Index

A

accepted_name_scope() (in module kg_microbe.utils.ingredient_identity) accession_to_gtdb_species (kg_microbe.transform_utils.metatraits_gtdb.MetaTraitsGTDBTransform attribute) accession_to_ncbi (kg_microbe.transform_utils.metatraits_gtdb.MetaTraitsGTDBTransform attribute) active_xrefs() (kg_microbe.utils.ingredient_bundle.ReviewedIngredientBundle method) add() (kg_microbe.transform_utils.prego.calibration.ScoreHistogram method) add_child() (kg_microbe.utils.mapping_file_utils.MetpoTreeNode method) add_cog_annotation() (kg_microbe.transform_utils.bakta.bakta.BaktaTransform method) (kg_microbe.transform_utils.bakta.BaktaTransform method) add_cog_node() (kg_microbe.transform_utils.cog.cog.COGTransform method) (kg_microbe.transform_utils.cog.COGTransform method) add_ec_annotation() (kg_microbe.transform_utils.bakta.bakta.BaktaTransform method) (kg_microbe.transform_utils.bakta.BaktaTransform method) add_edge() (kg_microbe.transform_utils.bakta.bakta.BaktaTransform method) (kg_microbe.transform_utils.bakta.BaktaTransform method) (kg_microbe.transform_utils.cog.cog.COGTransform method) (kg_microbe.transform_utils.cog.COGTransform method) (kg_microbe.transform_utils.kegg.kegg.KEGGTransform method) (kg_microbe.transform_utils.kegg.KEGGTransform method) add_functional_annotations() (kg_microbe.transform_utils.bakta.bakta.BaktaTransform method) (kg_microbe.transform_utils.bakta.BaktaTransform method) add_functional_category_node() (kg_microbe.transform_utils.cog.cog.COGTransform method) (kg_microbe.transform_utils.cog.COGTransform method) add_gene_node() (kg_microbe.transform_utils.bakta.bakta.BaktaTransform method) (kg_microbe.transform_utils.bakta.BaktaTransform method) add_go_annotation() (kg_microbe.transform_utils.bakta.bakta.BaktaTransform method) (kg_microbe.transform_utils.bakta.BaktaTransform method) add_group_node() (kg_microbe.transform_utils.cog.cog.COGTransform method) (kg_microbe.transform_utils.cog.COGTransform method) add_kegg_annotation() (kg_microbe.transform_utils.bakta.bakta.BaktaTransform method) (kg_microbe.transform_utils.bakta.BaktaTransform method) add_ko_node() (kg_microbe.transform_utils.kegg.kegg.KEGGTransform method) (kg_microbe.transform_utils.kegg.KEGGTransform method) add_module_node() (kg_microbe.transform_utils.kegg.kegg.KEGGTransform method) (kg_microbe.transform_utils.kegg.KEGGTransform method)

add_organism_node() (kg_microbe.transform_utils.bakta.bakta.BaktaTransform method) (kg_microbe.transform_utils.bakta.BaktaTransform method) add_pathway_node() (kg_microbe.transform_utils.kegg.kegg.KEGGTransform method) (kg_microbe.transform_utils.kegg.KEGGTransform method) add_protein_node() (kg_microbe.transform_utils.bakta.bakta.BaktaTransform method) (kg_microbe.transform_utils.bakta.BaktaTransform method) advance() (kg_microbe.merge_utils.progress.MergeProgress method) alternate_ids (kg_microbe.utils.go_authority.GoTerm attribute) alternative_id() (in module kg_microbe.utils.ingredient_bundle_contract) ancestors() (kg_microbe.utils.ontology_resolution.CategoryAdapter method) annotate() (in module kg_microbe.utils.ner_utils) annotate_graph_stats() (in module kg_microbe.merge_utils.stats_provenance) annotation_document() (kg_microbe.utils.ingredient_bundle.ReviewedIngredientBundle method) annotation_id() (in module kg_microbe.utils.ingredient_bundle_contract) annotation_table() (in module kg_microbe.utils.ingredient_bundle_contract) archive_sha256 (kg_microbe.utils.postprocess_artifacts.ArtifactStatus attribute) ArtifactStatus (class in kg_microbe.utils.postprocess_artifacts) as_row() (kg_microbe.transform_utils.prego.calibration.ScoreHistogram method) assay_edges_generated (kg_microbe.transform_utils.bacdive.BacDiveTransform attribute) assay_nodes_generated (kg_microbe.transform_utils.bacdive.BacDiveTransform attribute) assay_raw_data (kg_microbe.transform_utils.bacdive.BacDiveTransform attribute) assay_target_nodes_generated (kg_microbe.transform_utils.bacdive.BacDiveTransform attribute) assembly_archive() (in module kg_microbe.transform_utils.gtdb.utils) assembly_curie() (in module kg_microbe.transform_utils.gtdb.utils) assert_chebi_version_alignment() (in module kg_microbe.utils.ontology_utils) assert_go_version_alignment() (in module kg_microbe.utils.ontology_utils) assert_ncbitaxon_version_alignment() (in module kg_microbe.utils.ontology_utils) atomic_write() (in module kg_microbe.utils.atomic_io) audit() (kg_microbe.utils.ingredient_bundle.ReviewedIngredientBundle method) authoritative_foodon_category() (in module kg_microbe.utils.foodon_classification) authority_path (kg_microbe.utils.go_authority.GoAuthority attribute) authority_sha256 (kg_microbe.utils.go_authority.GoAuthority attribute)

B

bacdive_record_url() (in module kg_microbe.utils.provenance) BacDiveTransform (class in kg_microbe.transform_utils.bacdive) (class in kg_microbe.transform_utils.bacdive.bacdive) BactoTraitsTransform (class in kg_microbe.transform_utils.bactotraits) (class in kg_microbe.transform_utils.bactotraits.bactotraits) BaktaTransform (class in kg_microbe.transform_utils.bakta) (class in kg_microbe.transform_utils.bakta.bakta) base_rate() (kg_microbe.transform_utils.prego.quality.LabelledEvidence method) baseline() (kg_microbe.transform_utils.prego.quality.GoldStandard method) begin_consumed_inputs() (kg_microbe.transform_utils.ontologies_stubs.ontologies_stubs_transform.OntologiesStubsTransform method) (kg_microbe.transform_utils.ontologies_stubs.OntologiesStubsTransform method) (kg_microbe.transform_utils.transform.Transform method)

begin_dependency_admission() (kg_microbe.transform_utils.transform.Transform method) bind_path() (kg_microbe.merge_utils.source_admission.SourceAdmission method) bind_to_transform() (kg_microbe.utils.ingredient_bundle.ReviewedIngredientBundle method) BiolinkHierarchy (class in kg_microbe.utils.biolink_hierarchy) bounded_file_fingerprint() (in module kg_microbe.utils.transform_fingerprint) build_cutoffs() (in module kg_microbe.transform_utils.prego.calibration) build_ingredient_lookup_bundle() (in module kg_microbe.utils.ingredient_bundle) build_nested_dict() (in module kg_microbe.bactotraits_to_mongo) build_provenance() (in module kg_microbe.merge_utils.artifact_manifest) built (kg_microbe.utils.ontology_utils.DbEnsureResult attribute)

C

cache_is_complete() (in module kg_microbe.utils.atomic_io) canonical_header() (in module kg_microbe.utils.graph_schema) canonical_id (kg_microbe.utils.go_authority.GoResolution attribute) canonical_json() (in module kg_microbe.utils.ingredient_bundle_contract) canonical_mapping_paths() (in module kg_microbe.utils.microbial_trait_mappings) canonical_node_category() (in module kg_microbe.utils.graph_canonicalization) canonical_owner() (kg_microbe.utils.ingredient_bundle.ReviewedIngredientBundle method) capture() (kg_microbe.merge_utils.source_admission.SourceAdmission method) capture_resolution() (kg_microbe.merge_utils.source_admission.SourceAdmission method) capture_tree() (kg_microbe.merge_utils.source_admission.SourceAdmission method) category (kg_microbe.utils.go_authority.GoResolution attribute) CategoryAdapter (class in kg_microbe.utils.ontology_resolution) channel_for_archive() (in module kg_microbe.transform_utils.prego.utils) chebi_categories (kg_microbe.transform_utils.bacdive.BacDiveTransform attribute) (kg_microbe.transform_utils.mediadive.MediaDiveTransform attribute) chebi_category() (in module kg_microbe.utils.ontology_resolution) chebi_labels (kg_microbe.transform_utils.mediadive.MediaDiveTransform attribute) chebi_role_edges (kg_microbe.transform_utils.mediadive.MediaDiveTransform attribute) chebi_roles (kg_microbe.transform_utils.mediadive.MediaDiveTransform attribute) ChebiDbUnavailableError (in module kg_microbe.utils.ontology_utils) check_for_file_existence_in_batch() (in module kg_microbe.utils.download_utils) check_merged_invariants() (in module kg_microbe.merge_utils.invariants) check_string_in_tar() (in module kg_microbe.utils.uniprot_utils) check_wanted_pairs() (in module kg_microbe.utils.unipathways_utils) ChemicalMappingLoader (class in kg_microbe.utils.chemical_mapping_utils) classify_evidence() (in module kg_microbe.transform_utils.prego.utils) classify_mapping_row() (in module kg_microbe.utils.sssom_identity_policy) classify_row() (in module kg_microbe.transform_utils.prego.utils) clean_field_name() (in module kg_microbe.bactotraits_to_mongo) clean_taxon_name() (in module kg_microbe.transform_utils.gtdb.utils) code_fingerprint() (in module kg_microbe.utils.transform_fingerprint) CODE_INPUTS (kg_microbe.transform_utils.metatraits_gtdb.metatraits_gtdb.MetaTraitsGTDBTransform attribute) (kg_microbe.transform_utils.metatraits_gtdb.MetaTraitsGTDBTransform attribute) (kg_microbe.transform_utils.transform.Transform attribute)

