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julielab-gnormplus from group de.julielab (version 1.0.4)

Group: de.julielab Artifact: julielab-gnormplus
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Artifact julielab-gnormplus
Group de.julielab
Version 1.0.4
Last update 21. August 2024
Organization not specified
URL https://www.ncbi.nlm.nih.gov/research/bionlp/Tools/gnormplus/
License not specified
Dependencies amount 2
Dependencies pengyifan-bioc, snowball-stemmer,
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jcore-gnormplus-ae from group de.julielab (version 2.6.10)

Wrapper for the JULIE Lab variant of the GNormPlus gene ID mapper.

Group: de.julielab Artifact: jcore-gnormplus-ae
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Artifact jcore-gnormplus-ae
Group de.julielab
Version 2.6.10
Last update 20. May 2024
Organization JULIE Lab Jena, Germany
URL https://github.com/JULIELab/jcore-base/tree/master/jcore-gnormplus-ae
License BSD 2-Clause
Dependencies amount 10
Dependencies julielab-gnormplus, jcore-gnp-bioc-writer, jcore-gnp-bioc-reader, jcore-xmi-db-reader, jcore-xml-db-reader, jcore-pmc-db-reader, slf4j-api, jcore-types, jcore-descriptor-creator, junit-jupiter-engine,
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jcore-pmc-db-reader from group de.julielab (version 2.6.3)

JeDIS database reader for PMC base documents.

Group: de.julielab Artifact: jcore-pmc-db-reader
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Artifact jcore-pmc-db-reader
Group de.julielab
Version 2.6.3
Last update 17. April 2024
Organization JULIE Lab Jena, Germany
URL https://github.com/JULIELab/jcore-base/tree/master/jcore-pmc-db-reader
License not specified
Dependencies amount 9
Dependencies slf4j-api, jcore-descriptor-creator, jcore-db-reader, jcore-pmc-reader, jcore-types, junit-jupiter-engine, jcore-db-test-utilities, assertj-core, jcore-utilities,
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jcore-xml-db-reader from group de.julielab (version 2.6.5)

A Collection Reader that converts XML, stored in a database, to CAS objects. The conversion is the same employed by the jcore-xml-reader, making use of the jcore-xml-mapper. The reader requires a configuration file which determines the database connection, the table schema and the PostgreSQL schema (namespace) to use.

Group: de.julielab Artifact: jcore-xml-db-reader
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Artifact jcore-xml-db-reader
Group de.julielab
Version 2.6.5
Last update 23. February 2024
Organization not specified
URL https://github.com/JULIELab/jcore-base/jcore-xml-db-reader
License BSD-2-Clause
Dependencies amount 12
Dependencies jcore-db-reader, costosys, slf4j-api, commons-lang3, guava, jcore-xml-mapper, jcore-utilities, jcore-types, junit-jupiter-engine, jcore-db-test-utilities, assertj-core, jcore-descriptor-creator,
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jcore-jsbd-ae from group de.julielab (version 2.6.2)

UIMA Wrapper for the JULIE Sentence Boundary Detector.

Group: de.julielab Artifact: jcore-jsbd-ae
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Artifact jcore-jsbd-ae
Group de.julielab
Version 2.6.2
Last update 22. February 2024
Organization JULIE Lab Jena, Germany
URL https://github.com/JULIELab/jcore-base/tree/master/jcore-jsbd-ae
License BSD-2-Clause
Dependencies amount 8
Dependencies assertj-core, jcore-types, slf4j-api, mallet, commons-lang3, jcore-utilities, jcore-descriptor-creator, junit-jupiter,
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jcore-xmi-db-reader from group de.julielab (version 2.6.3)

Reads CAS XMI data from a relational database (Postgres). Thus, the stored CASes may then be processed further.

Group: de.julielab Artifact: jcore-xmi-db-reader
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Artifact jcore-xmi-db-reader
Group de.julielab
Version 2.6.3
Last update 22. February 2024
Organization JULIE Lab Jena, Germany
URL https://github.com/JULIELab/jcore-base/tree/master/jcore-xmi-db-reader
License BSD-2-Clause
Dependencies amount 7
Dependencies jcore-db-reader, testng, jcore-types, jcore-xmi-splitter, jcore-utilities, julie-xml-tools, jcore-descriptor-creator,
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jcore-db-reader from group de.julielab (version 2.6.3)

Abstract database reader for database driven processing

Group: de.julielab Artifact: jcore-db-reader
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Artifact jcore-db-reader
Group de.julielab
Version 2.6.3
Last update 22. February 2024
Organization not specified
URL Not specified
License BSD-2-Clause
Dependencies amount 5
Dependencies costosys, slf4j-api, jcore-descriptor-creator, junit-jupiter-engine, uima-ducc-user,
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jcore-db-checkpoint-ae from group de.julielab (version 2.6.3)

This is a JeDIS component. It can be used to set the 'last component' column in a subset table. This help to keep track of the pipeline status.

Group: de.julielab Artifact: jcore-db-checkpoint-ae
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Artifact jcore-db-checkpoint-ae
Group de.julielab
Version 2.6.3
Last update 22. February 2024
Organization JULIE Lab Jena, Germany
URL https://github.com/JULIELab/jcore-base/tree/master/jcore-db-checkpoint-ae
License BSD-2-Clause
Dependencies amount 6
Dependencies slf4j-api, jcore-types, costosys, jcore-utilities, jcore-descriptor-creator, testng,
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jcore-xmi-db-writer from group de.julielab (version 2.6.3)

Writes CAS data in XMI format into a relational (PostgreSQL) database. It is possible to write the whole XMI for each document into the database. However, it is also possible to define a list of annotations that should be written into separate tables. The JCoRe XMI Database Reader can then be used to assemble XMI data from a given set of annotations.

Group: de.julielab Artifact: jcore-xmi-db-writer
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Artifact jcore-xmi-db-writer
Group de.julielab
Version 2.6.3
Last update 22. February 2024
Organization not specified
URL https://github.com/JULIELab/jcore-base/tree/master/jcore-xmi-db-writer
License BSD-2-Clause
Dependencies amount 10
Dependencies costosys, jcore-descriptor-creator, jcore-types, uima-ducc-user, jcore-xmi-splitter, commons-codec, jcore-db-checkpoint-ae, jcore-db-test-utilities, assertj-core, annotations,
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jcore-pubmed-db-reader from group de.julielab (version 2.6.1)

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.

Group: de.julielab Artifact: jcore-pubmed-db-reader
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Artifact jcore-pubmed-db-reader
Group de.julielab
Version 2.6.1
Last update 20. February 2024
Organization JULIE Lab, Germany
URL https://github.com/JULIELab/jcore-projects/tree/master/jcore-pubmed-db-reader
License BSD-2-Clause
Dependencies amount 3
Dependencies jcore-xml-db-reader, jcore-descriptor-creator, junit-jupiter-engine,
There are maybe transitive dependencies!

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