Index

Symbols

--about runoak-axioms command line option --adapter-mapping runoak-validate-definitions command line option runoak-validate-mappings command line option runoak-validate-subset command line option runoak-validate-synonyms command line option --add runoak command line option --add-closure-fields runoak-associations command line option runoak-associations-counts command line option --add-labels runoak-lexmatch command line option --add-mrcas runoak-tree command line option runoak-viz command line option --additional-metadata runoak-definitions command line option runoak-term-metadata command line option --all runoak-ontology-metadata command line option runoak-ontology-versions command line option runoak-taxon-constraints command line option --all-languages runoak-labels command line option --allow-labels runoak-enrichment command line option --allow-missing runoak-fill-table command line option --analyze runoak-generate-logical-definitions command line option --annotated-roots runoak-roots command line option --apply-patch runoak-generate-definitions command line option runoak-generate-lexical-replacements command line option runoak-generate-synonyms command line option runoak-synonymize command line option --association-predicates runoak-associations command line option runoak-associations-counts command line option runoak-associations-matrix command line option runoak-enrichment command line option --associations runoak command line option runoak-diff-associations command line option --associations-type runoak command line option --autolabel runoak-associations command line option runoak-associations-counts command line option runoak-associations-matrix command line option runoak-definitions command line option runoak-diff-associations command line option runoak-diff-via-mappings command line option runoak-disjoints command line option runoak-enrichment command line option runoak-fill-table command line option runoak-generate-disjoints command line option runoak-generate-logical-definitions command line option runoak-logical-definitions command line option runoak-mappings command line option runoak-normalize command line option runoak-paths command line option runoak-query command line option runoak-relationships command line option runoak-rollup command line option runoak-search command line option runoak-similarity command line option runoak-similarity-pair command line option runoak-termset-similarity command line option runoak-usages command line option runoak-validate-mappings command line option runoak-validate-subset command line option runoak-validate-synonyms command line option --autosave runoak command line option --axiom-type runoak-axioms command line option --background-file runoak-enrichment command line option --bidirectional runoak-diff-via-mappings command line option --caching runoak command line option --category runoak-annotate command line option --category-system runoak-term-categories command line option --change-type runoak-diff command line option --changes-format runoak-apply command line option --changes-input runoak-apply command line option --changes-output runoak-apply command line option --comment runoak-fill-table command line option --compare-with runoak-statistics command line option --config-file runoak-dump command line option runoak-transform command line option --config-yaml runoak-validate-subset command line option --configuration-file runoak-annotate command line option runoak-validate-definitions command line option runoak-validate-mappings command line option runoak-validate-subset command line option runoak-validate-synonyms command line option --configure runoak-paths command line option runoak-tree command line option runoak-viz command line option --contributor runoak-apply command line option --cutoff runoak-enrichment command line option runoak-validate command line option runoak-validate-multiple command line option --dangling runoak-extract command line option --days-old runoak-cache-clear command line option --delimiter runoak-fill-table command line option --direct runoak-taxon-constraints command line option --directed runoak-paths command line option --direction runoak-relationships command line option --display runoak-definitions command line option runoak-descendants command line option runoak-info command line option runoak-labels command line option runoak-tree command line option --down runoak-tree command line option runoak-viz command line option --dry-run runoak-apply command line option runoak-lint command line option --endpoint runoak-set-apikey command line option --enforce-canonical-ordering runoak-dump command line option --ensure-strict-prefixes runoak-lexmatch command line option --evolution-file runoak-apply-taxon-constraints command line option --exclude-defined runoak-generate-definitions command line option --exclude-existing runoak-generate-disjoints command line option --exclude-mapped runoak-lexmatch command line option --exclude-predicates runoak-paths command line option --exclude-query runoak-validate-subset command line option --exclude-tokens runoak-annotate command line option --expand runoak-apply command line option runoak-apply-obsolete command line option --fill runoak-generate-logical-definitions command line option --filter runoak-associations-counts command line option --filter-category-identical runoak-diff-via-mappings command line option --filter-obsoletes runoak-leafs command line option runoak-singletons command line option runoak-terms command line option --filter-redundant runoak-enrichment command line option --gap-fill runoak-tree command line option runoak-viz command line option --graph-traversal-method runoak-ancestors command line option runoak-apply-taxon-constraints command line option runoak-descendants command line option runoak-taxon-constraints command line option --group-by runoak-associations-counts command line option runoak-diff-associations command line option --group-by-defined-by runoak-diff command line option runoak-statistics command line option --group-by-obo-namespace runoak-diff command line option runoak-statistics command line option --group-by-prefix runoak-diff command line option runoak-statistics command line option --group-by-property runoak-diff command line option runoak-statistics command line option --has-prefix runoak-roots command line option runoak-statistics command line option --if-absent runoak-associations command line option runoak-definitions command line option runoak-labels command line option runoak-logical-definitions command line option runoak-relationships command line option --ignore-invalid-changes runoak-apply command line option runoak-apply-obsolete command line option --import-depth runoak command line option --include-abox runoak-relationships command line option --include-aliases runoak-annotate command line option --include-entailed runoak-relationships command line option --include-entities runoak-associations-matrix command line option --include-identity-mappings runoak-diff-via-mappings command line option --include-merged runoak-obsoletes command line option --include-metadata runoak-extract command line option runoak-relationships command line option --include-predicates runoak-paths command line option --include-redundant runoak-taxon-constraints command line option --include-residuals runoak-statistics command line option --include-tbox runoak-relationships command line option --include-unused runoak-usages command line option --information-content-adapter runoak-validate-subset command line option --information-content-file runoak-similarity command line option runoak-termset-similarity command line option runoak-validate-subset command line option --input runoak command line option --input-type runoak command line option --intra runoak-diff-via-mappings command line option --label-fields runoak-query command line option --lexical-index-file runoak-annotate command line option runoak-lexmatch command line option --limit runoak-associations-counts command line option --lookup-references runoak-definitions command line option --main-score-field runoak-associations-matrix command line option runoak-similarity command line option --mapper runoak-mappings command line option --mapping-input runoak-diff-via-mappings command line option --maps-to-source runoak-mappings command line option runoak-normalize command line option --match-column runoak-annotate command line option --matches-whole-text runoak-annotate command line option --matrix-axes runoak-logical-definitions command line option --max-hops runoak-tree command line option runoak-viz command line option --merge runoak command line option --meta runoak-viz command line option --metamodel-mappings runoak command line option --min-ancestor-information-content runoak-similarity command line option --min-descendants runoak-generate-disjoints command line option --min-facet-count runoak-associations-counts command line option --min-jaccard-similarity runoak-similarity command line option --missing-value-token runoak-fill-table command line option --model runoak-annotate command line option --named-classes-only runoak-disjoints command line option --named-prefix-map runoak command line option --narrow runoak-paths command line option --new-date runoak-diff-associations command line option --no-A runoak-roots command line option runoak-taxon-constraints command line option --no-add-closure-fields runoak-associations command line option runoak-associations-counts command line option --no-add-labels runoak-lexmatch command line option --no-add-mrcas runoak-tree command line option runoak-viz command line option --no-additional-metadata runoak-definitions command line option runoak-term-metadata command line option --no-all runoak-ontology-metadata command line option runoak-ontology-versions command line option runoak-taxon-constraints command line option --no-all-languages runoak-labels command line option --no-allow-labels runoak-enrichment command line option --no-allow-missing runoak-fill-table command line option --no-analyze runoak-generate-logical-definitions command line option --no-annotated-roots runoak-roots command line option --no-apply-patch runoak-generate-definitions command line option runoak-generate-lexical-replacements command line option runoak-generate-synonyms command line option runoak-synonymize command line option --no-autolabel runoak-associations command line option runoak-associations-counts command line option runoak-associations-matrix command line option runoak-definitions command line option runoak-diff-associations command line option runoak-diff-via-mappings command line option runoak-disjoints command line option runoak-enrichment command line option runoak-fill-table command line option runoak-generate-disjoints command line option runoak-generate-logical-definitions command line option runoak-logical-definitions command line option runoak-mappings command line option runoak-normalize command line option runoak-paths command line option runoak-query command line option runoak-relationships command line option runoak-rollup command line option runoak-search command line option runoak-similarity command line option runoak-similarity-pair command line option runoak-termset-similarity command line option runoak-usages command line option runoak-validate-mappings command line option runoak-validate-subset command line option runoak-validate-synonyms command line option --no-autosave runoak command line option --no-bidirectional runoak-diff-via-mappings command line option --no-dangling runoak-extract command line option --no-direct runoak-taxon-constraints command line option --no-directed runoak-paths command line option --no-down runoak-tree command line option runoak-viz command line option --no-dry-run runoak-apply command line option runoak-lint command line option --no-enforce-canonical-ordering runoak-dump command line option --no-ensure-strict-prefixes runoak-lexmatch command line option --no-exclude-defined runoak-generate-definitions command line option --no-exclude-existing runoak-generate-disjoints command line option --no-exclude-mapped runoak-lexmatch command line option --no-expand runoak-apply command line option runoak-apply-obsolete command line option --no-fill runoak-generate-logical-definitions command line option --no-filter-category-identical runoak-diff-via-mappings command line option --no-filter-obsoletes runoak-leafs command line option runoak-singletons command line option runoak-terms command line option --no-filter-redundant runoak-enrichment command line option --no-gap-fill runoak-tree command line option runoak-viz command line option --no-group-by-defined-by runoak-diff command line option runoak-statistics command line option --no-group-by-obo-namespace runoak-diff command line option runoak-statistics command line option --no-group-by-prefix runoak-diff command line option runoak-statistics command line option --no-ignore-invalid-changes runoak-apply command line option runoak-apply-obsolete command line option --no-include-abox runoak-relationships command line option --no-include-aliases runoak-annotate command line option --no-include-entailed runoak-relationships command line option --no-include-entities runoak-associations-matrix command line option --no-include-identity-mappings runoak-diff-via-mappings command line option --no-include-merged runoak-obsoletes command line option --no-include-metadata runoak-extract command line option runoak-relationships command line option --no-include-predicates runoak-paths command line option --no-include-redundant runoak-taxon-constraints command line option --no-include-residuals runoak-statistics command line option --no-include-tbox runoak-relationships command line option --no-include-unused runoak-usages command line option --no-intra runoak-diff-via-mappings command line option --no-lookup-references runoak-definitions command line option --no-matches-whole-text runoak-annotate command line option --no-merge runoak command line option --no-meta runoak-viz command line option --no-named-classes-only runoak-disjoints command line option --no-narrow runoak-paths command line option --no-non-redundant-entailed runoak-relationships command line option --no-obo-model runoak-aliases command line option --no-ontology-only runoak-enrichment command line option --no-overwrite runoak-apply command line option --no-parse runoak-generate-logical-definitions command line option --no-pivot-languages runoak-labels command line option --no-profile runoak command line option --no-quiet runoak command line option --no-recreate runoak-lexmatch command line option --no-replace runoak-migrate-curies command line option --no-show-extract runoak-generate-logical-definitions command line option --no-show-migration-relationships runoak-obsoletes command line option --no-simple runoak-diff command line option --no-skip-ontology-rules runoak-validate command line option --no-skip-structural-validation runoak-validate command line option --no-skip-text-annotation runoak-validate-definitions command line option --no-stacktrace runoak command line option --no-statistics runoak-ancestors command line option runoak-diff command line option --no-unmelt runoak-generate-logical-definitions command line option runoak-logical-definitions command line option --no-use-associations runoak-information-content command line option --no-used-only runoak-prefixes command line option --no-view runoak-viz command line option --no-viz runoak-paths command line option --no-W runoak-annotate command line option --non-redundant-entailed runoak-relationships command line option --object-group runoak-rollup command line option --obo-model runoak-aliases command line option --old-date runoak-diff-associations command line option --ontology-only runoak-enrichment command line option --other-associations runoak-diff-associations command line option --other-input runoak-diff-via-mappings command line option --other-input-type runoak-diff-via-mappings command line option --other-languages runoak command line option --other-ontology runoak-diff command line option runoak-diff-terms command line option --output runoak-aliases command line option runoak-ancestors command line option runoak-annotate command line option runoak-apply command line option runoak-apply-obsolete command line option runoak-apply-taxon-constraints command line option runoak-associations command line option, [1] runoak-associations-counts command line option, [1] runoak-associations-matrix command line option, [1] runoak-axioms command line option runoak-definitions command line option runoak-descendants command line option runoak-diff command line option runoak-diff-associations command line option, [1] runoak-diff-terms command line option runoak-diff-via-mappings command line option runoak-disjoints command line option runoak-dump command line option runoak-enrichment command line option, [1] runoak-expand-subsets command line option runoak-extract command line option runoak-fill-table command line option runoak-generate-definitions command line option runoak-generate-disjoints command line option runoak-generate-lexical-replacements command line option runoak-generate-logical-definitions command line option runoak-generate-synonyms command line option runoak-info command line option runoak-information-content command line option runoak-labels command line option runoak-leafs command line option runoak-lexmatch command line option runoak-lint command line option runoak-logical-definitions command line option runoak-mappings command line option runoak-migrate-curies command line option runoak-normalize command line option runoak-obsoletes command line option runoak-ontologies command line option runoak-ontology-metadata command line option runoak-ontology-versions command line option runoak-paths command line option runoak-prefixes command line option runoak-query command line option runoak-relationships command line option runoak-rollup command line option runoak-roots command line option runoak-search command line option runoak-siblings command line option runoak-similarity command line option runoak-similarity-pair command line option runoak-singletons command line option runoak-statistics command line option runoak-subsets command line option runoak-synonymize command line option runoak-taxon-constraints command line option runoak-term-categories command line option runoak-term-metadata command line option runoak-term-subsets command line option runoak-terms command line option runoak-termset-similarity command line option runoak-transform command line option runoak-tree command line option runoak-usages command line option, [1] runoak-validate command line option runoak-validate-definitions command line option runoak-validate-mappings command line option runoak-validate-multiple command line option runoak-validate-subset command line option runoak-validate-synonyms command line option runoak-viz command line option

