CultureMech - Microbial Growth Media Schema

Classes (47)

`MediaRecipe`

A complete growth medium formulation for culturing microorganisms. This is the root entity - one per YAML file.

Attribute	Range	Cardinality	Status	Description
`id`	`string`	single	required	Stable canonical external CultureMech identifier for this media recipe. Immutable after issuance and never reused; lifecycle is published in data/culturemech_recipe_catalog.tsv.
`id_lineage_token`	`string`	single	optional	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.
`name`	`string`	single	required	Human-readable medium name (e.g., "LB Broth", "M9 Minimal Medium")
`original_name`	`string`	single	optional	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.
`category`	`CategoryEnum`	single	recommended	Broad category for organization
`categories`	`CategoryEnum`	list	optional	All categories this recipe appears in (for cross-category merges)
`high_metal`	`boolean`	single	optional	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.
`high_ree`	`boolean`	single	optional	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.
`synonyms`	`RecipeSynonym`	list	optional	Alternate names from merged duplicate recipes
`merged_from`	`string`	list	optional	Original recipe IDs that were merged into this record
`merge_fingerprint`	`string`	single	optional	SHA256 hash of ingredient set for deduplication tracking
`chemical_fingerprint`	`string`	single	optional	SHA256 hash using parent ingredients (hierarchy-aware)
`variant_fingerprint`	`string`	single	optional	SHA256 hash preserving variant distinctions
`fingerprint_version`	`string`	single	optional	Version of fingerprinting algorithm used
`merge_metadata`	`MergeMetadata`	single	optional	Metadata about merge process and quality
`media_term`	`MediaTypeDescriptor`	single	recommended	Reference to authoritative media database
`kg_microbe_match`	`string`	single	optional	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).
`description`	`string`	single	optional	Overview of the medium and its purpose
`target_organisms`	`OrganismDescriptor`	list	recommended	Organisms for which this medium is designed
`source_environment`	`SourceEnvironmentDescriptor`	list	optional	Environment(s) from which target organisms originate or for which this medium is designed. Enables environment-based queries and linking to CommunityMech environmental metadata.
`organism_culture_type`	`OrganismCultureTypeEnum`	single	recommended	Whether this medium targets a pure isolate culture or a mixed microbial community
`record_kind`	`RecordKindEnum`	single	optional	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.
`medium_type`	`MediumTypeEnum`	single	optional	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.
`composition_type`	`MediumCompositionTypeEnum`	single	recommended	Composition axis — how chemically defined the medium is (DEFINED / UNDEFINED / SEMI_DEFINED). Supersedes the DEFINED/COMPLEX values of the deprecated medium_type slot.
`nutritional_class`	`MediumNutritionalClassEnum`	single	optional	Nutritional-level axis — MINIMAL / RICH / GENERAL_PURPOSE. Orthogonal to composition_type and functional_role.
`functional_role`	`MediumFunctionalRoleEnum`	list	optional	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.
`physical_state`	`PhysicalStateEnum`	single	required	Physical form of the medium
`ph_value`	`float`	single	optional	Target pH value
`ph_range`	`PhRange`	single	optional	Acceptable pH range. Structured as PhRange (min/max floats; notes for unparseable values).
`light_intensity`	`string`	single	optional	Light intensity for photosynthetic organisms (e.g., "50 µmol photons m⁻² s⁻¹")
`light_cycle`	`string`	single	optional	Photoperiod light:dark cycle (e.g., "16:8", "continuous light", "24:0")
`light_quality`	`string`	single	optional	Light spectrum or wavelength (e.g., "cool white fluorescent", "red LED 660nm")
`temperature_range`	`string`	single	optional	Optimal temperature range (e.g., "20-25°C", "room temperature")
`temperature_value`	`float`	single	optional	Specific culture temperature in Celsius
`salinity`	`string`	single	optional	Salt concentration for marine/brackish media (e.g., "35 ppt", "3.5%")
`aeration`	`string`	single	optional	Gas exchange method (e.g., "0.5% CO2 in air", "bubbling", "shaking at 150 rpm")
`culture_vessel`	`string`	single	optional	Recommended culture container (e.g., "Erlenmeyer flask", "test tube", "petri dish")
`ingredients`	`IngredientDescriptor`	list	required	Chemical and biological ingredients
`solutions`	`SolutionDescriptor`	list	optional	Pre-prepared stock solutions used as ingredients
`preparation_steps`	`PreparationStep`	list	recommended	Ordered steps to prepare the medium
`sterilization`	`SterilizationDescriptor`	single	recommended	Sterilization method and parameters
`storage`	`StorageConditions`	single	optional	Storage conditions for prepared medium
`applications`	`string`	list	optional	Use cases and applications
`variants`	`MediaVariant`	list	optional	Related formulations or modifications
`parent_media`	`MediaRecipeReference`	single	optional	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.
`variant_children`	`MediaRecipeReference`	list	optional	Child MediaRecipe YAML records that are variants of this canonical parent medium.
`variant_relationship`	`MediaVariantRelationshipEnum`	single	optional	Relationship type to the parent medium when this recipe is a child variant record.
`variant_modifications`	`string`	list	optional	Summary of how this child formulation differs from its parent medium.
`references`	`PublicationReference`	list	optional	Original literature sources
`notes`	`string`	single	optional	Additional context, historical notes, tips
`evidence`	`EvidenceItem`	list	optional	Evidence supporting formulation claims
`datasets`	`Dataset`	list	optional	Public datasets (omics/sequence/phenotype) generated using this medium
`discussions`	`Discussion`	list	optional	Open questions, knowledge gaps, controversies, and curation todos attached to this medium (shared Discussion supertype; anchor `attaches_to` into e.g. `composition#<ingredient>` / `conditions#<x>`).
`import_metadata`	`ImportMetadata`	single	recommended	Import tracking and versioning information. Enables reproducible imports, provenance tracking, and update workflows.
`curation_history`	`CurationEvent`	list	optional	Audit trail of curation events
`data_quality_flags`	`string`	list	optional	Data quality indicators for transparency
`sources`	`SourceReference`	list	optional	Upstream database attribution(s) for this record (e.g. MediaDive, CultureBotHT). Multivalued for cross-listings.
`incubation_atmosphere`	`AtmosphereEnum`	single	optional	Atmospheric conditions for incubation
`source_data`	`SourceData`	single	optional	Provenance tracking for records imported from other repositories

