id: https://w3id.org/culturemech name: culturemech title: CultureMech - Microbial Growth Media Schema description: | LinkML schema for modeling microbial culture media recipes and formulations. Follows the dismech architecture pattern with descriptor classes for ontology grounding. license: BSD-3-Clause prefixes: linkml: https://w3id.org/linkml/ culturemech: https://w3id.org/culturemech/ biolink: https://w3id.org/biolink/vocab/ rdfs: http://www.w3.org/2000/01/rdf-schema# # Chemicals CHEBI: http://purl.obolibrary.org/obo/CHEBI_ # Organisms NCBITaxon: http://purl.obolibrary.org/obo/NCBITaxon_ # Media databases (authoritative sources) DSMZ: https://mediadive.dsmz.de/medium/ TOGO: http://togodb.org/db/medium/ ATCC: https://www.atcc.org/products/ NCIT: http://purl.obolibrary.org/obo/NCIT_ # Algae culture collections UTEX: https://utex.org/products/ CCAP: https://www.ccap.ac.uk/catalogue/strain- SAG: https://sagdb.uni-goettingen.de/detailedList.php?str_number= # Lab procedures OBI: http://purl.obolibrary.org/obo/OBI_ # Environmental conditions ENVO: http://purl.obolibrary.org/obo/ENVO_ # Units UO: http://purl.obolibrary.org/obo/UO_ # Anatomy (for tissue extracts) UBERON: http://purl.obolibrary.org/obo/UBERON_ # Food products (peptone, yeast extract, wheat germ, etc.) FOODON: http://purl.obolibrary.org/obo/FOODON_ # Upstream MediaDive compound URI (kept alongside CHEBI grounding on solution composition entries) mediadive.compound: https://mediadive.dsmz.de/compound/ # References PMID: http://www.ncbi.nlm.nih.gov/pubmed/ DOI: https://doi.org/ # Pathways KEGG: https://www.genome.jp/entry/ EC: https://enzyme.expasy.org/EC/ # Data repositories geo: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= sra: https://www.ncbi.nlm.nih.gov/sra/ # Genomic taxonomy GTDB: https://gtdb.ecogenomic.org/genome?gid= # Genome assemblies RefSeq: https://www.ncbi.nlm.nih.gov/datasets/genome/ GenBank: https://www.ncbi.nlm.nih.gov/assembly/ BioSample: https://www.ncbi.nlm.nih.gov/biosample/ # Suppliers sigma: https://www.sigmaaldrich.com/catalog/product/ thermofisher: https://www.thermofisher.com/order/catalog/product/ default_prefix: culturemech default_range: string imports: - linkml:types # Shared, byte-identical Mech module: Discussion (knowledge gaps) + Dataset # (+ DatasetTypeEnum/DatasetRepositoryEnum). Replaces the former local Dataset # class + DatasetTypeEnum. Vendored + sha-pinned across the Mechs — claw#7. - mech_shared # MIM-authored ingredient role facet enums (NutritionalRoleEnum / # PhysicochemicalRoleEnum / CellularMetabolicRoleEnum). Vendored + sha-pinned; # source of truth lives in MediaIngredientMech#129 + #134. Referenced by the # three faceted role slots on IngredientDescriptor. - mim_roles # ================================================================ # ROOT CLASS # ================================================================ classes: MediaRecipe: class_uri: culturemech:MediaRecipe description: >- A complete growth medium formulation for culturing microorganisms. This is the root entity - one per YAML file. attributes: id: description: >- Stable canonical external CultureMech identifier for this media recipe. Immutable after issuance and never reused; lifecycle is published in data/culturemech_recipe_catalog.tsv. range: string identifier: true required: true pattern: "^CultureMech:(?!000000)\\d{6}$" id_lineage_token: description: >- Internal immutable lineage witness for legacy records that predate the ID-assignment curation event. This is not an external identifier and must never be copied to another record or changed after publication. range: string pattern: "^legacy:[0-9a-f]{64}$" name: description: Human-readable medium name (e.g., "LB Broth", "M9 Minimal Medium") required: true range: string original_name: description: >- Original name from source database before filename sanitization. May contain special characters like /, :, %, (, ), ', ", <, >, &, #, etc. This field preserves the exact name as it appears in the source database. range: string required: false category: description: Broad category for organization range: CategoryEnum recommended: true categories: description: All categories this recipe appears in (for cross-category merges) range: CategoryEnum multivalued: true comments: - Used when recipes from different categories are merged based on identical ingredients - Preserves all original category assignments high_metal: description: >- Indicates media with total metal concentration above the 90th percentile threshold (≥1049.84 mM). Metals include Fe, Cu, Zn, Mn, Co, Ni, Mo, Se, W, V, Cr, Ca, Mg, K, Na. Based on automated concentration analysis of ingredient composition. range: boolean recommended: false comments: - Threshold computed from distribution of 9,599 media with detectable metal content - Useful for identifying high-metal media for metal toxicity studies or bioremediation applications high_ree: description: >- Indicates media with total rare earth element (REE) concentration above the 90th percentile threshold (≥1030.48 mM). REEs include lanthanides (La, Ce, Pr, Nd, Pm, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu) plus Sc and Y. Based on automated concentration analysis of ingredient composition. range: boolean recommended: false comments: - Threshold computed from distribution of 9,130 media with detectable REE content - Useful for identifying specialized media for REE extraction or bioaccumulation research synonyms: description: Alternate names from merged duplicate recipes range: RecipeSynonym multivalued: true inlined_as_list: true comments: - Populated during merge process when duplicate recipes are consolidated - Tracks all non-canonical names with their source provenance merged_from: description: Original recipe IDs that were merged into this record range: string multivalued: true comments: - List of recipe file IDs that were consolidated into this canonical record - "Format: source_id_sanitized_name (e.g., TOGO_M3236_Luria_Bertani_LB_medium)" merge_fingerprint: description: SHA256 hash of ingredient set for deduplication tracking range: string comments: - Generated from sorted list of CHEBI IDs and normalized ingredient names - Includes both direct ingredients and solution compositions - Order-independent, concentration-independent chemical_fingerprint: description: SHA256 hash using parent ingredients (hierarchy-aware) range: string comments: - Treats chemical variants as equivalent (CaCl2·2H2O = CaCl2) - Uses parent CHEBI IDs from MediaIngredientMech hierarchy - Enables smart merging of hydrates, salt forms, and anhydrous variants - Generated only when hierarchy enrichment is available variant_fingerprint: description: SHA256 hash preserving variant distinctions range: string comments: - Keeps hydrates separate from anhydrous forms - Uses parent CHEBI + variant type (HYDRATE, ANHYDROUS, SALT_FORM, etc.) - Preserves important chemical specificity during merge - Generated only when hierarchy enrichment is available fingerprint_version: description: Version of fingerprinting algorithm used range: string comments: - Example "hierarchy-chemical-v1.0" or "original-v1.0" - Enables tracking algorithm changes over time - Used to determine which fingerprints are comparable merge_metadata: description: Metadata about merge process and quality range: MergeMetadata inlined: true comments: - Provides transparency about merge decisions - Enables quality analysis and debugging - Populated during hierarchy-aware merge pipeline media_term: description: Reference to authoritative media database range: MediaTypeDescriptor recommended: true kg_microbe_match: description: >- KG-Microbe mediadive.medium node ID for exact ingredient match. Populated when this recipe's ingredients exactly match a medium in KG-Microbe (ignoring concentrations, considering hierarchical ingredient resolution). range: string required: false pattern: "^mediadive\\.medium:[0-9a-zA-Z_-]+$" comments: - Format mediadive.medium:514, mediadive.medium:693, mediadive.medium:92 - Match criteria same ingredient set (CHEBI/FOODON IDs) regardless of concentrations - Handles hierarchical ingredients (commercial products vs constituent chemicals) - Enables validation against authoritative DSMZ formulations description: description: Overview of the medium and its purpose range: string multivalued: false target_organisms: description: Organisms for which this medium is designed range: OrganismDescriptor multivalued: true recommended: true inlined_as_list: true source_environment: description: >- Environment(s) from which target organisms originate or for which this medium is designed. Enables environment-based queries and linking to CommunityMech environmental metadata. range: SourceEnvironmentDescriptor multivalued: true required: false inlined_as_list: true comments: - Optional field for backward compatibility - Multivalued to support media used for multiple environments - Use when environment is known or can be inferred from target organisms - Enables queries like "find all media for marine organisms" organism_culture_type: description: >- Whether this medium targets a pure isolate culture or a mixed microbial community range: OrganismCultureTypeEnum recommended: true record_kind: description: >- What kind of record this is: a growth MEDIUM, or a standalone stock SOLUTION. Normally inferred from the `term.id` prefix (`mediadive.solution:*`), and only stated explicitly for solutions that carry no upstream solution identifier — 202 records imported from KOMODO as media ("Trace element solution (medium 929)", "10 x M9 salts") whose composition was flattened into their parent medium. A curated assertion, written by `just retype-solution-records` and reviewable in the diff. It is NOT derived from the name at read time: matching "*solution*" would silently reclassify a genuine medium such as Ringer's solution. range: RecordKindEnum medium_type: description: >- MAINTAINED compatibility axis, derived from composition_type. It is the single-valued classification published to downstream consumers: kgx_export emits one edge per record from this slot, so it is load-bearing rather than vestigial. Populate it on every record, and keep it consistent with composition_type — DEFINED maps to DEFINED, UNDEFINED and SEMI_DEFINED both map to COMPLEX. BUFFER and NEGATIVE_CONTROL have no composition_type counterpart and are curated directly. Use `just curate-medium-type` to stamp it; a guard fails the build if any record is missing it or contradicts composition_type. range: MediumTypeEnum composition_type: description: >- Composition axis — how chemically defined the medium is (DEFINED / UNDEFINED / SEMI_DEFINED). Supersedes the DEFINED/COMPLEX values of the deprecated medium_type slot. range: MediumCompositionTypeEnum recommended: true nutritional_class: description: >- Nutritional-level axis — MINIMAL / RICH / GENERAL_PURPOSE. Orthogonal to composition_type and functional_role. range: MediumNutritionalClassEnum functional_role: description: >- Functional-role axis — what the medium is designed to do (SELECTIVE, DIFFERENTIAL, ENRICHMENT, GENERAL_PURPOSE, TRANSPORT, ASSAY, ENUMERATION). Multivalued: a medium may have more than one role. range: MediumFunctionalRoleEnum multivalued: true physical_state: description: Physical form of the medium range: PhysicalStateEnum required: true ph_value: description: Target pH value range: float ph_range: description: Acceptable pH range. Structured as PhRange (min/max floats; notes for unparseable values). range: PhRange inlined: true # Algae-specific culture conditions light_intensity: description: Light intensity for photosynthetic organisms (e.g., "50 µmol photons m⁻² s⁻¹") range: string comments: - For algae and cyanobacteria cultures - "Common units: µE/m²/s, µmol photons m⁻² s⁻¹, lux, or foot-candles" light_cycle: description: Photoperiod light:dark cycle (e.g., "16:8", "continuous light", "24:0") range: string comments: - For algae and cyanobacteria cultures - "Format: hours_light:hours_dark" light_quality: description: Light spectrum or wavelength (e.g., "cool white fluorescent", "red LED 660nm") range: string comments: - For algae and cyanobacteria cultures temperature_range: description: Optimal temperature range (e.g., "20-25°C", "room temperature") range: string temperature_value: description: Specific culture temperature in Celsius range: float salinity: description: Salt concentration for marine/brackish media (e.g., "35 ppt", "3.5%") range: string comments: - For marine algae and halophilic organisms aeration: description: Gas exchange method (e.g., "0.5% CO2 in air", "bubbling", "shaking at 150 rpm") range: string culture_vessel: description: Recommended culture container (e.g., "Erlenmeyer flask", "test tube", "petri dish") range: string ingredients: description: Chemical and biological ingredients range: IngredientDescriptor multivalued: true required: true inlined_as_list: true solutions: description: Pre-prepared stock solutions used as ingredients range: SolutionDescriptor multivalued: true inlined_as_list: true preparation_steps: description: Ordered steps to prepare the medium range: PreparationStep multivalued: true recommended: true inlined_as_list: true sterilization: description: Sterilization method and parameters range: SterilizationDescriptor recommended: true inlined: true storage: description: Storage conditions for prepared medium range: StorageConditions inlined: true applications: description: Use cases and applications range: string multivalued: true variants: description: Related formulations or modifications range: MediaVariant multivalued: true inlined_as_list: true parent_media: description: >- Canonical parent medium when this record is a child/variant formulation. Used for parent-child media variant modeling where each variant remains a full MediaRecipe YAML record. range: MediaRecipeReference inlined: true variant_children: description: >- Child MediaRecipe YAML records that are variants of this canonical parent medium. range: MediaRecipeReference multivalued: true inlined_as_list: true variant_relationship: description: >- Relationship type to the parent medium when this recipe is a child variant record. range: MediaVariantRelationshipEnum variant_modifications: description: >- Summary of how this child formulation differs from its parent medium. range: string multivalued: true references: description: Original literature sources range: PublicationReference multivalued: true inlined_as_list: true notes: description: Additional context, historical notes, tips range: string evidence: description: Evidence supporting formulation claims range: EvidenceItem multivalued: true recommended: false inlined_as_list: true datasets: description: Public datasets (omics/sequence/phenotype) generated using this medium range: Dataset multivalued: true inlined_as_list: true discussions: description: >- Open questions, knowledge gaps, controversies, and curation todos attached to this medium (shared Discussion supertype; anchor `attaches_to` into e.g. `composition#` / `conditions#`). range: Discussion multivalued: true inlined_as_list: true import_metadata: description: >- Import tracking and versioning information. Enables reproducible imports, provenance tracking, and update workflows. range: ImportMetadata inlined: true recommended: true comments: - Populated for all imported media (excludes manually created recipes) - Essential for tracking source database versions and updates - Enables reproducibility and audit trails curation_history: description: Audit trail of curation events range: CurationEvent multivalued: true inlined_as_list: true data_quality_flags: description: Data quality indicators for transparency range: string multivalued: true comments: - Used to mark recipes with known quality issues - "Common values: incomplete_composition, pending_curation, low_confidence" sources: description: >- Upstream database attribution(s) for this record (e.g. MediaDive, CultureBotHT). Multivalued for cross-listings. range: SourceReference multivalued: true inlined_as_list: true incubation_atmosphere: description: Atmospheric conditions for incubation range: AtmosphereEnum comments: - Indicates whether the organism requires aerobic, anaerobic, or microaerophilic conditions - Imported from CommunityMech when available source_data: description: Provenance tracking for records imported from other repositories range: SourceData inlined: true comments: - Records imported from CommunityMech include community IDs and evidence - Preserves bidirectional linking between repositories SolutionRecipe: class_uri: culturemech:SolutionRecipe description: >- A standalone stock-solution record (one per YAML file). Used for pre-prepared solutions that are referenced as ingredients by MediaRecipes — e.g. MediaDive's "Main sol." or "Trace metals SL10" records. SolutionDescriptor is the inlined-in-recipe form; this is the root form with its own id, curation history, and provenance. attributes: id: description: >- Stable canonical external CultureMech identifier for this solution record. Immutable after issuance and never reused; lifecycle is published in data/culturemech_recipe_catalog.tsv. range: string identifier: true required: true pattern: "^CultureMech:(?!000000)\\d{6}$" id_lineage_token: description: >- Internal immutable lineage witness for legacy records that predate the ID-assignment curation event. This is not an external identifier and must never be copied to another record or changed after publication. range: string pattern: "^legacy:[0-9a-f]{64}$" preferred_term: description: Solution name (e.g., "Trace Metal Solution", "Vitamin Stock") required: true range: string term: description: Ontology term identifying this solution range: Term inlined: true mediaingredientmech_term: description: Legacy MediaIngredientMech:NNNNNN identifier for this solution (pre-CHEBI-keying). range: MediaIngredientMechTerm recommended: false inlined: true mediaingredientmech_chebi_term: description: CHEBI-keyed linkage to a curated MediaIngredientMech ingredient (current MIM schema). range: MediaIngredientMechChebiTerm recommended: false inlined: true culturemech_term: description: Reference to another CultureMech recipe (if this solution is also catalogued there) range: CultureMechTerm recommended: false inlined: true category: description: Source / collection category (algae, bacterial, fungal, …) range: CategoryEnum composition: description: Ingredients in the stock solution range: IngredientDescriptor multivalued: true required: true inlined_as_list: true solutions: description: Nested stock solutions added while preparing this stock solution range: SolutionDescriptor multivalued: true inlined_as_list: true ingredients: description: >- Placeholder/stub ingredient entries from upstream imports (kept alongside the authoritative `composition`). Intended to be empty or carry a "See source for composition" marker. range: IngredientDescriptor multivalued: true recommended: false inlined_as_list: true concentration: description: Working concentration when added to a medium range: ConcentrationValue inlined: true preparation_notes: description: How to prepare the stock solution range: string storage_conditions: description: Storage requirements range: StorageConditions inlined: true shelf_life: description: Stability duration (e.g., "6 months at 4°C") range: string references: description: Source references for this solution range: PublicationReference multivalued: true inlined_as_list: true source_data: description: Provenance tracking for imported solution records range: SourceData inlined: true curation_history: description: Audit trail of curation events range: CurationEvent multivalued: true inlined_as_list: true data_quality_flags: description: Data quality indicators range: string multivalued: true sources: description: Upstream database attribution(s) for this solution record. range: SourceReference multivalued: true inlined_as_list: true notes: description: Additional free-text notes range: string evidence: description: >- Evidence for solution-level formulation, nested stock additions and preparation claims. Ingredient concentration evidence belongs on the relevant composition entry. Scope each claim to its exact field path and preparation stage in the evidence explanation. range: EvidenceItem multivalued: true recommended: false inlined_as_list: true categories: description: All categories this solution recipe appears in (for cross-category merges) range: CategoryEnum multivalued: true synonyms: description: Alternate names from merged duplicate solution recipes range: RecipeSynonym multivalued: true inlined_as_list: true merged_from: description: Original recipe IDs that were merged into this solution record range: string multivalued: true merge_fingerprint: description: SHA256 hash of ingredient set for deduplication tracking range: string chemical_fingerprint: description: SHA256 hash using parent ingredients (hierarchy-aware) range: string variant_fingerprint: description: SHA256 hash including concentration and preparation variant details range: string RecipeSynonym: description: An alternate name for a recipe from a specific source attributes: name: description: Alternate recipe name (non-canonical) required: true range: string source: description: Source database (KOMODO, MediaDive, TOGO, etc.) required: true range: string source_id: description: Original identifier in source database range: string original_category: description: Original category assignment before merge range: CategoryEnum MergeMetadata: description: Metadata about merge process and quality attributes: merge_version: description: Version of