--output-type runoak-aliases command line option runoak-ancestors command line option runoak-annotate command line option runoak-apply command line option runoak-apply-obsolete command line option runoak-associations command line option runoak-associations-counts command line option runoak-associations-matrix command line option runoak-axioms command line option runoak-definitions command line option runoak-descendants command line option runoak-diff command line option runoak-diff-associations command line option runoak-diff-via-mappings command line option runoak-disjoints command line option runoak-dump command line option runoak-enrichment command line option runoak-extract command line option runoak-generate-definitions command line option runoak-generate-disjoints command line option runoak-generate-lexical-replacements command line option runoak-generate-logical-definitions command line option runoak-generate-synonyms command line option runoak-info command line option runoak-information-content command line option runoak-labels command line option runoak-lint command line option runoak-logical-definitions command line option runoak-mappings command line option runoak-migrate-curies command line option runoak-normalize command line option runoak-obsoletes command line option runoak-ontology-metadata command line option runoak-paths command line option runoak-prefixes command line option runoak-query command line option runoak-relationships command line option runoak-rollup command line option runoak-roots command line option runoak-search command line option runoak-siblings command line option runoak-similarity command line option runoak-similarity-pair command line option runoak-statistics command line option runoak-taxon-constraints command line option runoak-term-categories command line option runoak-term-metadata command line option runoak-term-subsets command line option runoak-termset-similarity command line option runoak-transform command line option runoak-tree command line option runoak-usages command line option runoak-validate command line option runoak-validate-definitions command line option runoak-validate-mappings command line option runoak-validate-subset command line option runoak-validate-synonyms command line option runoak-viz command line option --overwrite runoak-apply command line option --owl-type runoak-terms command line option --parse runoak-generate-logical-definitions command line option --patch runoak-generate-definitions command line option runoak-generate-lexical-replacements command line option runoak-generate-synonyms command line option runoak-synonymize command line option --patch-format runoak-generate-definitions command line option runoak-generate-lexical-replacements command line option runoak-generate-synonyms command line option --patterns-file runoak-generate-logical-definitions command line option --pivot-languages runoak-labels command line option --predicate-weights runoak-paths command line option --predicates runoak-ancestors command line option runoak-apply-taxon-constraints command line option runoak-associations command line option runoak-associations-counts command line option runoak-associations-matrix command line option runoak-descendants command line option runoak-diff-associations command line option runoak-diff-via-mappings command line option runoak-disjoints command line option runoak-enrichment command line option runoak-expand-subsets command line option runoak-extract command line option runoak-generate-disjoints command line option runoak-information-content command line option runoak-leafs command line option runoak-logical-definitions command line option runoak-paths command line option runoak-relationships command line option runoak-rollup command line option runoak-roots command line option runoak-siblings command line option runoak-similarity command line option runoak-similarity-pair command line option runoak-singletons command line option runoak-taxon-constraints command line option runoak-term-metadata command line option runoak-termset-similarity command line option runoak-tree command line option runoak-validate-subset command line option runoak-viz command line option --preferred-language runoak command line option --prefix runoak command line option --prefixes runoak-query command line option --profile runoak command line option --query runoak-query command line option --quiet runoak command line option --recreate runoak-lexmatch command line option --references runoak-axioms command line option --relation runoak-fill-table command line option --relation-file runoak-fill-table command line option --replace runoak-migrate-curies command line option --report-format runoak-lint command line option --requests-cache-db runoak command line option --root runoak-tree command line option --rule runoak-validate command line option --rules-expression runoak-generate-lexical-replacements command line option --rules-file runoak-annotate command line option runoak-generate-lexical-replacements command line option runoak-generate-synonyms command line option runoak-lexmatch command line option runoak-synonymize command line option runoak-validate-synonyms command line option --sample-file runoak-enrichment command line option --save-as runoak command line option --schema runoak-fill-table command line option runoak-validate-multiple command line option --set-value runoak-associations command line option runoak-definitions command line option runoak-labels command line option runoak-logical-definitions command line option runoak-relationships command line option --set1-file runoak-similarity command line option --set2-file runoak-similarity command line option --show-extract runoak-generate-logical-definitions command line option --show-migration-relationships runoak-obsoletes command line option --simple runoak-diff command line option --skip runoak-tree command line option --skip-ontology-rules runoak-validate command line option --skip-structural-validation runoak-validate command line option --skip-text-annotation runoak-validate-definitions command line option --source runoak-diff-via-mappings command line option --stacktrace runoak command line option --statistics runoak-ancestors command line option runoak-diff command line option --style-hints runoak-generate-definitions command line option --stylemap runoak-paths command line option runoak-tree command line option runoak-viz command line option --target runoak-paths command line option --terms-role runoak-associations command line option runoak-associations-counts command line option runoak-associations-matrix command line option --text-file runoak-annotate command line option --transform runoak-transform command line option --unmelt runoak-generate-logical-definitions command line option runoak-logical-definitions command line option --use-associations runoak-information-content command line option --used-by-prefix runoak-usages command line option --used-only runoak-prefixes command line option --verbose runoak command line option --view runoak-viz command line option --viz runoak-paths command line option --wrap-adapter runoak command line option -A runoak-annotate command line option runoak-roots command line option runoak-taxon-constraints command line option -a runoak command line option -B runoak-enrichment command line option -C runoak-annotate command line option runoak-paths command line option runoak-tree command line option runoak-validate-definitions command line option runoak-validate-mappings command line option runoak-validate-subset command line option runoak-validate-synonyms command line option runoak-viz command line option -c runoak-dump command line option runoak-transform command line option -D runoak-definitions command line option runoak-descendants command line option runoak-info command line option runoak-labels command line option runoak-tree command line option -E runoak-apply-taxon-constraints command line option -e runoak-set-apikey command line option -F runoak-associations-counts command line option -G runoak command line option -g runoak command line option runoak-diff-associations command line option -I runoak command line option -i runoak command line option -L runoak-annotate command line option runoak-associations-counts command line option runoak-lexmatch command line option runoak-query command line option -l runoak command line option -M runoak-ancestors command line option runoak-apply-taxon-constraints command line option runoak-descendants command line option runoak-generate-disjoints command line option runoak-mappings command line option runoak-normalize command line option runoak-taxon-constraints command line option -m runoak-annotate command line option -O runoak-aliases command line option runoak-ancestors command line option runoak-annotate command line option runoak-apply command line option runoak-apply-obsolete command line option runoak-associations command line option runoak-associations-counts command line option runoak-associations-matrix command line option runoak-axioms command line option runoak-definitions command line option runoak-descendants command line option runoak-diff command line option runoak-diff-associations command line option runoak-diff-via-mappings command line option runoak-disjoints command line option runoak-dump command line option runoak-enrichment command line option runoak-extract command line option runoak-generate-definitions command line option runoak-generate-disjoints command line option runoak-generate-lexical-replacements command line option runoak-generate-logical-definitions command line option runoak-generate-synonyms command line option runoak-info command line option runoak-information-content command line option runoak-labels command line option runoak-lint command line option runoak-logical-definitions command line option runoak-mappings command line option runoak-migrate-curies command line option runoak-normalize command line option runoak-obsoletes command line option runoak-ontology-metadata command line option runoak-paths command line option runoak-prefixes command line option runoak-query command line option runoak-relationships command line option runoak-rollup command line option runoak-roots command line option runoak-search command line option runoak-siblings command line option runoak-similarity command line option runoak-similarity-pair command line option runoak-statistics command line option runoak-taxon-constraints command line option runoak-term-categories command line option runoak-term-metadata command line option runoak-term-subsets command line option runoak-termset-similarity command line option runoak-transform command line option runoak-tree command line option runoak-usages command line option runoak-validate command line option runoak-validate-definitions command line option runoak-validate-mappings command line option runoak-validate-subset command line option runoak-validate-synonyms command line option runoak-viz command line option -o runoak-aliases command line option runoak-ancestors command line option runoak-annotate command line option runoak-apply command line option runoak-apply-obsolete command line option runoak-apply-taxon-constraints command line option runoak-associations command line option, [1] runoak-associations-counts command line option, [1] runoak-associations-matrix command line option, [1] runoak-axioms command line option runoak-definitions command line option runoak-descendants command line option runoak-diff command line option runoak-diff-associations command line option, [1] runoak-diff-terms command line option runoak-diff-via-mappings command line option runoak-disjoints command line option runoak-dump command line option runoak-enrichment command line option, [1] runoak-expand-subsets command line option runoak-extract command line option runoak-fill-table command line option runoak-generate-definitions command line option runoak-generate-disjoints command line option runoak-generate-lexical-replacements command line option runoak-generate-logical-definitions command line option runoak-generate-synonyms command line option runoak-info command line option runoak-information-content command line option runoak-labels command line option runoak-leafs command line option runoak-lexmatch command line option runoak-lint command line option runoak-logical-definitions command line option runoak-mappings command line option runoak-migrate-curies command line option runoak-normalize command line option runoak-obsoletes command line option runoak-ontologies command line option runoak-ontology-metadata command line option runoak-ontology-versions command line option runoak-paths command line option runoak-prefixes command line option runoak-query command line option runoak-relationships command line option runoak-rollup command line option runoak-roots command line option runoak-search command line option runoak-siblings command line option runoak-similarity command line option runoak-similarity-pair command line option runoak-singletons command line option runoak-statistics command line option runoak-subsets command line option runoak-synonymize command line option runoak-taxon-constraints command line option runoak-term-categories command line option runoak-term-metadata command line option runoak-term-subsets command line option runoak-terms command line option runoak-termset-similarity command line option runoak-transform command line option runoak-tree command line option runoak-usages command line option, [1] runoak-validate command line option runoak-validate-definitions command line option runoak-validate-mappings command line option runoak-validate-multiple command line option runoak-validate-subset command line option runoak-validate-synonyms command line option runoak-viz command line option -P runoak-definitions command line option runoak-generate-logical-definitions command line option runoak-query command line option runoak-roots command line option runoak-statistics command line option runoak-usages command line option -p runoak-ancestors command line option runoak-apply-taxon-constraints command line option runoak-associations command line option runoak-associations-counts command line option runoak-associations-matrix command line option runoak-descendants command line option runoak-diff-associations command line option runoak-diff-via-mappings command line option runoak-disjoints command line option runoak-enrichment command line option runoak-expand-subsets command line option runoak-extract command line option runoak-generate-disjoints command line option runoak-information-content command line option runoak-leafs command line option runoak-logical-definitions command line option runoak-paths command line option runoak-relationships command line option runoak-rollup command line option runoak-roots command line option runoak-siblings command line option runoak-similarity command line option runoak-similarity-pair command line option runoak-singletons command line option runoak-taxon-constraints command line option runoak-term-metadata command line option runoak-termset-similarity command line option runoak-tree command line option runoak-validate-subset command line option runoak-viz command line option -Q runoak-associations command line option runoak-associations-counts command line option runoak-associations-matrix command line option -q runoak command line option runoak-query command line option -R runoak-annotate command line option runoak-generate-lexical-replacements command line option runoak-generate-synonyms command line option runoak-lexmatch command line option runoak-synonymize command line option runoak-validate command line option runoak-validate-synonyms command line option -S runoak-associations command line option runoak-associations-matrix command line option runoak-definitions command line option runoak-diff-via-mappings command line option runoak-labels command line option runoak-logical-definitions command line option runoak-paths command line option runoak-relationships command line option runoak-tree command line option runoak-viz command line option -s runoak-validate-multiple command line option -T runoak-enrichment command line option -t runoak-transform command line option -U runoak-enrichment command line option -v runoak command line option -W runoak command line option runoak-annotate command line option -X runoak-diff command line option runoak-diff-associations command line option runoak-diff-via-mappings command line option runoak-statistics command line option runoak-validate-subset command line option -x runoak-annotate command line option -Y runoak-generate-lexical-replacements command line option

