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gene-species-assignment from group de.julielab (version 1.0.0)

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.

Group: de.julielab Artifact: gene-species-assignment
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Artifact gene-species-assignment
Group de.julielab
Version 1.0.0
Last update 03. December 2022
Organization JULIE Lab Jena, Germany
URL Not specified
License BSD-2-Clause
Dependencies amount 8
Dependencies gene-mapper-experimental-base, gene-candidate-retrieval, jcore-types, junit-jupiter-engine, assertj-core, lucene-suggest, ruta-core, jcore-utilities,
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index from group org.dbpedia.spotlight (version 1.1)

Group: org.dbpedia.spotlight Artifact: index
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Artifact index
Group org.dbpedia.spotlight
Version 1.1
Last update 26. January 2022
Organization not specified
URL Not specified
License not specified
Dependencies amount 11
Dependencies core, core, rio, commons-compress, commons-io, weka, trove, jdbm, mahout-collections, kryo, jackson-core-asl,
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spotlight from group org.dbpedia.spotlight (version 1.1)

DBpedia Spotlight is a tool for automatically annotating mentions of DBpedia resources in text, providing a solution for linking unstructured information sources to the Linked Open Data cloud through DBpedia.

Group: org.dbpedia.spotlight Artifact: spotlight
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Artifact spotlight
Group org.dbpedia.spotlight
Version 1.1
Last update 26. January 2022
Organization not specified
URL https://github.com/dbpedia-spotlight/dbpedia-spotlight-model
License The Apache License, Version 2.0
Dependencies amount 0
Dependencies No dependencies
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core from group org.dbpedia.spotlight (version 1.1)

Group: org.dbpedia.spotlight Artifact: core
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Artifact core
Group org.dbpedia.spotlight
Version 1.1
Last update 26. January 2022
Organization not specified
URL Not specified
License not specified
Dependencies amount 33
Dependencies core, slf4j-simple, jcs, xercesImpl, solr-analysis-extras, commons-lang, guava, nekohtml, httpclient, nxparser, cloud9, kea-goss-weka, weka, lift-json_2.10, junit, opencsv, hsqldb, fastutil, maxent, opennlp-tools, json, scalatest_2.10, kryo, jdbm, trove, mahout-collections, commons-math, spotter-aho, scalaz-core_2.10, scala-actors, breeze_2.10, akka-actor_2.10, lombok,
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rest from group org.dbpedia.spotlight (version 1.1)

Group: org.dbpedia.spotlight Artifact: rest
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Artifact rest
Group org.dbpedia.spotlight
Version 1.1
Last update 26. January 2022
Organization not specified
URL Not specified
License not specified
Dependencies amount 22
Dependencies core, jersey-bundle, jersey-server, velocity-engine-core, jersey-client, jersey-grizzly, grizzly-servlet-webserver, xom, xmlParserAPIs, xml-apis, json-lib, xstream, jettison, stax-api, boilerpipe, nif, lombok, mockito-core, gson, jaxb-core, jaxb-api, jaxb-impl,
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org.apache.stanbol.enhancer.engines.entitycomention from group org.apache.stanbol (version 1.0.0)

An engine that find co-mentions of Entities earlier mentioned on the Text. NOTE: This Engine does NOT use NLP level co-reference detection. Therefore it will not link Pronouns with the correct Entity.

Group: org.apache.stanbol Artifact: org.apache.stanbol.enhancer.engines.entitycomention
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Artifact org.apache.stanbol.enhancer.engines.entitycomention
Group org.apache.stanbol
Version 1.0.0
Last update 16. September 2016
Organization not specified
URL Not specified
License not specified
Dependencies amount 4
Dependencies org.apache.stanbol.commons.namespaceprefix.service, org.apache.stanbol.enhancer.engines.entitylinking.engine, org.apache.felix.scr.annotations, slf4j-api,
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jcore-bionlpgold-pred-gene-merge-ae from group de.julielab (version 2.6.0)

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.

Group: de.julielab Artifact: jcore-bionlpgold-pred-gene-merge-ae
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Artifact jcore-bionlpgold-pred-gene-merge-ae
Group de.julielab
Version 2.6.0
Last update 25. November 2022
Organization JULIE Lab Jena, Germany
URL https://github.com/JULIELab/jcore-base/tree/master/jcore-bionlpgold-pred-gene-merge-ae
License BSD 2-Clause
Dependencies amount 5
Dependencies jcore-utilities, slf4j-api, jcore-types, jcore-descriptor-creator, junit-jupiter-engine,
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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,
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jcore-mutationfinder-ae from group de.julielab (version 2.6.1)

An analysis engine to recognize mentions of gene point mutations in document text. This is a wrapper around the original MutationFinder (http://mutationfinder.sourceforge.net/), published in the following paper: MutationFinder: A high-performance system for extracting point mutation mentions from text J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, and Lawrence Hunter; Bioinformatics, 2007 23(14):1862-1865; doi:10.1093/bioinformatics/btm235;

Group: de.julielab Artifact: jcore-mutationfinder-ae
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Artifact jcore-mutationfinder-ae
Group de.julielab
Version 2.6.1
Last update 18. December 2022
Organization not specified
URL Not specified
License BSD-2-Clause
Dependencies amount 6
Dependencies oro, junit-jupiter-engine, jcore-types, jcore-descriptor-creator, slf4j-api, assertj-core,
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gene-mapper-experimental-base from group de.julielab (version 1.0.0)

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.

Group: de.julielab Artifact: gene-mapper-experimental-base
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Artifact gene-mapper-experimental-base
Group de.julielab
Version 1.0.0
Last update 03. December 2022
Organization JULIE Lab Jena, Germany
URL Not specified
License BSD-2-Clause
Dependencies amount 21
Dependencies commons-lang3, commons-text, julielab-java-utilities, slf4j-api, lucene-analyzers-common, guava, julielab-ranklib-mallet, jcore-mallet-2.0.9, libsvm, spark-core, guice, julie-xml-tools, julielab-entity-evaluator, ehcache, cache-api, annotations, commons-codec, commons-io, junit-jupiter-engine, assertj-core, com.wcohen.secondstring,
There are maybe transitive dependencies!

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