oaklib 0.6.2__tar.gz → 0.6.4__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {oaklib-0.6.2 → oaklib-0.6.4}/PKG-INFO +2 -1
- {oaklib-0.6.2 → oaklib-0.6.4}/pyproject.toml +4 -3
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/cli.py +294 -136
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/converters/obo_graph_to_obo_format_converter.py +41 -18
- oaklib-0.6.4/src/oaklib/datamodels/ontology_metadata.py +2179 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/ontology_metadata.yaml +27 -2
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/validation_datamodel.py +221 -481
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/validation_datamodel.yaml +20 -1
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/llm_implementation.py +101 -1
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/simpleobo/simple_obo_implementation.py +32 -5
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/simpleobo/simple_obo_parser.py +18 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/interfaces/obograph_interface.py +55 -0
- oaklib-0.6.4/src/oaklib/interfaces/validator_interface.py +315 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/io/streaming_obo_writer.py +12 -44
- oaklib-0.6.4/src/oaklib/utilities/publication_utils/doi_wrapper.py +142 -0
- oaklib-0.6.4/src/oaklib/utilities/publication_utils/pubdb_wrapper.py +36 -0
- oaklib-0.6.4/src/oaklib/utilities/publication_utils/pubmed_wrapper.py +167 -0
- oaklib-0.6.4/src/oaklib/utilities/validation/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/utilities/validation/definition_ontology_rule.py +72 -50
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/utilities/validation/rule_runner.py +2 -2
- oaklib-0.6.2/src/oaklib/datamodels/ontology_metadata.py +0 -3390
- oaklib-0.6.2/src/oaklib/interfaces/validator_interface.py +0 -122
- {oaklib-0.6.2 → oaklib-0.6.4}/LICENSE +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/README.md +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/go-human-input-spec.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/go-pombase-input-spec.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/hpoa-g2p-input-spec.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/hpoa-input-spec.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/lexmatch-rules-oboinowl-default.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/mondo-g2d-input-spec.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/mondo-gencc-input-spec.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/mondo-hpoa-g2d-input-spec.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/mondo-medgen-g2d-input-spec.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/obograph-style.json +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/omo-to-skos.sssom.tsv +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/value-set-expander.conf.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/constants.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/converters/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/converters/data_model_converter.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/converters/logical_definition_flattener.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/converters/obo_graph_to_cx_converter.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/converters/obo_graph_to_fhir_converter.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/converters/obo_graph_to_rdf_owl_converter.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/association.owl.ttl +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/association.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/association.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/class_enrichment.owl.ttl +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/class_enrichment.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/class_enrichment.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/cross_ontology_diff.owl.ttl +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/cross_ontology_diff.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/cross_ontology_diff.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/cx.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/cx.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/fhir.owl.ttl +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/fhir.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/fhir.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/input_specification.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/input_specification.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/item_list.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/item_list.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/lexical_index.owl.ttl +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/lexical_index.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/lexical_index.schema.json +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/lexical_index.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/mapping_cluster_datamodel.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/mapping_cluster_datamodel.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/mapping_rules_datamodel.owl.ttl +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/mapping_rules_datamodel.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/mapping_rules_datamodel.schema.json +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/mapping_rules_datamodel.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/obograph.owl.ttl +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/obograph.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/obograph.schema.json +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/obograph.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/ontology_metadata.owl.ttl +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/ontology_metadata.schema.json +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/oxo.owl.ttl +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/oxo.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/oxo.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/search.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/search_datamodel.owl.ttl +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/search_datamodel.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/search_datamodel.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/settings.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/similarity.owl.ttl +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/similarity.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/similarity.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/summary_statistics_datamodel.owl.ttl +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/summary_statistics_datamodel.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/summary_statistics_datamodel.schema.json +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/summary_statistics_datamodel.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/synonymizer_datamodel.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/synonymizer_datamodel.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/taxon_constraints.owl.ttl +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/taxon_constraints.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/taxon_constraints.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/text_annotator.owl.ttl +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/text_annotator.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/text_annotator.schema.json +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/text_annotator.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/validation_datamodel.owl.ttl +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/validation_datamodel.schema.json +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/value_set_configuration.owl.ttl +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/value_set_configuration.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/value_set_configuration.yaml +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/vocabulary.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/aggregator/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/aggregator/aggregator_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/agrkb/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/agrkb/agrkb_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/amigo/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/amigo/amigo_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/cx/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/cx/cx_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/eutils/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/eutils/eutils_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/eutils/pubmed_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/fhir/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/funowl/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/funowl/funowl_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/gilda.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/kgx/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/kgx/kgx_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/monarch/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/monarch/monarch_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ncbi/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ncbi/ncbi_gene_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/neo4j/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/obograph/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/obograph/obograph_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ols/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ols/constants.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ols/ols_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ols/oxo_utils.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ontobee/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ontobee/ontobee_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ontoportal/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ontoportal/agroportal_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ontoportal/bioportal_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ontoportal/ecoportal_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ontoportal/matportal_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ontoportal/ontoportal_implementation_base.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/owlery/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/owlery/owlery_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/pantherdb/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/pantherdb/pantherdb_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/pronto/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/pronto/pronto_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/robot/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/scigraph/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/semsimian/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/semsimian/profiler.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/semsimian/semsimian_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/simpleobo/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/skos/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/solor/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/solr/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/sparql/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/sparql/abstract_sparql_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/sparql/lov_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/sparql/oak_metamodel_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/sparql/sparql_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/sparql/sparql_query.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/sqldb/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/sqldb/sql_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/sqldb/sqlite_utils.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/tabular/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/tabular/robot_template_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/tabular/tabular_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/tccm/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/translator/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/translator/translator_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ubergraph/__init__.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ubergraph/ubergraph_implementation.py +0 -0
- {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/umls/__init__.py +0 -0
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