JarCastingProject Group: de.julielab
julielab-java-utilities
de.julielab : julielab-java-utilitiesThe Parent POM for all JULIE Lab projects.
Last Version: 1.4.5
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Last Version: 1.0.3
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Last Version: 0.6.4
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JULIE Entity Evaluator
de.julielab : julielab-entity-evaluatorA small library aiming at a standardized way to do entity recognition evaluations.
Last Version: 1.3.0
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julielab-neo4j-plugins-concepts-representation
de.julielab : julielab-neo4j-plugins-concepts-representationThis project contains Neo4j server plugins used by the Julie Lab team.
Last Version: 3.0.1
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JULIE Lab Neo4j Concept Management Plugin
de.julielab : julielab-neo4j-plugins-conceptsThis project includes multiple plugins for the Neo4j server to support to import, management and query of concepts.
Last Version: 3.0.1
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JULIE Lab Concept Database Manager Core
de.julielab : julielab-concept-db-manager-coreThe central interfaces and services for the concept database manager.
Last Version: 1.1.1
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JULIE Lab Neo4j Server Plugin Utilities
de.julielab : julielab-neo4j-plugins-utilitiesThis project contains various utilities used for the Neo4j server plugins developed at the JULIE lab.
Last Version: 3.0.1
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JULIE Lab Neo4j Server Plugins
de.julielab : julielab-neo4j-server-pluginsThis project contains Neo4j server plugins used by the Julie Lab team.
Last Version: 3.0.1
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JULIE Lab Concept DB Manager Application
de.julielab : julielab-concept-db-applicationThis project is a collection of tools with the goal to import ontological concepts into a graph database. The graph database then allows to traverse the imported data with a graph-specific query language. In case of a Neo4j database, which is the one employed by this tool, uses the Cypher query language.
Last Version: 1.1.1
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JULIE Lab Concept Creation for NCBI Gene
de.julielab : julielab-concept-creation-ncbi-geneThis project uses internal JULIE Lab files to create database concepts for the NCBI Gene database.
Last Version: 1.1.1
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JULIE Lab Concept Database Manager
de.julielab : julielab-concept-db-managerThis project is a collection of tools with the goal to import ontological concepts into a graph database. The graph database then allows to traverse the imported data with a graph-specific query language. In case of a Neo4j database, which is the one employed by this tool, uses the Cypher query language.
Last Version: 1.1.1
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JULIE Lab Concept Creation Provider MeSH
de.julielab : julielab-concept-creation-meshThis project contains algorithms to create database concepts from the XML version of the MeSH. There is a full API to work with MeSH XML in this project.
Last Version: 1.1.1
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JULIE Lab Concept Creation for BioPortal
de.julielab : julielab-concept-creation-bioportalThis project uses the JULIE Lab BioPortal Tools to create database concepts for ontology classes.
Last Version: 1.1.1
Release Date:julielab-smac-utilities
de.julielab : julielab-smac-utilitiesThe Parent POM for all JULIE Lab projects.
Last Version: 1.0.0
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Last Version: 2.5.0
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jcore-db-test-utilities
de.julielab : jcore-db-test-utilitiesThe POM for the JCoRe Dependencies projects.
Last Version: 2.5.2
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Corpus Storage System
de.julielab : costosysA 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. For more sophisticated tasks, a user configuration file can be delivered which can take control of the table schema to use, the PostgreSQL schema to use and the actual database server to connect to as well as the concrete database.
Last Version: 1.5.2
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JCoRe OpenNLP POS Tagger, Biomedical English
de.julielab : jcore-opennlp-postag-ae-biomedical-englishThis project employs the OpenNLP wrapper (jcore-opennlp-postag-ae) with a model trained on the PennBioIE corpus.
Last Version: 2.5.1
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JCoRe Sentence Annotator, Biomedical English
de.julielab : jcore-jsbd-ae-biomedical-englishUIMA Wrapper for the JCoRe Sentence Boundary Detector (jcore-jsbd-ae) with a model trained on data from both the GENIA and PennBioIE corpus as well as additional material from MedLine abstracts.
Last Version: 2.5.1
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JCoRe Linnaeus Species AE Proxies Dictionary
de.julielab : jcore-linnaeus-species-ae-proxies-dictThis 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.