COGTransform (class in kg_microbe.transform_utils.cog) (class in kg_microbe.transform_utils.cog.cog) collect_stub_curies() (in module kg_microbe.utils.stub_curie_collection) compact_identifier() (in module kg_microbe.utils.graph_canonicalization) consider (kg_microbe.utils.go_authority.GoResolution attribute) (kg_microbe.utils.go_authority.GoTerm attribute) consolidate_node_categories() (in module kg_microbe.utils.consolidate_categories) consume_bulk_input() (kg_microbe.transform_utils.mediadive.mediadive.MediaDiveTransform method) (kg_microbe.transform_utils.mediadive.MediaDiveTransform method) consume_input() (kg_microbe.transform_utils.transform.Transform method) consume_optional_input() (kg_microbe.transform_utils.transform.Transform method) consumed_input_snapshots (kg_microbe.transform_utils.transform.Transform property) contains() (kg_microbe.transform_utils.prego.quality.GoldStandard method) content_sha256() (in module kg_microbe.utils.ingredient_bundle_contract) contested_deposit_description() (in module kg_microbe.transform_utils.bacdive.emission) contract_resource() (in module kg_microbe.utils.ingredient_bundle_contract) convert_omim_diseases() (in module kg_microbe.utils.uniprot_utils) convert_to_json() (in module kg_microbe.utils.robot_utils) count_raw_predicates() (in module kg_microbe.merge_utils.stats_provenance) covers() (kg_microbe.transform_utils.prego.quality.GoldStandard method) create_df_from_pair() (in module kg_microbe.utils.unipathways_utils) create_field_path() (in module kg_microbe.bactotraits_to_mongo) create_gene_id() (in module kg_microbe.transform_utils.bakta.utils) create_mapping_file() (in module kg_microbe.transform_utils.bakta.create_samn_mapping) create_pool() (in module kg_microbe.utils.uniprot_utils) crosswalk_curie() (in module kg_microbe.transform_utils.microbedecoder.utils) CTDTransform (class in kg_microbe.transform_utils.ctd) (class in kg_microbe.transform_utils.ctd.ctd) cutoff() (kg_microbe.transform_utils.prego.calibration.ScoreHistogram method) cutoff_bin() (kg_microbe.transform_utils.prego.calibration.ScoreHistogram method)

D

DATA_DIR (kg_microbe.transform_utils.transform.Transform attribute) data_fingerprint() (in module kg_microbe.utils.transform_fingerprint) DATA_INPUTS (kg_microbe.transform_utils.bacdive.bacdive.BacDiveTransform attribute) (kg_microbe.transform_utils.bacdive.BacDiveTransform attribute) (kg_microbe.transform_utils.ctd.ctd.CTDTransform attribute) (kg_microbe.transform_utils.ctd.CTDTransform attribute) (kg_microbe.transform_utils.gold.gold.GOLDTransform attribute) (kg_microbe.transform_utils.gold.GOLDTransform attribute) (kg_microbe.transform_utils.gtdb.gtdb.GTDBTransform attribute) (kg_microbe.transform_utils.gtdb.GTDBTransform attribute) (kg_microbe.transform_utils.madin_etal.madin_etal.MadinEtAlTransform attribute) (kg_microbe.transform_utils.madin_etal.MadinEtAlTransform attribute) (kg_microbe.transform_utils.mediadive.mediadive.MediaDiveTransform attribute) (kg_microbe.transform_utils.mediadive.MediaDiveTransform attribute) (kg_microbe.transform_utils.metatraits.metatraits.MetaTraitsTransform attribute) (kg_microbe.transform_utils.metatraits.MetaTraitsTransform attribute) (kg_microbe.transform_utils.metatraits_gtdb.metatraits_gtdb.MetaTraitsGTDBTransform attribute) (kg_microbe.transform_utils.metatraits_gtdb.MetaTraitsGTDBTransform attribute) (kg_microbe.transform_utils.microbedecoder.microbedecoder.MicrobeDecoderTransform attribute) (kg_microbe.transform_utils.ontologies.ontologies_transform.OntologiesTransform attribute) (kg_microbe.transform_utils.ontologies.OntologiesTransform attribute) (kg_microbe.transform_utils.ontologies_stubs.ontologies_stubs_transform.OntologiesStubsTransform attribute) (kg_microbe.transform_utils.ontologies_stubs.OntologiesStubsTransform attribute) (kg_microbe.transform_utils.transform.Transform attribute) DbEnsureResult (class in kg_microbe.utils.ontology_utils) declared_data_inputs() (in module kg_microbe.utils.transform_fingerprint) decompress() (kg_microbe.transform_utils.ontologies.ontologies_transform.OntologiesTransform method) (kg_microbe.transform_utils.ontologies.OntologiesTransform method) DEFAULT_INPUT_DIR (kg_microbe.transform_utils.mediadive.mediadive.MediaDiveTransform attribute) (kg_microbe.transform_utils.mediadive.MediaDiveTransform attribute) (kg_microbe.transform_utils.transform.Transform attribute)

DEFAULT_OUTPUT_DIR (kg_microbe.transform_utils.transform.Transform attribute) definition (kg_microbe.utils.go_authority.GoResolution attribute) (kg_microbe.utils.go_authority.GoTerm attribute) DEPOSIT_CONFLICT_HEADER (in module kg_microbe.transform_utils.bacdive.emission) deposit_conflict_rows() (in module kg_microbe.transform_utils.bacdive.emission) deprecated (kg_microbe.utils.go_authority.GoResolution attribute) (kg_microbe.utils.go_authority.GoTerm attribute) deprecated_metpo_terms() (in module kg_microbe.utils.metpo_liveness) detail (kg_microbe.utils.postprocess_artifacts.ArtifactStatus attribute) DisbiomeTransform (class in kg_microbe.transform_utils.disbiome) (class in kg_microbe.transform_utils.disbiome.disbiome) discovered_data_inputs() (kg_microbe.transform_utils.metatraits.metatraits.MetaTraitsTransform class method) (kg_microbe.transform_utils.metatraits.MetaTraitsTransform class method) disposition (kg_microbe.utils.go_authority.GoResolution attribute) download() (in module kg_microbe) (in module kg_microbe.download) download_detailed_media() (in module kg_microbe.utils.mediadive_bulk_download) download_from_api() (in module kg_microbe.utils.download_utils) download_from_yaml() (in module kg_microbe.utils.download_utils) download_mediadive_bulk() (in module kg_microbe.utils.mediadive_bulk_download) download_medium_strains() (in module kg_microbe.utils.mediadive_bulk_download) download_yaml_and_get_json() (kg_microbe.transform_utils.mediadive.mediadive.MediaDiveTransform method) (kg_microbe.transform_utils.mediadive.MediaDiveTransform method) drop_duplicates() (in module kg_microbe.utils.pandas_utils) drop_stale() (in module kg_microbe.utils.download_manifest) DummyTqdm (class in kg_microbe.utils.dummy_tqdm) dump_ont_nodes_from() (in module kg_microbe.utils.pandas_utils)

E

edge_metadata_for() (in module kg_microbe.transform_utils.prego.utils) elastic_search_query() (in module kg_microbe.utils.download_utils) enrich_node() (kg_microbe.utils.ingredient_bundle.ReviewedIngredientBundle method) enrichment_by_window() (in module kg_microbe.transform_utils.prego.quality) entailed_by_every_claim() (in module kg_microbe.transform_utils.bacdive.emission) entity_to_curie() (in module kg_microbe.transform_utils.prego.utils) ENVIRONMENT_ID_CORRECTIONS_FILE (in module kg_microbe.transform_utils.madin_etal.madin_etal) establish_transitive_relationship() (in module kg_microbe.utils.pandas_utils) establish_transitive_relationship_multiple() (in module kg_microbe.utils.pandas_utils)

estimate_retention() (in module kg_microbe.transform_utils.prego.calibration) EXPECTED_STUB_PATTERNS (in module kg_microbe.merge_utils.invariants) EXPECTED_STUB_PREFIXES (in module kg_microbe.merge_utils.invariants) expected_stub_reason() (in module kg_microbe.merge_utils.invariants) extract_accession_type() (in module kg_microbe.transform_utils.gtdb.utils) extract_compounds_from_media() (in module kg_microbe.utils.mediadive_bulk_download) extract_convert_to_json() (in module kg_microbe.utils.robot_utils) extract_ko_ids_from_list() (in module kg_microbe.transform_utils.kegg.utils) extract_samn_from_path() (in module kg_microbe.transform_utils.bakta.utils) extract_solutions_from_media() (in module kg_microbe.utils.mediadive_bulk_download)

