v1.9.8

Added

• Add --clean-obo option to convert #995
• Allow interpolation of ontology IRI and version IRI within annotation values #1241
• Allow selecting punned entities in remove and filter #1251
• Add support for predicate-object pairs to ROBOT template #1249

Changed

• Updated Apache POI #1252
• Support SPLIT=\n #1246
• Include SubObjectPropertyOf axioms when reducing #1248

Fixed

• Update owl-diff dependency for stable ordering and to avoid large string creation #1227
• Exclude deprecated from lowercase_definition check #1224
• Improve disambiguation of properties in QuotedEntityChecker #1226
• Skip "non-robot" columns in templates for the purposes of axiom annotations #1216
• Fix but that caused logical axioms with axiom annotations not to be processed correctly when merging axiom annotations #1223
• Correctly merge unannotated and annotated duplicated axioms #1239
• Fix reading of default queries from embedded Jar resources #1212
• Fix repair --merge-axiom-annotations #1240
• Allow interpolation of placeholders in annotation values. #1242
• Subproperties being ignored when evaluating redundancy in reduce #1014, #1208

v1.9.7

Fixed

• Output inferred object property assertions using Whelk reasoner, by updating to Whelk 1.1.3. #1121

Changed

• Update Whelk to 1.2.1 #1221
• Treat raw IRI as an OWLClass in logical template cells #1211

v1.9.6

Added

• Added option to input template strings from external file #1152

Changed

• Updated duplicate_exact_syonym report query to be case-insensitive and ignore synoyms annotated as abbreviation or acronym synonym types #1179
• Extend --drop-axiom-annotations option to support value-specific removal of axiom annotations #1193
• Add --enforce-obo-format, --exclude-named-classes and --include-subclass-of features to relax command #1060, #1183
• Updated obographs to version 0.3.1(https://github.com/geneontology/obographs/releases/tag/v0.3.1)
• Updated OWL API to 4.5.29. This includes a major update to OBO Format which now supports IDSPACE declarations(owlcs/owlapi#1102) (non-OBO Foundry prefixes).
• Updated Elk to version 0.6.0, see here(liveontologies/elk-reasoner#48 (comment)).

Fixed

• '--annotate-with-source true' does not work with extract --method subset #1160
• Fix how Template adds entities to the QuotedEntityChecker #1104
• merge and 'annotate' operations '--annotate-defined-by' excludes reserved OWL 2 vocabularies #1171
• Handle IRIs that are not entities in export #1168
• Fix integration tests #1181
• robot repair is fixed to be more flexible, to enable partial repairs #1194
• Invalid Xrefs test has been fixed to recognise invalid CURIEs correctly #1127
• Fix issue with correctly determining base entities #1108

v1.9.5

Added

• Updated ELK from 0.4.3 to 0.5.0. #999. This is an important change as ELK 0.5.0 is more complete than 0.4.3, which means that it will potentially uncover inferences, in particular unsatisfiable classes, which were not recognised by ELK 0.4.3.
• Add support for pluggable commands #1119

Changed

• Migrate to OWL API 4.5.26 to deal with broken turtle serialiser(#1129). #1135
• Improvements to export and report for XLSX format #1148

v1.9.4

Changed

• Speed up unsatisfiable object-property check on certain reasoners including HermiT #1100
• Update HermiT from 1.3.8.413 to 1.4.5.456 #1073

Fixed

• Preserve prefixes across ontology load and save #1101

v1.9.3

Added

• Subset method added to extract #1000

Changed

• Upgrade OWLAPI to 4.5.25 #1093

Fixed

• Restore logging details for CLI #1091
• Fix OBO Serialiser bug where built in vocabulary was introduced as annotation properties #1089
• Fix OBO Serialiser erroneous logging #1088

v1.9.2

Changed

• Upgrade OWLAPI to 4.5.24 #1086

Fixed

• Downgrade SnakeYaml to 1.31 #1071
• Don't check for disjoint annotation properties #1084

This ROBOT release synchronizes with Protégé 5.6.0 which has updated to OWL API 4.5.24. This version of OWL API includes several changes to some serializers (notably the OBO-format serializer), which will likely result in large diffs when ontology files are saved with this version of ROBOT or Protégé for the first time. To minimize the annoyance caused by such diffs, it is advised to:

• save your ontology with ROBOT 1.9.2 or Protégé 5.6.0 without introducing any changes to the logic or annotations, and commit the resulting ontology files; consider saving to OFN syntax and then OWL (RDF/XML) format, as explained in #1090
• once the ontology files have been saved once with ROBOT 1.9.2 or Protégé 5.6.0, avoid editing it again with older versions of ROBOT or Protégé.

v1.9.1 with ELK 0.5.0

This version of ROBOT includes a snapshot of ELK 0.5.0, based on #999. ELK 0.5.0 is more strict than ELK 0.4.3 that was previously included with ROBOT, and so ROBOT may report more logical problems such as unsatisfiable classes when using the new ELK. This pre-release is for testing with ELK 0.5.0 in ROBOT workflows.

v1.9.1

Added

• extract and merge should optionally inject provenance #977
• Checking for empty strings in addition to missing ones in missing_label.rq #1017
• Add "domain" and "range" support to export #1061

Fixed

• Fixed report serialization in JSON #1016
• Fix missing labels in diff output. #1026
• input IRI now takes catalog file into account #1030

v1.9.0

Added

• Add new command: expand #964

Fixed

• Fix OBOGraphs by updating guava #1009