merge pipeline used range: string comments: - Example "hierarchy-v1.0" - Enables tracking pipeline changes merge_mode: description: Merge mode used (conservative/aggressive/variant-aware) range: MergeModeEnum comments: - CONSERVATIVE - Only merge with explicit rules or exact match - AGGRESSIVE - Merge all variants with same parent - VARIANT_AWARE - Balanced approach, merge some variants merge_reason: description: Why these recipes were merged together range: MergeReasonEnum comments: - Indicates which merge rule triggered the merge - Used for quality analysis and debugging merge_confidence: description: Confidence score for merge decision (0.0-1.0) range: float comments: - 1.0 = Explicit merge rule (highest confidence) - 0.9 = Identical fingerprint - 0.8 = Same parent ingredients - 0.7 = Hydration variant only hierarchy_conflicts: description: Ingredients with conflicting merge signals range: string multivalued: true comments: - Used to flag potential quality issues - Example "CaCl2 has multiple parent assignments" fingerprint_mode: description: Fingerprinting mode used (chemical/variant/original) range: FingerprintModeEnum comments: - Indicates which fingerprint algorithm was used - Enables comparing merge results across modes # ================================================================ # BASE DESCRIPTOR PATTERN (following dismech) # ================================================================ Descriptor: abstract: true description: >- Base class for descriptor pattern. Descriptors have a human-readable preferred_term and optional ontology term. Term: abstract: true description: >- Base class for ontology term references. Subclasses specify id_prefixes for validation. attributes: id: description: Ontology identifier (CURIE) identifier: true required: true range: string label: slot_uri: rdfs:label description: >- CANONICAL ontology label for `id` (e.g. "magnesium sulfate" for CHEBI:32599). Verified against the ontology by the id↔label gate; the sibling `preferred_term` holds the free/source name. range: string confidence: description: Confidence score for the mapping (0.0-1.0). Populated by automated grounding pipelines. range: float match_type: description: Provenance/method of the term mapping (e.g. "kg_fallback", "exact", "manual_curated"). range: TermMatchTypeEnum # ================================================================ # DESCRIPTOR CLASSES # ================================================================ MediaTypeDescriptor: is_a: Descriptor description: Classification and authoritative database reference for the medium attributes: preferred_term: description: Medium designation in source database (e.g., "DSMZ Medium 1", "LB") required: true range: string term: description: Authoritative media database identifier range: MediaDatabaseTerm recommended: true inlined: true IngredientDescriptor: is_a: Descriptor description: Chemical or biological ingredient in a medium attributes: preferred_term: description: Human-readable ingredient name (e.g., "Glucose", "Yeast Extract") required: true range: string term: description: Primary ontology grounding (CHEBI, FOODON, UBERON, ENVO, or upstream mediadive.compound). range: ChemicalEntityTerm # NOTE: intentionally NO `binds_value_of: id` canonical-label binding. # `term`/`chebi_term` carry CURATOR-intended formula/common-name labels # (e.g. CHEBI:15377 "Distilled water", CHEBI:26710 "NaCl") that are # deliberately not the OBO canonical label. Enforcing the canonical # label here (linkml-term-validator --labels, Engine A) would directly # contradict the Engine-B label waiver (conf/id_label_targets.yaml: # label_waived_keys: [term, chebi_term]) and flag the very rows that # waiver exists to accept. id-existence is still checked by Engine B. # Canonical-label bindings ARE kept on organism/environment/precursor/ # substrate terms, whose labels are canonical. recommended: true inlined: true chebi_term: description: CHEBI-only grounding kept alongside `term` when `term` carries the upstream identifier (e.g. mediadive.compound on solution compositions). range: ChebiTerm # No canonical-label binding — see the `term` slot note above; same # curator-label policy and Engine-B waiver apply. recommended: false inlined: true mediaingredientmech_term: description: Legacy MediaIngredientMech:NNNNNN identifier for this ingredient (pre-CHEBI-keying). range: MediaIngredientMechTerm recommended: false inlined: true mediaingredientmech_chebi_term: description: CHEBI-keyed linkage to a curated MediaIngredientMech ingredient (current MIM schema). range: MediaIngredientMechChebiTerm recommended: false inlined: true culturemech_term: description: Reference to another CultureMech media recipe used as component range: CultureMechTerm recommended: false inlined: true comments: - Used when this ingredient is actually a complete medium or stock solution - "Example: A medium that uses BG-11 as a base would reference CultureMech:009592" parent_ingredient: description: Reference to parent chemical entity from MediaIngredientMech range: IngredientReference recommended: false inlined: true comments: - Links to canonical parent in MediaIngredientMech hierarchy - Example CaCl2·2H2O → parent is "Calcium chloride" variant_type: description: Type of chemical variant range: VariantTypeEnum recommended: false comments: - Describes relationship to parent (HYDRATE, SALT_FORM, ANHYDROUS, etc.) - Populated from MediaIngredientMech metadata concentration: description: >- Amount of ingredient. Recommended but not required: pH-adjustment ingredients (HCl/H2SO4/NaOH/KOH titrated "to pH") and similar "to-effect" reagents legitimately lack a fixed concentration. range: ConcentrationValue recommended: true inlined: true modifier: description: Modification in variants (INCREASED, DECREASED) range: ModifierEnum chemical_formula: description: Molecular formula (e.g., "C6H12O6") range: string synonyms: description: >- Alternate names for this ingredient (e.g. brand names, abbreviations). Each entry is an `IngredientSynonym` with `synonym_text` and `synonym_type`. range: IngredientSynonym multivalued: true inlined_as_list: true source: description: Provenance attribution for this ingredient entry. range: string curation_metadata: description: >- Structured curation metadata for this ingredient mapping (mapping quality, confidence score, ontology source, etc.). range: IngredientCurationMetadata inlined: true data_quality_flags: description: Ingredient-level data quality indicators. range: string multivalued: true molecular_weight: description: Molecular weight in g/mol range: float supplier_catalog: description: Supplier information for sourcing range: SupplierInfo inlined: true notes: description: Preparation notes specific to this ingredient range: string nutritional_roles: description: >- What element or macronutrient this ingredient supplies to the medium (facet 1 of 3). Multiple values allowed — L-cysteine → [AMINO_ACID_SOURCE, SULFUR_SOURCE]. Vocabulary imported from MIM (`mim_roles.NutritionalRoleEnum`); MIM owns the ingredient identity layer + evidence-bearing assignment surface, this slot carries CultureMech recipe-scoped assertions or overrides. range: NutritionalRoleEnum multivalued: true physicochemical_roles: description: >- Chemical or physical function this ingredient performs in the medium (facet 2 of 3), independent of what element it supplies — BUFFER, CHELATOR, REDUCING_AGENT, PH_INDICATOR, etc. Vocabulary imported from MIM (`mim_roles.PhysicochemicalRoleEnum`). range: PhysicochemicalRoleEnum multivalued: true cellular_metabolic_roles: description: >- Role of this ingredient inside/on the cultured microbe (facet 3 of 3) — SUBSTRATE, ELECTRON_DONOR, COFACTOR, INHIBITOR, etc. Often organism-conditional (e.g., methanol → ELECTRON_DONOR only for methylotrophs). Vocabulary imported from MIM (`mim_roles.CellularMetabolicRoleEnum`). range: CellularMetabolicRoleEnum multivalued: true role_curie: description: >- Escape-hatch CURIE(s) for out-of-vocabulary role terms not covered by the three facet enums. Should resolve within a recognized role namespace (CHEBI role subtree under CHEBI:50906, METPO, ENVO, GO, PATO, NCIT). Use sparingly — prefer a facet enum value where one fits. range: uriorcurie multivalued: true cofactors_provided: description: Cofactors supplied by this ingredient range: CofactorDescriptor multivalued: true inlined_as_list: true evidence: description: Evidence for this ingredient's role range: EvidenceItem multivalued: true inlined_as_list: true SolutionDescriptor: is_a: Descriptor description: A pre-prepared stock solution used as an ingredient attributes: preferred_term: description: Solution name (e.g., "Trace Metal Solution", "Vitamin Stock") required: true range: string name: description: Human-readable solution label (kept alongside preferred_term). range: string notes: description: Free-text notes about this solution as used in the parent recipe. range: string source: description: Provenance attribution for this solution entry. range: string term: description: Ontology term if available range: Term inlined: true mediaingredientmech_term: description: Legacy MediaIngredientMech:NNNNNN identifier for this solution component (pre-CHEBI-keying). range: MediaIngredientMechTerm recommended: false inlined: true mediaingredientmech_chebi_term: description: CHEBI-keyed linkage to a curated MediaIngredientMech ingredient (current MIM schema). range: MediaIngredientMechChebiTerm recommended: false inlined: true culturemech_term: description: Reference to another CultureMech media recipe for this solution range: CultureMechTerm recommended: false inlined: true comments: - Used when this solution is defined as a complete recipe in CultureMech - "Example: Bold Trace Stock (CultureMech:015441)" composition: description: >- Ingredients in the stock solution. Optional when the solution is referenced by name only (no inline composition copied from the source). range: IngredientDescriptor multivalued: true inlined_as_list: true solutions: description: Nested stock solutions added while preparing this stock solution range: SolutionDescriptor multivalued: true inlined_as_list: true concentration: description: Working concentration when added to medium range: ConcentrationValue inlined: true comments: - >- ASSERTED values only — a figure read from this medium's own source. A value inferred from other media goes in `concentration_candidates` and must never be written here, so a reader can always tell what the source said from what a tool concluded. concentration_candidates: description: >- Proposed working concentrations that are NOT asserted — each carries the basis it rests on and the evidence for it. Never overwrites `concentration`; a curator promotes one by hand after checking it. range: ConcentrationCandidate multivalued: true recommended: