SSSOM-Java 0.7.1

This is a bugfix release.

The documentation of the SSSOM/T-OWL dialect used by the inject ROBOT command states that all axiom-generating functions accept an optional argument describing how to annotate the generated axioms, but this was not true for the direct() function, which accepted no such argument.

The only change from version 0.7.0 is that the direct() function now accepts the same optional argument as all the other axiom-generating functions. The default behaviour, when the function is called without argument, is still to generate direct axiom annotations for all the mapping metadata except mapping_cardinality.

SSSOM-Java 0.7.0

Changes since version 0.6.2:

• New ROBOT command to rename entities in a OWL ontology, using a mapping set as data source.
• New SSSOM/T preprocessing function to edit mappings on the fly.

SSSOM-Java 0.6.2

Changes since version 0.6.1:

• Fix erroneous inversion of object_source slot when inverting a mapping.
• sssom-cli:
  • Provide a self-executable Jar file (for Unix-like systems only).
  • Add the --rule option to specify a single SSSOM/T rule directly from the command line.
• sssom-inject:
  • Allow to create annotated axioms using the mapping metadata.

Full Changelog: sssom-java-0.6.1...sssom-java-0.6.2

SSSOM-Java 0.6.1

Changes since version 0.6.0:

• TSV writer:
  • Write out a default license value if no license is explicitly set.
  • Write out an automatically generated ID if no ID is explicitly set.
• SSSOM/T:
  • Fix filtering on mapping cardinality to ensure it works correctly even when mappings are dropped during the processing.
• xref-extract:
  • Try to infer mapping ID and license from the source ontology.
  • New options --set-id and --set-license.
• sssom-inject:
  • Renamed to inject.

Full Changelog: sssom-java-0.6.0...sssom-java-0.6.1

SSSOM-Java 0.6.0

Changes since version 0.5.0:

• SSSOM/T can now filter on all available slots.
• Changes to the TSV reader:
  • Silently ignores unknown slots.
  • Recognises and converts slots from older versions of the specification.
  • Propagates slots down to individual mappings.
• Changes to the TSV writer:
  • Condenses slots up to the level of the mapping set.
• SSSOM-to-OWL:
  • Excludes mapping_cardinality from OWL serialisation.
  • Use dc/terms rather than dc/elements/1.1 for dispatch table metadata.
• Addition of sssom-cli, a command-line tool to manipulate mapping sets.

Full Changelog: sssom-java-0.5.0...sssom-java-0.6.0

SSSOM-Java 0.5.0

Changes since version 0.4.3:

• Fix sssom-inject crash when using --direct option under certain conditions.
• Fix parsing of multi-valued slots in mappings.
• Make the output of the TSV writer fully predictable:
  • Sort mapping set metadata by “spec order”.
  • Sort Curie map entries by alphabetical order.
  • Sort mappings using all available slots.
  • Write the effective Curie map only.
• Add SlotVisitor interface.
• Add test suite.

SSSOM-Java 0.4.3

Changes since version 0.4.2

• Update model to sssom-0.15.
• Fix writing of date fields.
• Fix bogus computation of mapping cardinality.
• xref-extract:
  • Ignore obsolete classes when extracting cross-references.
  • Allow reusing an existing mapping set (or its metadata).

SSSOM-Java 0.4.2

Changes since version 0.4.1

• Allow filtering on mapping cardinality (e.g. mapping_cardinality==1:n).
• Add option --drop-duplicates to xref-extract.
• Allow to set default ontology ID/version in a dispatch table.
• Dispatch table filenames are relative to the directory containing the table.

Release artifacts

• sssom-core-0.4.2.jar is the base Java library containing only the code from this project (dependencies are not included);
• sssom-robot-plugin-0.4.2.jar is a plugin for ROBOT providing the sssom-inject and xref-extract commands, to be used with a version ROBOT that supports plugins (no such version has been released yet);
• sssom-robot-standalone-0.4.2.jar includes a full distribution of ROBOT 1.9.4, where the sssom-inject and xref-extract commands from this project are readily available as built-in commands.

SSSOM-Java 0.4.1

Changes since version 0.4.0

This version brings some helper options to sssom-inject, intended to allow avoiding the use of SSSOM/Transform rules for some simple use cases:

• --invert to invert the mapping set before generating any bridging axioms.
• --bridge-iri to specify the ontology IRI of the bridge file created with --bridge-file.
• --only-subject-in to filter mappings on their subject ID.
• --only-object-in to filter mappings on their object ID.

In addition, the command now is by default aware of all prefixes that are known to ROBOT when it is called. Use the --no-default-prefixes to revert to the previous behaviour where all prefixes had to be explicitly declared.

Release artifacts

• sssom-core-0.4.1.jar is the base Java library containing only the code from this project (dependencies are not included);
• sssom-robot-plugin-0.4.1.jar is a plugin for ROBOT providing the sssom-inject and xref-extract commands, to be used with a version ROBOT that supports plugins (no such version has been released yet);
• sssom-robot-standalone-0.4.1.jar includes a full distribution of ROBOT 1.9.4, where the sssom-inject and xref-extract commands from this project are readily available as built-in commands.

SSSOM-Java 0.4.0

Changes since version 0.3.1

• SSSOM/T-OWL:
  • New preprocessing functions check_subject_existence() and check_object_existence().
  • New function set_var() to declare mapping-dependent variables.
• New ROBOT command xref-extract to get extract mappings from oboInOwl:hasDbXref annotations in an ontology.
• New in sssom-inject:
  • Allow loading multiple mapping sets by repeating --sssom option as needed.
  • New option --extract to get a mapping set directly from oboInOwl:hasDbXref annotations in the ontology (may be combined with --sssom).
  • New add-axiom key in dispatch table entries.

Release artifacts

• sssom-core-0.4.0.jar is the base Java library containing only the code from this project (dependencies are not included);
• sssom-robot-plugin-0.4.0.jar is a plugin for ROBOT providing the sssom-inject and xref-extract commands, to be used with a version ROBOT that supports plugins (no such version has been released yet);
• sssom-robot-standalone-0.4.0.jar includes a full distribution of ROBOT 1.9.4, where the sssom-inject and xref-extract commands from this project are readily available as built-in commands.