F

FatalOntologyError fetch_taxon_page() (in module kg_microbe.transform_utils.lpsn_api.lpsn_api) finalization_inputs_current() (in module kg_microbe.utils.transform_fingerprint) finalize() (kg_microbe.transform_utils.transform.Transform method) finalize_selected_sources() (in module kg_microbe.utils.source_finalization) finalize_source() (in module kg_microbe.utils.source_finalization) find_bakta_tsv() (in module kg_microbe.transform_utils.bakta.utils) find_biolink_equivalent_parent() (kg_microbe.utils.mapping_file_utils.MetpoTreeNode method) find_chebi_by_formula() (in module kg_microbe.utils.chemical_mapping_utils) (kg_microbe.utils.chemical_mapping_utils.ChemicalMappingLoader method) find_chebi_by_name() (in module kg_microbe.utils.chemical_mapping_utils) (kg_microbe.utils.chemical_mapping_utils.ChemicalMappingLoader method) find_chebi_by_xref() (in module kg_microbe.utils.chemical_mapping_utils) (kg_microbe.utils.chemical_mapping_utils.ChemicalMappingLoader method) find_multi_parent_strains() (in module kg_microbe.merge_utils.invariants) find_stub_nodes() (in module kg_microbe.merge_utils.invariants)

find_synonym_node() (kg_microbe.utils.mapping_file_utils.MetpoTreeNode method) FINGERPRINT_FILE (in module kg_microbe.utils.transform_fingerprint) FINGERPRINT_VERSION (in module kg_microbe.utils.transform_fingerprint) fix_list_field() (in module kg_microbe.utils.fix_list_representations) fix_tsv() (in module kg_microbe.utils.fix_list_representations) flat_channel_star() (in module kg_microbe.transform_utils.prego.calibration) fold_enrichment() (in module kg_microbe.transform_utils.prego.quality) foodon_category() (in module kg_microbe.utils.ontology_resolution) foodon_dispositions() (in module kg_microbe.utils.foodon_classification) foodon_organism_classes() (in module kg_microbe.utils.foodon_classification) format_citation() (in module kg_microbe.transform_utils.microbedecoder.utils) format_organism_report() (in module kg_microbe.query_utils) (in module kg_microbe.query_utils.utils) forward_fill_headers() (in module kg_microbe.bactotraits_to_mongo) from_ingredient_lookup_bundle() (kg_microbe.utils.chemical_mapping_utils.ChemicalMappingLoader class method) from_statements() (kg_microbe.utils.go_authority.GoAuthority class method)

G

generate_assay_entity_edges() (in module kg_microbe.utils.mapping_file_utils) generate_assay_entity_nodes() (in module kg_microbe.utils.mapping_file_utils) generate_assay_nodes() (in module kg_microbe.utils.mapping_file_utils) get_all_samn_directories() (in module kg_microbe.transform_utils.bakta.utils) get_all_samn_ids() (in module kg_microbe.transform_utils.bakta.create_samn_mapping) get_ancestors() (kg_microbe.utils.biolink_hierarchy.BiolinkHierarchy method) get_biolink_category_for_go() (in module kg_microbe.transform_utils.bakta.utils) get_biolink_predicate_for_go() (in module kg_microbe.transform_utils.bakta.utils) get_canonical_name() (in module kg_microbe.utils.chemical_mapping_utils) (kg_microbe.utils.chemical_mapping_utils.ChemicalMappingLoader method) get_category() (in module kg_microbe.utils.chemical_mapping_utils) (kg_microbe.utils.chemical_mapping_utils.ChemicalMappingLoader method) get_category_group_name() (in module kg_microbe.transform_utils.cog.utils) get_chebi_adapter() (in module kg_microbe.utils.ontology_utils) get_chebi_category() (in module kg_microbe.utils.ontology_utils) get_compounds_of_solution() (kg_microbe.transform_utils.mediadive.mediadive.MediaDiveTransform method) (kg_microbe.transform_utils.mediadive.MediaDiveTransform method) get_curie_id() (in module kg_microbe.utils.validation_utils) get_curie_prefix() (in module kg_microbe.utils.validation_utils) get_depth() (kg_microbe.utils.biolink_hierarchy.BiolinkHierarchy method) get_disease_direction() (kg_microbe.transform_utils.wallen_etal.wallen_etal.WallenEtAlTransform method) (kg_microbe.transform_utils.wallen_etal.WallenEtAlTransform method) get_ec_adapter() (in module kg_microbe.utils.ontology_utils) get_foodon_category() (in module kg_microbe.utils.ontology_utils) get_formula() (in module kg_microbe.utils.chemical_mapping_utils) (kg_microbe.utils.chemical_mapping_utils.ChemicalMappingLoader method) get_go_adapter() (in module kg_microbe.utils.ontology_utils) get_go_aspect() (in module kg_microbe.transform_utils.bakta.utils) (in module kg_microbe.utils.ontology_utils) get_go_category_by_aspect() (in module kg_microbe.utils.ontology_utils) get_go_category_trees() (in module kg_microbe.utils.uniprot_utils) get_go_relation_and_obsolete_terms() (in module kg_microbe.utils.uniprot_utils) get_hydrate_equivalents() (in module kg_microbe.utils.chemical_mapping_utils) get_identifier_annotation_owners() (kg_microbe.utils.chemical_mapping_utils.ChemicalMappingLoader method) get_ingredients_overlap() (in module kg_microbe.utils.pandas_utils) get_jobs() (in module kg_microbe.utils.download_utils) get_json_from_api() (in module kg_microbe.utils.mediadive_bulk_download) get_json_object() (kg_microbe.transform_utils.mediadive.mediadive.MediaDiveTransform method) (kg_microbe.transform_utils.mediadive.MediaDiveTransform method) get_kegg_ko_details() (in module kg_microbe.transform_utils.kegg.utils) get_kegg_ko_list() (in module kg_microbe.transform_utils.kegg.utils) get_key_from_value() (in module kg_microbe.utils.unipathways_utils) get_label() (in module kg_microbe.utils.oak_utils) get_mapping_load_audit() (in module kg_microbe.utils.chemical_mapping_utils) get_media_composition() (in module kg_microbe.query_utils.organism_queries) get_media_preferences() (in module kg_microbe.query_utils.organism_queries)

get_most_specific_category() (kg_microbe.utils.biolink_hierarchy.BiolinkHierarchy method) get_ncbitaxon_adapter() (in module kg_microbe.utils.ontology_utils) get_ncbitaxon_category() (in module kg_microbe.utils.ontology_utils) get_ncbitaxon_id() (kg_microbe.transform_utils.bakta.bakta.BaktaTransform method) (kg_microbe.transform_utils.bakta.BaktaTransform method) get_node_enrichment() (in module kg_microbe.utils.chemical_mapping_utils) (kg_microbe.utils.chemical_mapping_utils.ChemicalMappingLoader method) get_nodes_and_edges() (in module kg_microbe.utils.uniprot_utils) get_ontology_adapter() (in module kg_microbe.utils.ontology_utils) get_or_create_database() (in module kg_microbe.query_utils) (in module kg_microbe.query_utils.duckdb_loader) get_organism_id() (kg_microbe.transform_utils.bakta.bakta.BaktaTransform method) (kg_microbe.transform_utils.bakta.BaktaTransform method) get_organism_traits() (in module kg_microbe.query_utils.organism_queries) get_parents() (in module kg_microbe.utils.chemical_mapping_utils) (kg_microbe.utils.chemical_mapping_utils.ChemicalMappingLoader method) get_pato_category() (in module kg_microbe.utils.ontology_utils) get_protein_id() (in module kg_microbe.transform_utils.bakta.utils) get_solution_recipe_occurrences() (kg_microbe.transform_utils.mediadive.mediadive.MediaDiveTransform method) (kg_microbe.transform_utils.mediadive.MediaDiveTransform method) get_strain_info() (in module kg_microbe.query_utils.organism_queries) get_synonyms() (in module kg_microbe.utils.chemical_mapping_utils) (kg_microbe.utils.chemical_mapping_utils.ChemicalMappingLoader method) get_uberon_category() (in module kg_microbe.utils.ontology_utils) get_unipathways_prefix() (in module kg_microbe.utils.unipathways_utils) get_uniprot_values_organism() (in module kg_microbe.utils.download_utils) get_xrefs() (in module kg_microbe.utils.chemical_mapping_utils) (kg_microbe.utils.chemical_mapping_utils.ChemicalMappingLoader method) git_commit() (in module kg_microbe.merge_utils.stats_provenance) go_category_for_namespace() (in module kg_microbe.utils.ontology_resolution) go_category_for_type() (in module kg_microbe.transform_utils.prego.utils) go_category_trees_is_complete() (in module kg_microbe.utils.uniprot_utils) GoAuthority (class in kg_microbe.utils.go_authority) GOLD_NODES_FILE (in module kg_microbe.transform_utils.gold.gold) GoldStandard (class in kg_microbe.transform_utils.prego.quality) GOLDTransform (class in kg_microbe.transform_utils.gold) (class in kg_microbe.transform_utils.gold.gold) GoReferenceError GoResolution (class in kg_microbe.utils.go_authority) GoTerm (class in kg_microbe.utils.go_authority) graph_rows() (in module kg_microbe.utils.source_finalization) GTDB_NCBI_POOLING_REPORT (in module kg_microbe.transform_utils.constants) gtdb_preferred_ncbi (kg_microbe.transform_utils.metatraits_gtdb.MetaTraitsGTDBTransform attribute) gtdb_to_ncbi (kg_microbe.transform_utils.metatraits_gtdb.MetaTraitsGTDBTransform attribute) GTDBTransform (class in kg_microbe.transform_utils.gtdb) (class in kg_microbe.transform_utils.gtdb.gtdb)

