Download JAR files tagged by species with all dependencies

A reader for the BioC format used by GNormPlus. Reads the text and the annotations, both species and genes.

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.

This is a mavenized version of the LINNAEUS Species Tagger by Martin Gerner with minor modifications. Refer to the README.md file for an overview of the changes.

The main project for the external domain-specific modeling language ML-Rules, which is used to model hierarchical biochemical reaction networks with nested and attributed species

Uses the Linnaeus software (http://linnaeus.sourceforge.net/) to detect species mentions and map them to NCBI taxonomy IDs. This project contains the UIMA wrapper around the original Linnaeus software but does not include any dictionaries. Since Linnaeus works with different dictionaries (e.g. concrete species name mention recognition, species proxy/clue recognition, ...) each of the different resource has been stored in a project of its own in jcore-projects. The default mention dictionary is stored in the jcore-linneaus-species-dict project, for example.

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.

This 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.

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.

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.