Last Version: 2.5.1
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JCoRe PubMed Reader
de.julielab : jcore-pubmed-readerLeveraging the JCoRe XML Reader, this project employs a PubMed-enabled mapping file to map PubMed XML documents to CAS instances. The input is a directory of single XML files, each containing exactly one XML PubmedArticle. The XML format is the one used by NCBI when displaying results in PubMed as XML.
Last Version: 2.5.1
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JCoRe Token Annotator, Biomedical English
de.julielab : jcore-jtbd-ae-biomedical-englishUIMA Wrapper for the JCoRe Token Boundary Detector with a model trained on a special biomedical corpus which consists of data from (manually annotated) material which we took from MedLine abstracts and a modified version of PennBioIE's underlying tokenization.
Last Version: 2.5.1
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JCoRe BioSem AE, BioNLP SharedTask 2011
de.julielab : jcore-biosem-ae-bionlp-st11This project employs the JCoRe BioSem wrapper (jcore-biosem-ae) with a BioSem database trained on the BioNLP SharedTask 2011 train and development (that is, "mixed") data for biological event extraction.
Last Version: 2.5.1
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JCoRe BioSem AE, BioNLP SharedTask 2009
de.julielab : jcore-biosem-ae-bionlp-st09This project employs the JCoRe BioSem wrapper (jcore-biosem-ae) with a BioSem database trained on the BioNLP SharedTask 2009 train data for biological event extraction.
Last Version: 2.5.1
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JCoRe JPOS AE, Medical German
de.julielab : jcore-jpos-ae-medical-germanThis project employs the jcore-jpos-ae (Part-of-Speech Tagger) with a model trained on the confidential FraMed corpus.
Last Version: 2.5.1
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JCoRe OpenNLP Sentence Splitter, Biomedical English
de.julielab : jcore-opennlp-sentence-ae-biomedical-englishThis project employs the UIMA wrapper (jcore-opennlp-sentence-ae) with a model trained on the PennBioIE and Genia corpora.
Last Version: 2.5.1
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JCoRe OpenNLP Parser, Biomedical English
de.julielab : jcore-opennlp-parser-ae-biomedical-englishThis project employs the OpenNLP wrapper (jcore-opennlp-parser-ae) with a model trained on the Genia corpus.
Last Version: 2.5.1
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JCoRe OpenNLP POS Tagger, Medical German
de.julielab : jcore-opennlp-postag-ae-medical-germanThis Model was trained on the confidential FraMed corpus.
Last Version: 2.5.1
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JCoRe OpenNLP Tokenizer, Medical German
de.julielab : jcore-opennlp-token-ae-medical-germanThis Model was trained on the confidential FraMed corpus.
Last Version: 2.5.1
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JCoRe MST Parser AE, Biomedical English
de.julielab : jcore-mstparser-ae-biomedical-englishThis project employs the jcore-mstparser-ae (Dependency Parser) with a model trained on the GENIA corpus.
Last Version: 2.5.1
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Last Version: 2.5.1
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JCoRe Lingpipe Gazetteer Dummy Implementation
de.julielab : jcore-lingpipegazetteer-ae-dummy-implementationThis is just a dummy implementation that can be adapted according to ones own need.
Last Version: 2.5.1
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JCoRe Sentence Annotator, Medical German
de.julielab : jcore-jsbd-ae-medical-germanUIMA Wrapper for the JCoRe Sentence Boundary Detector (jcore-jsbd-ae) with a model trained on data from the confidential FraMed corpus
Last Version: 2.5.1
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JCoRe BioSem AE, BioNLP SharedTask 2013
de.julielab : jcore-biosem-ae-bionlp-st13This project employs the JCoRe BioSem wrapper (jcore-biosem-ae) with a BioSem database trained on the BioNLP SharedTask 2013 train and development (mix) data for biological event extraction.
Last Version: 2.5.1
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JCoRe OpenNLP Chunker, Biomedical English
de.julielab : jcore-opennlp-chunk-ae-biomedical-englishThis project employs the OpenNLP wrapper (jcore-opennlp-chunker-ae) with a model trained on the Genia corpus.