A

add_associations() (in module oaklib.selector) (oaklib.interfaces.association_provider_interface.AssociationProviderInterface method) add_metadata() (oaklib.interfaces.obograph_interface.OboGraphInterface method) add_missing_property_values() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) AggregatorImplementation (class in oaklib.implementations.aggregator.aggregator_implementation) alias_map_by_curie() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) aliases_by_curie() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) all_by_all_pairwise_similarity() (oaklib.interfaces.semsim_interface.SemanticSimilarityInterface method) all_entity_curies() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) all_obsolete_curies() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) all_ontology_curies() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) all_relationships() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) all_sssom_mappings() (oaklib.interfaces.mapping_provider_interface.MappingProviderInterface method) all_subset_curies() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) Ancestor ancestor_graph() (oaklib.interfaces.obograph_interface.OboGraphInterface method) ancestors() (oaklib.interfaces.obograph_interface.OboGraphInterface method) annotate_file() (oaklib.interfaces.text_annotator_interface.TextAnnotatorInterface method) annotate_tabular_file() (oaklib.interfaces.text_annotator_interface.TextAnnotatorInterface method) annotate_text() (oaklib.interfaces.text_annotator_interface.TextAnnotatorInterface method)

Annotation annotation_assertion_axioms() (oaklib.interfaces.owl_interface.OwlInterface method) AnnotationProperty apply_patch() (oaklib.interfaces.patcher_interface.PatcherInterface method) as_bytes_io() (oaklib.converters.obo_graph_to_obo_format_converter.OboGraphToOboFormatConverter method) as_obograph() (oaklib.interfaces.obograph_interface.OboGraphInterface method) Asserted Association association_counts() (oaklib.interfaces.association_provider_interface.AssociationProviderInterface method) association_pairwise_coassociations() (oaklib.interfaces.association_provider_interface.AssociationProviderInterface method) association_subject_counts() (oaklib.interfaces.association_provider_interface.AssociationProviderInterface method) AssociationProviderInterface (class in oaklib.interfaces.association_provider_interface) associations() (oaklib.interfaces.association_provider_interface.AssociationProviderInterface method) associations_subject_search() (oaklib.interfaces.association_provider_interface.AssociationProviderInterface method) associations_subjects() (oaklib.interfaces.association_provider_interface.AssociationProviderInterface method) auto_add_contributor_using (oaklib.interfaces.patcher_interface.PatcherInterface attribute) auto_relax_axioms (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface attribute) autosave (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface attribute) axiom_is_about() (oaklib.interfaces.owl_interface.OwlInterface method) axiom_references() (oaklib.interfaces.owl_interface.OwlInterface method)

