Group: JULIELab

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Labels LDA Topics estimated from project julielab-topic-modeling to infer document topics for PubMed articles

This project employs the OpenNLP wrapper (jcore-opennlp-parser-ae) with a model trained on the Genia corpus.

JCoRe Pipeline Runner

JCoRe Version Normalizer

Reader for embeddings.

This 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 ...

This 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.

Writes acronym annotations from the CAS to a text file format.

This component allows to read gene annotations provided in the BioCreative II Gene Mention format.

This 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.

Reads MS doc files; derived from UIMA example "FileSystemCollectionReader" and the JCoRe component File Reader

An analysis engine to recognize mentions of gene point mutations in document text. This is a wrapper around the original MutationFinder (http://mutationfinder.sourceforge.net/), published in the following paper: MutationFinder: A high-performance system for extracting point mutation mentions from text J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, and Lawrence Hunter; Bioinformatics, 2007 23(14):1862-1865; ...

Analysis Engine to detect epistemic modal expressions and assign the appropriate likelihood category.

Reader for DTA files (German digital humanities corpus)

Jffs Module Concept Database

UIMA Wrapper for the Stanford CoreNLP Lemmatizer.

This component writes CAS data to the piped text annotation format.

JULIE Lab JSON Tools

This is an intermediate parent POM between the jcore-base parent and the components belonging to the Jena Document Information (JeDIS) infrastructure. This POM determines the version of CoStoSys to use.

This 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.