Python Module Index

k | q | t


	k
	`kg_microbe`
	`kg_microbe.bactotraits_to_mongo`
	`kg_microbe.download`
	`kg_microbe.merge_utils`
	`kg_microbe.merge_utils.artifact_manifest`
	`kg_microbe.merge_utils.external_node_closure`
	`kg_microbe.merge_utils.invariants`
	`kg_microbe.merge_utils.local_context`
	`kg_microbe.merge_utils.merge_contract`
	`kg_microbe.merge_utils.merge_kg`
	`kg_microbe.merge_utils.progress`
	`kg_microbe.merge_utils.source_admission`
	`kg_microbe.merge_utils.source_freshness`
	`kg_microbe.merge_utils.stats_provenance`
	`kg_microbe.query`
	`kg_microbe.query_utils`
	`kg_microbe.query_utils.duckdb_loader`
	`kg_microbe.query_utils.organism_queries`
	`kg_microbe.query_utils.utils`
	`kg_microbe.run`
	`kg_microbe.transform`
	`kg_microbe.transform_utils`
	`kg_microbe.transform_utils.bacdive`
	`kg_microbe.transform_utils.bacdive.ancestry_authority`
	`kg_microbe.transform_utils.bacdive.bacdive`
	`kg_microbe.transform_utils.bacdive.clinical_categories`
	`kg_microbe.transform_utils.bacdive.csv_field_limit`
	`kg_microbe.transform_utils.bacdive.ec_substrate_corrections`
	`kg_microbe.transform_utils.bacdive.emission`
	`kg_microbe.transform_utils.bacdive.fallback_evidence`
	`kg_microbe.transform_utils.bacdive.fallback_native_authority`
	`kg_microbe.transform_utils.bacdive.fallback_selection`
	`kg_microbe.transform_utils.bacdive.isolation_categories`
	`kg_microbe.transform_utils.bacdive.ncit_category_claims`
	`kg_microbe.transform_utils.bacdive.references`
	`kg_microbe.transform_utils.bacdive.supplied_taxid_policy`
	`kg_microbe.transform_utils.bacdive.taxonomy_evidence`
	`kg_microbe.transform_utils.bactotraits`
	`kg_microbe.transform_utils.bactotraits.bactotraits`
	`kg_microbe.transform_utils.bakta`
	`kg_microbe.transform_utils.bakta.bakta`
	`kg_microbe.transform_utils.bakta.create_samn_mapping`
	`kg_microbe.transform_utils.bakta.utils`
	`kg_microbe.transform_utils.cog`
	`kg_microbe.transform_utils.cog.cog`
	`kg_microbe.transform_utils.cog.utils`
	`kg_microbe.transform_utils.constants`
	`kg_microbe.transform_utils.ctd`
	`kg_microbe.transform_utils.ctd.ctd`
	`kg_microbe.transform_utils.disbiome`
	`kg_microbe.transform_utils.disbiome.disbiome`
	`kg_microbe.transform_utils.example_transform`
	`kg_microbe.transform_utils.gold`
	`kg_microbe.transform_utils.gold.alias_observations`
	`kg_microbe.transform_utils.gold.crosswalk_quarantine`
	`kg_microbe.transform_utils.gold.fold_restoration`
	`kg_microbe.transform_utils.gold.gold`
	`kg_microbe.transform_utils.gold.selected_taxon_aliases`
	`kg_microbe.transform_utils.gold.taxon_dispositions`
	`kg_microbe.transform_utils.gtdb`
	`kg_microbe.transform_utils.gtdb.gtdb`
	`kg_microbe.transform_utils.gtdb.utils`
	`kg_microbe.transform_utils.kegg`
	`kg_microbe.transform_utils.kegg.kegg`
	`kg_microbe.transform_utils.kegg.utils`
	`kg_microbe.transform_utils.lpsn`
	`kg_microbe.transform_utils.lpsn.lpsn`
	`kg_microbe.transform_utils.lpsn_api`
	`kg_microbe.transform_utils.lpsn_api.lpsn_api`
