├── .github └── workflows │ ├── publish.yml │ └── test.yml ├── .gitignore ├── .gitreview ├── .pylintrc ├── .readthedocs.yml ├── AUTHORS.md ├── Contributing.rst ├── LICENSE-3RD-PARTY.txt ├── LICENSE.txt ├── README.rst ├── binder └── postBuild ├── docs ├── Makefile └── source │ ├── api.rst │ ├── archetypes.rst │ ├── architecture.rst │ ├── assets │ ├── bbnforge │ └── nexus-forge-architecture.png │ ├── conf.py │ ├── configuration.rst │ ├── contributing.rst │ ├── index.rst │ ├── interaction.rst │ ├── releases │ ├── release-notes.rst │ ├── v0.3-release-notes.rst │ ├── v0.3.3-release-notes.rst │ ├── v0.4.0-release-notes.rst │ ├── v0.5.0-release-notes.rst │ ├── v0.5.1-release-notes.rst │ ├── v0.5.2-release-notes.rst │ ├── v0.6.0-release-notes.rst │ ├── v0.6.1-release-notes.rst │ ├── v0.6.2-release-notes.rst │ ├── v0.6.3-release-notes.rst │ └── v0.7.0-release-notes.rst │ ├── releasesfile.rst │ ├── specializations.rst │ └── tutorials.rst ├── examples ├── configurations │ ├── demo-resolver │ │ ├── entity-to-resource-mapping.hjson │ │ └── term-to-resource-mapping.hjson │ ├── demo-store │ │ ├── demo-config-with-resolvers.yml │ │ └── file-to-resource-mapping.hjson │ ├── entitylinking-resolver │ │ ├── entitylinking-mapper-encoder.hjson │ │ ├── entitylinking-mapper-es.hjson │ │ └── entitylinking-mapper.hjson │ ├── nexus-resolver │ │ ├── agent-to-resource-mapping.hjson │ │ └── term-to-resource-mapping.hjson │ └── nexus-store │ │ ├── file-to-resource-mapping.hjson │ │ └── publishing-file-to-resource-mapping.hjson ├── data │ ├── associations.tsv │ ├── my_data.xwz │ ├── my_data_derived.txt │ ├── non_existing_person.jpg │ ├── persons-with-id.csv │ ├── persons.csv │ ├── scientists-database │ │ ├── albert_einstein.txt │ │ └── marie_curie.txt │ └── tfidfvectorizer_model_schemaorg_linking ├── mappings │ ├── DemoDB │ │ └── mappings │ │ │ └── DictionaryMappings │ │ │ └── Example.hjson │ ├── LICENSE │ ├── MouseLight │ │ ├── mappings │ │ │ └── DictionaryMapping │ │ │ │ └── NeuronMorphology.hjson │ │ └── metadata.json │ ├── NeuroMorpho │ │ ├── jsonld_context.json │ │ ├── mappings │ │ │ └── DictionaryMapping │ │ │ │ └── NeuronMorphology.hjson │ │ └── metadata.json │ ├── README.md │ ├── UniProt │ │ ├── jsonld_context.json │ │ ├── mappings │ │ │ └── DictionaryMapping │ │ │ │ ├── Gene.hjson │ │ │ │ └── Protein.hjson │ │ └── metadata.json │ ├── allen-cell-types-database │ │ └── mappings │ │ │ └── DictionaryMapping │ │ │ ├── NeuronMorphology.hjson │ │ │ ├── PatchedCell.hjson │ │ │ └── Subject.hjson │ └── scientists-database │ │ └── DictionaryMapping │ │ ├── Association.hjson │ │ └── Contribution.hjson ├── models │ └── neuroshapes_context.json └── notebooks │ ├── getting-started │ ├── 00 - Initialization.ipynb │ ├── 01 - Resources.ipynb │ ├── 02 - Datasets.ipynb │ ├── 03 - Storing.ipynb │ ├── 04 - Querying.ipynb │ ├── 05 - Versioning.ipynb │ ├── 06 - JSON IO.ipynb │ ├── 07 - DataFrame IO.ipynb │ ├── 08 - Formatting.ipynb │ ├── 09 - Resolving.ipynb │ ├── 10 - Reshaping.ipynb │ ├── 11 - Modeling.ipynb │ ├── 12 - Mapping.ipynb │ ├── 13 - JSON-LD IO.ipynb │ ├── 14 - RDF IO.ipynb │ ├── 15 - SQL IO.ipynb │ ├── 16 - Debugging.ipynb │ └── README.md │ └── use-cases │ ├── BBP KG Create Datasets.ipynb │ ├── BBP KG Creating and Modifying Schemas.ipynb │ ├── BBP KG Forge retrieval.ipynb │ ├── BBP KG Ontology Brain Building Workflow Search and Exploration.ipynb │ ├── BBP KG Ontology types Search and Exploration.ipynb │ ├── BBP KG Schema changes.ipynb │ ├── BBP KG Search and Download.ipynb │ ├── BBP-KG-Search-and-Download-Data-at-a-given-tag.ipynb │ ├── EntityLinkerElastic-forge-demo-config.yml │ ├── EntityLinkerSkLearn-forge-demo-config.yml │ ├── MOOC_Content_based_Recommender_System_using_Blue_Brain_Nexus.ipynb │ ├── ResolvingStrategies.ipynb │ ├── bbp-staging-forge.yml │ ├── copy-token.png │ ├── dataset_from_different_sources.ipynb │ ├── forge.yml │ ├── login-ui.png │ ├── mappings │ ├── allen_ephys_dataset.hjson │ ├── allen_morphology_dataset.hjson │ └── mouselight_dataset.hjson │ ├── nsg-forge-nexus.yml │ ├── one_cell_minds.ipynb │ ├── prod-forge-nexus.yml │ └── rdfmodel │ └── jsonldcontext.json ├── kgentitylinkingsklearn ├── __init__.py ├── entity_linking_sklearn.py └── entity_linking_sklearn_service.py ├── kgforge ├── __init__.py ├── core │ ├── __init__.py │ ├── archetypes │ │ ├── __init__.py │ │ ├── dataset_store.py │ │ ├── mapper.py │ │ ├── mapping.py │ │ ├── model.py │ │ ├── read_only_store.py │ │ ├── resolver.py │ │ └── store.py │ ├── commons │ │ ├── __init__.py │ │ ├── actions.py │ │ ├── attributes.py │ │ ├── constants.py │ │ ├── context.py │ │ ├── dictionaries.py │ │ ├── es_query_builder.py │ │ ├── exceptions.py │ │ ├── execution.py │ │ ├── files.py │ │ ├── formatter.py │ │ ├── imports.py │ │ ├── parser.py │ │ ├── query_builder.py │ │ ├── sparql_query_builder.py │ │ └── strategies.py │ ├── conversions │ │ ├── __init__.py │ │ ├── dataframe.py │ │ ├── json.py │ │ └── rdf.py │ ├── forge.py │ ├── reshaping.py │ ├── resource.py │ └── wrappings │ │ ├── __init__.py │ │ ├── dict.py │ │ └── paths.py └── specializations │ ├── __init__.py │ ├── mappers │ ├── __init__.py │ ├── dictionaries.py │ ├── r2rml.py │ ├── resources.py │ └── tables.py │ ├── mappings │ ├── __init__.py │ └── dictionaries.py │ ├── models │ ├── __init__.py │ ├── demo_model.py │ ├── rdf │ │ ├── __init__.py │ │ ├── collectors.py │ │ ├── directory_service.py │ │ ├── node_properties.py │ │ ├── service.py │ │ ├── store_service.py │ │ └── utils.py │ └── rdf_model.py │ ├── resolvers │ ├── __init__.py │ ├── agent_resolver.py │ ├── demo_resolver.py │ ├── entity_linking │ │ ├── __init__.py │ │ ├── entity_linker.py │ │ ├── entity_linker_elastic.py │ │ └── service │ │ │ ├── __init__.py │ │ │ ├── entity_linking_elastic_service.py │ │ │ └── entity_linking_service.py │ ├── ontology_resolver.py │ └── store_service.py │ ├── resources │ ├── __init__.py │ ├── datasets.py │ └── entity_linking_candidate.py │ └── stores │ ├── __init__.py │ ├── bluebrain_nexus.py │ ├── demo_store.py │ ├── nexus │ ├── __init__.py │ ├── batch_request_handler.py │ ├── http_helpers.py │ ├── prepare_methods.py │ └── service.py │ ├── rdflib_graph.py │ ├── sparql │ ├── __init__.py │ └── sparql_service.py │ └── sparql_store.py ├── setup.py ├── tests ├── KGForge Setup.ipynb ├── __init__.py ├── conftest.py ├── core │ ├── __init__.py │ ├── archetypes │ │ ├── test_dataset_store.py │ │ ├── test_read_only_store.py │ │ └── test_store.py │ ├── commons │ │ ├── __init__.py │ │ ├── test_actions.py │ │ ├── test_attributes.py │ │ ├── test_context.py │ │ ├── test_dictionaries.py │ │ ├── test_es_query_builder.py │ │ ├── test_execution.py │ │ └── test_sparql_query_builder.py │ ├── conversions │ │ ├── conftest.py │ │ ├── test_dataframe.py │ │ ├── test_json.py │ │ └── test_rdf.py │ ├── resource.feature │ ├── test_forge.py │ ├── test_reshaping.py │ ├── test_resolving.py │ ├── test_resource.py │ └── wrappings │ │ ├── test_dict.py │ │ └── test_paths.py ├── data │ ├── dbpedia-model │ │ ├── context.json │ │ └── mappings │ │ │ └── DictionaryMapping │ │ │ └── Example.hjson │ ├── demo-model │ │ ├── mappings │ │ │ ├── allen-cell-types-database │ │ │ │ └── DictionaryMapping │ │ │ │ │ ├── NeuronMorphology.hjson │ │ │ │ │ ├── PatchedCell.hjson │ │ │ │ │ └── Subject.hjson │ │ │ └── scientists-database │ │ │ │ └── DictionaryMapping │ │ │ │ ├── Association.hjson │ │ │ │ └── Contribution.hjson │ │ ├── namespaces.json │ │ ├── schemas.json │ │ └── vocabulary.json │ ├── demo-resolver │ │ ├── agents.json │ │ ├── cell_types.json │ │ ├── sex.json │ │ ├── species.json │ │ └── structure_layer.json │ ├── nexus-store │ │ ├── file-to-resource-mapping.hjson │ │ └── publishing-file-to-resource-mapping.hjson │ └── shacl-model │ │ ├── commons │ │ ├── schemaorg-v26.0.json │ │ ├── shapes-1.json │ │ ├── shapes-2.json │ │ ├── shapes-3.json │ │ └── shapes-4.json │ │ └── context.json └── specializations │ ├── mappers │ └── test_mappers.py │ ├── mappings │ └── test_mappings.py │ ├── models │ ├── data.py 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