H

has_data_rows() (in module kg_microbe.utils.atomic_io)

has_optional_inputs() (in module kg_microbe.utils.optional_consumed_inputs)

I

identifier (kg_microbe.utils.go_authority.GoTerm attribute) identifier_claims() (kg_microbe.utils.ingredient_bundle.ReviewedIngredientBundle method) identifier_owners() (kg_microbe.utils.ingredient_bundle.ReviewedIngredientBundle method) indeterminate_traits_file (kg_microbe.transform_utils.metatraits.metatraits.MetaTraitsTransform property) (kg_microbe.transform_utils.metatraits.MetaTraitsTransform property) ingredient_authority_label() (in module kg_microbe.utils.ingredient_identity) ingredient_cas_annotations() (in module kg_microbe.utils.ingredient_identity) ingredient_case_sensitive_name_scope() (in module kg_microbe.utils.ingredient_identity) ingredient_graph_id() (in module kg_microbe.utils.ingredient_kgx) ingredient_hydration_compatible() (in module kg_microbe.utils.ingredient_identity) ingredient_identity_policy() (in module kg_microbe.utils.ingredient_identity) ingredient_kgx_profile() (in module kg_microbe.utils.ingredient_kgx) ingredient_mapping_allowed() (in module kg_microbe.utils.ingredient_identity) ingredient_name_scopes() (in module kg_microbe.utils.ingredient_identity) ingredient_name_target() (in module kg_microbe.utils.ingredient_identity)

ingredient_xref_allowed() (in module kg_microbe.utils.ingredient_identity) initialize_robot() (in module kg_microbe.utils.robot_utils) inspect_artifact() (in module kg_microbe.utils.postprocess_artifacts) invalid_cas_identifier() (in module kg_microbe.utils.cas) is_continuous_channel() (in module kg_microbe.transform_utils.prego.calibration) is_empty_cell() (in module kg_microbe.transform_utils.microbedecoder.utils) is_float() (in module kg_microbe.utils.uniprot_utils) is_monotone_increasing() (in module kg_microbe.transform_utils.prego.quality) is_more_specific() (kg_microbe.utils.biolink_hierarchy.BiolinkHierarchy method) isolation_source_mappings (kg_microbe.transform_utils.bacdive.BacDiveTransform attribute) item_publications() (in module kg_microbe.transform_utils.bacdive.references) iter_calibration_rows() (in module kg_microbe.transform_utils.prego.calibration) iter_database_pairs() (in module kg_microbe.transform_utils.prego.utils) iter_dictionary_entities() (in module kg_microbe.transform_utils.prego.utils) iter_dictionary_names() (in module kg_microbe.transform_utils.prego.utils) iter_metabolism_columns() (in module kg_microbe.transform_utils.microbedecoder.utils)

J

json_scalar() (in module kg_microbe.utils.ingredient_kgx)

K

keep_row() (in module kg_microbe.transform_utils.prego.calibration) KEGGTransform (class in kg_microbe.transform_utils.kegg) (class in kg_microbe.transform_utils.kegg.kegg) KeptTarget (class in kg_microbe.utils.ontology_utils) kg_microbe module kg_microbe.bactotraits_to_mongo module kg_microbe.download module kg_microbe.merge_utils module kg_microbe.merge_utils.artifact_manifest module kg_microbe.merge_utils.external_node_closure module kg_microbe.merge_utils.invariants module kg_microbe.merge_utils.local_context module kg_microbe.merge_utils.merge_kg module kg_microbe.merge_utils.progress module kg_microbe.merge_utils.source_admission module kg_microbe.merge_utils.source_freshness module kg_microbe.merge_utils.stats_provenance module kg_microbe.query module kg_microbe.query_utils module kg_microbe.query_utils.duckdb_loader module kg_microbe.query_utils.organism_queries module kg_microbe.query_utils.utils module kg_microbe.run module kg_microbe.transform module kg_microbe.transform_utils module kg_microbe.transform_utils.bacdive module kg_microbe.transform_utils.bacdive.bacdive module kg_microbe.transform_utils.bacdive.emission module kg_microbe.transform_utils.bacdive.references module kg_microbe.transform_utils.bactotraits module kg_microbe.transform_utils.bactotraits.bactotraits module kg_microbe.transform_utils.bakta module kg_microbe.transform_utils.bakta.bakta module kg_microbe.transform_utils.bakta.create_samn_mapping module kg_microbe.transform_utils.bakta.utils module kg_microbe.transform_utils.cog module kg_microbe.transform_utils.cog.cog module kg_microbe.transform_utils.cog.utils module kg_microbe.transform_utils.constants module kg_microbe.transform_utils.ctd module kg_microbe.transform_utils.ctd.ctd module kg_microbe.transform_utils.disbiome module kg_microbe.transform_utils.disbiome.disbiome module kg_microbe.transform_utils.example_transform module kg_microbe.transform_utils.gold module kg_microbe.transform_utils.gold.gold module kg_microbe.transform_utils.gtdb module kg_microbe.transform_utils.gtdb.gtdb module kg_microbe.transform_utils.gtdb.utils module kg_microbe.transform_utils.kegg module kg_microbe.transform_utils.kegg.kegg module kg_microbe.transform_utils.kegg.utils module kg_microbe.transform_utils.lpsn module kg_microbe.transform_utils.lpsn.lpsn module kg_microbe.transform_utils.lpsn_api module kg_microbe.transform_utils.lpsn_api.lpsn_api module kg_microbe.transform_utils.madin_etal module kg_microbe.transform_utils.madin_etal.madin_etal module kg_microbe.transform_utils.mediadive module kg_microbe.transform_utils.mediadive.bulk_inputs module kg_microbe.transform_utils.mediadive.mediadive module kg_microbe.transform_utils.metatraits module kg_microbe.transform_utils.metatraits.io module kg_microbe.transform_utils.metatraits.metatraits module kg_microbe.transform_utils.metatraits_gtdb module kg_microbe.transform_utils.metatraits_gtdb.metatraits_gtdb module kg_microbe.transform_utils.microbedecoder module kg_microbe.transform_utils.microbedecoder.microbedecoder module kg_microbe.transform_utils.microbedecoder.utils module kg_microbe.transform_utils.mim_ingredients module kg_microbe.transform_utils.mim_ingredients.mim_ingredients module

kg_microbe.transform_utils.ontologies module kg_microbe.transform_utils.ontologies.ontologies_transform module kg_microbe.transform_utils.ontologies_stubs module kg_microbe.transform_utils.ontologies_stubs.ncit_category_projection module kg_microbe.transform_utils.ontologies_stubs.ontologies_stubs_transform module kg_microbe.transform_utils.prego module kg_microbe.transform_utils.prego.calibration module kg_microbe.transform_utils.prego.prego module kg_microbe.transform_utils.prego.quality module kg_microbe.transform_utils.prego.utils module kg_microbe.transform_utils.rhea_mappings module kg_microbe.transform_utils.rhea_mappings.rhea_mappings module kg_microbe.transform_utils.transform module kg_microbe.transform_utils.uniprot_functional_microbes module kg_microbe.transform_utils.uniprot_functional_microbes.uniprot_functional_microbes module kg_microbe.transform_utils.uniprot_human module kg_microbe.transform_utils.uniprot_human.uniprot_human module kg_microbe.transform_utils.wallen_etal module kg_microbe.transform_utils.wallen_etal.wallen_etal module kg_microbe.utils module kg_microbe.utils.atomic_io module kg_microbe.utils.biolink_hierarchy module kg_microbe.utils.biolink_model module kg_microbe.utils.cas module kg_microbe.utils.chemical_mapping_utils module kg_microbe.utils.consolidate_categories module kg_microbe.utils.download_manifest module kg_microbe.utils.download_utils module kg_microbe.utils.dummy_tqdm module kg_microbe.utils.external_identifiers module kg_microbe.utils.fix_list_representations module kg_microbe.utils.foodon_classification module kg_microbe.utils.go_authority module kg_microbe.utils.graph_canonicalization module kg_microbe.utils.graph_schema module kg_microbe.utils.ingredient_bundle module kg_microbe.utils.ingredient_bundle_contract module kg_microbe.utils.ingredient_identity module kg_microbe.utils.ingredient_kgx module kg_microbe.utils.ingredient_scope module kg_microbe.utils.isolation_source_mapping_utils module kg_microbe.utils.lpsn_utils module kg_microbe.utils.mapping_file_utils module kg_microbe.utils.mediadive_bulk_download module kg_microbe.utils.metpo_liveness module kg_microbe.utils.metpo_predicates module kg_microbe.utils.microbial_trait_mappings module kg_microbe.utils.ner_utils module kg_microbe.utils.oak_utils module kg_microbe.utils.ontology_resolution module kg_microbe.utils.ontology_utils module kg_microbe.utils.optional_consumed_inputs module kg_microbe.utils.pandas_utils module kg_microbe.utils.postprocess_artifacts module kg_microbe.utils.provenance module kg_microbe.utils.review_claims module kg_microbe.utils.robot_utils module kg_microbe.utils.sanitize_curies module kg_microbe.utils.source_finalization module kg_microbe.utils.sssom_identity_policy module kg_microbe.utils.string_coding module kg_microbe.utils.stub_curie_collection module kg_microbe.utils.transform_fingerprint module kg_microbe.utils.tsv_io module kg_microbe.utils.unipathways_utils module kg_microbe.utils.uniprot_utils module kg_microbe.utils.validation_utils module knowledge_source_tokens() (in module kg_microbe.utils.provenance) KNOWN_DEPRECATED (in module kg_microbe.utils.metpo_liveness)