	`kg_microbe.transform_utils.madin_etal`
	`kg_microbe.transform_utils.madin_etal.madin_etal`
	`kg_microbe.transform_utils.mediadive`
	`kg_microbe.transform_utils.mediadive.bulk_inputs`
	`kg_microbe.transform_utils.mediadive.material_scope_audit`
	`kg_microbe.transform_utils.mediadive.mediadive`
	`kg_microbe.transform_utils.mediadive.recipe_identity`
	`kg_microbe.transform_utils.metatraits`
	`kg_microbe.transform_utils.metatraits.io`
	`kg_microbe.transform_utils.metatraits.metatraits`
	`kg_microbe.transform_utils.metatraits_gtdb`
	`kg_microbe.transform_utils.metatraits_gtdb.metatraits_gtdb`
	`kg_microbe.transform_utils.microbedecoder`
	`kg_microbe.transform_utils.microbedecoder.bacdive_join_dispositions`
	`kg_microbe.transform_utils.microbedecoder.chemical_curation`
	`kg_microbe.transform_utils.microbedecoder.crosswalk_quarantine`
	`kg_microbe.transform_utils.microbedecoder.crosswalk_witnesses`
	`kg_microbe.transform_utils.microbedecoder.curation`
	`kg_microbe.transform_utils.microbedecoder.gold_crosswalk_dispositions`
	`kg_microbe.transform_utils.microbedecoder.material_dispositions`
	`kg_microbe.transform_utils.microbedecoder.microbedecoder`
	`kg_microbe.transform_utils.microbedecoder.phenotype_curation`
	`kg_microbe.transform_utils.microbedecoder.process_scopes`
	`kg_microbe.transform_utils.microbedecoder.source_annotations`
	`kg_microbe.transform_utils.microbedecoder.utils`
	`kg_microbe.transform_utils.mim_ingredients`
	`kg_microbe.transform_utils.mim_ingredients.mim_ingredients`
	`kg_microbe.transform_utils.ontologies`
	`kg_microbe.transform_utils.ontologies.ontologies_transform`
	`kg_microbe.transform_utils.ontologies_stubs`
	`kg_microbe.transform_utils.ontologies_stubs.ncit_category_projection`
	`kg_microbe.transform_utils.ontologies_stubs.ontologies_stubs_transform`
	`kg_microbe.transform_utils.prego`
	`kg_microbe.transform_utils.prego.calibration`
	`kg_microbe.transform_utils.prego.envo_identity`
	`kg_microbe.transform_utils.prego.native_inputs`
	`kg_microbe.transform_utils.prego.prego`
	`kg_microbe.transform_utils.prego.quality`
	`kg_microbe.transform_utils.prego.utils`
	`kg_microbe.transform_utils.rhea_mappings`
	`kg_microbe.transform_utils.rhea_mappings.label_inputs`
	`kg_microbe.transform_utils.rhea_mappings.legacy_xrefs`
	`kg_microbe.transform_utils.rhea_mappings.native_graph`
	`kg_microbe.transform_utils.rhea_mappings.native_inputs`
	`kg_microbe.transform_utils.rhea_mappings.native_rdf`
	`kg_microbe.transform_utils.rhea_mappings.reaction_families`
	`kg_microbe.transform_utils.rhea_mappings.rhea_mappings`
	`kg_microbe.transform_utils.rhea_mappings.stage_snapshot`
	`kg_microbe.transform_utils.transform`
	`kg_microbe.transform_utils.uniprot_functional_microbes`
	`kg_microbe.transform_utils.uniprot_functional_microbes.uniprot_functional_microbes`
	`kg_microbe.transform_utils.uniprot_human`
	`kg_microbe.transform_utils.uniprot_human.uniprot_human`
	`kg_microbe.transform_utils.wallen_etal`