B

basic_search() (oaklib.interfaces.search_interface.SearchInterface method) BasicOntologyInterface (class in oaklib.interfaces.basic_ontology_interface) Bioportal

branch_summary_statistics() (oaklib.interfaces.summary_statistics_interface.SummaryStatisticsInterface method) BRANCHES runoak-statistics command line option

C

cache_directory (oaklib.interfaces.text_annotator_interface.TextAnnotatorInterface attribute) cache_lookups (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface attribute) cached_information_content_map (oaklib.interfaces.semsim_interface.SemanticSimilarityInterface attribute) Category Class ClassEnrichmentCalculationInterface (class in oaklib.interfaces.class_enrichment_calculation_interface) clone() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) Closure code() (oaklib.converters.obo_graph_to_fhir_converter.OboGraphToFHIRConverter method) COMMANDS runoak-apply command line option comments() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) common_ancestors() (oaklib.interfaces.semsim_interface.SemanticSimilarityInterface method) compare_ontology_term_lists() (oaklib.interfaces.differ_interface.DifferInterface method) Concept CONSTRAINTS runoak-apply-taxon-constraints command line option

convert() (oaklib.converters.data_model_converter.DataModelConverter method) (oaklib.converters.obo_graph_to_cx_converter.OboGraphToCXConverter method) (oaklib.converters.obo_graph_to_fhir_converter.OboGraphToFHIRConverter method) (oaklib.converters.obo_graph_to_obo_format_converter.OboGraphToOboFormatConverter method) converter (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface property) create() (oaklib.implementations.sqldb.sql_implementation.SqlImplementation class method) create_entity() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) create_normalization_map() (oaklib.interfaces.mapping_provider_interface.MappingProviderInterface method) create_search_configuration() (in module oaklib.datamodels.search) create_self_associations() (oaklib.interfaces.class_enrichment_calculation_interface.ClassEnrichmentCalculationInterface method) CURIE curie_converter (oaklib.converters.data_model_converter.DataModelConverter attribute) CURIE_PAIRS runoak-migrate-curies command line option curie_to_uri() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) curies_by_label() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) curies_by_subset() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)

D

dangling() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) Datamodel DataModelConverter (class in oaklib.converters.data_model_converter) DatatypeProperty DBS runoak-validate-multiple command line option default_language (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface property) defined_by() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) defined_bys() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) definition() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) definitions() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) delete_entity() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) Descendant descendant_count() (oaklib.interfaces.obograph_interface.OboGraphInterface method) descendant_graph() (oaklib.interfaces.obograph_interface.OboGraphInterface method)

descendants() (oaklib.interfaces.obograph_interface.OboGraphInterface method) Diff diff() (oaklib.interfaces.differ_interface.DifferInterface method) diff_summary() (oaklib.interfaces.differ_interface.DifferInterface method) DifferInterface (class in oaklib.interfaces.differ_interface) direct_graph() (oaklib.interfaces.obograph_interface.OboGraphInterface method) disable_transitive_query_cache() (oaklib.interfaces.obograph_interface.OboGraphInterface method) disjoint_class_expressions_axioms() (oaklib.interfaces.obograph_interface.OboGraphInterface method) disjoint_pairs() (oaklib.interfaces.owl_interface.OwlInterface method) dump() (oaklib.converters.data_model_converter.DataModelConverter method) (oaklib.converters.obo_graph_to_cx_converter.OboGraphToCXConverter method) (oaklib.converters.obo_graph_to_fhir_converter.OboGraphToFHIRConverter method) (oaklib.converters.obo_graph_to_obo_format_converter.OboGraphToOboFormatConverter method) (oaklib.interfaces.dumper_interface.DumperInterface method) DumperInterface (class in oaklib.interfaces.dumper_interface) dumps() (oaklib.converters.obo_graph_to_obo_format_converter.OboGraphToOboFormatConverter method)

E

Edge (class in semsql.sqla.semsql) edge_index (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface property) edges() (oaklib.interfaces.obograph_interface.OboGraphInterface method) enable_transitive_query_cache() (oaklib.interfaces.obograph_interface.OboGraphInterface method) enforce_canonical_ordering (oaklib.converters.data_model_converter.DataModelConverter attribute) enriched_classes() (oaklib.interfaces.class_enrichment_calculation_interface.ClassEnrichmentCalculationInterface method) Entailed entailed_edge_index (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface property) entailed_incoming_relationships() (oaklib.interfaces.relation_graph_interface.RelationGraphInterface method) entailed_outgoing_relationships() (oaklib.interfaces.relation_graph_interface.RelationGraphInterface method) entailed_relationships_between() (oaklib.interfaces.relation_graph_interface.RelationGraphInterface method)

EntailedEdge (class in semsql.sqla.semsql) entities() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) entities_metadata_statements() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) entity_alias_map() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) entity_aliases() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) entity_metadata_map() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) equivalence_axioms() (oaklib.interfaces.owl_interface.OwlInterface method) exclude_owl_top_and_bottom (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface attribute) expand_change() (oaklib.interfaces.patcher_interface.PatcherInterface method) expand_changes() (oaklib.interfaces.patcher_interface.PatcherInterface method) extract_graph() (oaklib.interfaces.obograph_interface.OboGraphInterface method) extract_subset_ontology() (oaklib.interfaces.subsetter_interface.SubsetterInterface method)

F

Functional Syntax

FunOWL FunOwlImplementation (class in oaklib.implementations.funowl.funowl_implementation)

G

gap_fill_relationships() (oaklib.interfaces.subsetter_interface.SubsetterInterface method) get_adapter() (in module oaklib.selector) get_curies_by_label() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) get_definition_by_curie() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) get_implementation_class_from_scheme() (in module oaklib.selector) get_implementation_from_shorthand() (in module oaklib.selector) get_information_content() (oaklib.interfaces.semsim_interface.SemanticSimilarityInterface method) get_label_by_curie() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) get_labels_for_curies() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)

get_prefix_map() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) get_resource_from_shorthand() (in module oaklib.selector) get_sssom_mappings_by_curie() (oaklib.interfaces.mapping_provider_interface.MappingProviderInterface method) get_transitive_mappings_by_curie() (oaklib.interfaces.mapping_provider_interface.MappingProviderInterface method) GildaImplementation (class in oaklib.implementations.gilda) global_summary_statistics() (oaklib.interfaces.summary_statistics_interface.SummaryStatisticsInterface method) Graph Graph Traversal grouped_diff() (oaklib.interfaces.differ_interface.DifferInterface method)

H

hierarchical_parents() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)

I

Identifier ignore_invalid_changes (oaklib.interfaces.patcher_interface.PatcherInterface attribute) Implementation incoming_relationship_map() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) incoming_relationships() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) Information Content information_content_scores() (oaklib.interfaces.semsim_interface.SemanticSimilarityInterface method)

Input Selector Interface IS_A: is_coherent() (oaklib.interfaces.validator_interface.ValidatorInterface method) is_disjoint() (oaklib.interfaces.owl_interface.OwlInterface method) is_satisfiable() (oaklib.interfaces.owl_interface.OwlInterface method) Iterator