L

label (kg_microbe.utils.go_authority.GoResolution attribute) (kg_microbe.utils.go_authority.GoTerm attribute) label() (kg_microbe.transform_utils.prego.quality.LabelledEvidence method) (kg_microbe.utils.ontology_resolution.CategoryAdapter method) LabelledEvidence (class in kg_microbe.transform_utils.prego.quality) LazyTransform (class in kg_microbe.transform) lift() (in module kg_microbe.transform_utils.prego.quality) LINE_TERMINATOR (in module kg_microbe.utils.tsv_io) link_target (kg_microbe.utils.ontology_utils.KeptTarget attribute) load_and_merge() (in module kg_microbe.merge_utils) (in module kg_microbe.merge_utils.merge_kg) load_assay_kit_mappings() (in module kg_microbe.utils.mapping_file_utils) load_assembly_aliases() (in module kg_microbe.utils.external_identifiers) load_basic_media_list() (in module kg_microbe.utils.mediadive_bulk_download) load_doid_to_mondo() (in module kg_microbe.transform_utils.prego.utils) load_existing_mapping() (in module kg_microbe.transform_utils.bakta.create_samn_mapping) load_go_authority() (in module kg_microbe.utils.go_authority)

load_ingredient_lookup_bundle() (in module kg_microbe.utils.ingredient_bundle) load_isolation_source_mappings() (in module kg_microbe.utils.isolation_source_mapping_utils) load_kegg_ko_details_from_cache() (in module kg_microbe.transform_utils.kegg.utils) load_metpo_enzyme_mappings() (in module kg_microbe.utils.mapping_file_utils) load_metpo_mappings() (in module kg_microbe.utils.mapping_file_utils) load_metpo_metabolite_production_mappings() (in module kg_microbe.utils.mapping_file_utils) load_metpo_metabolite_utilization_mappings() (in module kg_microbe.utils.mapping_file_utils) load_microbial_trait_mappings() (in module kg_microbe.utils.microbial_trait_mappings) load_samn_to_ncbitaxon_mapping() (in module kg_microbe.transform_utils.bakta.utils) load_taxid_merges() (in module kg_microbe.utils.external_identifiers) load_unified_mappings() (in module kg_microbe.utils.chemical_mapping_utils) load_valid_kgm_terms() (in module kg_microbe.utils.validation_utils) local_prefix_context() (in module kg_microbe.merge_utils.local_context) LPSN_CORRECT_NAME (in module kg_microbe.utils.lpsn_utils) LPSN_GENUS_COLUMN (in module kg_microbe.transform_utils.microbedecoder.utils) LPSN_MAX_SYNONYM_HOPS (in module kg_microbe.utils.lpsn_utils) LPSNAPITransform (class in kg_microbe.transform_utils.lpsn_api.lpsn_api) LPSNTransform (class in kg_microbe.transform_utils.lpsn.lpsn)

M

MadinEtAlTransform (class in kg_microbe.transform_utils.madin_etal) (class in kg_microbe.transform_utils.madin_etal.madin_etal) main() (in module kg_microbe.bactotraits_to_mongo) (in module kg_microbe.transform_utils.bakta.create_samn_mapping) (in module kg_microbe.utils.consolidate_categories) (in module kg_microbe.utils.fix_list_representations) MANIFEST_NAME (in module kg_microbe.utils.download_manifest) manifest_path() (in module kg_microbe.utils.download_manifest) mappings() (kg_microbe.utils.ingredient_bundle.ReviewedIngredientBundle method) MEASUREMENT_TRAITS (kg_microbe.transform_utils.metatraits.metatraits.MetaTraitsTransform attribute) (kg_microbe.transform_utils.metatraits.MetaTraitsTransform attribute) MediaDiveTransform (class in kg_microbe.transform_utils.mediadive) (class in kg_microbe.transform_utils.mediadive.mediadive) members (kg_microbe.utils.postprocess_artifacts.ArtifactStatus attribute) merge() (in module kg_microbe.merge_utils.merge_kg) merge_dicts() (in module kg_microbe.bactotraits_to_mongo) merge_phase() (in module kg_microbe.merge_utils.progress) MergeProgress (class in kg_microbe.merge_utils.progress) METAMODEL_NODE_PREFIXES (in module kg_microbe.transform_utils.ontologies.ontologies_transform) MetaTraitsGTDBTransform (class in kg_microbe.transform_utils.metatraits_gtdb) (class in kg_microbe.transform_utils.metatraits_gtdb.metatraits_gtdb) MetaTraitsTransform (class in kg_microbe.transform_utils.metatraits) (class in kg_microbe.transform_utils.metatraits.metatraits) metpo_json_path() (in module kg_microbe.utils.metpo_liveness) MetpoTreeNode (class in kg_microbe.utils.mapping_file_utils) MicrobeDecoderTransform (class in kg_microbe.transform_utils.microbedecoder.microbedecoder) migrate_markers() (in module kg_microbe.utils.transform_fingerprint) MIMIngredientsTransform (class in kg_microbe.transform_utils.mim_ingredients.mim_ingredients) mirror_to_bucket() (in module kg_microbe.utils.download_utils) module 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_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.bacdive kg_microbe.transform_utils.bacdive.emission kg_microbe.transform_utils.bacdive.references 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.gold 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.mediadive 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.microbedecoder 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.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.rhea_mappings 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.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.fix_list_representations kg_microbe.utils.foodon_classification kg_microbe.utils.go_authority kg_microbe.utils.graph_canonicalization kg_microbe.utils.graph_schema kg_microbe.utils.ingredient_bundle kg_microbe.utils.ingredient_bundle_contract 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.lpsn_utils kg_microbe.utils.mapping_file_utils kg_microbe.utils.mediadive_bulk_download kg_microbe.utils.metpo_liveness kg_microbe.utils.metpo_predicates kg_microbe.utils.microbial_trait_mappings kg_microbe.utils.ner_utils kg_microbe.utils.oak_utils 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.provenance kg_microbe.utils.review_claims kg_microbe.utils.robot_utils kg_microbe.utils.sanitize_curies kg_microbe.utils.source_finalization 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.unipathways_utils kg_microbe.utils.uniprot_utils kg_microbe.utils.validation_utils query_utils query_utils.query tests tests.test_transform_class

N

NAMED_THING_CATEGORY (in module kg_microbe.merge_utils.invariants) namespace (kg_microbe.utils.go_authority.GoResolution attribute) (kg_microbe.utils.go_authority.GoTerm attribute) native_contract() (in module kg_microbe.transform_utils.ontologies_stubs.ncit_category_projection) ncbitaxon_category() (in module kg_microbe.utils.ontology_resolution) ncbitaxon_fallback_cache (kg_microbe.transform_utils.bacdive.BacDiveTransform attribute) ncbitaxon_labels (kg_microbe.transform_utils.bacdive.BacDiveTransform attribute) ncbitaxon_name_to_id (kg_microbe.transform_utils.bacdive.BacDiveTransform attribute) (kg_microbe.transform_utils.metatraits.MetaTraitsTransform attribute) (kg_microbe.transform_utils.metatraits_gtdb.MetaTraitsGTDBTransform attribute)

ncbitaxon_synonyms (kg_microbe.transform_utils.bacdive.BacDiveTransform attribute) node_fields() (kg_microbe.utils.go_authority.GoResolution method) normalize_biolink_category() (in module kg_microbe.utils.mapping_file_utils) normalize_chemical_primes() (in module kg_microbe.utils.chemical_mapping_utils) normalize_go_bundle() (in module kg_microbe.utils.go_authority) normalize_isolation_source_label() (in module kg_microbe.utils.isolation_source_mapping_utils) normalize_name() (in module kg_microbe.utils.chemical_mapping_utils)

