├── .cruft.json ├── .github └── workflows │ ├── check-links.yaml │ ├── deploy-docs.yaml │ ├── main.yaml │ ├── pypi-publish.yaml │ └── test-pages-build.yaml ├── .gitignore ├── .linkmllint-root.yaml ├── .linkmllint.yaml ├── .pylintrc ├── CLAUDE.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── DEVELOPMENT.md ├── Dockerfile ├── LICENSE ├── MAINTAINERS.md ├── Makefile ├── README.md ├── about.yaml ├── assets ├── blanklines.txt ├── changesheet_examples │ ├── data_generation_id_inst_changesheet.tsv │ └── omics_processing_id_inst_changesheet.tsv ├── enum_pv_template.tsv ├── from-sssom-dir │ ├── README.md │ ├── biosample_ebs_water_packages_unclassified_taxa_sssom.tsv │ ├── biosample_env_package_normalizastion.tsv │ └── per_biosample_scoped_ebs_mapping_results.tsv ├── import_mixs_slots_regardless.tsv ├── jsons-for-mongodb │ └── .gitkeep ├── misc │ ├── .env.template │ ├── .gitkeep │ ├── README_cookiecutter.md │ ├── data_prefix_expansions.context.jsonld │ ├── gold_seqMethod_to_nmdc_instrument_set.tsv │ ├── legacy_migration_notes.md │ ├── linter_config_default.yaml │ ├── neon_nmdc_term_mapping.tsv │ ├── neon_raw_data_file_mappings.tsv │ └── neon_sequencingMethod_to_nmdc_instrument_set.tsv ├── mongodb_queries │ ├── data_qc │ │ ├── biosample_part_of_study.js │ │ ├── data_generation_has_input_biosample_or_processed_sample.js │ │ ├── data_generation_has_output_data_objects.js │ │ ├── data_object_was_generated_by_workflow_execution_or_data_generation.js │ │ ├── functional_annotation_agg_metagenome_metatranscriptome_annotation_id.js │ │ └── material_processing_has_input_biosample_or_processed_sample.js │ ├── delete_bioscales_data_objects.js │ ├── delete_data_generation_has_output_ref_integrity_exceptions.js │ └── find_id_nonconforming_data_objects.js ├── my_emsl_prefix.ttl ├── ncbi_mappings │ ├── README.md │ ├── ncbi_attribute_mappings.tsv │ ├── ncbi_attribute_mappings_filled.tsv │ ├── ncbi_pg_db_field_mappings.tsv │ ├── ncbi_pg_db_field_mappings_filled.tsv │ └── ncbi_pg_db_fields.txt ├── neon_mixs_env_triad_mappings │ ├── README.md │ ├── neon-nlcd-local-broad-mappings.tsv │ └── neon-site-env_medium.tsv ├── neon_table_types.tsv ├── other_mixs_yaml_files │ ├── TargetGeneEnum.yaml │ ├── cur_land_use_enum.yaml │ ├── mixs_env_triad_field_slot.yaml │ ├── mixs_template.yaml │ └── nmdc_mixs_env_triad_tooltips.yaml ├── pref-unit-slots-claude-ucum-expanded-curated-with-has-problem.tsv ├── schema_pattern_linting.txt ├── sparql │ ├── OmicsProcessing-to-Biosample-pairwise.rq │ ├── OmicsProcessing-to-catted-Biosamples.rq │ ├── OmicsProcessing.rq │ ├── Study.rq │ ├── mongodb-slots-to-units.rq │ ├── objects-that-are-never-subjects.rq │ ├── subjects-lacking-rdf-types.rq │ ├── tdb-graph-list.rq │ ├── tdb-test.rq │ ├── undefined-non-procs-inputs.rq │ └── undesc-ununsed-slots.rq └── yq-for-mixs_subset_modified.txt ├── docker-compose.yml ├── docs └── images │ ├── NMDC_metadata_img1.png │ ├── NMDC_metadata_img2.png │ ├── NMDC_metadata_img3.png │ ├── NMDC_metadata_img4.png │ ├── NMDC_metadata_img5.png │ └── NMDC_metadata_img6.png ├── gen-project-config.yaml ├── images └── nmdc_logo_long.jpeg ├── local └── .gitkeep ├── mkdocs.yml ├── nmdc_schema ├── README.md ├── __init__.py ├── anyuri_strings_to_iris.py ├── dump_single_modality.py ├── get_json_schema.py ├── get_nmdc_view.py ├── gold-to-mixs.sssom.tsv ├── id_helpers.py ├── migration_recursion.py ├── migrators │ ├── .docker │ │ ├── .env.example │ │ ├── docker-compose.yaml │ │ ├── mongoKeyFile │ │ ├── mongo_init │ │ │ └── initialize_replica_set.sh │ │ └── wait-for-it.sh │ ├── README.md │ ├── __init__.py │ ├── adapters │ │ ├── adapter_base.py │ │ ├── dictionary_adapter.py │ │ ├── mongo_adapter.py │ │ ├── test_dictionary_adapter.py │ │ └── test_mongo_adapter.py │ ├── assets │ │ ├── migrator_from_10_2_0_to_11_0_0_part_08 │ │ │ └── instrument_set.yaml │ │ ├── migrator_from_11_7_to_11_8 │ │ │ └── data_category_map.yaml │ │ ├── migrator_from_8_1_to_9_0 │ │ │ └── study_dois_changes.yaml │ │ └── migrator_from_9_1_to_9_2 │ │ │ └── websites_dois.yaml │ ├── cli │ │ ├── README.md │ │ ├── __init__.py │ │ ├── create_migrator.py │ │ ├── migrator.py.template │ │ └── run_migrator.py │ ├── helpers.py │ ├── migration_reporter.py │ ├── migrator_base.py │ ├── migrator_from_10_0_0_to_10_1_2.py │ ├── migrator_from_10_2_0_to_11_0_0.py │ ├── migrator_from_10_3_0_to_10_4_0.py │ ├── migrator_from_10_4_0_to_10_5_4.py │ ├── migrator_from_10_5_4_to_10_5_5.py │ ├── migrator_from_10_5_5_to_10_5_6.py │ ├── migrator_from_10_5_6_to_10_6_0.py │ ├── migrator_from_10_6_0_to_10_7_0.py │ ├── migrator_from_11_0_3_to_11_1_0.py │ ├── migrator_from_11_10_0_to_11_11_0.py │ ├── migrator_from_11_11_0_to_11_13_0.py │ ├── migrator_from_11_13_0_to_11_14_0.py │ ├── migrator_from_11_1_0_to_11_2_0.py │ ├── migrator_from_11_3_0_to_11_4_0.py │ ├── migrator_from_11_4_0_to_11_5_0.py │ ├── migrator_from_11_5_0_to_11_5_1.py │ ├── migrator_from_11_5_1_to_11_6_0.py │ ├── migrator_from_11_6_0_to_11_6_1.py │ ├── migrator_from_11_6_1_to_11_7_0.py │ ├── migrator_from_11_7_0_to_11_8_0.py │ ├── migrator_from_11_8_0_to_11_9_0.py │ ├── migrator_from_11_9_1_to_11_10_0.py │ ├── migrator_from_1_0_0_to_EXAMPLE.py │ ├── migrator_from_7_7_2_to_7_8_0.py │ ├── migrator_from_7_8_0_to_8_0_0.py │ ├── migrator_from_8_0_to_8_1.py │ ├── migrator_from_8_1_to_9_0.py │ ├── migrator_from_9_1_to_9_2.py │ ├── migrator_from_9_3_to_10_0.py │ └── partials │ │ ├── README.md │ │ ├── migrator_from_10_2_0_to_11_0_0 │ │ ├── __init__.py │ │ ├── migrator_from_10_2_0_to_11_0_0_part_01.py │ │ ├── migrator_from_10_2_0_to_11_0_0_part_02.py │ │ ├── migrator_from_10_2_0_to_11_0_0_part_03.py │ │ ├── migrator_from_10_2_0_to_11_0_0_part_04.py │ │ ├── migrator_from_10_2_0_to_11_0_0_part_05.py │ │ ├── migrator_from_10_2_0_to_11_0_0_part_06.py │ │ ├── migrator_from_10_2_0_to_11_0_0_part_07.py │ │ ├── migrator_from_10_2_0_to_11_0_0_part_08.py │ │ ├── migrator_from_10_2_0_to_11_0_0_part_09.py │ │ ├── migrator_from_10_2_0_to_11_0_0_part_10.py │ │ ├── migrator_from_10_2_0_to_11_0_0_part_11.py │ │ ├── migrator_from_10_2_0_to_11_0_0_part_12.py │ │ ├── migrator_from_10_2_0_to_11_0_0_part_13.py │ │ ├── migrator_from_10_2_0_to_11_0_0_part_14.py │ │ ├── migrator_from_10_2_0_to_11_0_0_part_15.py │ │ └── migrator_from_10_2_0_to_11_0_0_part_16.py │ │ ├── migrator_from_11_0_3_to_11_1_0 │ │ ├── __init__.py │ │ ├── migrator_from_11_0_3_to_11_1_0_part_1.py │ │ ├── migrator_from_11_0_3_to_11_1_0_part_2.py │ │ └── migrator_from_11_0_3_to_11_1_0_part_3.py │ │ ├── migrator_from_11_10_0_to_11_11_0 │ │ ├── __init__.py │ │ ├── migrator_from_11_10_0_to_11_11_0_part_1.py │ │ └── migrator_from_11_10_0_to_11_11_0_part_2.py │ │ ├── migrator_from_11_11_0_to_11_13_0 │ │ ├── __init__.py │ │ ├── migrator_from_11_11_0_to_11_13_0_part_1.py │ │ ├── migrator_from_11_11_0_to_11_13_0_part_2.py │ │ └── migrator_from_11_11_0_to_11_13_0_part_3.py │ │ ├── migrator_from_11_13_0_to_11_14_0 │ │ ├── __init__.py │ │ ├── migrator_from_11_13_0_to_11_14_0_part_1.py │ │ └── migrator_from_11_13_0_to_11_14_0_part_2.py │ │ ├── migrator_from_11_1_0_to_11_2_0 │ │ ├── __init__.py │ │ ├── migrator_from_11_1_0_to_11_2_0_part_1.py │ │ └── migrator_from_11_1_0_to_11_2_0_part_2.py │ │ ├── migrator_from_11_5_1_to_11_6_0 │ │ ├── __init__.py │ │ ├── migrator_from_11_5_1_to_11_6_0_part_1.py │ │ └── migrator_from_11_5_1_to_11_6_0_part_2.py │ │ ├── migrator_from_11_7_0_to_11_8_0 │ │ ├── __init__.py │ │ ├── migrator_from_11_7_0_to_11_8_0_part_1.py │ │ ├── migrator_from_11_7_0_to_11_8_0_part_2.py │ │ ├── migrator_from_11_7_0_to_11_8_0_part_3.py │ │ ├── migrator_from_11_7_0_to_11_8_0_part_4.py │ │ └── migrator_from_11_7_0_to_11_8_0_part_5.py │ │ ├── migrator_from_11_8_0_to_11_9_0 │ │ ├── __init__.py │ │ ├── migrator_from_11_8_0_to_11_9_0_part_1.py │ │ └── migrator_from_11_8_0_to_11_9_0_part_2.py │ │ └── migrator_from_11_9_1_to_11_10_0 │ │ ├── __init__.py │ │ ├── migrator_from_11_9_1_to_11_10_0_part_1.py │ │ ├── migrator_from_11_9_1_to_11_10_0_part_2.py │ │ └── migrator_from_11_9_1_to_11_10_0_part_3.py ├── nmdc-pydantic.py ├── nmdc.py ├── nmdc.schema.json ├── nmdc_data.py ├── nmdc_materialized_patterns.json ├── nmdc_materialized_patterns.schema.json ├── nmdc_materialized_patterns.yaml ├── nmdc_schema_validation_plugin.py ├── nmdc_version.py └── validate_nmdc_json.py ├── notebooks ├── ReadQcAnalysisActivity_slots.ipynb ├── find-ControlledTermValue-usages.ipynb ├── mongo_doc_top_slot_usage_counts.ipynb ├── nist_bioeconomy_lexicon_scraper.ipynb ├── schema-view-based-documentation.ipynb └── test-schema-view.ipynb ├── poetry.lock ├── project.Makefile ├── pyproject.toml ├── src ├── __init__.py ├── data │ ├── invalid │ │ ├── .gitkeep │ │ ├── Biosample-caps-IGSN.yaml │ │ ├── Biosample-incomplete_napa_id.yaml │ │ ├── Biosample-invalid-infiltrations.yaml │ │ ├── Biosample-invalid-source-system.yaml │ │ ├── Biosample-invalid_fire.yaml │ │ ├── Biosample-invalid_id-1.yaml │ │ ├── Biosample-invalid_id-2.yaml │ │ ├── Biosample-minimal-invalid-type.yaml │ │ ├── Biosample-minimal-no-id-but-with-type.yaml │ │ ├── Biosample-minimal-no-type.yaml │ │ ├── Biosample-non_boolean_embargo.yaml │ │ ├── CalibrationInformation-GC-missing-calibration_object.yaml │ │ ├── CalibrationInformation-GC-missing-calibration_standard.yaml │ │ ├── CalibrationInformation-incorrect-calibration_target.yaml │ │ ├── ChromatograohyConfiguration-invalid-no_sp.yaml │ │ ├── ChromatographyConfiguration-invalid-no_CC.yaml │ │ ├── DataGeneration-invalid-class_is_abstract.yaml │ │ ├── DataObject-in_manifest-invalid.yaml │ │ ├── DataObject-invalid-data_object_type-2.yaml │ │ ├── DataObject-invalid-data_object_type.yaml │ │ ├── DataObject-invalid_id-1.yaml │ │ ├── DataObject-invalid_id-2.yaml │ │ ├── DataObject-invalid_was_generated_by.yaml │ │ ├── DataObject-no-data_category.yaml │ │ ├── DataObject-no-data_object_type.yaml │ │ ├── DataObject-no-id.yaml │ │ ├── DataObject-no-name.yaml │ │ ├── DataObject-no-type.yaml │ │ ├── Database-Biosample-invalid_id.yaml │ │ ├── Database-Biosample-missing_longitude.yaml │ │ ├── Database-MetabolomicsAnalysis-no_metabolomics_category.yaml │ │ ├── Database-ReadQcAnalysisActivity-invalid.yaml │ │ ├── Database-WorkflowExecution-was-informed-by-not-a-list.yaml │ │ ├── Database-WorkflowExecutionActivity-invalid.yaml │ │ ├── Database-biosample_gold_id_list_as_primary_key.yaml │ │ ├── Database-biosample_undeclared_slot.yaml │ │ ├── Database-biosamples-lat_lon-with-GLV-missing-latitude.yaml │ │ ├── Database-biosamples-lat_lon-with-GLV-missing-longitude.yaml │ │ ├── Database-functional_annotation_agg-missing_gene_function_id.yaml │ │ ├── Database-invalid-functional-annotation.yaml │ │ ├── Database-invalid_calibration_slot.yaml │ │ ├── Database-mags-img_identifiers-exceeds-cardinality.yaml │ │ ├── Database-metatranscriptome_workflow-invalidDatabase.yaml │ │ ├── Database-plannedprocess-non-string-end_datet.yaml │ │ ├── Database-polymorphic-invalid-typed-LibraryPreparation.yaml │ │ ├── Database-studies-legacy-gold-study-id.yaml │ │ ├── Database-studies-missing-study_category.yaml │ │ ├── Database-studies-undefined-doi-slot.yaml │ │ ├── Database-studies-undefined-foo-slot.yaml │ │ ├── Database-studies-undefined-principal_investigator_name-slot.yaml │ │ ├── Database-study-include-abstract.yaml │ │ ├── Database-study_set-bad-emsl-doi-slot-name.yaml │ │ ├── Database-using-undefined-analytical_sample_set-slot.yaml │ │ ├── Database-with-deprecated-MetagenomeSequencing.yaml │ │ ├── Database_processed-sample-bad-portion.yaml │ │ ├── DissolvingProcess-minimal-invalid-substance.yaml │ │ ├── Doi-invalid-award-without-provider.yaml │ │ ├── Doi-invalid-dataset-without-provider.yaml │ │ ├── Extraction-extraction_method-slot-retired.yaml │ │ ├── Extraction-invalid_extraction_targets.yaml │ │ ├── Extraction-metabolomics-concentration-without-compound.yaml │ │ ├── Extraction-metabolomics-string-extractant.yaml │ │ ├── Extraction-sample_mass-now_input_mass.yaml │ │ ├── FiltrationProcess-invalid_non-numeric-pore-size-num-val.yaml │ │ ├── FiltrationProcess-invalid_non-string-conditioning.yaml │ │ ├── FunctionalAnnotation-invalid-function.yaml │ │ ├── FunctionalAnnotationAggMember-invalid-no_count.yaml │ │ ├── FunctionalAnnotationAggMember-invalid_cog_id.yaml │ │ ├── FunctionalAnnotationAggMember-invalid_kegg_id.yaml │ │ ├── FunctionalAnnotationAggMember-invalid_pfam_id.yaml │ │ ├── FunctionalAnnotationAggMember-invalid_pfam_id_length.yaml │ │ ├── Instrument-invalid_model.yaml │ │ ├── LibraryPreparation-invalid-target_gene.yaml │ │ ├── LibraryPreparation-missing-protocol-type.yaml │ │ ├── MagsAnalysis-invalid-bin_qulity.yaml │ │ ├── MagsAnalysis-invalid-float-for-16s.yaml │ │ ├── MagsAnalysis-invalid-missing-bin-name.yaml │ │ ├── MagsAnalysis-invalid-negative-int.yaml │ │ ├── MagsAnalysisActivity-invalid_ncbi_lineage_tax_ids.yaml │ │ ├── MagsAnalysis_invalid-newer-version.yaml │ │ ├── MassSpectrometry-incl-nucleotideseq-slots.yaml │ │ ├── MassSpectrometry-invalid-gc-without-config.yaml │ │ ├── MassSpectrometry-invalid-lc-without-config.yaml │ │ ├── MassSpectrometry-invalid_no_eic.yaml │ │ ├── MassSpectrometry-invalid_no_hms_config.yaml │ │ ├── MassSpectrometry-no-analyte_category.yaml │ │ ├── MassSpectrometry-working.yaml │ │ ├── MassSpectrometryConfiguration-invalid-no_is.yaml │ │ ├── MassSpectrometryConfiguration-invalid-no_ma.yaml │ │ ├── MassSpectrometryConfiguration-invalid-no_msas.yaml │ │ ├── MassSpectrometryConfiguration-invalid-no_mscm.yaml │ │ ├── MassSpectrometryConfiguration-invalid-no_pm.yaml │ │ ├── MassSpectrometryConfiguration-invalid-no_rc.yaml │ │ ├── MetabolomicsAnalysis-invalid-has-slot-used.yaml │ │ ├── MetabolomicsAnalysis-invalid-missing_execution_resource.yaml │ │ ├── MetabolomicsAnalysis-invalid_execution_resource_not_in_enum.yaml │ │ ├── MetabolomicsAnalysis-invalid_id-1.yaml │ │ ├── MetabolomicsAnalysis-invalid_id-2.yaml │ │ ├── MetabolomicsAnalysis-invalid_id-3.yaml │ │ ├── MetabolomicsAnalysis-invalid_id-4.yaml │ │ ├── MetabolomicsAnalysis-invalid_no_informed_by.yaml │ │ ├── MetabolomicsAnalysis-metab_quantified.yaml │ │ ├── MetagenomeAssembly-invalid-qc-status-rules.yaml │ │ ├── MetaproteomicsAnalysis-invalid-missing-metap-cat.yaml │ │ ├── MetatranscriptomeExpressionAnalysis-invalid-type.yaml │ │ ├── NomAnalysis-incomplete-string-ended_at_time.yaml │ │ ├── NomAnalysis-non-string-ended_at_time.yaml │ │ ├── NomAnalysis-remove_used.yaml │ │ ├── NucleotideSequencing-instrument_name-retired.yaml │ │ ├── NucleotideSequencing-invalid-prefix.yaml │ │ ├── NucleotideSequencing-invalid-target_gene.yaml │ │ ├── NucleotideSequencing-invalid_parthood.yaml │ │ ├── NucleotideSequencing-no-id.yaml │ │ ├── NucleotideSequencing-omics-type-slot-retired.yaml │ │ ├── NucleotideSequencing-undefined-omics-processing.yaml │ │ ├── NucleotideSequencing-working.yaml │ │ ├── Pooling-invalid_id-1.yaml │ │ ├── ReadQcAnalysis-invalid-has-part_of.yaml │ │ ├── ReadQcAnalysis-invalid.yaml │ │ ├── ReadQcAnalysis-invalid_execution_resource.yaml │ │ ├── ReadQcAnalysis-no_processing_institution.yaml │ │ ├── Study-emsl-bad-local.yaml │ │ ├── Study-has-abstract.yaml │ │ ├── Study-has-missing_doi_provider.yaml │ │ ├── Study-has-publications.yaml │ │ ├── Study-include-emsl_project_dois.yaml │ │ ├── Study-invalid-homepage-website.yaml │ │ ├── Study-invalid-neon-identifier.yaml │ │ ├── Study-invalid_id-1.yaml │ │ ├── Study-invalid_id-2.yaml │ │ ├── Study-using-retired-relevant_protocols-slot.yaml │ │ ├── Study-using-undefined-genome_portal_identifiers-slot.yaml │ │ ├── TextValue-forbidden-processed-value.yaml │ │ └── TextValue-was_generated_by.yaml │ ├── problem │ │ ├── .gitkeep │ │ ├── invalid │ │ │ └── .gitkeep │ │ └── valid │ │ │ └── .gitkeep │ └── valid │ │ ├── .gitkeep │ │ ├── Biosample-PropertyAssertion-examples.yaml │ │ ├── Biosample-amplicon.yaml │ │ ├── Biosample-embargoed.yaml │ │ ├── Biosample-minimal.yaml │ │ ├── Biosample-possibly-exhaustive.yaml │ │ ├── Biosample-soil_horizon.yaml │ │ ├── Biosample-with-fire.yaml │ │ ├── CalibrationInformation-GC.yaml │ │ ├── ChemicalConversionProcess-digest.yaml │ │ ├── ChemicalConversionProcess-minimal.yaml │ │ ├── ChromatographicSeparationProcess-SPE.yaml │ │ ├── ChromatographyConfiguration-GC.yaml │ │ ├── ChromatographyConfiguration-LC.yaml │ │ ├── CreditAssociation-1.yaml │ │ ├── DataObject-1.yaml │ │ ├── DataObject-3.yaml │ │ ├── DataObject-Crisper-Terms-data_object_type.yaml │ │ ├── DataObject-calibration.yaml │ │ ├── DataObject-exhaustive.yaml │ │ ├── DataObject-gen_by_omics.yaml │ │ ├── DataObject-mass_spec.yaml │ │ ├── DataObject-metatranscriptome-expression.yaml │ │ ├── DataObject-minimal.yaml │ │ ├── DataObject-my_emsl_prefix.yaml │ │ ├── Database-AssemblyAnalysis-1.yaml │ │ ├── Database-DataObject_expression_output.yaml │ │ ├── Database-GOLD_amplicon.yaml │ │ ├── Database-MassSpectrometry-NucleotideSequencing.yaml │ │ ├── Database-MassSpectrometry-dgms-minimal.yaml │ │ ├── Database-Metabolomics-configuration.yaml │ │ ├── Database-MetabolomicsAnalysis-1.yaml │ │ ├── Database-NOM-material-processing.yaml │ │ ├── Database-ProcessedSample-sampled_portion.yaml │ │ ├── Database-ReadQcAnalysisActivity-quality_fail.yaml │ │ ├── Database-WorkflowExecution.yaml │ │ ├── Database-amplicon_example.yaml │ │ ├── Database-analytical_sample-extract-EDITED-TO_PASS.yaml │ │ ├── Database-biosamples-1.yaml │ │ ├── Database-biosamples-infiltrations.yaml │ │ ├── Database-biosamples-minimal.yaml │ │ ├── Database-biosamples-sites.yaml │ │ ├── Database-data-generations.yaml │ │ ├── Database-data_object_singleM.yaml │ │ ├── Database-data_objects_genomad.yaml │ │ ├── Database-extraction_set-exhaustive.yaml │ │ ├── Database-extraction_set-minimal.yaml │ │ ├── Database-functional-annotations.yaml │ │ ├── Database-functional_annotation_agg.yaml │ │ ├── Database-gen_from_omics.yaml │ │ ├── Database-instrument_set.yaml │ │ ├── Database-interleaved.yaml │ │ ├── Database-library-prep-exhausive.yaml │ │ ├── Database-librarypreparation_rna_option1.yaml │ │ ├── Database-lipid-workflow.yaml │ │ ├── Database-mags.yaml │ │ ├── Database-mass-spectrometry.yaml │ │ ├── Database-mass_spectrometry_gc.yaml │ │ ├── Database-metabolomics_calibration_example.yaml │ │ ├── Database-metagenome-assembly.yaml │ │ ├── Database-metatranscriptome_workflow.yaml │ │ ├── Database-multi-id-study.yaml │ │ ├── Database-multiple-paths.yaml │ │ ├── Database-neon-story.yaml │ │ ├── Database-neon_Biosample_to_DataObject_NEON.yaml │ │ ├── Database-nmdc-example.yaml │ │ ├── Database-nom-alt_id.yaml │ │ ├── Database-nom_analysis_set.yaml │ │ ├── Database-nom_calibration_example.yaml │ │ ├── Database-nucleic-extraction.yaml │ │ ├── Database-polymorphic-planned-process-set.yaml │ │ ├── Database-pooling_set-exhaustive.yaml │ │ ├── Database-pooling_set-minimal.yaml │ │ ├── Database-processed_sample-extract-exhaustive.yaml │ │ ├── Database-processed_sample-minimal.yaml │ │ ├── Database-study-set-with-consortia-and-parents.yaml │ │ ├── Database-study-set-with-dois.yaml │ │ ├── Database-study-set-with-gnps-id.yaml │ │ ├── Database-study_test.yaml │ │ ├── DissolvingProcess-minimal.yaml │ │ ├── Doi-valid-award-with-provider.yaml │ │ ├── Doi-valid-dataset-with-provider.yaml │ │ ├── Doi-valid-dmp-without-provider.yaml │ │ ├── Doi-valid-publication-without-provider.yaml │ │ ├── Extraction-NEON.yaml │ │ ├── Extraction-Target-NOM.yaml │ │ ├── Extraction-metabolomics.yaml │ │ ├── Extraction-proteomics.yaml │ │ ├── FiltrationProcess-minimal_pressurized.yaml │ │ ├── FunctionalAnnotation-exhaustive.yaml │ │ ├── FunctionalAnnotation-minimal.yaml │ │ ├── FunctionalAnnotationAggMember-metatranscriptome.yaml │ │ ├── FunctionalAnnotationAggMember-minimal.yaml │ │ ├── GeneProduct-minimal.yaml │ │ ├── ImageValue-1.yaml │ │ ├── Instrument-basic.yaml │ │ ├── LibraryPreparation-amplicon.yaml │ │ ├── LibraryPreparation.yaml │ │ ├── MagsAnalysis-exhaustive.yaml │ │ ├── MagsAnalysis.yaml │ │ ├── MassSpectrometry-NOM.yaml │ │ ├── MassSpectrometry-dgms-minimal.yaml │ │ ├── MassSpectrometry-omprc-minimal.yaml │ │ ├── MassSpectrometry-valid-gc-with-config.yaml │ │ ├── MassSpectrometry-valid-lc-with-config.yaml │ │ ├── MassSpectrometry-valid-syringe-without-config.yaml │ │ ├── MassSpectrometryConfiguration-NOM.yaml │ │ ├── MetabolomicsAnalysis-1.yaml │ │ ├── MetabolomicsAnalysis-2.yaml │ │ ├── MetatranscriptomeAnnotation-1.yaml │ │ ├── MixingProcess-minimal.yaml │ │ ├── MobilePhaseSegment-1.yaml │ │ ├── NucleotideSequencing-2.yaml │ │ ├── NucleotideSequencing-dgns-minimal.yaml │ │ ├── NucleotideSequencing-ndsdc-bioproject.yaml │ │ ├── NucleotideSequencing-omprc-minimal.yaml │ │ ├── NucleotideSequencing-processing-institution.yaml │ │ ├── NucleotideSequencing-valid.yaml │ │ ├── OntologyClass-chebi.yaml │ │ ├── OntologyClass-envo.yaml │ │ ├── Pooling-exhaustive.yaml │ │ ├── Pooling-minimal.yaml │ │ ├── PortionOfSubstance-1.yaml │ │ ├── Protocol-minimal.yaml │ │ ├── QuantityValue-1.yaml │ │ ├── ReadQcAnalysis-1.yaml │ │ ├── StorageProcess-minimal.yaml │ │ ├── Study-credit-1.yaml │ │ ├── Study-emsl.yaml │ │ ├── Study-exhaustive.yaml │ │ ├── Study-minimal.yaml │ │ ├── Study-tidy.yaml │ │ ├── SubSamplingProcess-minimal.yaml │ │ └── TextValue-raw_value.yaml ├── doc-templates │ ├── class.md.jinja2 │ ├── class_diagram.md.jinja2 │ ├── common_metadata.md.jinja2 │ ├── enum.md.jinja2 │ ├── index.md.jinja2 │ ├── slot.md.jinja2 │ └── subset.md.jinja2 ├── docs │ ├── Information.md │ ├── Metadata_Documentation_Overview.md │ ├── about.md │ ├── collaboration.md │ ├── developer-docs.md │ ├── identifiers.md │ ├── images │ │ ├── Activity.png │ │ ├── AttributeValue10.png │ │ ├── AttributeValue11.png │ │ ├── Configuration.png │ │ ├── DOE_logo.png │ │ ├── InformationObject.png │ │ ├── MaterialProcessing.png │ │ ├── MobilePhaseSegment.png │ │ ├── NMDC_logo.png │ │ ├── NMDC_metadata_img1.png │ │ ├── NMDC_metadata_img2.png │ │ ├── NMDC_metadata_img3.png │ │ ├── NMDC_metadata_img4.png │ │ ├── NMDC_metadata_img5.png │ │ ├── NMDC_metadata_img6.png │ │ ├── PortionOfSubstance.png │ │ ├── ProtocolExecution.png │ │ └── favicon.ico │ ├── maintaining-the-schema.md │ ├── migrations.md │ ├── schema-validation.md │ ├── schema_element_deprecation_guide.md │ ├── schemaview.md │ ├── typecode-to-class-map.md │ ├── v10-vs-v11-retrospective.md │ ├── validation.md │ └── visualizations.md ├── schema │ ├── annotation.yaml │ ├── attribute_values.yaml │ ├── basic_classes.yaml │ ├── basic_slots.yaml │ ├── core.yaml │ ├── deprecated.yaml │ ├── external_identifiers.yaml │ ├── mixs.yaml │ ├── nmdc.yaml │ ├── nmdc_subsets.yaml │ ├── nmdc_types.yaml │ ├── portal_enums.yaml │ ├── portal_mixs_inspired.yaml │ ├── portal_sample_id.yaml │ ├── portal_user_facility.yaml │ └── workflow_execution_activity.yaml └── scripts │ ├── __init__.py │ ├── analyze_mentions_of_ids.py │ ├── check_examples_class_coverage.py │ ├── class_instantiation_counts.py │ ├── database_to_json_list_files.py │ ├── date_created_blank_node.py │ ├── experimental │ ├── __init__.py │ ├── class_sparql.py │ └── partial_imports_graph.py │ ├── extract_numeric_values.py │ ├── get_study_id_from_filename.py │ ├── interleave_yaml.py │ ├── iterative-validation.sh │ ├── json-dir-to-mongodb.sh │ ├── make_typecode_to_class_map.py │ ├── ncbi_nmdc_exact_term_matching.py │ ├── ncbi_postgres_nmdc_exact_term_matching.py │ ├── nmdc_database_tools.py │ ├── report_biosamples_per_study.py │ ├── report_usages.py │ ├── schema_pattern_linting.py │ ├── schema_view_relation_graph.py │ ├── scrutinize_elements.py │ ├── slot_range_type_reporter.py │ ├── tablesort.js │ └── task_specific_code │ ├── README.md │ ├── create_legacy_orphan_deletion_requests.py │ └── insert_many_pymongo.py ├── sssom └── gold-to-mixs.sssom.tsv ├── tests ├── __init__.py ├── test_all_classes_assert_a_class_uri.py ├── test_all_classes_can_use_type_slot.py ├── test_all_multivalued_class_range_slots_are_inlined_as_list.py ├── test_annotations.py ├── test_any_of_forbidden.py ├── test_database.py ├── test_enums.py ├── test_getters.py ├── test_has_unit_enum.py ├── test_inherited_slots_not_reiterated.py ├── test_json_schema_artifact.py ├── test_nmdc_data.py ├── test_nmdc_schema_validation_plugin.py └── test_units_alignment.py ├── units ├── Makefile ├── docs │ ├── .~lock.removed-storage-units-annotations.tsv# │ ├── README.md │ ├── legacy-data-strategy.md │ ├── migration-guide.md │ ├── removed-storage-units-annotations.tsv │ ├── units-ecosystem-overview.md │ └── units-problems-definitive.md ├── output │ ├── schema_qv_complete_table.txt │ ├── schema_qv_storage_counts.tsv │ ├── schema_qv_with_storage.txt │ ├── schema_qv_without_storage.txt │ ├── schema_units_excuses.tsv │ └── user_friendly_units.tsv ├── scripts │ └── __init__.py ├── semi-static-inputs │ ├── mongodb-slots-to-units.csv │ └── mongodb-slots-to-units_remediated.csv ├── slow-outputs │ └── 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