K

KEYVAL runoak-set-apikey command line option

KGCL

L

Label label() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) labeler (oaklib.converters.data_model_converter.DataModelConverter attribute) labels() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) languages() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) leafs() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)

lexical_index (oaklib.interfaces.text_annotator_interface.TextAnnotatorInterface attribute) load_graph() (oaklib.interfaces.obograph_interface.OboGraphInterface method) load_information_content_scores() (oaklib.interfaces.semsim_interface.SemanticSimilarityInterface method) Logical Definition logical_definitions() (oaklib.interfaces.obograph_interface.OboGraphInterface method) lookup_references() (oaklib.interfaces.validator_interface.ValidatorInterface method)

M

map_associations() (oaklib.interfaces.association_provider_interface.AssociationProviderInterface method) Mapping MappingProviderInterface (class in oaklib.interfaces.mapping_provider_interface) metadata_property_summary_statistics() (oaklib.interfaces.summary_statistics_interface.SummaryStatisticsInterface method) migrate_curies() (oaklib.interfaces.patcher_interface.PatcherInterface method) module oaklib.datamodels.search oaklib.selector oaklib.utilities.apikey_manager oaklib.utilities.graph.networkx_bridge oaklib.utilities.graph.relationship_walker oaklib.utilities.lexical.lexical_indexer oaklib.utilities.obograph_utils oaklib.utilities.subsets.slimmer_utils oaklib.utilities.table_filler oaklib.utilities.taxon.taxon_constraint_utils

most_recent_common_ancestors() (oaklib.interfaces.semsim_interface.SemanticSimilarityInterface method) MRCA multilingual (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface property) multilingual_labels() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) multiset_most_recent_common_ancestors() (oaklib.interfaces.semsim_interface.SemanticSimilarityInterface method) multiterm_search() (oaklib.interfaces.search_interface.SearchInterface method)

N

Name Named Individual Node node() (oaklib.interfaces.obograph_interface.OboGraphInterface method) nodes() (oaklib.interfaces.obograph_interface.OboGraphInterface method)

non_redundant_entailed_relationships() (oaklib.interfaces.obograph_interface.OboGraphInterface method) normalize() (oaklib.interfaces.mapping_provider_interface.MappingProviderInterface method) normalize_association() (oaklib.interfaces.association_provider_interface.AssociationProviderInterface method) normalize_associations() (oaklib.interfaces.association_provider_interface.AssociationProviderInterface method) normalize_prefix() (oaklib.interfaces.mapping_provider_interface.MappingProviderInterface method)

O

oaklib.datamodels.search module oaklib.selector module oaklib.utilities.apikey_manager module oaklib.utilities.graph.networkx_bridge module oaklib.utilities.graph.relationship_walker module oaklib.utilities.lexical.lexical_indexer module oaklib.utilities.obograph_utils module oaklib.utilities.subsets.slimmer_utils module oaklib.utilities.table_filler module oaklib.utilities.taxon.taxon_constraint_utils module Object Object Closure ObjectProperty OBO Format OBO Graphs OboGraphImplementation (class in oaklib.implementations.obograph.obograph_implementation) OboGraphInterface (class in oaklib.interfaces.obograph_interface) OboGraphToCXConverter (class in oaklib.converters.obo_graph_to_cx_converter) OboGraphToFHIRConverter (class in oaklib.converters.obo_graph_to_fhir_converter)

OboGraphToOboFormatConverter (class in oaklib.converters.obo_graph_to_obo_format_converter) obsoletes() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) obsoletes_migration_relationships() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) OLS OlsImplementation (class in oaklib.implementations.ols.ols_implementation) Ontobee OntobeeImplementation (class in oaklib.implementations.ontobee.ontobee_implementation) OntoGPT ONTOLOGIES runoak-ontology-metadata command line option runoak-ontology-versions command line option ontologies() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) Ontology Ontology Element Ontology Format Ontology Graph Projection ontology_curies() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) ontology_metadata_map() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) ontology_metamodel_mapper (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface attribute) ontology_versions() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) OntoPortal outgoing_relationship_map() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) outgoing_relationships() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) OWL OWL Annotation owl_type() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) owl_types() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) OwleryImplementation (class in oaklib.implementations.owlery.owlery_implementation) OwlInterface (class in oaklib.interfaces.owl_interface)

P

pairwise_similarity() (oaklib.interfaces.semsim_interface.SemanticSimilarityInterface method) PantherDBImplementation (class in oaklib.implementations.pantherdb.pantherdb_implementation) Part Of Patch PatcherInterface (class in oaklib.interfaces.patcher_interface) paths() (oaklib.interfaces.obograph_interface.OboGraphInterface method)

precompute_lookups() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) Predicate prefix_map() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) Pronto ProntoImplementation (class in oaklib.implementations.pronto.pronto_implementation) Property property_characteristics() (oaklib.interfaces.owl_interface.OwlInterface method)

Q

query() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)