O

occurrence_id() (in module kg_microbe.utils.ingredient_bundle_contract) occurrences() (kg_microbe.utils.ingredient_bundle.ReviewedIngredientBundle method) OntologiesStubsTransform (class in kg_microbe.transform_utils.ontologies_stubs) (class in kg_microbe.transform_utils.ontologies_stubs.ontologies_stubs_transform) OntologiesTransform (class in kg_microbe.transform_utils.ontologies) (class in kg_microbe.transform_utils.ontologies.ontologies_transform) ontology_db_path() (in module kg_microbe.utils.ontology_utils) ONTOLOGY_KNOWLEDGE_SOURCES (kg_microbe.transform_utils.ontologies.ontologies_transform.OntologiesTransform attribute) (kg_microbe.transform_utils.ontologies.OntologiesTransform attribute) OntologyDbUnavailableError OntologyVersionMismatchError

open_jsonl() (in module kg_microbe.transform_utils.metatraits.io) open_maybe_gzipped() (in module kg_microbe.transform_utils.metatraits.io) OPTIONAL_CONSUMED_INPUTS (kg_microbe.transform_utils.metatraits.metatraits.MetaTraitsTransform attribute) (kg_microbe.transform_utils.metatraits.MetaTraitsTransform attribute) (kg_microbe.transform_utils.transform.Transform attribute) optional_consumed_inputs (kg_microbe.transform_utils.transform.Transform property) optional_input_paths() (in module kg_microbe.utils.optional_consumed_inputs) OPTIONAL_RAW_CONSUMED_INPUTS (kg_microbe.transform_utils.mediadive.mediadive.MediaDiveTransform attribute) (kg_microbe.transform_utils.mediadive.MediaDiveTransform attribute) (kg_microbe.transform_utils.transform.Transform attribute) organism_classes() (in module kg_microbe.utils.foodon_classification) original_id (kg_microbe.utils.go_authority.GoResolution attribute)

P

parse() (kg_microbe.transform_utils.ontologies.ontologies_transform.OntologiesTransform method) (kg_microbe.transform_utils.ontologies.OntologiesTransform method) parse_bactotraits_to_mongo() (in module kg_microbe.bactotraits_to_mongo) parse_bakta_tsv() (in module kg_microbe.transform_utils.bakta.utils) parse_binding_site() (in module kg_microbe.utils.uniprot_utils) parse_cog_definitions() (in module kg_microbe.transform_utils.cog.utils) parse_dbxrefs() (in module kg_microbe.transform_utils.bakta.utils) parse_disease() (in module kg_microbe.utils.uniprot_utils) parse_ec() (in module kg_microbe.utils.uniprot_utils) parse_functional_categories() (in module kg_microbe.transform_utils.cog.utils) parse_gene() (in module kg_microbe.utils.uniprot_utils) parse_go_entry() (in module kg_microbe.utils.uniprot_utils) parse_kegg_entry() (in module kg_microbe.transform_utils.kegg.utils) parse_kegg_ko_list_file() (in module kg_microbe.transform_utils.kegg.utils) parse_list_representation() (in module kg_microbe.utils.fix_list_representations) parse_load_config() (in module kg_microbe.merge_utils) (in module kg_microbe.merge_utils.merge_kg) parse_ncbitaxon_json() (in module kg_microbe.utils.download_utils) parse_query_yaml() (in module kg_microbe.query) parse_response() (in module kg_microbe.utils.download_utils) parse_rhea_entry() (in module kg_microbe.utils.uniprot_utils) parse_taxon_page() (in module kg_microbe.transform_utils.lpsn_api.lpsn_api) parse_taxonomy_string() (in module kg_microbe.transform_utils.gtdb.utils) parse_url() (in module kg_microbe.utils.download_utils) parse_value() (in module kg_microbe.bactotraits_to_mongo) pass_through() (kg_microbe.transform_utils.transform.Transform method) path (kg_microbe.utils.postprocess_artifacts.ArtifactStatus attribute) pathogenicity_mappings (kg_microbe.transform_utils.bacdive.BacDiveTransform attribute)

pato_category() (in module kg_microbe.utils.ontology_resolution) payload_sha256() (in module kg_microbe.utils.review_claims) phenotype_routing (kg_microbe.transform_utils.bacdive.BacDiveTransform attribute) policy_parity() (kg_microbe.utils.ingredient_bundle.ReviewedIngredientBundle method) post_process() (kg_microbe.transform_utils.ontologies.ontologies_transform.OntologiesTransform method) (kg_microbe.transform_utils.ontologies.OntologiesTransform method) precision_by_window() (in module kg_microbe.transform_utils.prego.quality) PREDICATE_SEMANTICS_KEY (in module kg_microbe.utils.chemical_mapping_utils) PregoTransform (class in kg_microbe.transform_utils.prego.prego) prepare_go_dictionary() (in module kg_microbe.utils.uniprot_utils) prepare_kgx() (in module kg_microbe.utils.biolink_model) prepare_mondo_dictionary() (in module kg_microbe.utils.uniprot_utils) prev_path (kg_microbe.utils.ontology_utils.KeptTarget attribute) primary_source_and_publications() (in module kg_microbe.utils.provenance) process_and_decode_label() (in module kg_microbe.utils.string_coding) process_gene() (kg_microbe.transform_utils.bakta.bakta.BaktaTransform method) (kg_microbe.transform_utils.bakta.BaktaTransform method) process_genome() (kg_microbe.transform_utils.bakta.bakta.BaktaTransform method) (kg_microbe.transform_utils.bakta.BaktaTransform method) process_lines() (in module kg_microbe.utils.uniprot_utils) producer_native_inputs (kg_microbe.transform_utils.mediadive.mediadive.MediaDiveTransform property) (kg_microbe.transform_utils.mediadive.MediaDiveTransform property) product_id() (in module kg_microbe.utils.ingredient_bundle_contract) products() (kg_microbe.utils.ingredient_bundle.ReviewedIngredientBundle method) profile_metadata() (in module kg_microbe.utils.ingredient_scope) project_category() (in module kg_microbe.transform_utils.ontologies_stubs.ncit_category_projection) project_ingredient_context() (in module kg_microbe.transform_utils.mim_ingredients.mim_ingredients) project_onto_header() (in module kg_microbe.utils.unipathways_utils) publication_doi() (in module kg_microbe.transform_utils.bacdive.references)

Q

Query (class in query_utils.query) query_ncbi_for_taxon() (in module kg_microbe.transform_utils.bakta.create_samn_mapping) query_organism_full() (in module kg_microbe.query_utils) (in module kg_microbe.query_utils.organism_queries)

query_utils module query_utils.query module

R

read_annotation_table() (in module kg_microbe.utils.ingredient_bundle_contract) read_dispositions() (in module kg_microbe.transform_utils.ontologies_stubs.ncit_category_projection) read_fingerprint() (in module kg_microbe.utils.transform_fingerprint) read_json() (in module kg_microbe.utils.ingredient_bundle_contract) (kg_microbe.merge_utils.source_admission.SourceAdmission method) read_manifest() (in module kg_microbe.utils.download_manifest) read_predicate_semantics() (in module kg_microbe.utils.chemical_mapping_utils) read_profile_table() (in module kg_microbe.utils.ingredient_scope) read_scope_metadata() (in module kg_microbe.utils.ingredient_scope) record() (in module kg_microbe.utils.download_manifest) records (kg_microbe.utils.go_authority.GoAuthority attribute) reference_dois() (in module kg_microbe.transform_utils.bacdive.references) relationships() (kg_microbe.utils.ontology_resolution.CategoryAdapter method) remove_convert_to_json() (in module kg_microbe.utils.robot_utils) remove_nextlines() (in module kg_microbe.utils.string_coding) remove_unwanted_prefixes_from_edges() (in module kg_microbe.utils.unipathways_utils) remove_unwanted_prefixes_from_node_xrefs() (in module kg_microbe.utils.unipathways_utils) replace_category_by_prefix() (in module kg_microbe.utils.ontology_resolution) replace_category_for_unipathways() (in module kg_microbe.utils.unipathways_utils) replace_category_ontology() (in module kg_microbe.utils.ontology_utils) replace_deprecated_categories() (in module kg_microbe.utils.ontology_utils) replace_deprecated_category_names() (in module kg_microbe.utils.ontology_resolution) replace_id_with_xref() (in module kg_microbe.utils.unipathways_utils) replace_triples_with_labels() (in module kg_microbe.utils.unipathways_utils) replaced_by (kg_microbe.utils.go_authority.GoTerm attribute) replacement_chain (kg_microbe.utils.go_authority.GoResolution attribute) report() (kg_microbe.merge_utils.progress.MergeProgress method) REQUIRED_CONSUMED_INPUTS (kg_microbe.transform_utils.bactotraits.bactotraits.BactoTraitsTransform attribute) (kg_microbe.transform_utils.bactotraits.BactoTraitsTransform attribute) (kg_microbe.transform_utils.mediadive.mediadive.MediaDiveTransform attribute) (kg_microbe.transform_utils.mediadive.MediaDiveTransform attribute) (kg_microbe.transform_utils.mim_ingredients.mim_ingredients.MIMIngredientsTransform attribute) (kg_microbe.transform_utils.transform.Transform attribute) resolution_asserts_a_parent() (in module kg_microbe.transform_utils.bacdive.emission) RESOLUTION_COLLAPSED (in module kg_microbe.transform_utils.bacdive.emission) RESOLUTION_SUPPRESSED (in module kg_microbe.transform_utils.bacdive.emission) RESOLUTION_SUPPRESSED_NO_ANCESTRY (in module kg_microbe.transform_utils.bacdive.emission) resolve() (kg_microbe.utils.go_authority.GoAuthority method) resolve_accepted_records() (in module kg_microbe.utils.lpsn_utils) resolve_adapter() (in module kg_microbe.utils.ontology_utils) resolve_data_input() (in module kg_microbe.utils.transform_fingerprint) resolve_deposit_parents() (in module kg_microbe.transform_utils.bacdive.emission) resolve_external_reference_bundle() (in module kg_microbe.merge_utils.external_node_closure) resolve_external_references() (in module kg_microbe.merge_utils.external_node_closure) resolve_ingredient_source() (kg_microbe.utils.chemical_mapping_utils.ChemicalMappingLoader method) resolve_organism_name() (in module kg_microbe.query_utils.organism_queries) resolve_replacement() (in module kg_microbe.utils.external_identifiers) resolve_source() (kg_microbe.utils.ingredient_bundle.ReviewedIngredientBundle method) result_dict_to_tsv() (in module kg_microbe.query) review_status() (in module kg_microbe.utils.postprocess_artifacts)

reviewed_products() (in module kg_microbe.utils.ingredient_bundle_contract) ReviewedIngredientBundle (class in kg_microbe.utils.ingredient_bundle) RheaMappingsTransform (class in kg_microbe.transform_utils.rhea_mappings) (class in kg_microbe.transform_utils.rhea_mappings.rhea_mappings) robust_fix_uri() (in module kg_microbe.utils.sanitize_curies) run() (kg_microbe.transform_utils.bacdive.bacdive.BacDiveTransform method) (kg_microbe.transform_utils.bacdive.BacDiveTransform method) (kg_microbe.transform_utils.bactotraits.bactotraits.BactoTraitsTransform method) (kg_microbe.transform_utils.bactotraits.BactoTraitsTransform method) (kg_microbe.transform_utils.bakta.bakta.BaktaTransform method) (kg_microbe.transform_utils.bakta.BaktaTransform method) (kg_microbe.transform_utils.cog.cog.COGTransform method) (kg_microbe.transform_utils.cog.COGTransform method) (kg_microbe.transform_utils.ctd.ctd.CTDTransform method) (kg_microbe.transform_utils.ctd.CTDTransform method) (kg_microbe.transform_utils.disbiome.disbiome.DisbiomeTransform method) (kg_microbe.transform_utils.disbiome.DisbiomeTransform method) (kg_microbe.transform_utils.gold.gold.GOLDTransform method) (kg_microbe.transform_utils.gold.GOLDTransform method) (kg_microbe.transform_utils.gtdb.gtdb.GTDBTransform method) (kg_microbe.transform_utils.gtdb.GTDBTransform method) (kg_microbe.transform_utils.kegg.kegg.KEGGTransform method) (kg_microbe.transform_utils.kegg.KEGGTransform method) (kg_microbe.transform_utils.lpsn.lpsn.LPSNTransform method) (kg_microbe.transform_utils.lpsn_api.lpsn_api.LPSNAPITransform method) (kg_microbe.transform_utils.madin_etal.madin_etal.MadinEtAlTransform method) (kg_microbe.transform_utils.madin_etal.MadinEtAlTransform method) (kg_microbe.transform_utils.mediadive.mediadive.MediaDiveTransform method) (kg_microbe.transform_utils.mediadive.MediaDiveTransform method) (kg_microbe.transform_utils.metatraits.metatraits.MetaTraitsTransform method) (kg_microbe.transform_utils.metatraits.MetaTraitsTransform method) (kg_microbe.transform_utils.metatraits_gtdb.metatraits_gtdb.MetaTraitsGTDBTransform method) (kg_microbe.transform_utils.metatraits_gtdb.MetaTraitsGTDBTransform method) (kg_microbe.transform_utils.microbedecoder.microbedecoder.MicrobeDecoderTransform method) (kg_microbe.transform_utils.mim_ingredients.mim_ingredients.MIMIngredientsTransform method) (kg_microbe.transform_utils.ontologies.ontologies_transform.OntologiesTransform method) (kg_microbe.transform_utils.ontologies.OntologiesTransform method) (kg_microbe.transform_utils.ontologies_stubs.ontologies_stubs_transform.OntologiesStubsTransform method) (kg_microbe.transform_utils.ontologies_stubs.OntologiesStubsTransform method) (kg_microbe.transform_utils.prego.prego.PregoTransform method) (kg_microbe.transform_utils.rhea_mappings.rhea_mappings.RheaMappingsTransform method) (kg_microbe.transform_utils.rhea_mappings.RheaMappingsTransform method) (kg_microbe.transform_utils.transform.Transform method) (kg_microbe.transform_utils.uniprot_functional_microbes.uniprot_functional_microbes.UniprotFunctionalMicrobesTransform method) (kg_microbe.transform_utils.uniprot_functional_microbes.UniprotFunctionalMicrobesTransform method) (kg_microbe.transform_utils.uniprot_human.uniprot_human.UniprotHumanTransform method) (kg_microbe.transform_utils.wallen_etal.wallen_etal.WallenEtAlTransform method) (kg_microbe.transform_utils.wallen_etal.WallenEtAlTransform method) (query_utils.query.Query method) run_query() (in module kg_microbe.query)

S

safe_member() (in module kg_microbe.utils.ingredient_bundle_contract) sanitize_id_or_uri() (in module kg_microbe.utils.sanitize_curies) sanitize_row() (in module kg_microbe.utils.sanitize_curies) sanitize_tsv() (in module kg_microbe.utils.sanitize_curies) save_json_file() (in module kg_microbe.utils.mediadive_bulk_download) SCHEMA_FILES (in module kg_microbe.utils.transform_fingerprint) schema_fingerprint() (in module kg_microbe.utils.transform_fingerprint) scope_profile() (in module kg_microbe.utils.ingredient_scope) ScoreHistogram (class in kg_microbe.transform_utils.prego.calibration) search_by_label() (in module kg_microbe.utils.oak_utils) select_artifact() (in module kg_microbe.utils.postprocess_artifacts) serialize_knowledge_sources() (in module kg_microbe.utils.provenance) set_description() (kg_microbe.utils.dummy_tqdm.DummyTqdm method) setUp() (tests.test_transform_class.TestTransform method) setup_cache() (in module kg_microbe.utils.mediadive_bulk_download) SHARED_CODE (in module kg_microbe.utils.transform_fingerprint) shared_code_fingerprint() (in module kg_microbe.utils.transform_fingerprint) sibling_imports() (in module kg_microbe.utils.biolink_model) SKOS_SEMANTICS (in module kg_microbe.utils.chemical_mapping_utils) slugify_label() (in module kg_microbe.transform_utils.microbedecoder.utils) snapshot_bulk_input() (in module kg_microbe.transform_utils.mediadive.bulk_inputs) snapshot_consumed_input() (in module kg_microbe.utils.source_finalization) snapshot_optional_input() (in module kg_microbe.utils.optional_consumed_inputs) source_markers() (in module kg_microbe.merge_utils.stats_provenance) source_paths (kg_microbe.utils.go_authority.GoAuthority attribute)

SourceAdmission (class in kg_microbe.merge_utils.source_admission) SourceFinalizationRequired split_functional_categories() (in module kg_microbe.transform_utils.cog.utils) split_list_values() (in module kg_microbe.bactotraits_to_mongo) split_multivalue() (in module kg_microbe.transform_utils.microbedecoder.utils) split_multivalue_comma_only() (in module kg_microbe.transform_utils.microbedecoder.utils) split_snapshot_values() (in module kg_microbe.transform_utils.microbedecoder.utils) SSSOM_CONSUMED_INPUT (kg_microbe.transform_utils.mim_ingredients.mim_ingredients.MIMIngredientsTransform attribute) stable_id() (in module kg_microbe.utils.ingredient_bundle_contract) stale_by_url() (in module kg_microbe.utils.download_manifest) standardize_compound_id() (kg_microbe.transform_utils.mediadive.mediadive.MediaDiveTransform method) (kg_microbe.transform_utils.mediadive.MediaDiveTransform method) star_for_row() (in module kg_microbe.transform_utils.prego.calibration) stats_filename_from_config() (in module kg_microbe.merge_utils.stats_provenance) status (kg_microbe.utils.postprocess_artifacts.ArtifactStatus attribute) STRAIN_PARENT_REPORT (in module kg_microbe.merge_utils.invariants) strain_parent_rows() (in module kg_microbe.merge_utils.invariants) StrainProvenanceWriter (class in kg_microbe.transform_utils.bacdive.emission) StreamingRowWriter (class in kg_microbe.transform_utils.metatraits.io) strip_gtdb_prefix() (in module kg_microbe.transform_utils.gtdb.utils) structural_edges (kg_microbe.utils.go_authority.GoAuthority attribute) stub_incident_rows() (in module kg_microbe.merge_utils.invariants) STUB_NODE_REPORT (in module kg_microbe.merge_utils.invariants) stub_node_rows() (in module kg_microbe.merge_utils.invariants) synthetic_nodes_metadata (kg_microbe.transform_utils.metatraits_gtdb.MetaTraitsGTDBTransform attribute)