false inlined_as_list: true comments: - >- Multivalued because the evidence genuinely disagrees. The DSMZ stock "Trace element solution SL-10" is added at 1 ml/L in ten MediaDive media and at 0.05 ml/L in J537 (TREPONEMA ISOPTEROCOLA) — a 20x spread. A single inferred-value slot would force a tool to pick one and hide the other; an array lets both stand with their support until someone reads that medium's own recipe. - >- Introduced for the #150 cocktail repair, where a flattened stock's addition volume is often recoverable only by inference. preparation_notes: description: How to prepare the stock solution range: string storage_conditions: description: Storage requirements for the stock range: StorageConditions inlined: true shelf_life: description: Stability duration (e.g., "6 months at 4°C") range: string OrganismDescriptor: is_a: Descriptor description: Target organism for the medium attributes: preferred_term: description: Organism name (e.g., "Escherichia coli") required: true identifier: true range: string term: description: NCBITaxon identifier range: OrganismTerm bindings: - binds_value_of: id obligation_level: REQUIRED required: false inlined: true scoped_to_variant: description: >- Name of the `variants[]` entry this organism's growth evidence is scoped to, when growth is verified only on a specific variant of the medium and NOT on the parent recipe. Must match a `variants[].name` on the same record. Downstream KG builds should attach the organism<->medium edge to the named variant rather than the parent, so variant-only evidence is not propagated as a parent-medium claim. range: string gtdb_term: description: GTDB genome or lineage identifier (alternative to NCBITaxon) range: GTDBTerm inlined: true genome_assembly_id: description: >- Genome assembly accession(s) for this organism, complementing gtdb_term. Accepts RefSeq (GCF_), GenBank (GCA_), or BioSample (SAMN) identifiers. range: string multivalued: true pattern: "^(GCF_|GCA_|SAMN)[0-9.]+$" comments: - "Examples: GCF_000005845.2, GCA_000005845.2, SAMN02604091" - Complements gtdb_term for cases where assembly accession is the primary genome reference strain: description: Specific strain designation (e.g., "K-12", "MG1655") range: string growth_phase: description: Target growth phase (e.g., "exponential", "stationary") range: GrowthPhaseEnum growth_metrics: description: Quantitative growth measurements observed for this organism on this medium range: GrowthMetrics multivalued: true inlined_as_list: true comments: - Captures empirical growth performance (max OD, doubling time, growth rate, etc.) - Each entry should be tied to a literature reference via its evidence list community_role: description: Functional role in microbial community (e.g., PRIMARY_DEGRADER, SYNERGIST, COMMENSAL, COMPETITOR). range: CommunityOrganismRoleEnum multivalued: true target_abundance: description: Target relative abundance in community (0.0-1.0) range: float community_function: description: Specific functional contribution to community range: string multivalued: true cofactor_requirements: description: Cofactors required by this organism range: CofactorRequirement multivalued: true inlined_as_list: true transporters: description: Annotated transport systems range: TransporterAnnotation multivalued: true inlined_as_list: true evidence: description: Evidence supporting growth on this medium range: EvidenceItem multivalued: true inlined_as_list: true strain_modifications: description: >- Genotype/phenotype modifications relative to the wild-type or type strain. Strain-level (carries across observations) and distinct from per-observation `growth_metrics[].perturbations`. range: StrainModification multivalued: true inlined_as_list: true SourceEnvironmentDescriptor: is_a: Descriptor description: >- Environment from which target organisms originate or for which the medium is designed. Enables environment-based discovery and cross-repository linking with CommunityMech. attributes: preferred_term: description: Human-readable environment name (e.g., "peatland", "marine", "soil") required: true range: string term: description: ENVO ontology term for the environment range: EnvironmentTerm bindings: - binds_value_of: id obligation_level: REQUIRED recommended: true inlined: true comments: - Recommended but not required to allow media without known environment - Use ENVO Browser to find appropriate terms notes: description: Additional environmental context, conditions, or specificity range: string required: false comments: - Follows dismech Descriptor pattern used throughout CultureMech - Multivalued when added to MediaRecipe (media can serve multiple environments) - Optional field - backward compatible with existing records CofactorDescriptor: is_a: Descriptor description: A cofactor or coenzyme required for enzymatic activity attributes: preferred_term: description: Human-readable cofactor name (e.g., "Thiamine pyrophosphate", "NAD") required: true range: string term: description: CHEBI term for the cofactor range: ChemicalEntityTerm bindings: - binds_value_of: id obligation_level: REQUIRED recommended: true inlined: true category: description: High-level classification range: CofactorCategoryEnum recommended: true precursor: description: Precursor molecule (e.g., thiamine → TPP) range: string precursor_term: description: CHEBI term for precursor range: ChemicalEntityTerm bindings: - binds_value_of: id obligation_level: REQUIRED inlined: true ec_associations: description: EC numbers of enzymes using this cofactor range: string multivalued: true kegg_pathways: description: KEGG pathway IDs for biosynthesis range: string multivalued: true enzyme_examples: description: Example enzymes requiring this cofactor range: string multivalued: true biosynthesis_genes: description: Genes involved in cofactor biosynthesis range: string multivalued: true bioavailability: description: Uptake and availability characteristics range: string notes: description: Additional information about the cofactor range: string # ================================================================ # SUPPORTING CLASSES # ================================================================ SourceReference: description: >- Upstream database attribution for a record. Carried alongside curation_history; multivalued because a record can have multiple upstream sources (e.g. originally from MediaDive, also catalogued in CultureBotHT). attributes: database: description: Source database/repository name (e.g. CultureBotHT, MediaDive). range: string required: true database_id: description: Identifier or name in the source database. range: string url: description: Direct URL to the source record. range: string IngredientSynonym: description: An alternate name for an ingredient (e.g. brand name, abbreviation). attributes: synonym_text: description: The alternate name string. range: string required: true synonym_type: description: Synonym match type (e.g. EXACT, RELATED, BROAD). range: SynonymTypeEnum IngredientCurationMetadata: description: >- Structured metadata describing how an ingredient mapping was produced (mapping quality, confidence, source). Populated by curation pipelines. attributes: mapping_quality: description: Quality tier of the mapping (e.g. EXACT, LLM_ASSISTED, KG_FALLBACK). range: string confidence_score: description: Confidence score for the mapping (0.0-1.0). range: float curation_date: description: When the curation was performed (ISO-8601). range: string ontology_source: description: Ontology used as the mapping target (e.g. CHEBI). range: string IngredientReference: description: Reference to canonical ingredient attributes: preferred_term: description: Name of parent ingredient required: true range: string mediaingredientmech_id: description: MediaIngredientMech ID range: string pattern: "^MediaIngredientMech:\\d{6}$" ConcentrationValue: description: Quantified concentration with units attributes: value: description: Numeric value or range range: string required: true unit: description: Concentration unit range: ConcentrationUnitEnum required: true per_volume: description: Volume basis (e.g., "per liter", "per 100 mL") range: string ConcentrationCandidate: description: >- A concentration that has been PROPOSED but not asserted, carrying the basis it rests on and the evidence for it. This exists so an inferred value can be recorded without being mistaken for one that was read from a source. A candidate never overwrites an asserted `concentration`; promoting it is a curation decision, made after checking the record's own source. attributes: value: description: Numeric value or range, as the evidence gives it. range: string required: true unit: description: Concentration unit range: ConcentrationUnitEnum required: true basis: description: What kind of claim this is — how the value was arrived at. range: ConcentrationBasisEnum required: true support: description: >- The evidence, stated so it can be re-checked, e.g. "10 of 11 MediaDive media citing this stock add it at this volume". range: string recommended: true counterevidence: description: >- Evidence AGAINST this candidate, where any is known. Recorded because a candidate offered without its known counterexample invites the reader to trust it more than the evidence allows. range: string source: description: Citation or URL the support was read from. range: string recommended: true proposed_by: description: Script or curator that proposed the value. range: string proposed_on: description: ISO-8601 date the proposal was made. range: string GrowthMetrics: description: >- Quantitative growth measurements for an organism on a medium. Captures empirical growth performance (max OD, doubling time, growth rate) observed under defined conditions. Every non-empty record must cite at least one literature reference via the evidence list. attributes: max_od600: description: Maximum optical density observed (default wavelength 600 nm) range: float max_od_wavelength_nm: description: Wavelength at which OD was measured, in nanometers (default 600) range: integer ifabsent: int(600) doubling_time_minutes: description: Population doubling time in minutes range: float growth_rate_per_hour: description: Specific growth rate μ in h⁻¹ (inverse hours) range: float temperature_celsius: description: Temperature at which the measurement was taken, in degrees Celsius range: float ph_at_measurement: description: Medium pH at the time of measurement range: float measurement_conditions: description: >- Free-text description of measurement context (e.g., "shake flask, 200 rpm", "microtiter plate, 96-well, plate reader Tecan Spark") range: string evidence: description: Literature evidence supporting these growth measurements range: EvidenceItem multivalued: true required: true inlined_as_list: true comments: - Required for any populated