Chunker
de.julielab : jcore-opennlp-chunk-aeUIMA 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.
Last Version: 2.5.0
Release Date:
JCoRe XML Database Reader
de.julielab : jcore-xml-db-readerA 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. The reader requires a configuration file which determines the database connection, the table schema and the PostgreSQL schema (namespace) to use.
Last Version: 2.5.0
Release Date:
JCoRe Token Annotator
de.julielab : jcore-jtbd-aeUIMA Wrapper for the JULIE Token Boundary Detector.
Last Version: 2.5.0
Release Date:
JCoRe Mantra XML Types
de.julielab : jcore-mantra-xml-typesAdditional types for the Mantra Challenge (see iexml-{reader,cosnumer}).
Last Version: 2.5.0
Release Date:
JCoRe Linnaeus Species Tagger
de.julielab : jcore-linnaeus-species-aeUses 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 default mention dictionary is stored in the jcore-linneaus-species-dict project, for example.
Last Version: 2.5.0
Release Date:
JCoRe OpenNLP Tokenizer
de.julielab : jcore-opennlp-token-aeUIMA 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.
Last Version: 2.5.0
Release Date:
JCoRe Sentence Annotator
de.julielab : jcore-jsbd-aeUIMA Wrapper for the JULIE Sentence Boundary Detector.
Last Version: 2.5.0
Release Date:
JCoRe XML Mapper
de.julielab : jcore-xml-mapperA generic XML mapper to create CAS instances reflecting contents of XML documents. Especially created to read PubMed/Medline XML.
Last Version: 2.5.0
Release Date:
JCoRe XML Reader
de.julielab : jcore-xml-readerA 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.
Last Version: 2.5.0
Release Date:
JCoRe Lingpipe Gazetteer AE
de.julielab : jcore-lingpipe-gazetteer-aeBasically used as NE tagger based on Lingpipe's dictionary-lookup tagger.
Last Version: 2.5.0
Release Date:
JCoRe Lingscope AE
de.julielab : jcore-lingscope-aeThis 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.
Last Version: 2.5.0
Release Date:
Last Version: 2.5.0
Release Date:
Last Version: 2.5.0
Release Date:
JCoRe Annotation Adder
de.julielab : jcore-annotation-adder-aeAdds annotations from external sources, e.g. files, into the CAS.
Last Version: 2.5.0
Release Date:
JCoRe BioLemmatizer
de.julielab : jcore-biolemmatizer-aeLemmatization tool for morphological analysis of biomedical literature downloaded from SourceForge
Last Version: 2.5.0
Release Date:
JCoRe Database Checkpoint AE
de.julielab : jcore-db-checkpoint-aeThis 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.
Last Version: 2.5.0
Release Date:
JCoRe OpenNLP Constituency Parser
de.julielab : jcore-opennlp-parser-aeUIMA 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.
Last Version: 2.5.0
Release Date:
JCoRe MST Parser AE
de.julielab : jcore-mstparser-aeSlightly modified version of the MST parser to fit into the UIMA framework. This dependency parser determines all syntactic dependencies between words within a sentence. Certain level of adaptation of the original source code was necessary to neatly integrate the parser in UIMA.
Last Version: 2.5.0
Release Date:
JCoRe Banner
de.julielab : jcore-banner-aeBanner gene tagging tool. Bases on version 0.0.12-SNAPSHOT from scm:git:[email protected]:oaqa/banner.git.
Last Version: 2.5.0
Release Date:
JCoRe XMI Database Reader
de.julielab : jcore-xmi-db-readerReads CAS XMI data from a relational database (Postgres). Thus, the stored CASes may then be processed further.
Last Version: 2.5.0
Release Date:JCoRe Analysis Engine Archetype
de.julielab : jcore-ae-archetypeAn archetype to quickly create new JCoRe UIMA analysis engines.
Last Version: 2.5.1
Release Date:JCoRe Consumer Archetype
de.julielab : jcore-cc-archetypeAn archetype to quickly create new JCoRe UIMA CAS consumers.
Last Version: 2.5.1
Release Date:JCoRe Collection Reader Archetype
de.julielab : jcore-cr-archetypeAn archetype to quickly create new JCoRe UIMA collection reader.
Last Version: 2.5.1
Release Date:
JCoRe CAS to IOB Consumer
de.julielab : jcore-iob-consumerA CAS Consumer that converts UIMA annotations into IOB format
Last Version: 2.5.0
Release Date:
JCoRe IGN Reader
de.julielab : jcore-ign-readerCollection Reader for the IGN corpus in BioC format as accessible at https://sites.google.com/site/hongjiedai/projects/the-ign-corpus.
Last Version: 2.5.0
Release Date:
JCoRe BioNLP Format Reader
de.julielab : jcore-bionlpformat-readerThis reader generates CAS' from data that adheres to the BioNLP-ST format.
Last Version: 2.5.0
Release Date:
JCoRe BioCreative II Gene Mention Format Writer
de.julielab : jcore-bc2gmformat-writerThis component allows to write CAS entity annotations into the format used for the BioCreative II Gene Mention challenge.
Last Version: 2.5.0
Release Date:
JCoRe Line Multiplier
de.julielab : jcore-line-multiplierA multiplier that splits files into lines.
Last Version: 2.5.0
Release Date:
JCoRe Likelihood Detection AE
de.julielab : jcore-likelihood-detection-aeAnalysis Engine to detect epistemic modal expressions and assign the appropriate likelihood category.
Last Version: 2.5.0
Release Date:
JCoRe PubTator Reader
de.julielab : jcore-pubtator-readerA collection reader to read the PubTator (https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/) format.
Last Version: 2.5.0
Release Date:
JCoRe JULIE Lab Entity Evaluator Converter
de.julielab : jcore-julielab-entity-evaluator-consumerThis component allows the output of entity mention data in documents in the format required by the JULIE Lab Entity Evaluator. This way, CAS annotations can be exported for evaluation purposes. The output format is a single tab-separated text file. For the exact format refer to the documentation of the julielab-entity-evaluator in the jcore-dependencies repository on https://github.com/JULIELab/.
Last Version: 2.5.0
Release Date:
JCoRe Feature Value Replacement AE
de.julielab : jcore-feature-value-replacement-aeThis analysis engine simply replaces feature values of feature structures with other values as defined by an external resource, e.g. file. For instance, all NCBI Gene IDs could be mapped to Ensemble IDs.
Last Version: 2.5.0
Release Date:
Last Version: 2.5.0
Release Date:JCoRe MSdoc Reader
de.julielab : jcore-msdoc-readerReads MS doc files; derived from UIMA example "FileSystemCollectionReader" and the JCoRe component File Reader
Last Version: 2.5.0
Release Date:
JCoRe Likelihood Assignment AE
de.julielab : jcore-likelihood-assignment-aeAnalysis Engine to assign likelihood indicators to their corresponding entities and events.
Last Version: 2.5.0
Release Date:
JCoRe BioNLP Format Consumer
de.julielab : jcore-bionlpformat-consumerThis consumer is used to generate BioNLP-ST (2009) compliant data from a CAS.
Last Version: 2.5.0
Release Date:
JCoRe IEXML Reader
de.julielab : jcore-iexml-readerReader for IEXML files as used in the Mantra project/challenge
Last Version: 2.5.0
Release Date: