Group: de.julielab - All Dependencies

JCoRe PubMed Central DB Reader · JeDIS database reader for PMC base documents.

JCoRe BioNLP Gold and Predicted Genes Merge AE · Given the gold BioNLP ST gene mentions and other gene mentions - possibly from gene recognizer - merges the two different sources of genes. For simplicity, this component employs two different types to represent genes. The BioNLP ST reader uses the de.julielab.jcore.types.Gene type. The other genes should be realized with de.julielab.jcore.types.Protein annotations.

Gene ID Mapper · Mapper to find database entries of gene entity mentions.

This project has a lot of business classes to work with genes and related named entities. Genes are part of a GeneDocument and may have gold IDs as well as mapped/predicted IDs. Another large part are species because most (all?) gene ID databases are species specific. So there are also classes or members to represent species mentions and the assignment of species IDs (taxonomy IDs) to genes. There is little to no business logic herein. This project is only useful as building block in other projects dealing with species assignment, gene ID mapping or similar efforts.

Gene Mapper Resources · This project assembles code and files required to build the dictionaries and indexes used by the JCoRe Gene Mapper.

GeNoSa · The task that is the subject of this project is the assignment of taxonomy identifiers to mentions of genes in text documents. The base for the assignment are mostly the mentions of species in the same document.

JULIE Lab Gene Mapper · Parent POM for: Mapper to find database entries of gene entity mentions

JCoRe GNormPlus PubMed Database Multiplier · This is the GNormPlus XML DB multiplier base component that is contained in the JCoRe GNormPlus AE project in jcore-base complemented by the pubmed XML mapping file. This is a drop-in replacement for the PubMed DB Multiplier that runs GNormPlus after the XML data has been added to the CAS. Note that running GNormPlus requires the presence of the GNormPlus resources and external programs in the working directory of the pipeline.