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Releases · gouttegd/kgcl-java · GitHub

Releases · gouttegd/kgcl-java

Changes since KGCL-Java 0.5.0:

• It is now possible to refer to object properties by their “OBO shorthands”, if they do have such a shorthand. For example, "part_of" would be understood to refer to BFO:0000050, if the part_of shorthand annotation is present in the ontology the changes are applied to.
• As a special case, "is_a" is accepted as a shorthand for rdfs:subClassOf.

Changes sinces KGCL-Java 0.4.0:

• It is now possible to refer to nodes in a KGCL instruction using their labels rather than their identifiers (e.g., obsolete 'my class rather than obsolete EX:0001).
• The KGCLReader and KGCLWriter classes now accept a Map<String,String> to use a custom prefix map, in addition to a OWLAPI PrefixManager object.
• The org.incenp.obofoundry.kgcl package has been restructured and several classes have been moved to subpackages (which may break existing code); in particular, all classes related to the application of KGCL changes to an OWL ontology have been moved to the org.incenp.obofoundry.kgcl.owl subpackage. Note that code that was using the KGCLHelper class to perform operations, rather than instanciating classes from the org.incenp.obofoundry.kgcl package, should remain unaffected by the restructuration.

Changes sinces KGCL-Java 0.3.2:

• Allow creating an edge that uses an annotation property (when the value is an entity rather than a literal).
• Allow creating new object properties (create relation...) and new annotation properties (create annotation property...).
• Support for explicit typing of literal values (e.g. "123"^^xsd:integer).
• Lax comparison of literal values when language tags are used (see INCATools/kgcl#60).
• New --create option for the kgcl:apply ROBOT command, to create a new ontology from scratch with the changes rather than working on an existing ontology.
• Support for auto-assignation of IDs for newly created entities (see INCATools/kgcl#56).
• New helper ROBOT command kgcl:mint to re-allocate permanent identifiers.

Changes since KGCL-Java 0.3.1:

• When obsoleting a class with a direct replacement, axioms referring to the obsolete class are now re-wired.
• Language tags in text values (e.g. for synonyms or labels) are better handled.
• Experimental support for applying changes in a “provisional” manner, by recording them in the ontology rather than applying them directory.

See INCATools/kgcl#49 for details about the “provisional mode”.

To record provisional changes in an ontology rather than applying them, pass the --provisional (-p) option to the ROBOT apply command.

To apply provisional changes that were previously recorded in an ontology, use the --pending DATE option, where DATE is either the special value all to apply all provisional changes, or a date in the YYYY-MM-DD format to apply all changes that were recorded prior to the indicated date.

Changes since KGCL-Java 0.3.0:

• Fix packaging of ROBOT plugin.
• Add support for node "unobsoletion" (unobsolete command).
• Add support for node deletion (delete command).
• Add support for node annotation change (change annotation command).

Changes since KGCL-Java 0.2.0:

• Support for edge deletion (delete edge command).
• Support for node move operations (move, deepen, shallow commands).
• Support for predicate change (change relationship command).

• Java library:
  • Do not fail to parse empty inputs.
  • Allow to use KGCLReader on strings in addition to files.
  • KGCLReader returns an empty list rather than null upon errors.
• ROBOT apply command:
  • Allow using -k and/or -K options more than once.
  • Add --(no-)reject-file options.

• kgcl-0.2.0.jar is the base Java library containing only the code from this project (dependencies are not included);
• kgcl-robot-plugin-0.2.0.jar additionally includes the dependencies that are not already provided by the standard ROBOT distribution; as such, that file is suitable for use as a ROBOT plugin, if you have a version of ROBOT that supports such plugins;
• kgcl-robot-standalone-0.2.0.jar includes a full distribution of ROBOT 1.9.4, where the apply command from this project is readily available as a built-in command.

This is the initial release of the KGCL Java library and ROBOT command. See the README for details of what is implemented in this version.

• kgcl-0.1.0.jar is the base Java library containing only the code from this project (dependencies are not included);
• kgcl-robot-plugin-0.1.0.jar additionally includes the dependencies that are not already provided by the standard ROBOT distribution; as such, that file is suitable for use as a ROBOT plugin, if you have a version of ROBOT that supports such plugins;
• kgcl-robot-standalone-0.1.0.jar includes a full distribution of ROBOT 1.9.4, where the apply command from this project is readily available as a built-in command.

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