`SolutionRecipe`

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.

Attribute	Range	Cardinality	Status	Description
`id`	`string`	single	required	Stable canonical external CultureMech identifier for this solution record. Immutable after issuance and never reused; lifecycle is published in data/culturemech_recipe_catalog.tsv.
`id_lineage_token`	`string`	single	optional	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.
`preferred_term`	`string`	single	required	Solution name (e.g., "Trace Metal Solution", "Vitamin Stock")
`term`	`Term`	single	optional	Ontology term identifying this solution
`mediaingredientmech_term`	`MediaIngredientMechTerm`	single	optional	Legacy MediaIngredientMech:NNNNNN identifier for this solution (pre-CHEBI-keying).
`mediaingredientmech_chebi_term`	`MediaIngredientMechChebiTerm`	single	optional	CHEBI-keyed linkage to a curated MediaIngredientMech ingredient (current MIM schema).
`culturemech_term`	`CultureMechTerm`	single	optional	Reference to another CultureMech recipe (if this solution is also catalogued there)
`category`	`CategoryEnum`	single	optional	Source / collection category (algae, bacterial, fungal, …)
`composition`	`IngredientDescriptor`	list	required	Ingredients in the stock solution
`solutions`	`SolutionDescriptor`	list	optional	Nested stock solutions added while preparing this stock solution
`ingredients`	`IngredientDescriptor`	list	optional	Placeholder/stub ingredient entries from upstream imports (kept alongside the authoritative `composition`). Intended to be empty or carry a "See source for composition" marker.
`concentration`	`ConcentrationValue`	single	optional	Working concentration when added to a medium
`preparation_notes`	`string`	single	optional	How to prepare the stock solution
`storage_conditions`	`StorageConditions`	single	optional	Storage requirements
`shelf_life`	`string`	single	optional	Stability duration (e.g., "6 months at 4°C")
`references`	`PublicationReference`	list	optional	Source references for this solution
`source_data`	`SourceData`	single	optional	Provenance tracking for imported solution records
`curation_history`	`CurationEvent`	list	optional	Audit trail of curation events
`data_quality_flags`	`string`	list	optional	Data quality indicators
`sources`	`SourceReference`	list	optional	Upstream database attribution(s) for this solution record.
`notes`	`string`	single	optional	Additional free-text notes
`evidence`	`EvidenceItem`	list	optional	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.
`categories`	`CategoryEnum`	list	optional	All categories this solution recipe appears in (for cross-category merges)
`synonyms`	`RecipeSynonym`	list	optional	Alternate names from merged duplicate solution recipes
`merged_from`	`string`	list	optional	Original recipe IDs that were merged into this solution record
`merge_fingerprint`	`string`	single	optional	SHA256 hash of ingredient set for deduplication tracking
`chemical_fingerprint`	`string`	single	optional	SHA256 hash using parent ingredients (hierarchy-aware)
`variant_fingerprint`	`string`	single	optional	SHA256 hash including concentration and preparation variant details