T

test_attributes (tests.test_transform_class.TestTransform attribute) test_attributes_0_source_name() (tests.test_transform_class.TestTransform method) test_attributes_1_node_header() (tests.test_transform_class.TestTransform method) test_attributes_2_edge_header() (tests.test_transform_class.TestTransform method) test_default_dirs_exist() (tests.test_transform_class.TestTransform method) test_path_attributes() (tests.test_transform_class.TestTransform method) test_reality() (tests.test_transform_class.TestTransform method) test_transform_child_classes (tests.test_transform_class.TestTransform attribute) test_transform_child_classes_00_mim_ingredients() (tests.test_transform_class.TestTransform method) test_transform_child_classes_01_ontologies() (tests.test_transform_class.TestTransform method) test_transform_child_classes_02_ontologies_stubs() (tests.test_transform_class.TestTransform method) test_transform_child_classes_03_bacdive() (tests.test_transform_class.TestTransform method) test_transform_child_classes_04_bakta() (tests.test_transform_class.TestTransform method) test_transform_child_classes_05_cog() (tests.test_transform_class.TestTransform method) test_transform_child_classes_06_gtdb() (tests.test_transform_class.TestTransform method) test_transform_child_classes_07_kegg() (tests.test_transform_class.TestTransform method) test_transform_child_classes_08_lpsn() (tests.test_transform_class.TestTransform method) test_transform_child_classes_09_lpsn_api() (tests.test_transform_class.TestTransform method) test_transform_child_classes_10_mediadive() (tests.test_transform_class.TestTransform method) test_transform_child_classes_11_madin_etal() (tests.test_transform_class.TestTransform method) test_transform_child_classes_12_metatraits() (tests.test_transform_class.TestTransform method) test_transform_child_classes_13_metatraits_gtdb() (tests.test_transform_class.TestTransform method) test_transform_child_classes_14_rhea_mappings() (tests.test_transform_class.TestTransform method) test_transform_child_classes_15_bactotraits() (tests.test_transform_class.TestTransform method) test_transform_child_classes_16_gold() (tests.test_transform_class.TestTransform method) test_transform_child_classes_17_microbedecoder() (tests.test_transform_class.TestTransform method) test_transform_child_classes_18_prego() (tests.test_transform_class.TestTransform method) tests module tests.test_transform_class module

TestTransform (class in tests.test_transform_class) to_biolink_predicate() (in module kg_microbe.utils.metpo_predicates) trait_mapping (kg_microbe.transform_utils.metatraits.MetaTraitsTransform attribute) (kg_microbe.transform_utils.metatraits_gtdb.MetaTraitsGTDBTransform attribute) Transform (class in kg_microbe.transform_utils.transform) transform() (in module kg_microbe.transform) transform_class (kg_microbe.transform.LazyTransform property) TRANSFORM_INPUTS (kg_microbe.transform_utils.bacdive.bacdive.BacDiveTransform attribute) (kg_microbe.transform_utils.bacdive.BacDiveTransform attribute) (kg_microbe.transform_utils.bactotraits.bactotraits.BactoTraitsTransform attribute) (kg_microbe.transform_utils.bactotraits.BactoTraitsTransform attribute) (kg_microbe.transform_utils.gold.gold.GOLDTransform attribute) (kg_microbe.transform_utils.gold.GOLDTransform attribute) (kg_microbe.transform_utils.lpsn.lpsn.LPSNTransform attribute) (kg_microbe.transform_utils.lpsn_api.lpsn_api.LPSNAPITransform attribute) (kg_microbe.transform_utils.mediadive.mediadive.MediaDiveTransform attribute) (kg_microbe.transform_utils.mediadive.MediaDiveTransform attribute) (kg_microbe.transform_utils.metatraits.metatraits.MetaTraitsTransform attribute) (kg_microbe.transform_utils.metatraits.MetaTraitsTransform attribute) (kg_microbe.transform_utils.metatraits_gtdb.metatraits_gtdb.MetaTraitsGTDBTransform attribute) (kg_microbe.transform_utils.metatraits_gtdb.MetaTraitsGTDBTransform attribute) (kg_microbe.transform_utils.microbedecoder.microbedecoder.MicrobeDecoderTransform attribute) (kg_microbe.transform_utils.prego.prego.PregoTransform attribute) (kg_microbe.transform_utils.transform.Transform attribute) TransformBatchError TransformChildClass (class in tests.test_transform_class) tsv_dict_writer() (in module kg_microbe.utils.tsv_io) TSV_QUOTING (kg_microbe.transform_utils.microbedecoder.microbedecoder.MicrobeDecoderTransform attribute) (kg_microbe.transform_utils.mim_ingredients.mim_ingredients.MIMIngredientsTransform attribute) tsv_writer() (in module kg_microbe.utils.tsv_io)

U

uberon_category() (in module kg_microbe.utils.ontology_resolution) UniprotFunctionalMicrobesTransform (class in kg_microbe.transform_utils.uniprot_functional_microbes) (class in kg_microbe.transform_utils.uniprot_functional_microbes.uniprot_functional_microbes) UniprotHumanTransform (class in kg_microbe.transform_utils.uniprot_human.uniprot_human)

UnknownDownloadTagError update() (kg_microbe.utils.dummy_tqdm.DummyTqdm method) upstream_fingerprint() (in module kg_microbe.utils.transform_fingerprint) uri_to_curie() (in module kg_microbe.utils.mapping_file_utils) usable (kg_microbe.utils.ontology_utils.DbEnsureResult attribute)

V

valid_cas() (in module kg_microbe.utils.cas) validate_bundle() (in module kg_microbe.utils.ingredient_bundle_contract) validate_canonical_tsv() (in module kg_microbe.utils.graph_schema) validate_curie() (in module kg_microbe.utils.validation_utils) validate_curie_prefix() (in module kg_microbe.utils.validation_utils) validate_graph_bundle() (in module kg_microbe.utils.source_finalization) validate_identifier() (in module kg_microbe.utils.source_finalization) validate_ingredient_fields() (in module kg_microbe.utils.ingredient_kgx) validate_kgm_term() (in module kg_microbe.utils.validation_utils) validate_member_hashes() (in module kg_microbe.utils.ingredient_bundle_contract) validate_native_contract() (in module kg_microbe.transform_utils.ontologies_stubs.ncit_category_projection) validate_node_representation() (in module kg_microbe.utils.source_finalization) validate_payload() (in module kg_microbe.utils.ingredient_bundle_contract) validate_primary_source_and_publications() (in module kg_microbe.utils.provenance) validate_review_decision() (in module kg_microbe.utils.review_claims) validate_scope_row() (in module kg_microbe.utils.ingredient_scope) validate_tau() (in module kg_microbe.transform_utils.prego.calibration) verify() (kg_microbe.merge_utils.source_admission.SourceAdmission method)

verify_bulk_inputs() (in module kg_microbe.transform_utils.mediadive.bulk_inputs) verify_consumed_inputs() (in module kg_microbe.utils.source_finalization) (kg_microbe.transform_utils.transform.Transform method) verify_current() (kg_microbe.utils.ingredient_bundle.ReviewedIngredientBundle method) verify_declared_dependencies() (kg_microbe.transform_utils.transform.Transform method) verify_finalized_source_files() (in module kg_microbe.utils.source_finalization) verify_native_inputs() (kg_microbe.transform_utils.mediadive.mediadive.MediaDiveTransform method) (kg_microbe.transform_utils.mediadive.MediaDiveTransform method) (kg_microbe.transform_utils.ontologies_stubs.ontologies_stubs_transform.OntologiesStubsTransform method) (kg_microbe.transform_utils.ontologies_stubs.OntologiesStubsTransform method) verify_optional_inputs() (in module kg_microbe.utils.optional_consumed_inputs) verify_recorded_bulk_inputs() (in module kg_microbe.transform_utils.mediadive.bulk_inputs) verify_recorded_native_inputs() (kg_microbe.transform_utils.mediadive.mediadive.MediaDiveTransform class method) (kg_microbe.transform_utils.mediadive.MediaDiveTransform class method) (kg_microbe.transform_utils.ontologies_stubs.ontologies_stubs_transform.OntologiesStubsTransform class method) (kg_microbe.transform_utils.ontologies_stubs.OntologiesStubsTransform class method) verify_recorded_optional_inputs() (in module kg_microbe.utils.optional_consumed_inputs) verify_source_freshness() (in module kg_microbe.merge_utils.source_freshness)

W

WallenEtAlTransform (class in kg_microbe.transform_utils.wallen_etal) (class in kg_microbe.transform_utils.wallen_etal.wallen_etal) WEB_RECORD_SOURCE_KEY (in module kg_microbe.transform_utils.lpsn_api.lpsn_api) write_annotations() (kg_microbe.utils.ingredient_bundle.ReviewedIngredientBundle method) write_empty_go_report() (in module kg_microbe.utils.go_authority) write_fingerprint() (in module kg_microbe.utils.transform_fingerprint) write_graph_archive() (in module kg_microbe.merge_utils.artifact_manifest) write_loose_manifest() (in module kg_microbe.merge_utils.artifact_manifest) write_merge_validation_report() (in module kg_microbe.utils.source_finalization) write_obsolete_file_header() (in module kg_microbe.utils.uniprot_utils)

write_output() (kg_microbe.transform_utils.bakta.bakta.BaktaTransform method) (kg_microbe.transform_utils.bakta.BaktaTransform method) (kg_microbe.transform_utils.cog.cog.COGTransform method) (kg_microbe.transform_utils.cog.COGTransform method) (kg_microbe.transform_utils.kegg.kegg.KEGGTransform method) (kg_microbe.transform_utils.kegg.KEGGTransform method) write_profile_table() (in module kg_microbe.utils.ingredient_scope) write_row() (kg_microbe.transform_utils.metatraits.io.StreamingRowWriter method) writerow() (kg_microbe.transform_utils.bacdive.emission.StrainProvenanceWriter method) writerows() (kg_microbe.transform_utils.bacdive.emission.StrainProvenanceWriter method)