Group: de.julielab - All Dependencies

JULIE ElasticSearch Query Components · This is a Tapestry 5 project that offers a Tapestry-IoC integrated query layer for an ElasticSearch server.

JCoRe Topics Writer · Writes the topic weights, given the jcore-topic-indexing-ae running before, into a simple text file. Thus, the output consists of a sequency of double numbers encodes as strings, separated by tab characters. The topic ID is just the 0-based index of each number, from left to right in the written file. The first entry of each file is the document ID.

JCoRe-Topic-Labeling-AE · Labels LDA Topics estimated from project julielab-topic-modeling to infer document topics for PubMed articles

JCoRe PubTator Reader · A collection reader to read the PubTator (https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/) format.

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

JCoRe Likelihood Detection AE · Analysis Engine to detect epistemic modal expressions and assign the appropriate likelihood category.

JCoRe Likelihood Assignment AE · Analysis Engine to assign likelihood indicators to their corresponding entities and events.

JCoRe JULIE Lab Entity Evaluator Converter · This component allows the output of entity mention data in documents in the format required by the JULIE Lab Entity Evaluator. This way, CAS annotations can be exported for evaluation purposes. The output format is a single tab-separated text file. For the exact format refer to the documentation of the julielab-entity-evaluator in the jcore-dependencies repository on https://github.com/JULIELab/.

JCoRe CAS to IOB Consumer · A CAS Consumer that converts UIMA annotations into IOB format

JCoRe IGN Reader · Collection Reader for the IGN corpus in BioC format as accessible at https://sites.google.com/site/hongjiedai/projects/the-ign-corpus.

JCoRe Feature Value Replacement AE · This analysis engine simply replaces feature values of feature structures with other values as defined by an external resource, e.g. file. For instance, all NCBI Gene IDs could be mapped to Ensemble IDs.

JCoRe Event Flattener AE · This component reads de.julielab.jcore.types.EventMention annotations and converts event structures into de.julielab.jcore.types.ext.FlattenedRelation annotation. The purpose of FlattenedRelations is to represent complex event structures in a more simple manner. This can be helpful for visualization or further processing.

JCoRe ElasticSearch Consumer · This component converts CAS annotations into a JSON format that originates from Solr's preanalyzed field type. At the JulieLab, there is an ElasticSearch plugin making this format accessible also by ElasticSearch. Configuration happens right in Java code. Note that the component is also able to generate perfectly valid ElasticSearch default JSON which does not require the plugin. Then, however, the preanalyzed data format cannot be used because this is the format that required the ElasticSearch plugin.

JCoRe Enzyme Commission Number AE · This component recognizes Enzyme Comission (EC) numbers.

JCoRe Collection Reader Archetype · An archetype to quickly create new JCoRe UIMA collection reader.

JCoRe Consumer Archetype · An archetype to quickly create new JCoRe UIMA CAS consumers.

JCoRe Analysis Engine Archetype · An archetype to quickly create new JCoRe UIMA analysis engines.