GrowthMetrics record - Each evidence item should cite the paper reporting the measurement is_max_attainment: description: >- TRUE when the metric represents max-attained / standard / textbook growth on this medium for this organism. FALSE when it's conditional on a perturbation, mutation, or non-default condition (in which case `perturbations` and/or the OrganismDescriptor's `strain_modifications` should be populated). Optional; absence means "not asserted either way". range: boolean growth_mode: description: Cultivation mode under which the metric was measured. range: GrowthModeEnum perturbations: description: >- Applied stresses, modifications, or non-default conditions that accompanied this growth observation. When non-empty, `is_max_attainment` should typically be FALSE. range: PerturbationContext multivalued: true inlined_as_list: true nutrient_overrides: description: >- C/N/S/electron-source nutrients used in this observation that differ from the recipe's prescribed ingredients (e.g., "succinate as sole carbon source", "L-phenylalanine as sole nitrogen source"). range: NutrientOverride multivalued: true inlined_as_list: true PerturbationContext: description: >- A non-default condition under which a growth metric was observed — chemical stress, temperature stress, nutrient limitation, adaptation, or non-batch culture mode. When PerturbationContext is non-empty, GrowthMetrics.is_max_attainment should be FALSE (the metric is conditional, not a max claim). attributes: perturbation_type: description: Class of perturbation applied during the observation. range: PerturbationTypeEnum required: true descriptor: description: >- Free-text description (e.g. "Cr(VI) at 10 mg/L", "magnetosome-deficient strain", "cellulose-adapted", "induced at OD600=0.6"). range: string target: description: >- Subject of the perturbation — gene/locus for genetic, stressor compound for chemical, limiting nutrient for nutritional, substrate for adaptation. range: string level: description: Quantitative level of the perturbation (e.g. 10.0 for 10 mg/L Cr(VI), 4.0 for 4 °C). range: float level_unit: description: Unit for `level` (e.g. "mg/L", "mM", "%", "°C", "µmol·m⁻²·s⁻¹"). range: string ontology_id: description: >- Optional ontology CURIE for the perturbation type or agent (CHEBI for chemical agents, ENVO for environmental stress, NCIT for genetic-modification class, PATO for phenotypic qualities). Curator-supplied; pipeline does not auto-resolve. Renamed from `ontology_term` (G13) to align with the `_id` convention used for bare-string CURIEs elsewhere in the schema. The typed-Term-object convention is `_term`. range: string pattern: "^[A-Za-z][A-Za-z0-9._-]*:[A-Za-z0-9._-]+$" evidence: description: Literature evidence supporting the perturbation claim. range: EvidenceItem multivalued: true inlined_as_list: true StrainModification: description: >- A genotype/phenotype modification of the OrganismDescriptor's strain relative to the wild-type or type strain. Applies to the strain itself (carries across all media on which it grows), as distinct from PerturbationContext which applies per-observation. attributes: modification_type: description: Class of modification applied to the strain. range: StrainModificationTypeEnum required: true target: description: >- Gene/locus name, phenotype label, or substrate the modification targets (e.g. "magnetosome operon", "spo0A", "cellulose utilization"). range: string description: description: Curator free-text describing the modification. range: string ontology_id: description: >- Optional CURIE — NCIT:C120956 (Knockout), NCIT:C17026 (Genetic Modification), PATO:0015009 (mutant), etc. Renamed from `ontology_term` (G13) to align with the `_id` convention used for bare-string CURIEs. range: string pattern: "^[A-Za-z][A-Za-z0-9._-]*:[A-Za-z0-9._-]+$" evidence: description: Literature evidence supporting the modification claim. range: EvidenceItem multivalued: true inlined_as_list: true NutrientOverride: description: >- A nutrient source used in this observation that differs from the medium's nominal recipe — typically a "sole carbon source", "sole nitrogen source", or specific electron donor/acceptor pairing the original recipe doesn't enforce. Distinct from the medium's prescribed `ingredients`; represents experimental substitution at observation time. attributes: role: description: >- Functional role the override supplies to the experiment (e.g. CARBON_SOURCE, NITROGEN_SOURCE, SULFUR_SOURCE, PHOSPHATE_SOURCE). Retargeted from the retired NutrientRoleEnum to the MIM-imported NutritionalRoleEnum (which is broader — 12 values covering all macronutrient / vitamin / cofactor supply categories). Values that used to fit under NutrientRoleEnum but not NutritionalRoleEnum (ELECTRON_DONOR, ELECTRON_ACCEPTOR) belong on the cellular-metabolic facet of the *ingredient* the override supplies, not on the override itself. range: NutritionalRoleEnum required: true source: description: e.g. "succinate", "L-phenylalanine", "acetate". range: string required: true ontology_id: description: Preferred CHEBI / FOODON CURIE for the source compound. range: string pattern: "^[A-Za-z][A-Za-z0-9._-]*:[A-Za-z0-9._-]+$" is_sole_source: description: TRUE when this is the only source for that role in the experiment. range: boolean evidence: description: Literature evidence supporting the nutrient-override claim. range: EvidenceItem multivalued: true inlined_as_list: true TemperatureValue: description: Temperature with units attributes: value: description: Numeric temperature value range: float required: true unit: description: Temperature unit range: TemperatureUnitEnum required: true PhRange: description: >- Acceptable pH range for a medium. Use `min` and `max` (floats) for parseable ranges; `notes` preserves the original free-text whenever a value can't be parsed cleanly (avoids data loss during migration). attributes: min: description: Lower bound of the acceptable pH range (inclusive). range: float max: description: Upper bound of the acceptable pH range (inclusive). range: float notes: description: >- Free-text qualifier or the original unparseable value (e.g. "varies by species", "alkaline 9-10 for halophiles"). range: string PreparationStep: description: A step in medium preparation attributes: step_number: description: Sequential order range: integer required: true action: description: Action type range: PreparationActionEnum required: true description: description: Detailed instruction range: string required: true temperature: description: Temperature for this step range: TemperatureValue inlined: true duration: description: Time duration (e.g., "15 minutes", "overnight") range: string equipment: description: Required equipment (e.g., "autoclave", "magnetic stirrer") range: string notes: description: Additional tips or warnings range: string SterilizationDescriptor: description: Sterilization method and parameters attributes: method: description: Sterilization technique range: SterilizationMethodEnum required: true temperature: description: Temperature setting range: TemperatureValue inlined: true pressure: description: Pressure in psi or kPa (for autoclaving) range: float duration: description: Sterilization duration range: string notes: description: Special instructions (e.g., "Filter-sterilize heat-labile components separately") range: string StorageConditions: description: Storage requirements for prepared medium attributes: temperature: description: Storage temperature range: TemperatureValue required: true inlined: true light_condition: description: Light exposure requirement range: LightConditionEnum shelf_life: description: Duration of stability range: string container_type: description: Recommended container (e.g., "glass bottle", "polypropylene tube") range: string notes: description: Additional storage tips range: string MediaVariant: description: A variant or modification of the base recipe attributes: name: description: Variant name (e.g., "Low Salt LB", "LB + Ampicillin") required: true identifier: true range: string relationship: description: >- Typed relationship to the base recipe, drawn from the same enum that MediaRecipeReference.relationship uses. Curators should set this whenever a clean enum value applies; the free-text `modifications` slot remains for nuance or for variants whose relationship is genuinely composite. range: MediaVariantRelationshipEnum recommended: true description: description: Purpose and context range: string modifications: description: What differs from base recipe range: string multivalued: true purpose: description: Why this variant exists range: string supplier_info: description: Commercial supplier if premix range: SupplierInfo inlined: true evidence: description: Evidence supporting the variant range: EvidenceItem multivalued: true inlined_as_list: true MediaRecipeReference: description: Reference to another CultureMech media recipe record attributes: id: description: Stable CultureMech identifier for the referenced media record range: string pattern: "^CultureMech:\\d{6}$" name: description: Referenced media recipe name range: string path: description: Repository-relative YAML path for the referenced media record range: string pattern: "^data/normalized_yaml/.