Uberon ROBOT plugin 0.5.0

Changes since version 0.4.0:

• New command uberon:inference-diff to generate a report highlighting the consequences of changes to logical definitions between two versions of an ontology.

Uberon ROBOT plugin 0.4.0

Changes since version 0.3.3:

• The uberon:obo-export command has been removed; the --clean-obo option of the standard convert command, available in ROBOT 1.9.8, should be used instead.

Uberon ROBOT plugin 0.3.3

This release adds a new command obo-export to produce customised OBO files.

Usage:

robot uberon:obo-export -i source.owl --strip-owl-axioms --strip-gci-axioms --merge-comments --obo-output destination.obo

• --strip-owl-axioms: Discard any axiom that cannot be represented in pure OBO (normally written in the owl-axioms header tag).
• --strip-gci-axioms: Discard any GCI axiom.
• --merge-comments: When a class has several rdfs:comment annotations (something that is not allowed in OBO), merge the comments into a single annotation.
• --obo-output FILE: Write the customised OBO to the indicated file.

Uberon ROBOT plugin 0.3.2

This release adds a --batch-file option to the merge-species command, allowing to perform several merges, for several species and/or over several linking properties, in a single invocation.

Uberon ROBOT plugin 0.3.1

This is a bug fix release. It fixes the create-species-subset command to ensure that root classes specified by the --root option are included in the subset, instead of only the descendants of the root classes.

Uberon ROBOT plugin 0.3.0

Changes since version 0.2.0:

• Unused command expand-curies has been removed.
• New command create-species-subset has been added.

Uberon ROBOT Plugin 0.2.0

Changes from version 0.1.0:

• Built for ROBOT 1.9.5, which has native support for plugins (consequently, the “standalone” build is no longer provided);
• New options for the merge-species command:
  • -d to delete class declaration axioms for classes that have been merged into another;
  • -x to translate more class expressions than just ObjectSomeValuesFrom;
  • -g to translate general class axioms (GCAs) that refer to classes that have been merged, when possible (axioms that cannot be translated are removed);
  • -G to always remove general class axioms that refer to classes that have been merged (without attempting to translate them).

Uberon ROBOT Plugin 0.1.0

Initial version of a ROBOT plugin intended to be used in Uberon pipelines.

The plugin provides replacement commands for two of OWLTools’ features:

• merge-species (replacement for --merge-species-ontology);
• merge-equivalent-sets (replacement for --merge-equivalence-sets).