	`kg_microbe.transform_utils.wallen_etal.wallen_etal`
	`kg_microbe.utils`
	`kg_microbe.utils.atomic_io`
	`kg_microbe.utils.biolink_hierarchy`
	`kg_microbe.utils.biolink_model`
	`kg_microbe.utils.cas`
	`kg_microbe.utils.chemical_mapping_utils`
	`kg_microbe.utils.clinical_mesh_categories`
	`kg_microbe.utils.consolidate_categories`
	`kg_microbe.utils.download_manifest`
	`kg_microbe.utils.download_utils`
	`kg_microbe.utils.dummy_tqdm`
	`kg_microbe.utils.external_identifiers`
	`kg_microbe.utils.finite_envo_po_categories`
	`kg_microbe.utils.finite_import_categories`
	`kg_microbe.utils.fix_list_representations`
	`kg_microbe.utils.foodon_anatomical_categories`
	`kg_microbe.utils.foodon_classification`
	`kg_microbe.utils.foodon_kernel_producer`
	`kg_microbe.utils.foodon_kernel_quarantine`
	`kg_microbe.utils.go_authority`
	`kg_microbe.utils.go_imported_restrictions`
	`kg_microbe.utils.graph_canonicalization`
	`kg_microbe.utils.graph_schema`
	`kg_microbe.utils.imported_gene_authority`
	`kg_microbe.utils.ingredient_bundle`
	`kg_microbe.utils.ingredient_bundle_contract`
	`kg_microbe.utils.ingredient_context`
	`kg_microbe.utils.ingredient_identity`
	`kg_microbe.utils.ingredient_kgx`
	`kg_microbe.utils.ingredient_scope`
	`kg_microbe.utils.isolation_source_mapping_utils`
	`kg_microbe.utils.kgm_validation_profile`
	`kg_microbe.utils.lpsn_utils`
	`kg_microbe.utils.mapping_file_utils`
	`kg_microbe.utils.mediadive_bulk_download`
	`kg_microbe.utils.mesh_finite_categories`
	`kg_microbe.utils.metpo_liveness`
	`kg_microbe.utils.metpo_predicates`
	`kg_microbe.utils.microbial_trait_mappings`
	`kg_microbe.utils.native_rdf`
	`kg_microbe.utils.native_ro_retention`
	`kg_microbe.utils.ncit_eight_categories`
	`kg_microbe.utils.ner_utils`
	`kg_microbe.utils.oak_utils`
	`kg_microbe.utils.ontology_category_authority`
	`kg_microbe.utils.ontology_metadata`
	`kg_microbe.utils.ontology_parent_quarantine`
	`kg_microbe.utils.ontology_resolution`
	`kg_microbe.utils.ontology_utils`
	`kg_microbe.utils.optional_consumed_inputs`
	`kg_microbe.utils.pandas_utils`
	`kg_microbe.utils.postprocess_artifacts`
	`kg_microbe.utils.producer_audits`
	`kg_microbe.utils.provenance`
	`kg_microbe.utils.release_binding`
	`kg_microbe.utils.release_preflight`
	`kg_microbe.utils.review_claims`
	`kg_microbe.utils.robot_utils`
	`kg_microbe.utils.sanitize_curies`
	`kg_microbe.utils.semsql_toolchain`
	`kg_microbe.utils.source_category_authority`
	`kg_microbe.utils.source_finalization`
	`kg_microbe.utils.sqlite_read`
	`kg_microbe.utils.sssom_identity_policy`
	`kg_microbe.utils.string_coding`
	`kg_microbe.utils.stub_curie_collection`
	`kg_microbe.utils.transform_fingerprint`
	`kg_microbe.utils.tsv_io`
	`kg_microbe.utils.uberon_temporal_categories`
	`kg_microbe.utils.unipathways_utils`
	`kg_microbe.utils.uniprot_utils`
	`kg_microbe.utils.upa_route_review`
	`kg_microbe.utils.validation_utils`

	q
	`query_utils`
	`query_utils.query`

	t
	`tests`
	`tests.test_transform_class`