`RecipeSynonym`

An alternate name for a recipe from a specific source

Attribute	Range	Cardinality	Status	Description
`name`	`string`	single	required	Alternate recipe name (non-canonical)
`source`	`string`	single	required	Source database (KOMODO, MediaDive, TOGO, etc.)
`source_id`	`string`	single	optional	Original identifier in source database
`original_category`	`CategoryEnum`	single	optional	Original category assignment before merge

`MergeMetadata`

Metadata about merge process and quality

Attribute	Range	Cardinality	Status	Description
`merge_version`	`string`	single	optional	Version of merge pipeline used
`merge_mode`	`MergeModeEnum`	single	optional	Merge mode used (conservative/aggressive/variant-aware)
`merge_reason`	`MergeReasonEnum`	single	optional	Why these recipes were merged together
`merge_confidence`	`float`	single	optional	Confidence score for merge decision (0.0-1.0)
`hierarchy_conflicts`	`string`	list	optional	Ingredients with conflicting merge signals
`fingerprint_mode`	`FingerprintModeEnum`	single	optional	Fingerprinting mode used (chemical/variant/original)

`Descriptor`

Base class for descriptor pattern. Descriptors have a human-readable preferred_term and optional ontology term.

No inline attributes.

`Term`

Base class for ontology term references. Subclasses specify id_prefixes for validation.

Attribute	Range	Cardinality	Status	Description
`id`	`string`	single	required	Ontology identifier (CURIE)
`label`	`string`	single	optional	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.
`confidence`	`float`	single	optional	Confidence score for the mapping (0.0-1.0). Populated by automated grounding pipelines.
`match_type`	`TermMatchTypeEnum`	single	optional	Provenance/method of the term mapping (e.g. "kg_fallback", "exact", "manual_curated").

`MediaTypeDescriptor`

Classification and authoritative database reference for the medium

Attribute	Range	Cardinality	Status	Description
`preferred_term`	`string`	single	required	Medium designation in source database (e.g., "DSMZ Medium 1", "LB")
`term`	`MediaDatabaseTerm`	single	recommended	Authoritative media database identifier

