Group: de.julielab - All Dependencies

JCoRe BioSem AE, BioNLP SharedTask 2013 · 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.

JCoRe BioSem AE, BioNLP SharedTask 2009 · 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.

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.

JCoRe PubMed DB Reader · An 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.

JCoRe MEDLINE DB Reader · An 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.

JCoRe Linnaeus Species AE with Species Dictionary · 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.

JCoRe Linnaeus Species AE Genera and Species Proxies Dictionaries · 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 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.

JCoRe BANNER AE for Biomedical English · The JCoRe BANNER Gene Tagger wrapper with a model for biomedical english.

JCoRe Stanford Lemmatizer · UIMA Wrapper for the Stanford CoreNLP Lemmatizer.

JCoRe Piped Format Writer · This component writes CAS data to the piped text annotation format.

JCoRe Mutation Finder AE · 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; doi:10.1093/bioinformatics/btm235;

JCoRe Lingscope Negation AE · This component uses Lingscope with the baseline negation cue tagger and a CRF scope detector.

JCoRe Clinical Trials Reader · A UIMA reader for clinical trials per ClinicalTrials.gov XML format.

JCoRe BioCreative II Gene Mention Format Writer · This component allows to write CAS entity annotations into the format used for the BioCreative II Gene Mention challenge.

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

JCoRe Line Multiplier · A multiplier that splits files into lines.

JCoRe Flair Token Embedding Annotator · Given a Flair compatible embedding file, computs the token embeddings of the CAS and sets them to the embeddingVector feature of the tokens.