R

RDF Reasoner reasoner_configurations() (oaklib.interfaces.owl_interface.OwlInterface method) Reasoning Reflexive Relation Graph RelationGraphEnum (class in oaklib.implementations.ubergraph.ubergraph_implementation) RelationGraphInterface (class in oaklib.interfaces.relation_graph_interface) Relationship Relationship Type relationships() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) relationships_metadata() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) relationships_to_graph() (oaklib.interfaces.obograph_interface.OboGraphInterface method) repair() (oaklib.interfaces.validator_interface.ValidatorInterface method) reverse_changes() (oaklib.interfaces.patcher_interface.PatcherInterface method) roots() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) rule_collection (oaklib.interfaces.text_annotator_interface.TextAnnotatorInterface attribute) runoak command line option --add --associations --associations-type --autosave --caching --import-depth --input --input-type --merge --metamodel-mappings --named-prefix-map --no-autosave --no-merge --no-profile --no-quiet --no-stacktrace --other-languages --preferred-language --prefix --profile --quiet --requests-cache-db --save-as --stacktrace --verbose --wrap-adapter -a -g -G -i -I -l -q -v -W runoak-aliases command line option --no-obo-model --obo-model --output --output-type -O -o TERMS runoak-ancestors command line option --graph-traversal-method --no-statistics --output --output-type --predicates --statistics -M -O -o -p TERMS runoak-annotate command line option --category --configuration-file --exclude-tokens --include-aliases --lexical-index-file --match-column --matches-whole-text --model --no-include-aliases --no-matches-whole-text --no-W --output --output-type --rules-file --text-file -A -C -L -m -o -O -R -W -x WORDS runoak-apply command line option --changes-format --changes-input --changes-output --contributor --dry-run --expand --ignore-invalid-changes --no-dry-run --no-expand --no-ignore-invalid-changes --no-overwrite --output --output-type --overwrite -o -O COMMANDS runoak-apply-obsolete command line option --expand --ignore-invalid-changes --no-expand --no-ignore-invalid-changes --output --output-type -o -O TERMS runoak-apply-taxon-constraints command line option --evolution-file --graph-traversal-method --output --predicates -E -M -o -p CONSTRAINTS runoak-associations command line option --add-closure-fields --association-predicates --autolabel --if-absent --no-add-closure-fields --no-autolabel --output, [1] --output-type --predicates --set-value --terms-role -o, [1] -O -p -Q -S TERMS runoak-associations-counts command line option --add-closure-fields --association-predicates --autolabel --filter --group-by --limit --min-facet-count --no-add-closure-fields --no-autolabel --output, [1] --output-type --predicates --terms-role -F -L -o, [1] -O -p -Q TERMS runoak-associations-matrix command line option --association-predicates --autolabel --include-entities --main-score-field --no-autolabel --no-include-entities --output, [1] --output-type --predicates --terms-role -o, [1] -O -p -Q -S TERMS runoak-axioms command line option --about --axiom-type --output --output-type --references -o -O TERMS runoak-cache-clear command line option --days-old runoak-definitions command line option --additional-metadata --autolabel --display --if-absent --lookup-references --no-additional-metadata --no-autolabel --no-lookup-references --output --output-type --set-value -D -o -O -P -S TERMS runoak-descendants command line option --display --graph-traversal-method --output --output-type --predicates -D -M -O -o -p TERMS runoak-diff command line option --change-type --group-by-defined-by --group-by-obo-namespace --group-by-prefix --group-by-property --no-group-by-defined-by --no-group-by-obo-namespace --no-group-by-prefix --no-simple --no-statistics --other-ontology --output --output-type --simple --statistics -o -O -X runoak-diff-associations command line option --associations --autolabel --group-by --new-date --no-autolabel --old-date --other-associations --output, [1] --output-type --predicates -g -o, [1] -O -p -X runoak-diff-terms command line option --other-ontology --output -o TERMS runoak-diff-via-mappings command line option --autolabel --bidirectional --filter-category-identical --include-identity-mappings --intra --mapping-input --no-autolabel --no-bidirectional --no-filter-category-identical --no-include-identity-mappings --no-intra --other-input --other-input-type --output --output-type --predicates --source -o -O -p -S -X TERMS runoak-disjoints command line option --autolabel --named-classes-only --no-autolabel --no-named-classes-only --output --output-type --predicates -O -o -p TERMS runoak-dump command line option --config-file --enforce-canonical-ordering --no-enforce-canonical-ordering --output --output-type -c -o -O TERMS runoak-enrichment command line option --allow-labels --association-predicates --autolabel --background-file --cutoff --filter-redundant --no-allow-labels --no-autolabel --no-filter-redundant --no-ontology-only --ontology-only --output, [1] --output-type --predicates --sample-file -B -o, [1] -O -p -T -U TERMS runoak-expand-subsets command line option --output --predicates -o -p SUBSETS runoak-extract command line option --dangling --include-metadata --no-dangling --no-include-metadata --output --output-type --predicates -o -O -p TERMS runoak-fill-table command line option --allow-missing --autolabel --comment --delimiter --missing-value-token --no-allow-missing --no-autolabel --output --relation --relation-file --schema -o TABLE_FILE runoak-generate-definitions command line option --apply-patch --exclude-defined --no-apply-patch --no-exclude-defined --output --output-type --patch --patch-format --style-hints -o -O TERMS runoak-generate-disjoints command line option --autolabel --exclude-existing --min-descendants --no-autolabel --no-exclude-existing --output --output-type --predicates -M -o -O -p TERMS runoak-generate-lexical-replacements command line option --apply-patch --no-apply-patch --output --output-type --patch --patch-format --rules-expression --rules-file -o -O -R -Y TERMS runoak-generate-logical-definitions command line option --analyze --autolabel --fill --no-analyze --no-autolabel --no-fill --no-parse --no-show-extract --no-unmelt --output --output-type --parse --patterns-file --show-extract --unmelt -o -O -P TERMS runoak-generate-synonyms command line option --apply-patch --no-apply-patch --output --output-type --patch --patch-format --rules-file -o -O -R TERMS runoak-info command line option --display --output --output-type -D -o -O TERMS runoak-information-content command line option --no-use-associations --output --output-type --predicates --use-associations -o -O -p TERMS runoak-labels command line option --all-languages --display --if-absent --no-all-languages --no-pivot-languages --output --output-type --pivot-languages --set-value -D -o -O -S TERMS

runoak-leafs command line option --filter-obsoletes --no-filter-obsoletes --output --predicates -o -p runoak-lexmatch command line option --add-labels --ensure-strict-prefixes --exclude-mapped --lexical-index-file --no-add-labels --no-ensure-strict-prefixes --no-exclude-mapped --no-recreate --output --recreate --rules-file -L -o -R TERMS runoak-lint command line option --dry-run --no-dry-run --output --output-type --report-format -o -O runoak-logical-definitions command line option --autolabel --if-absent --matrix-axes --no-autolabel --no-unmelt --output --output-type --predicates --set-value --unmelt -O -o -p -S TERMS runoak-mappings command line option --autolabel --mapper --maps-to-source --no-autolabel --output --output-type -M -o -O TERMS runoak-migrate-curies command line option --no-replace --output --output-type --replace -O -o CURIE_PAIRS runoak-normalize command line option --autolabel --maps-to-source --no-autolabel --output --output-type -M -o -O TERMS runoak-obsoletes command line option --include-merged --no-include-merged --no-show-migration-relationships --output --output-type --show-migration-relationships -O -o TERMS runoak-ontologies command line option --output -o runoak-ontology-metadata command line option --all --no-all --output --output-type -o -O ONTOLOGIES runoak-ontology-versions command line option --all --no-all --output -o ONTOLOGIES runoak-paths command line option --autolabel --configure --directed --exclude-predicates --include-predicates --narrow --no-autolabel --no-directed --no-include-predicates --no-narrow --no-viz --output --output-type --predicate-weights --predicates --stylemap --target --viz -C -O -o -p -S TERMS runoak-prefixes command line option --no-used-only --output --output-type --used-only -o -O TERMS runoak-query command line option --autolabel --label-fields --no-autolabel --output --output-type --prefixes --query -L -o -O -P -q runoak-relationships command line option --autolabel --direction --if-absent --include-abox --include-entailed --include-metadata --include-tbox --no-autolabel --no-include-abox --no-include-entailed --no-include-metadata --no-include-tbox --no-non-redundant-entailed --non-redundant-entailed --output --output-type --predicates --set-value -O -o -p -S TERMS runoak-rollup command line option --autolabel --no-autolabel --object-group --output --output-type --predicates -o -O -p TERMS runoak-roots command line option --annotated-roots --has-prefix --no-A --no-annotated-roots --output --output-type --predicates -A -o -O -p -P runoak-search command line option --autolabel --no-autolabel --output --output-type -O -o TERMS runoak-set-apikey command line option --endpoint -e KEYVAL runoak-siblings command line option --output --output-type --predicates -o -O -p TERMS runoak-similarity command line option --autolabel --information-content-file --main-score-field --min-ancestor-information-content --min-jaccard-similarity --no-autolabel --output --output-type --predicates --set1-file --set2-file -o -O -p TERMS runoak-similarity-pair command line option --autolabel --no-autolabel --output --output-type --predicates -o -O -p TERMS runoak-singletons command line option --filter-obsoletes --no-filter-obsoletes --output --predicates -o -p runoak-statistics command line option --compare-with --group-by-defined-by --group-by-obo-namespace --group-by-prefix --group-by-property --has-prefix --include-residuals --no-group-by-defined-by --no-group-by-obo-namespace --no-group-by-prefix --no-include-residuals --output --output-type -O -o -P -X BRANCHES runoak-subsets command line option --output -o runoak-synonymize command line option --apply-patch --no-apply-patch --output --patch --rules-file -o -R TERMS runoak-taxon-constraints command line option --all --direct --graph-traversal-method --include-redundant --no-A --no-all --no-direct --no-include-redundant --output --output-type --predicates -A -M -o -O -p TERMS runoak-term-categories command line option --category-system --output --output-type -o -O TERMS runoak-term-metadata command line option --additional-metadata --no-additional-metadata --output --output-type --predicates -o -O -p TERMS runoak-term-subsets command line option --output --output-type -o -O TERMS runoak-terms command line option --filter-obsoletes --no-filter-obsoletes --output --owl-type -o runoak-termset-similarity command line option --autolabel --information-content-file --no-autolabel --output --output-type --predicates -o -O -p TERMS runoak-transform command line option --config-file --output --output-type --transform -c -o -O -t TERMS runoak-tree command line option --add-mrcas --configure --display --down --gap-fill --max-hops --no-add-mrcas --no-down --no-gap-fill --output --output-type --predicates --root --skip --stylemap -C -D -O -o -p -S TERMS runoak-usages command line option --autolabel --include-unused --no-autolabel --no-include-unused --output, [1] --output-type --used-by-prefix -o, [1] -O -P TERMS runoak-validate command line option --cutoff --no-skip-ontology-rules --no-skip-structural-validation --output --output-type --rule --skip-ontology-rules --skip-structural-validation -o -O -R TERMS runoak-validate-definitions command line option --adapter-mapping --configuration-file --no-skip-text-annotation --output --output-type --skip-text-annotation -C -O -o TERMS runoak-validate-mappings command line option --adapter-mapping --autolabel --configuration-file --no-autolabel --output --output-type -C -O -o TERMS runoak-validate-multiple command line option --cutoff --output --schema -o -s DBS runoak-validate-subset command line option --adapter-mapping --autolabel --config-yaml --configuration-file --exclude-query --information-content-adapter --information-content-file --no-autolabel --output --output-type --predicates -C -O -o -p -X TERMS runoak-validate-synonyms command line option --adapter-mapping --autolabel --configuration-file --no-autolabel --output --output-type --rules-file -C -O -o -R TERMS runoak-viz command line option --add-mrcas --configure --down --gap-fill --max-hops --meta --no-add-mrcas --no-down --no-gap-fill --no-meta --no-view --output --output-type --predicates --stylemap --view -C -O -o -p -S TERMS