+\\.ya?ml$" relationship: description: Parent-child relationship type for this link range: MediaVariantRelationshipEnum notes: description: Curator notes about the relationship or unresolved mapping range: string evidence: description: Evidence supporting the media parent-child relationship range: EvidenceItem multivalued: true inlined_as_list: true SupplierInfo: description: Commercial supplier information attributes: supplier_name: description: Vendor name (e.g., "Sigma-Aldrich", "Thermo Fisher") range: string required: true catalog_number: description: Product catalog number range: string product_url: description: Direct product link range: uri notes: description: Additional sourcing notes range: string PublicationReference: description: Literature reference attributes: reference: description: Citation (PMID, DOI, or historical reference) range: string required: true implements: - linkml:authoritative_reference comments: - Use format PMID:12345678 or doi:10.1038/... for automatic validation. title: description: Publication title range: string authors: description: Author list range: string year: description: Publication year range: integer notes: description: Additional context about the reference range: string EvidenceItem: description: Evidence supporting a claim about media formulation or performance attributes: reference: description: Citation (PMID, DOI, or historical reference) range: string required: true identifier: true implements: - linkml:authoritative_reference comments: - This is automatically validated by the linkml-reference-validator tool. - Use format PMID:12345678 or doi:10.1038/... for automatic validation. - Acts as the natural identifier inside an `evidence:` list (no duplicates within a single record's evidence array). supports: description: Level of support range: EvidenceItemSupportEnum required: true snippet: description: Exact quote from paper (if PMID/DOI available) range: string implements: - linkml:excerpt comments: - This is automatically validated by the linkml-reference-validator tool. - Must be an exact substring of the cited paper's text. explanation: description: Why this evidence supports the claim range: string required: true CurationEvent: description: Audit trail entry for curation attributes: timestamp: description: ISO 8601 timestamp with a plausible 21st-century curation year range: string required: true pattern: "^20[0-9]{2}-" curator: description: Name or identifier of curator range: string required: true action: description: Action taken (created, updated, validated, etc.) range: string required: true notes: description: Additional context range: string changes: description: >- Structured summary of what changed in this event (free-text or semi-structured; used by automated curators e.g. `Set category to 'bacterial' (was: MISSING)`). range: string source: description: >- Source attribution for this curation event (e.g. a source PDF, a sibling CultureMech recipe, an external dataset). range: string SourceData: description: Provenance information for imported records attributes: origin: description: Source repository name range: string required: true examples: - value: CommunityMech comments: - Indicates which X-Mech repository this record was imported from community_ids: description: List of CommunityMech IDs this recipe was derived from range: string multivalued: true comments: - Enables bidirectional linking from CultureMech to CommunityMech - Format CommunityMech:NNNNNN import_date: description: Date of import (ISO 8601) range: string comments: - ISO 8601 date format YYYY-MM-DD evidence: description: Evidence records from source repository range: EvidenceItem multivalued: true inlined_as_list: true comments: - Preserves evidence from original CommunityMech record - Maintains literature references and provenance notes: description: Import notes and additional context range: string mediaingredientmech_id: description: >- MediaIngredientMech identifier for this imported solution record (carried when origin is `MediaIngredientMech`). Format `UNMAPPED_NNNN` or `MediaIngredientMech:NNNNNN`. range: string CofactorRequirement: description: Cofactor requirement for an organism attributes: cofactor: description: Required cofactor range: CofactorDescriptor required: true inlined: true can_biosynthesize: description: Whether organism can synthesize this cofactor range: boolean required: true confidence: description: Confidence level (0.0-1.0) based on genome annotation range: float evidence: description: Supporting evidence for requirement range: EvidenceItem multivalued: true inlined_as_list: true genes: description: Genes related to biosynthesis or utilization range: string multivalued: true TransporterAnnotation: description: Annotation of a transporter or transport system attributes: name: description: Transporter name or gene name required: true range: string transporter_type: description: Classification of transporter range: TransporterTypeEnum required: true substrates: description: Transported substrates range: string multivalued: true substrate_terms: description: CHEBI terms for substrates range: ChemicalEntityTerm bindings: - binds_value_of: id obligation_level: REQUIRED multivalued: true inlined_as_list: true direction: description: Transport direction (import, export, bidirectional) range: string genes: description: Gene names or locus tags range: string multivalued: true ec_number: description: EC number if enzymatic range: string notes: description: Additional functional notes range: string # ================================================================ # ONTOLOGY TERM CLASSES # ================================================================ ChemicalEntityTerm: is_a: Term description: >- A term identifying a chemical or biological ingredient. Primarily CHEBI, with FOODON / UBERON / ENVO accepted for ingredients (food products, anatomical tissues, environmental samples) where no CHEBI equivalent exists upstream. `mediadive.compound:*` is also accepted as the upstream MediaDive grounding kept alongside CHEBI mappings on solution-composition entries. MICRO (Ontology of Prokaryotic Phenotypic and Metabolic Characters) is accepted for enzymatic protein digests (tryptone, peptone, proteose peptone, soy peptone, casein hydrolysate) which ChEBI cannot represent because CHEBI:59999 "chemical substance" requires constant composition. slot_usage: id: pattern: "^(CHEBI|FOODON|MICRO|UBERON|ENVO|mediadive\\.compound):\\w+$" id_prefixes: - CHEBI - FOODON - MICRO - UBERON - ENVO - mediadive.compound ChebiTerm: is_a: Term description: >- A strictly-CHEBI term reference. Use for the `chebi_term` slot where the contract is "this is the CHEBI grounding specifically" — distinct from the polymorphic `ChemicalEntityTerm` used by `term` slots that may carry upstream non-CHEBI IDs. slot_usage: id: pattern: "^CHEBI:\\d+$" id_prefixes: - CHEBI OrganismTerm: is_a: Term description: An NCBITaxon term representing an organism slot_usage: id: pattern: "^NCBITaxon:\\d+$" id_prefixes: - NCBITaxon GTDBTerm: is_a: Term description: >- A GTDB genome identifier. id = GTDB accession (e.g. GTDB:RS_GCF_000006945.2), label = full GTDB lineage string (e.g. d__Bacteria;p__Proteobacteria;...) id_prefixes: - GTDB MediaDatabaseTerm: is_a: Term description: Identifier from authoritative media database id_prefixes: - mediadive.medium # MediaDive REST API format (for kg-microbe compatibility) - komodo.medium # KOMODO ModelSEED format (for kg-microbe compatibility) - DSMZ - TOGO - ATCC - NCIT MediaIngredientMechTerm: is_a: Term description: >- A legacy MediaIngredientMech identifier (MediaIngredientMech:NNNNNN) for a media ingredient. MediaIngredientMech has since migrated to a CHEBI-keyed schema and no longer mints these IDs; for new linkages use `mediaingredientmech_chebi_term` instead. Retained for the existing corpus, which still carries these IDs. slot_usage: id: pattern: "^MediaIngredientMech:\\d{6}$" id_prefixes: - MediaIngredientMech MediaIngredientMechChebiTerm: is_a: Term description: >- CHEBI-keyed linkage to a MediaIngredientMech curated ingredient. MediaIngredientMech migrated from minting `MediaIngredientMech:NNNNNN` ids to keying its curated ingredient entities by CHEBI; this term records the matched MIM entity's CHEBI identifier (with the MIM `preferred_term` as label). Distinct from the ingredient's own `term`/`chebi_term` grounding: it asserts "this ingredient corresponds to a curated MIM ingredient", even though the id coincides with the CHEBI grounding. slot_usage: id: pattern: "^CHEBI:\\d+$" id_prefixes: - CHEBI CultureMechTerm: is_a: Term description: A CultureMech identifier for a media recipe used as component slot_usage: id: pattern: "^CultureMech:\\d{6}$" description: CultureMech identifier (e.g., "CultureMech:009592") id_prefixes: - CultureMech comments: - Used when one medium references another medium as an ingredient or component - "Example: BG-11 Trace Metals Solution (CultureMech:015441) used in BG-11 Medium" EnvironmentTerm: is_a: Term description: An ENVO term representing an environmental system or biome slot_usage: id: pattern: "^ENVO:\\d{7,8}$" description: ENVO identifier (7-8 digit format) id_prefixes: - ENVO comments: - ENVO prefix already defined in schema prefixes - Pattern allows both 7 and 8 digit ENVO IDs - "Examples: ENVO:00000044 (peatland), ENVO:00002149 (sea water)" ImportMetadata: description: >- Tracking information for imported media records. Enables versioning, provenance tracking, and reproducible updates. attributes: source_database: description: Source database from which this medium was imported range: SourceDatabaseEnum required: true source_id: description: >- Original identifier in source database (e.g., "Medium 1234", "M3205"). Preserved for traceability and update tracking. range: string required: true import_version: description: >- Import version following format vMAJOR.MINOR.PATCH_YYYY-MM-DD. Example: v1.0.0_2026-01-27 range: string required: true pattern: "^v\\d+\\.\\d+\\.\\d+_\\d{4}-\\d{2}-\\d{2}$" import_date: description: ISO 8601 timestamp when this record was imported range: string required: true import_skill: description: >- Name of the skill or script that performed the import. Example: "import-mediadive", "import-togo-skill" range: string last_updated: description: ISO 8601 timestamp of most recent update range: string update_history: description: >- Chronological log of all updates applied to this record. Enables full audit trail from initial import to present. range: UpdateEvent multivalued: true inlined_as_list: true UpdateEvent: description: >- Record of a single update to an imported media recipe. Captures what changed, when, and why. attributes: timestamp: description: ISO 8601 timestamp when update was applied range: string required: true import_version: description: Import version that applied this update range: string required: true action: description: Type of update action performed range: UpdateActionEnum required: true fields_changed: description: >- List of field names that were modified in this update. Example: ["ingredients", "ph_value", "description"] range: string multivalued: true notes: description: >- Human-readable explanation of the update. Why was this change made? What was the context? range: string # ================================================================ # ENUMERATIONS # ================================================================ enums: RecordKindEnum: description: >- Whether a normalized_yaml record describes a growth medium or a standalone stock solution. See the `record_kind` slot: this is stated only where the `term.id` prefix cannot carry the distinction. permissible_values: MEDIUM: description: A growth medium. SOLUTION: description: >- A standalone stock solution (trace elements, vitamins, buffers). Excluded from media-level audits and from the deep-research ranking. MediumTypeEnum: description: >- Single-axis classification of culture medium, MAINTAINED alongside the three orthogonal axes rather than replaced by them. It conflates composition, nutritional level and functional role into one slot, which is why MediumCompositionTypeEnum (composition_type), MediumNutritionalClassEnum (nutritional_class) and MediumFunctionalRoleEnum (functional_role) exist and are the primary axes for new curation. This enum remains the published single-valued view: populate BOTH, and keep this slot derived from composition_type. The