JCoRe Flair NER AE · This component uses the Zalando Flair toolkit (https://github.com/zalandoresearch/flair) for named entity recognition. Since FLAIR is a python library, this component must use python for the actual NER part.
JCoRe Embedding Writer · This component takes as input a number of precomputed embeddings that are compatible with Flair and a UIMA type. If any annotations of the given type are found in a CAS, the embedding vectors for the words covered by the annotations are computed and written to file.
JCoRe CORD-19 Reader · A reader for the JSON format delivered by the CORD-19 corpus.
JULIE Lab Concept Database Manager · This 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.
JULIE Lab Concept Creation for NCBI Gene · This project uses internal JULIE Lab files to create database concepts for the NCBI Gene database.
JULIE Lab Concept Creation Provider MeSH · This 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.
Gene Name Mapping Resource Creation · This project assembles code and files required to build the dictionaries and indexes used by the Gene Mapper.
Gene Name Mapping Parent · Parent POM for: Mapper to find database entries of gene entity mentions
JULIELAB MMAX2 to IOB or IEXML Converter · Converts MMAX to IOB or IEXML
JCoRe Acronym Writer · Writes acronym annotations from the CAS to a text file format.
JCoRe Coreference Writer · Writes coreference annotations from the CAS to a text file format.
JCoRe Annotation Removal AE · Removes annotations from the CAS that belong to one of the types specified as a parameter value in the descriptor.
JCoRe Flow Controllers · Flow controllers can be used to control the route a (J)CAS takes through an aggregate analysis engine. This project contains Flow Controllers developed at the JULIE Lab.
JCoRe GNormPlus Annotator · Wrapper for the JULIE Lab variant of the GNormPlus gene ID mapper.
JCoRe GNormPlus BioC Reader · A reader for the BioC format used by GNormPlus. Reads the text and the annotations, both species and genes.
JCoRe GNormPlus BioC Writer · Writes CAS documents into the BioC XML format used by the gene tagger and normalizer GNormPlus.
JCoRe Neo4j Relations Consumer · Writes EventMentions to Neo4j.
JCoRe MMAX2 reader. · Collection reader for MMAX2 annotation projects.
JCoRe NLM-Gene Reader · Collection reader for the BioC format of the NLM-Gene corpus.
