├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md └── workflows │ ├── check-pull-request.yaml │ ├── codespell.yml │ ├── doc_pages.yaml │ └── pypi-publish.yml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE ├── Makefile ├── README.md ├── docs ├── Makefile ├── _static │ └── .gitkeep ├── cli.rst ├── conf.py ├── index.rst ├── install.rst ├── introduction.rst ├── make.bat ├── metamodels │ └── index.rst └── packages │ ├── annotators.rst │ ├── generalizers.rst │ ├── importers.rst │ ├── index.rst │ └── utilities.rst ├── local └── README.md ├── notebooks └── images │ └── FRED.png ├── poetry.lock ├── pyproject.toml ├── schema_automator ├── __init__.py ├── annotators │ ├── __init__.py │ ├── curated_to_enums.py │ ├── enum_annotator.py │ ├── enums_to_curateable.py │ ├── jsonld_annotator.py │ ├── llm_annotator.py │ └── schema_annotator.py ├── cli.py ├── generalizers │ ├── __init__.py │ ├── csv_data_generalizer.py │ ├── generalizer.py │ ├── infer_model_from_rdftab.py │ ├── json_instance_generalizer.py │ ├── pandas_generalizer.py │ ├── rdf_data_generalizer.py │ └── toml_instance_generalizer.py ├── importers │ ├── __init__.py │ ├── cadsr_import_engine.py │ ├── dbml_import_engine.py │ ├── dosdp_import_engine.py │ ├── frictionless_import_engine.py │ ├── import_engine.py │ ├── jsonschema_import_engine.py │ ├── kwalify_import_engine.py │ ├── owl_import_engine.py │ ├── rdfs_import_engine.py │ ├── sql_import_engine.py │ └── tabular_import_engine.py ├── jsonschema │ └── __init__.py ├── metamodels │ ├── __init__.py │ ├── cadsr.py │ ├── cadsr.yaml │ ├── dosdp │ │ ├── __init__.py │ │ ├── dosdp_linkml.yaml │ │ └── model.py │ ├── frictionless.py │ ├── frictionless.yaml │ └── jsonschema.py └── utils │ ├── __init__.py │ ├── enums_pvs_tsv.py │ ├── instance_extractor.py │ ├── schema_extractor.py │ └── schemautils.py ├── target └── placeholder └── tests ├── __init__.py ├── outputs └── README.md ├── resources ├── BioMRLs-table.html ├── C2M2_datapackage.json ├── MPLEx.toml ├── NWT_wildfires_biophysical_2016.tsv ├── bio.obo ├── biobank-specimens.tsv ├── biopax-level3.db ├── biopax-level3.nt ├── biopax-level3.ofn ├── biopax-level3.owl ├── biopax3.yaml ├── biosamples.tsv ├── books.tsv ├── cadsr-cde-12137353.json ├── cadsr-cde-2179609.json ├── cadsr-cde-2721353.json ├── cadsr-cde-2724331.json ├── cadsr-cde-996.json ├── cadsr-swagger.json ├── dad-is-metadata.tsv ├── data-package.json ├── data_to_import.tsv ├── db-xrefs.yaml ├── dosdp │ ├── OMIM_disease_series_by_gene.yaml │ ├── OMIM_phenotypic_series.yaml │ ├── acquired.yaml │ ├── acute.yaml │ ├── adenocarcinoma.yaml │ ├── adenoma.yaml │ ├── adenosquamous_carcinoma.yaml │ ├── adult.yaml │ ├── allergic_form_of_disease.yaml │ ├── allergy.yaml │ ├── autoimmune.yaml │ ├── autoimmune_inflammation.yaml │ ├── autosomal_dominant.yaml │ ├── autosomal_recessive.yaml │ ├── basis_in_disruption_of_process.yaml │ ├── benign.yaml │ ├── benign_neoplasm.yaml │ ├── cancer.yaml │ ├── carcinoma.yaml │ ├── carcinoma_in_situ.yaml │ ├── childhood.yaml │ ├── chronic.yaml │ ├── congenital.yaml │ ├── consequence_of_infectious_disease.yaml │ ├── dependence_on_substance.yaml │ ├── disease_by_dysfunctional_structure.yaml │ ├── disease_series_by_gene.yaml │ ├── disease_series_by_gene_and_inheritance.yaml │ ├── disrupts_process.yaml │ ├── environmental_stimulus.yaml │ ├── genetic.yaml │ ├── hemangioma.yaml │ ├── hereditary.yaml │ ├── idiopathic.yaml │ ├── inborn_metabolic.yaml │ ├── inborn_metabolic_disrupts.yaml │ ├── infantile.yaml │ ├── infectious_disease_by_agent.yaml │ ├── infectious_inflammation.yaml │ ├── inflammatory_disease_by_site.yaml │ ├── inherited_susceptibility.yaml │ ├── isolated.yaml │ ├── juvenile.yaml │ ├── leiomyoma.yaml │ ├── leiomyosarcoma.yaml │ ├── lipoma.yaml │ ├── location.yaml │ ├── location_top.yaml │ ├── lymphoma.yaml │ ├── malignant.yaml │ ├── melanoma.yaml │ ├── meningioma.yaml │ ├── mitochondrial_subtype.yaml │ ├── mucoepidermoid_carcinoma.yaml │ ├── neoplasm.yaml │ ├── neoplasm_by_origin.yaml │ ├── neuroendocrine_neoplasm.yaml │ ├── neuroendocrine_neoplasm_grade1.yaml │ ├── nuclear_subtype.yaml │ ├── poisoning.yaml │ ├── postinfectious_disease.yaml │ ├── primary_infectious.yaml │ ├── rare.yaml │ ├── rare_genetic.yaml │ ├── realized_in_response_to_environmental_exposure.yaml │ ├── refractory.yaml │ ├── rhabdomyosarcoma.yaml │ ├── sarcoma.yaml │ ├── small_cell_carcinoma.yaml │ ├── specific_disease_by_disrupted_process.yaml │ ├── specific_disease_by_dysfunctional_structure.yaml │ ├── specific_infectious_disease_by_agent.yaml │ ├── specific_infectious_disease_by_location.yaml │ ├── specific_inflammatory_disease_by_site.yaml │ ├── squamous_cell_carcinoma.yaml │ ├── substance_abuse.yaml │ ├── susceptibility_by_gene.yaml │ ├── syndromic.yaml │ ├── vectorBorneDisease.yaml │ ├── x_linked.yaml │ └── y_linked.yaml ├── envo.tsv ├── foaf_snippet.ttl ├── hca │ ├── README.md │ ├── core │ │ ├── biomaterial │ │ │ └── biomaterial_core.json │ │ ├── file │ │ │ └── file_core.json │ │ ├── process │ │ │ └── process_core.json │ │ ├── project │ │ │ └── project_core.json │ │ └── protocol │ │ │ └── protocol_core.json │ ├── module │ │ ├── biomaterial │ │ │ ├── cell_morphology.json │ │ │ ├── death.json │ │ │ ├── familial_relationship.json │ │ │ ├── growth_conditions.json │ │ │ ├── human_specific.json │ │ │ ├── medical_history.json │ │ │ ├── mouse_specific.json │ │ │ ├── preservation_storage.json │ │ │ ├── state_of_specimen.json │ │ │ └── timecourse.json │ │ ├── ontology │ │ │ ├── biological_macromolecule_ontology.json │ │ │ ├── cell_cycle_ontology.json │ │ │ ├── cell_type_ontology.json │ │ │ ├── cellular_component_ontology.json │ │ │ ├── contributor_role_ontology.json │ │ │ ├── development_stage_ontology.json │ │ │ ├── disease_ontology.json │ │ │ ├── enrichment_ontology.json │ │ │ ├── ethnicity_ontology.json │ │ │ ├── file_content_ontology.json │ │ │ ├── file_format_ontology.json │ │ │ ├── instrument_ontology.json │ │ │ ├── length_unit_ontology.json │ │ │ ├── library_amplification_ontology.json │ │ │ ├── library_construction_ontology.json │ │ │ ├── mass_unit_ontology.json │ │ │ ├── microscopy_ontology.json │ │ │ ├── organ_ontology.json │ │ │ ├── organ_part_ontology.json │ │ │ ├── process_type_ontology.json │ │ │ ├── protocol_type_ontology.json │ │ │ ├── sequencing_ontology.json │ │ │ ├── species_ontology.json │ │ │ ├── strain_ontology.json │ │ │ ├── target_pathway_ontology.json │ │ │ ├── time_unit_ontology.json │ │ │ └── treatment_method_ontology.json │ │ ├── process │ │ │ ├── purchased_reagents.json │ │ │ └── sequencing │ │ │ │ ├── S10x.json │ │ │ │ ├── barcode.json │ │ │ │ ├── insdc_experiment.json │ │ │ │ └── plate_based_sequencing.json │ │ ├── project │ │ │ ├── contact.json │ │ │ ├── funder.json │ │ │ └── publication.json │ │ └── protocol │ │ │ ├── channel.json │ │ │ ├── matrix.json │ │ │ └── probe.json │ ├── property_migrations.json │ ├── system │ │ ├── file_descriptor.json │ │ ├── license.json │ │ ├── links.json │ │ └── provenance.json │ ├── type │ │ ├── biomaterial │ │ │ ├── cell_line.json │ │ │ ├── cell_suspension.json │ │ │ ├── donor_organism.json │ │ │ ├── imaged_specimen.json │ │ │ ├── organoid.json │ │ │ └── specimen_from_organism.json │ │ ├── file │ │ │ ├── analysis_file.json │ │ │ ├── image_file.json │ │ │ ├── reference_file.json │ │ │ ├── sequence_file.json │ │ │ └── supplementary_file.json │ │ ├── process │ │ │ ├── analysis │ │ │ │ └── analysis_process.json │ │ │ └── process.json │ │ ├── project │ │ │ └── project.json │ │ └── protocol │ │ │ ├── analysis │ │ │ └── analysis_protocol.json │ │ │ ├── biomaterial_collection │ │ │ ├── aggregate_generation_protocol.json │ │ │ ├── collection_protocol.json │ │ │ ├── differentiation_protocol.json │ │ │ ├── dissociation_protocol.json │ │ │ ├── enrichment_protocol.json │ │ │ ├── ipsc_induction_protocol.json │ │ │ └── treatment_protocol.json │ │ │ ├── imaging │ │ │ ├── imaging_preparation_protocol.json │ │ │ └── imaging_protocol.json │ │ │ ├── protocol.json │ │ │ └── sequencing │ │ │ ├── library_preparation_protocol.json │ │ │ └── sequencing_protocol.json │ ├── update_log.csv │ └── versions.json ├── hpo-fhir.json ├── jsonschema │ ├── dosdp_schema.yaml │ └── vrs.schema.json ├── kitchen_sink.yaml ├── mixs │ ├── air.yaml │ ├── built_environment.yaml │ ├── checklists.yaml │ ├── core.yaml │ ├── host_associated.yaml │ ├── human_associated.yaml │ ├── human_gut.yaml │ ├── human_oral.yaml │ ├── human_skin.yaml │ ├── human_vaginal.yaml │ ├── hydrocarbon_resources_cores.yaml │ ├── hydrocarbon_resources_fluids_swabs.yaml │ ├── microbial_mat_biofilm.yaml │ ├── miscellaneous_natural_or_artificial_environment.yaml │ ├── mixs.yaml │ ├── plant_associated.yaml │ ├── ranges.yaml │ ├── sediment.yaml │ ├── soil.yaml │ ├── terms.yaml │ ├── wastewater_sludge.yaml │ └── water.yaml ├── model_card.schema.json ├── neon-in-gold.json.gz ├── obo-pred-summary.tsv ├── obo_registry.context.jsonld ├── obo_registry.schema.json ├── omo-pred-summary.tsv ├── phenopackets │ ├── any.proto │ ├── api.proto │ ├── base.proto │ ├── biosample.proto │ ├── descriptor.proto │ ├── disease.proto │ ├── duration.proto │ ├── empty.proto │ ├── field_mask.proto │ ├── genome.proto │ ├── individual.proto │ ├── interpretation.proto │ ├── measurement.proto │ ├── medical_action.proto │ ├── meta_data.proto │ ├── mme.proto │ ├── pedigree.proto │ ├── phenopackets.proto │ ├── phenopackets.schema.json │ ├── phenotypic_feature.proto │ ├── plugin.proto │ ├── source_context.proto │ ├── struct.proto │ ├── timestamp.proto │ ├── type.proto │ ├── vrsatile.proto │ └── wrappers.proto ├── prov.ofn ├── prov.ttl ├── reproschema.ofn ├── reproschema.ttl ├── sample.tsv ├── sbol.ofn ├── schemaorg-robot.ofn ├── shacl.ofn ├── shacl.owl ├── shacl.ttl ├── so-mini.obo ├── sosa.ttl ├── ssn.ttl ├── synonymizer.yaml ├── test-anon-individual.ofn ├── test.kwalify.yaml ├── test2.kwalify.yaml ├── users.yaml ├── webmap_enums.tsv └── zfa-pred-summary.tsv ├── test_annotators ├── __init__.py ├── test_bioportal_schema_annotator.py ├── test_jsonld_annotator.py ├── test_lov_schema_annotator.py └── test_schema_enricher.py ├── test_cli └── __init__.py ├── test_generalizers ├── __init__.py ├── test_csv_data_generalizer.py ├── test_fk_inference.py ├── test_from_robot_template.py ├── test_json_data_generalizer.py ├── test_pandas_data_generalizer.py └── test_rdf_data_generalizer.py ├── test_importers ├── __init__.py ├── test_cadsr_importer.py ├── test_convert_shacl_owl_representation.py ├── test_dbml_importer.py ├── test_dosdp_importer.py ├── test_frictionless_importer.py ├── test_from_owl_schemaorg.py ├── test_jsonschema_importer.py ├── test_kwalify_importer.py ├── test_owl_importer.py ├── test_rdfs_importer.py ├── test_sql_importer.py └── test_tabular_importer.py └── test_utils ├── __init__.py └── test_instance_extractor.py /.gitattributes: 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