per-value "Migrates to" notes below define that derivation and are parsed by the consistency guard, so they are load-bearing documentation rather than historical commentary. permissible_values: DEFINED: description: Chemically defined medium with known composition. Migrates to composition_type=DEFINED. meaning: NCIT:C64372 COMPLEX: description: Medium with undefined components (e.g., yeast extract). Migrates to composition_type=UNDEFINED. meaning: NCIT:C64371 SELECTIVE: description: Medium that selects for specific organisms. Migrates to functional_role=[SELECTIVE]. DIFFERENTIAL: description: Medium that differentiates organism types. Migrates to functional_role=[DIFFERENTIAL]. ENRICHMENT: description: Medium that enriches for specific organisms. Migrates to functional_role=[ENRICHMENT]. MINIMAL: description: Medium with minimal nutrients required for growth. Migrates to nutritional_class=MINIMAL. BUFFER: description: Buffer solution (e.g. PBS) — not a growth medium per se but stored alongside media for context. NEGATIVE_CONTROL: description: Negative-control "medium" used as an experimental baseline (e.g. distilled water). MediumCompositionTypeEnum: description: >- Composition axis: how chemically defined the medium is. Single-valued and orthogonal to nutritional level (MediumNutritionalClassEnum) and functional role (MediumFunctionalRoleEnum). permissible_values: DEFINED: description: Chemically defined (synthetic) medium; every component and its exact quantity is known. Synonyms —synthetic. meaning: NCIT:C64372 UNDEFINED: description: Medium containing one or more chemically undefined components (e.g. yeast extract, peptone, casamino acids, tissue or plant extracts). Multi-axis counterpart of MediumTypeEnum value COMPLEX, which remains maintained and derived from this slot. Synonyms —complex. meaning: NCIT:C64371 SEMI_DEFINED: description: Predominantly defined medium supplemented with a small amount of one or more undefined components (e.g. a defined base plus a trace of yeast extract). Synonyms —semisynthetic. MediumNutritionalClassEnum: description: >- Nutritional-level axis: how nutrient-rich the medium is. Single-valued and orthogonal to composition (MediumCompositionTypeEnum) and functional role (MediumFunctionalRoleEnum). permissible_values: MINIMAL: description: Provides only the minimal nutrients required for growth of the target organism — typically a defined medium with a single carbon/energy source plus essential salts (e.g. M9). RICH: description: Provides nutrients in excess (abundant amino acids, peptides, vitamins, and carbon sources), supporting rapid growth of fastidious or general organisms (e.g. LB, TSB, BHI). GENERAL_PURPOSE: description: Standard nutrient level for routine cultivation — neither deliberately minimal nor deliberately enriched. Use when a medium is not clearly MINIMAL or RICH. MediumFunctionalRoleEnum: description: >- Functional-role axis: what the medium is designed to do. MULTIVALUED — a medium may be both selective and differential, etc. Orthogonal to composition (MediumCompositionTypeEnum) and nutritional level (MediumNutritionalClassEnum). permissible_values: GENERAL_PURPOSE: description: Non-selective, non-differential medium for routine growth of a broad range of organisms. Synonyms —non-selective, basal. SELECTIVE: description: Suppresses or prevents growth of unwanted organisms (via antibiotics, dyes, bile salts, NaCl, pH, etc.) to favor a target group. DIFFERENTIAL: description: Distinguishes organism types by a visible biochemical reaction (e.g. color change from fermentation, or hemolysis) without necessarily inhibiting growth. ENRICHMENT: description: Promotes growth of a target organism to detectable numbers from a mixed population, typically prior to isolation. TRANSPORT: description: Maintains organism viability without significant multiplication during transport or storage. ASSAY: description: Standardized medium for a specific assay (e.g. antibiotic potency, vitamin or growth-factor bioassay). ENUMERATION: description: Supports viable-count / colony enumeration (e.g. heterotrophic plate count media such as R2A). PhysicalStateEnum: description: Physical form of the medium permissible_values: LIQUID: description: Liquid broth medium SOLID_AGAR: description: Solidified with agar SEMISOLID: description: Reduced agar concentration for motility testing BIPHASIC: description: Both liquid and solid phases ConcentrationBasisEnum: description: >- How a proposed concentration was arrived at. Ordered from strongest to weakest, because the distinction is the whole point of recording a candidate rather than an asserted value. permissible_values: READ_FROM_THIS_MEDIUM: description: >- Printed in this medium's own source. This is an asserted value and belongs in `concentration`, not here; the term exists so a promotion can record what it was promoted on. READ_FROM_STOCK_DEFINITION: description: >- Read from the cited definition of the stock solution itself (e.g. DSMZ medium 84 defines its trace element solution and the volume it is added at), for a medium that references that stock by name. CROSS_MEDIUM_INFERENCE: description: >- Taken from OTHER media that use the same named stock, not from this medium's own source. Defensible when the stock's volume is consistent across many media, and wrong whenever a medium departs from the norm — which does happen (SL-10 is 1 ml/L in ten media and 0.05 ml/L in J537). TYPICAL_VALUE: description: >- A conventional value for this class of stock, with no per-medium evidence at all. The weakest basis; recorded only to be checked. comments: - >- A candidate whose basis is CROSS_MEDIUM_INFERENCE or TYPICAL_VALUE must not be promoted into `concentration` without reading the record's own source — that is the check the basis exists to prompt. ConcentrationUnitEnum: description: Units for concentration permissible_values: G_PER_L: description: grams per liter meaning: UO:0000175 MG_PER_L: description: milligrams per liter MICROG_PER_L: description: micrograms per liter MOLAR: description: moles per liter meaning: UO:0000062 MILLIMOLAR: description: millimoles per liter MICROMOLAR: description: micromoles per liter PERCENT_W_V: description: percent weight per volume PERCENT_W_W: description: percent weight per weight PERCENT_V_V: description: percent volume per volume ML_PER_L: description: milliliters per liter (for solution/component additions) MG_PER_ML: description: milligrams per milliliter FOLD_DILUTION: description: dilution factor expressed as 1:N (e.g. "10-fold dilution") L: description: liters — used for volume-only entries like "Make up to 1 L" final-volume markers. VARIABLE: description: variable or unspecified concentration TemperatureUnitEnum: description: Units for temperature permissible_values: CELSIUS: description: Degrees Celsius meaning: UO:0000027 FAHRENHEIT: description: Degrees Fahrenheit KELVIN: description: Kelvin meaning: UO:0000012 AtmosphereEnum: description: Atmospheric conditions for incubation permissible_values: AEROBIC: description: Oxygen-rich atmosphere ANAEROBIC: description: Oxygen-free atmosphere MICROAEROPHILIC: description: Low oxygen atmosphere (typically 2-10% O2) PreparationActionEnum: description: Controlled vocabulary for preparation steps permissible_values: DISSOLVE: description: Dissolve ingredients in solvent MIX: description: Mix or stir components HEAT: description: Apply heat COOL: description: Cool to specified temperature AUTOCLAVE: description: Steam sterilization under pressure FILTER: description: Remove solids or particles by filtration FILTER_STERILIZE: description: Filter through 0.22 μm membrane ADJUST_PH: description: Adjust pH with acid or base ADD_AGAR: description: Add agar for solidification POUR_PLATES: description: Dispense into petri dishes ALIQUOT: description: Divide into smaller portions STORE: description: Store under specified conditions SterilizationMethodEnum: description: Sterilization techniques permissible_values: AUTOCLAVE: description: Steam sterilization under pressure (121°C, 15 psi, 15-20 min) FILTER: description: Filtration through 0.22 μm filter DRY_HEAT: description: Dry heat sterilization (160-180°C) TYNDALLIZATION: description: Intermittent sterilization for heat-sensitive media NONE: description: No sterilization (non-sterile media) LightConditionEnum: description: Light exposure requirements permissible_values: DARK: description: Store in complete darkness LIGHT_PROTECTED: description: Protect from light (amber bottle or foil wrap) AMBIENT: description: Normal laboratory lighting ModifierEnum: description: Modification type for variants permissible_values: INCREASED: description: Elevated concentration relative to base recipe DECREASED: description: Reduced concentration relative to base recipe ABSENT: description: Ingredient omitted in this variant EvidenceItemSupportEnum: description: Level of evidence support permissible_values: SUPPORT: description: Evidence supports the claim REFUTE: description: Evidence refutes the claim PARTIAL: description: Evidence partially supports the claim NO_EVIDENCE: description: No evidence found WRONG_STATEMENT: description: Statement is incorrect CategoryEnum: description: Organizational category for media recipes permissible_values: bacterial: description: Media for bacterial cultivation fungal: description: Media for fungal cultivation archaea: description: Media for archaeal cultivation specialized: description: Specialized or multi-domain media algae: description: Media for algal cultivation imported: description: Imported from external sources (to be recategorized) OrganismCultureTypeEnum: description: Whether the medium targets a pure isolate or a mixed microbial community permissible_values: isolate: description: Pure culture of one or more specific strains community: description: Mixed/consortium culture of multiple organisms CofactorCategoryEnum: description: High-level classification of cofactor types permissible_values: VITAMINS: description: Vitamins and vitamin-derived cofactors METALS: description: Metal ions and metal-containing cofactors NUCLEOTIDES: description: Nucleotide cofactors ENERGY_TRANSFER: description: Energy transfer and group transfer cofactors OTHER_SPECIALIZED: description: Specialized cofactors (PQQ, F420, etc.) CommunityOrganismRoleEnum: description: >- Role an organism plays in a microbial community (formerly `CellularRoleEnum`; renamed 2026-07-19 for consistency with the MIM #120 rename and to disambiguate from a forthcoming `CellularMetabolicRoleEnum` on ingredient records — these values describe organisms, not ingredients). permissible_values: PRIMARY_DEGRADER: description: Primary degrader with direct substrate degradation capability (40-60% abundance) REDUCTIVE_DEGRADER: description: Specialized degrader using reductive