S

save() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) (oaklib.interfaces.patcher_interface.PatcherInterface method) SearchConfiguration (class in oaklib.datamodels.search) (class in oaklib.interfaces.search_interface) SearchInterface (class in oaklib.interfaces.search_interface) Semantic Similarity Semantic SQL SemanticSimilarityInterface (class in oaklib.interfaces.semsim_interface) set_information_content_scores() (oaklib.interfaces.semsim_interface.SemanticSimilarityInterface method) set_label() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) set_metamodel_mappings() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) setwise_most_recent_common_ancestors() (oaklib.interfaces.semsim_interface.SemanticSimilarityInterface method) simple_mappings() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) simple_mappings_by_curie() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) simple_subproperty_of_chains() (oaklib.interfaces.owl_interface.OwlInterface method) SimpleOboImplementation (class in oaklib.implementations.simpleobo.simple_obo_implementation) singletons() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) SPARQL SparqlImplementation (class in oaklib.implementations.sparql.sparql_implementation) SQL

SqlImplementation (class in oaklib.implementations.sqldb.sql_implementation) SSSOM sssom_mappings() (oaklib.interfaces.mapping_provider_interface.MappingProviderInterface method) sssom_mappings_by_source() (oaklib.interfaces.mapping_provider_interface.MappingProviderInterface method) Statements (class in semsql.sqla.semsql) strict (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface attribute) subclass_axioms() (oaklib.interfaces.owl_interface.OwlInterface method) subgraph_from_traversal() (oaklib.interfaces.obograph_interface.OboGraphInterface method) Subject Subject Closure Subset subset_curies() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) subset_members() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) SUBSETS runoak-expand-subsets command line option subsets() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) SubsetterInterface (class in oaklib.interfaces.subsetter_interface) summary_statistic_description() (oaklib.interfaces.summary_statistics_interface.SummaryStatisticsInterface method) SummaryStatisticsInterface (class in oaklib.interfaces.summary_statistics_interface) synonym_map_for_curies() (oaklib.interfaces.obograph_interface.OboGraphInterface method)

T

TABLE_FILE runoak-fill-table command line option Tautology Term term_curies_without_definitions() (oaklib.interfaces.validator_interface.ValidatorInterface method) TERMS runoak-aliases command line option runoak-ancestors command line option runoak-apply-obsolete command line option runoak-associations command line option runoak-associations-counts command line option runoak-associations-matrix command line option runoak-axioms command line option runoak-definitions command line option runoak-descendants command line option runoak-diff-terms command line option runoak-diff-via-mappings command line option runoak-disjoints command line option runoak-dump command line option runoak-enrichment command line option runoak-extract command line option runoak-generate-definitions command line option runoak-generate-disjoints command line option runoak-generate-lexical-replacements command line option runoak-generate-logical-definitions command line option runoak-generate-synonyms command line option runoak-info command line option runoak-information-content command line option runoak-labels command line option runoak-lexmatch command line option runoak-logical-definitions command line option runoak-mappings command line option runoak-normalize command line option runoak-obsoletes command line option runoak-paths command line option runoak-prefixes command line option runoak-relationships command line option runoak-rollup command line option runoak-search command line option runoak-siblings command line option runoak-similarity command line option runoak-similarity-pair command line option runoak-synonymize command line option runoak-taxon-constraints command line option runoak-term-categories command line option runoak-term-metadata command line option runoak-term-subsets command line option runoak-termset-similarity command line option runoak-transform command line option runoak-tree command line option runoak-usages command line option runoak-validate command line option runoak-validate-definitions command line option runoak-validate-mappings command line option runoak-validate-subset command line option runoak-validate-synonyms command line option runoak-viz command line option

terms_categories() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) terms_subsets() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method) Text Annotation TextAnnotation (class in oaklib.datamodels.text_annotator) TextAnnotatorInterface (class in oaklib.interfaces.text_annotator_interface) transitive_object_properties() (oaklib.interfaces.owl_interface.OwlInterface method) TraversalConfiguration (class in oaklib.interfaces.obograph_interface) Triple Triplestore

U

Ubergraph UbergraphImplementation (class in oaklib.implementations.ubergraph.ubergraph_implementation) undo() (oaklib.interfaces.patcher_interface.PatcherInterface method)

unsatisfiable_classes() (oaklib.interfaces.validator_interface.ValidatorInterface method) URI uri_to_curie() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)

V

validate() (oaklib.interfaces.validator_interface.ValidatorInterface method) validate_definitions() (oaklib.interfaces.validator_interface.ValidatorInterface method)

validate_mappings() (oaklib.interfaces.validator_interface.ValidatorInterface method) validate_synonyms() (oaklib.interfaces.validator_interface.ValidatorInterface method) ValidatorInterface (class in oaklib.interfaces.validator_interface)

W

walk_up_relationship_graph() (oaklib.interfaces.obograph_interface.OboGraphInterface method)

WORDS runoak-annotate command line option