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Revision History

This file was last reviewed on 2024-02-07. Please, keep this note up to date.

7.0.2-SNAPSHOT

  • IMPORTANT: RDF Exporter and components relying on URI generation for concepts and relations: URIs are now built using the ONDEX internal integer ID.
  • Neo4j exporter: ondexId added to the indexes.

7.0.1

  • Various dependencies upgraded.

7.0

  • Spring migrated to version 6. No backward compatibility guaranteed
  • Addition to jaxb.properties, to cope with older Jakarta bugs.

6.0

  • Migrated to Java 17. WARNING: no backward compatibility guaranteed.

5.2

Bugfixes

  • Fixing problem (via dependency upgrade) with rdfutils and null literals.

5.1

  • Metadata descriptor (still experimental).
  • Text mining plug-in:
    • stop words added to the text mining plug-in, #65.
    • various bugfixes.
  • GraphLabelsUtils, case for selecting names with specie prefix added and used for the Cytoscape exporter #681
  • CytoscapeJS exporter:
  • (Hopefully) all logging messages sent to the logger, not to System.out anymore.
  • Indexing functionality added to OndexPluginUtils.
  • Various dependency upgrades (eg, Jena, RDF utils)

Internal changes

  • KnetMiner initialiser module added from code in KnetMiner (#51).
  • Lucene module: bugfixing for certain non-working queries.
  • Maven Assembly plug-in upgraded to latest version, many related files fixed.
  • javax.xml.bind + jaxb-runtime replaced with jakarta.xml.bind-api + jaxb-impl, due to problems with J17 compatibility (moreover, the previous modules are a dead projects).

5.0

  • Big changes to migrate to Java 11.
  • New version of rd2neo integrated into the neo4j-export component.
  • GraphSamplingPlugIn, better criteria to sample a representative graph.
  • Code changes:
    • git submodules eliminated, we went back to a single repository codebase
    • POMs cleaning/refactoring
    • Some code cleaning/refactoring
    • Graph manipulation and access utilities added
    • CI Migration to GitHub Actions, common CI script from rdf-common
  • Bugfixes and improvements to tab parser
  • Bugfixes and improvements to Lucene indexing module
  • Miscellanea:
    • Windows scripts updated
    • Some diagnostic messages added to the OXL parser
    • FASTA importer: AA sequence no longer imported
    • JSON exporter: minor changes to the output, to reflect Knetminer needs

3.0

  • Various bugfixes in the components:
    • Neo4j-export
  • Internal changes
    • Maven artifactory migrated to our new Nexus.
    • Maven POM linked to
    • Cleaning and improvement of both code and Maven files

2.1

  • Improvements to OWL/Ondex mappings (example).
  • Minor changes to the launching scripts (example).
  • Fixing problems with OXL Import/Export (#12, #14).
  • Fixing issues with the FASTA parser (1, 2).
  • Internal changes:

2.0

  • Graph Databases and Linked Data support:
  • OWL Parser and base components for developers:
    • Complete review of the generic parser architecture, which now has clear separation between data source decomposition and mapping.
    • The OWL Parser was changed accordingly.
    • Generic packages (ie, the generic parser library and a few utilities) were migrated from the owl parser module to proper places.
    • Several mappings for common ontologies added.
  • All ONDEX code reviewed and migrated to Lucene 6.0.0.
  • Berkeley support removed from the main build.
  • Bugfixing and Enhancements:
    • Text mining module (to support new PubMed XML, #12, #13).
    • New Concept Classes and and relation types added.

1.2

  • OWL parser
    • Some debugging and improvements in parsing GO, TO, FYPO ontologies
    • Options to customise accession prefixes in the final ONDEX graph
  • UniProt parser
  • Graph-merge options added to the tab-parser-2 to the tabular parser