pathways OXIDATIVE_DEGRADER: description: Specialized degrader using oxidative pathways BIOTRANSFORMER: description: Converts substrates to intermediates without complete degradation SYNERGIST: description: Provides complementary metabolic functions (15-30% abundance) BRIDGE_ORGANISM: description: Biosynthesizes and provides essential cofactors to community ELECTRON_SHUTTLE: description: Facilitates electron transfer between community members DETOXIFIER: description: Handles and detoxifies metabolic intermediates COMMENSAL: description: General commensal organism COMPETITOR: description: Competitive organism TransporterTypeEnum: description: Classification of membrane transporter systems permissible_values: ABC: description: ATP-binding cassette transporter MFS: description: Major facilitator superfamily transporter PTS: description: Phosphotransferase system TONB: description: TonB-dependent receptor SYMPORTER: description: Symporter or co-transporter ANTIPORTER: description: Antiporter or exchanger UNIPORTER: description: Uniporter or channel PORIN: description: Porin or outer membrane protein SIDEROPHORE_RECEPTOR: description: Siderophore receptor for iron uptake DEHALOGENASE: description: Dehalogenase enzyme for halogenated compounds FLUORIDE_EXPORTER: description: Fluoride-specific exporter VariantTypeEnum: description: Type of chemical variant relationship to parent permissible_values: HYDRATE: description: Hydrated form of parent chemical SALT_FORM: description: Different salt form of parent chemical ANHYDROUS: description: Anhydrous form of parent chemical NAMED_HYDRATE: description: Named hydrate (monohydrate, heptahydrate, etc.) CHEMICAL_VARIANT: description: Other chemical variant of parent MediaVariantRelationshipEnum: description: Type of parent-child relationship between media recipes permissible_values: CONCENTRATION_VARIANT: description: Same recognizable base medium with one or more concentration changes PHYSICAL_STATE_VARIANT: description: Same recognizable base medium with broth, agar, semisolid, or biphasic state change SUPPLEMENTED_VARIANT: description: Parent medium plus added supplement, antibiotic, blood, serum, carbon source, or other component OMITTED_COMPONENT_VARIANT: description: Parent medium with one or more components omitted SUBSTITUTED_COMPONENT_VARIANT: description: Parent medium with one or more components substituted PH_VARIANT: description: Parent medium adjusted to a different pH or pH range SALINITY_VARIANT: description: Parent medium adjusted to a different salt or salinity level STRAIN_SPECIFIC_VARIANT: description: Parent medium modified for a specific organism or strain SOURCE_DUPLICATE: description: Separate source record for the same formulation as the parent DERIVED_FROM: description: Broad parent-child relationship when a more specific relationship is not yet curated UNCERTAIN: description: Candidate relationship that requires additional source or formulation review MergeReasonEnum: description: Reason why recipes were merged together permissible_values: EXPLICIT_MERGE_RULE: description: Merged due to explicit rule from MediaIngredientMech IDENTICAL_FINGERPRINT: description: Merged due to identical ingredient fingerprints SAME_PARENT_INGREDIENTS: description: Merged due to same parent ingredients (aggressive mode) HYDRATION_VARIANT_ONLY: description: Merged due to only hydration differences (variant-aware mode) NO_MATCH: description: Not merged - no matching criteria met SourceDatabaseEnum: description: External databases from which media recipes are imported permissible_values: MEDIADIVE: description: MediaDive (DSMZ) media database meaning: https://mediadive.dsmz.de/ TOGO: description: TOGO Medium database (Japan) meaning: http://togodb.org/db/medium/ KOMODO: description: KOMODO media database (Korea) MEDIADB: description: MediaDB database UTEX: description: UTEX Culture Collection of Algae meaning: https://utex.org/ CCAP: description: Culture Collection of Algae and Protozoa meaning: https://www.ccap.ac.uk/ SAG: description: Culture Collection of Algae at Göttingen University meaning: https://sagdb.uni-goettingen.de/ CULTUREBOTHT: description: CultureBotHT repository COMMUNITYMECH: description: CommunityMech (X-Mech) integration BACDIVE: description: BacDive bacterial database meaning: https://bacdive.dsmz.de/ NBRC: description: NITE Biological Resource Center meaning: https://www.nite.go.jp/nbrc/ ATCC: description: American Type Culture Collection meaning: https://www.atcc.org/ MANUAL: description: Manually curated (not imported from external database) UpdateActionEnum: description: Type of update action applied to an imported record permissible_values: INITIAL_IMPORT: description: First import from source database ENRICHED: description: Additional metadata or enrichment added CORRECTED: description: Errors or inconsistencies corrected MERGED: description: Merged with duplicate or related records REFRESHED: description: Updated from source database refresh NORMALIZED: description: Format or structure normalized to schema PerturbationTypeEnum: description: >- Class of perturbation applied during a growth observation. Used by PerturbationContext.perturbation_type to flag conditional growth claims so downstream consumers can distinguish them from max-attainment / standard-condition observations. permissible_values: GENETIC_MODIFICATION: description: Knockout, deletion, insertion, or point mutation acting at observation time. meaning: NCIT:C17026 CHEMICAL_STRESS: description: Heavy metals, antibiotics, oxidative agents, salts at non-default levels. meaning: NCIT:C25574 TEMPERATURE_STRESS: description: Temperature outside the organism's optimum range (heat or cold shock). OXIDATIVE_STRESS: description: Reactive oxygen species, peroxide, paraquat, etc. NUTRIENT_LIMITATION: description: Sole-source / depletion / unusual substrate as growth driver. ADAPTATION: description: Serial passage / experimental evolution to grow on a substrate or condition. GROWTH_PHASE: description: Slow-growth, lag, or stationary-phase observations distinct from exponential max. CULTURE_MODE: description: Chemostat, fed-batch, or biofilm vs. standard batch. PH_STRESS: description: pH outside the organism's optimum. OTHER: description: Use sparingly; prefer a more specific value above. StrainModificationTypeEnum: description: >- Class of genetic or selection-derived modification carried by a strain relative to the wild-type or type strain. permissible_values: KNOCKOUT: description: Targeted gene disruption (most commonly via insertion). meaning: NCIT:C120956 DELETION: description: Targeted gene or operon deletion. INSERTION: description: Targeted gene or marker insertion. POINT_MUTATION: description: Single-nucleotide or small-residue substitution. OVEREXPRESSION: description: Gene placed under stronger promoter / on multi-copy vector. COMPLEMENTATION: description: Wild-type allele restored on knockout background. ADAPTATION: description: Serial selection / experimental evolution producing a stable phenotype. SELECTION: description: Strain isolated by selective pressure (e.g. plate selection, enrichment). OTHER: description: Use sparingly; prefer a more specific value above. GrowthModeEnum: description: >- Cultivation mode under which a growth metric was measured. Distinct from MediaRecipe.culture_vessel which describes the vessel itself. permissible_values: BATCH: description: Standard closed-system batch culture. CHEMOSTAT: description: Continuous culture with controlled dilution rate. TURBIDOSTAT: description: Continuous culture controlled to maintain a target turbidity. CONTINUOUS_FLOW: description: Other continuous-flow cultivation modes. FED_BATCH: description: Batch culture with controlled nutrient feed. BIOFILM: description: Surface-attached / biofilm cultivation. SOLID_SURFACE: description: Plate / agar / solid-substrate cultivation. UNSPECIFIED: description: Mode not stated in the source paper. # ---------------------------------------------------------------------- # Audit-followup enums (G12). All values are derived from existing slot # descriptions / observed in-corpus values; introducing them turns the # corresponding `range: string` slots into typed enums so the linkml # validator (and downstream consumers) get real type checking. # ---------------------------------------------------------------------- MergeModeEnum: description: Merge pipeline mode used by `MergeMetadata.merge_mode`. permissible_values: CONSERVATIVE: description: Only merge on identical fingerprints. AGGRESSIVE: description: Merge across hydration / parent-ingredient equivalence. VARIANT_AWARE: description: Use the hierarchy-aware variant fingerprint to merge. FingerprintModeEnum: description: Algorithm used to compute the ingredient fingerprint. permissible_values: ORIGINAL: description: Original ingredient set, no hierarchy resolution. CHEMICAL: description: Parent CHEBI IDs from MediaIngredientMech hierarchy. VARIANT: description: Parent CHEBI + variant type (HYDRATE / ANHYDROUS / SALT_FORM). GrowthPhaseEnum: description: Target microbial growth phase for a measurement / inoculum. permissible_values: LAG: description: Lag phase (no significant net growth). EXPONENTIAL: description: Exponential / log phase. STATIONARY: description: Stationary phase. DEATH: description: Death / decline phase. UNSPECIFIED: description: Phase not stated by the source. TermMatchTypeEnum: description: >- Provenance of an ontology-term mapping (`Term.match_type`). Values use the lowercase-snake convention emitted by upstream grounding pipelines (kg-microbe, manual curation). Three values are observed in the current corpus (kg_fallback, exact_match, synonym_match_ambiguous); the others are reserved for explicit curator use. permissible_values: exact_match: description: Exact label / synonym match. kg_fallback: description: Inferred from the kg-microbe ingredient graph as a fallback. synonym_match_ambiguous: description: Multiple equally-good synonym matches; mapping is uncertain. manual_curated: description: Human curator selected this term. automated_expert_mapping: description: Produced by an automated expert-mapping pipeline (e.g. LLM-assisted). fuzzy: description: Fuzzy / approximate string match. corpus_consensus: description: >- Borrowed from the unanimous reliable grounding of the same ingredient label elsewhere in the corpus (G25 Phase 1) — used to replace a low-confidence kg_fallback chebi_term without an external lookup. SynonymTypeEnum: description: Type of synonym relationship for an IngredientSynonym. permissible_values: EXACT: description: Exact synonym. RELATED: description: Related but not interchangeable. BROAD: description: Broader concept. NARROW: description: Narrower concept. ABBREVIATION: description: Abbreviation or shorthand (e.g. "TSB" for "Tryptic Soy Broth").