Last Version: 2.5.1
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JCoRe Linnaeus Species AE with Species Dictionary
de.julielab : jcore-linnaeus-species-ae-species-dictThis project is a project for the JCoRe 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. It does not contain species proxies, i.e. indirect clues to a species like the word "patient" which most likely refers to a human. For this task there is the project jcore-linnaeus-species-ae-proxies-dict.
Last Version: 2.5.1
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JCoRe Lingscope Negation AE
de.julielab : jcore-lingscope-negation-aeThis component uses Lingscope with the baseline negation cue tagger and a CRF scope detector.
Last Version: 2.5.1
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JCoRe OpenNLP Token AE, Biomedical English
de.julielab : jcore-opennlp-token-ae-biomedical-englishThis project employes the JCoRe OpenNLP tokenizer wrapper with a model trained on the PennBioIE corpus and data from MedLine abstracts.
Last Version: 2.5.1
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JCoRe JNET AE, Biomedical English
de.julielab : jcore-jnet-ae-biomedical-englishThis project employs the jcore-jnet-ae (Named Entity Tagger) with a model trained on the PennBioIE corpus.
Last Version: 2.5.1
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JCoRe Medline Reader
de.julielab : jcore-medline-readerLeveraging the JCoRe XML Reader, this project employs a Medline-enabled mapping file to map Medline XML documents to CAS instances. The input is a directory of single XML files, each containing exactly one XML MedlineCitation. The XML format is the one used by NCBI when downloading Medline documents in large batches from the NCBI FTP server. However, the component currently expects single documents instead of whole MedlineCitationSets containing sets of MedlineCitations.
Last Version: 2.5.1
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JCoRe OpenNLP Sentence Segmenter, Medical German
de.julielab : jcore-opennlp-sentence-ae-medical-germanThis Model was trained on the confidential FraMed corpus.
Last Version: 2.5.1
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JCoRe MEDLINE DB Reader
de.julielab : jcore-medline-db-readerAn instantiation of the jcore-db-reader that uses the jcore-xml-mapper to retrieve and parse MEDLINE XML from a PostgreSQL database. The XML format of retrieved documents is expected to follow the MEDLINE XML schema that was used until inclusive 2016. I.e. the root element of MEDLINE documents must be MedlineCitation and not, as it is since 2017, PubmedArticle.
Last Version: 2.5.1
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JCoRe Linnaeus Species AE Genera and Species Proxies Dictionaries
de.julielab : jcore-linnaeus-species-ae-genera-species-proxies-dictsThis project is a resource for the JCoRe Linnaeus Annotator. The dictionaries contained herein are 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. Additionally to such rather clear proxies, this project also includes a small dictionary containing maximum-frequency-proxies for genus expressions like "Drosophila" which will be mapped to "D. melanogaster". For the task of only finding concrete species names in text, there is the project jcore-linnaeus-species-ae-species-dict.
Last Version: 2.5.1
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JCoRe BANNER AE for Biomedical English
de.julielab : jcore-banner-ae-biomedical-englishThe JCoRe BANNER Gene Tagger wrapper with a model for biomedical english.
Last Version: 2.5.1
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JCoRe PubMed DB Reader
de.julielab : jcore-pubmed-db-readerAn instantiation of the jcore-db-reader that uses the jcore-xml-mapper to retrieve and parse PubMed XML from a PostgreSQL database. The XML format of retrieved documents is expected to follow the PubMed/MEDLINE XML schema that was used beginning from 2017. I.e. the root document of a document must be PubmedArticle and not, as it was for MEDLINE until 2017, MedlineCitation.
Last Version: 2.5.1
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JCoRe Token Annotator, Medical German
de.julielab : jcore-jtbd-ae-medical-germanUIMA Wrapper for the JCoRe Token Boundary Detector with a model trained on the confidential FraMed corpus.
Last Version: 2.5.1
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Learning to Rank
de.julielab : learning-to-rankThis 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.
Last Version: 2.11.1
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julielab-ranklib-mallet
de.julielab : julielab-ranklib-malletThe Parent POM for all JULIE Lab projects.
Last Version: 1.0.0
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Plugin: Mapper: Preanalyzed
de.julielab : elasticsearch-mapper-preanalyzedProvides the preanalyzed field datatype. The plugin allows to specify the exact terms of a field in JSON format without any further analysis being done.
Last Version: 7.0.1
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