Download JAR files tagged by ncbi with all dependencies

ddi-bioproject-reader from group uk.ac.ebi.ddi.api.readers (version 1.9)

Retrireve all NCBI datasests

Group: uk.ac.ebi.ddi.api.readers Artifact: ddi-bioproject-reader
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Artifact ddi-bioproject-reader
Group uk.ac.ebi.ddi.api.readers
Version 1.9
Last update 14. September 2022
Organization not specified
URL Not specified
License not specified
Dependencies amount 17
Dependencies spring-web, spring-test, spring-context-support, spring-retry, google-collections, slf4j-api, jcl-over-slf4j, logback-core, logback-classic, junit, jackson-databind, commons-io, jaxb-impl, jaxb-xjc, commons-lang3, ddi-api-readers, ddi-service-db,
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julielab-concept-creation-ncbi-gene from group de.julielab (version 1.3.1)

This project uses internal JULIE Lab files to create database concepts for the NCBI Gene database.

Group: de.julielab Artifact: julielab-concept-creation-ncbi-gene
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Artifact julielab-concept-creation-ncbi-gene
Group de.julielab
Version 1.3.1
Last update 23. January 2023
Organization not specified
URL Not specified
License not specified
Dependencies amount 4
Dependencies julielab-concept-db-manager-core, guava, julielab-java-utilities, commons-io,
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jcore-pubtator-reader from group de.julielab (version 2.6.1)

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

Group: de.julielab Artifact: jcore-pubtator-reader
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Artifact jcore-pubtator-reader
Group de.julielab
Version 2.6.1
Last update 18. December 2022
Organization JULIE Lab Jena, Germany
URL https://github.com/JULIELab/jcore-base/tree/master/jcore-pubtator-reader
License BSD-2-Clause
Dependencies amount 5
Dependencies slf4j-api, jcore-types, julielab-java-utilities, commons-lang3, junit-jupiter-engine,
There are maybe transitive dependencies!

jcore-biosem-ae from group de.julielab (version 2.6.2)

A UIMA wrapper around the BioSem Event Extractor from the University of Amsterdam. http://www.ncbi.nlm.nih.gov/pubmed/22859502

Group: de.julielab Artifact: jcore-biosem-ae
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Artifact jcore-biosem-ae
Group de.julielab
Version 2.6.2
Last update 04. January 2024
Organization JULIE Lab Jena, Germany
URL https://github.com/JULIELab/jcore-base/tree/master/jcore-biosem-ae
License BSD-2-Clause
Dependencies amount 5
Dependencies jcore-descriptor-creator, commons-lang3, biosem-event-extractor, jcore-types, junit-jupiter-engine,
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jcore-feature-value-replacement-ae from group de.julielab (version 2.6.1)

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.

Group: de.julielab Artifact: jcore-feature-value-replacement-ae
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Artifact jcore-feature-value-replacement-ae
Group de.julielab
Version 2.6.1
Last update 18. December 2022
Organization JULIE Lab Jena, Germany
URL https://github.com/JULIELab/jcore-base/tree/master/jcore-feature-value-replacement-ae
License BSD-2-Clause
Dependencies amount 3
Dependencies jcore-utilities, jcore-descriptor-creator, junit-jupiter-engine,
There are maybe transitive dependencies!

ner-import from group de.cit-ec.scie (version 2.0.1)

Tool used to import ontologies from various file formats (native simple XML used for the small ontologies, NCBI MeSH, NCBI Taxonomy) into the internal NER ontology database.

Group: de.cit-ec.scie Artifact: ner-import
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Artifact ner-import
Group de.cit-ec.scie
Version 2.0.1
Last update 10. December 2014
Organization not specified
URL http://openresearch.cit-ec.de/projects/scie/
License The GNU Affero General Public License, Version 3
Dependencies amount 2
Dependencies ner-core, ner-mapdb,
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fastcontext from group edu.utah.bmi.nlp (version 2.0.0.0-jdk11)

FastContext is an optimized Java implementation of ConText algorithm (https://www.ncbi.nlm.nih.gov/pubmed/23920642). It runs two orders of magnitude faster than previous two popular implementations: JavaConText and GeneralConText. Version 2.0 includes UIMA wrapper

Group: edu.utah.bmi.nlp Artifact: fastcontext
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Artifact fastcontext
Group edu.utah.bmi.nlp
Version 2.0.0.0-jdk11
Last update 05. February 2024
Organization not specified
URL Not specified
License not specified
Dependencies amount 1
Dependencies nlp-core,
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jcore-pubmed-reader from group de.julielab (version 2.6.0)

Leveraging the JCoRe XML Reader, this project employs a PubMed-enabled mapping file to map PubMed XML documents to CAS instances. The input is a directory of single XML files, each containing exactly one XML PubmedArticle. The XML format is the one used by NCBI when displaying results in PubMed as XML.

Group: de.julielab Artifact: jcore-pubmed-reader
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Artifact jcore-pubmed-reader
Group de.julielab
Version 2.6.0
Last update 18. December 2022
Organization JULIE Lab, Germany
URL https://github.com/JULIELab/jcore-projects/tree/master/jcore-pubmed-reader
License BSD-2-Clause
Dependencies amount 5
Dependencies jcore-xml-reader, logback-classic, jcore-descriptor-creator, jcore-utilities, junit-jupiter-engine,
There are maybe transitive dependencies!

jcore-linnaeus-species-ae from group de.julielab (version 2.6.1)

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.

Group: de.julielab Artifact: jcore-linnaeus-species-ae
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Artifact jcore-linnaeus-species-ae
Group de.julielab
Version 2.6.1
Last update 18. December 2022
Organization JULIE Lab Jena, Germany
URL https://github.com/JULIELab/jcore-base/tree/master/jcore-linnaeus-species-ae
License BSD-2-Clause
Dependencies amount 6
Dependencies linnaeus, slf4j-api, jcore-types, jcore-utilities, jcore-descriptor-creator, junit-jupiter-engine,
There are maybe transitive dependencies!

jcore-medline-reader from group de.julielab (version 2.6.0)

Leveraging the JCoRe XML Reader, this project employs a Medline-enabled mapping file to map Medline XML documents to CAS instances. The input is a directory of single XML files, each containing exactly one XML MedlineCitation. The XML format is the one used by NCBI when downloading Medline documents in large batches from the NCBI FTP server. However, the component currently expects single documents instead of whole MedlineCitationSets containing sets of MedlineCitations.

Group: de.julielab Artifact: jcore-medline-reader
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Artifact jcore-medline-reader
Group de.julielab
Version 2.6.0
Last update 18. December 2022
Organization JULIE Lab, Germany
URL https://github.com/JULIELab/jcore-projects/tree/master/jcore-medline-reader
License BSD-2-Clause
Dependencies amount 3
Dependencies jcore-descriptor-creator, jcore-xml-reader, junit-jupiter-engine,
There are maybe transitive dependencies!

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