`IngredientDescriptor`

Chemical or biological ingredient in a medium

Attribute	Range	Cardinality	Status	Description
`preferred_term`	`string`	single	required	Human-readable ingredient name (e.g., "Glucose", "Yeast Extract")
`term`	`ChemicalEntityTerm`	single	recommended	Primary ontology grounding (CHEBI, FOODON, UBERON, ENVO, or upstream mediadive.compound).
`chebi_term`	`ChebiTerm`	single	optional	CHEBI-only grounding kept alongside `term` when `term` carries the upstream identifier (e.g. mediadive.compound on solution compositions).
`mediaingredientmech_term`	`MediaIngredientMechTerm`	single	optional	Legacy MediaIngredientMech:NNNNNN identifier for this ingredient (pre-CHEBI-keying).
`mediaingredientmech_chebi_term`	`MediaIngredientMechChebiTerm`	single	optional	CHEBI-keyed linkage to a curated MediaIngredientMech ingredient (current MIM schema).
`culturemech_term`	`CultureMechTerm`	single	optional	Reference to another CultureMech media recipe used as component
`parent_ingredient`	`IngredientReference`	single	optional	Reference to parent chemical entity from MediaIngredientMech
`variant_type`	`VariantTypeEnum`	single	optional	Type of chemical variant
`concentration`	`ConcentrationValue`	single	recommended	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.
`modifier`	`ModifierEnum`	single	optional	Modification in variants (INCREASED, DECREASED)
`chemical_formula`	`string`	single	optional	Molecular formula (e.g., "C6H12O6")
`synonyms`	`IngredientSynonym`	list	optional	Alternate names for this ingredient (e.g. brand names, abbreviations). Each entry is an `IngredientSynonym` with `synonym_text` and `synonym_type`.
`source`	`string`	single	optional	Provenance attribution for this ingredient entry.
`curation_metadata`	`IngredientCurationMetadata`	single	optional	Structured curation metadata for this ingredient mapping (mapping quality, confidence score, ontology source, etc.).
`data_quality_flags`	`string`	list	optional	Ingredient-level data quality indicators.
`molecular_weight`	`float`	single	optional	Molecular weight in g/mol
`supplier_catalog`	`SupplierInfo`	single	optional	Supplier information for sourcing
`notes`	`string`	single	optional	Preparation notes specific to this ingredient
`nutritional_roles`	`NutritionalRoleEnum`	list	optional	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.
`physicochemical_roles`	`PhysicochemicalRoleEnum`	list	optional	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`).
`cellular_metabolic_roles`	`CellularMetabolicRoleEnum`	list	optional	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`).
`role_curie`	`uriorcurie`	list	optional	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.
`cofactors_provided`	`CofactorDescriptor`	list	optional	Cofactors supplied by this ingredient
`evidence`	`EvidenceItem`	list	optional	Evidence for this ingredient's role

`SolutionDescriptor`

A pre-prepared stock solution used as an ingredient

Attribute	Range	Cardinality	Status	Description
`preferred_term`	`string`	single	required	Solution name (e.g., "Trace Metal Solution", "Vitamin Stock")
`name`	`string`	single	optional	Human-readable solution label (kept alongside preferred_term).
`notes`	`string`	single	optional	Free-text notes about this solution as used in the parent recipe.
`source`	`string`	single	optional	Provenance attribution for this solution entry.
`term`	`Term`	single	optional	Ontology term if available
`mediaingredientmech_term`	`MediaIngredientMechTerm`	single	optional	Legacy MediaIngredientMech:NNNNNN identifier for this solution component (pre-CHEBI-keying).
`mediaingredientmech_chebi_term`	`MediaIngredientMechChebiTerm`	single	optional	CHEBI-keyed linkage to a curated MediaIngredientMech ingredient (current MIM schema).
`culturemech_term`	`CultureMechTerm`	single	optional	Reference to another CultureMech media recipe for this solution
`composition`	`IngredientDescriptor`	list	optional	Ingredients in the stock solution. Optional when the solution is referenced by name only (no inline composition copied from the source).
`solutions`	`SolutionDescriptor`	list	optional	Nested stock solutions added while preparing this stock solution
`concentration`	`ConcentrationValue`	single	optional	Working concentration when added to medium
`concentration_candidates`	`ConcentrationCandidate`	list	optional	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.
`preparation_notes`	`string`	single	optional	How to prepare the stock solution
`storage_conditions`	`StorageConditions`	single	optional	Storage requirements for the stock
`shelf_life`	`string`	single	optional	Stability duration (e.g., "6 months at 4°C")

`OrganismDescriptor`

Target organism for the medium

Attribute	Range	Cardinality	Status	Description
`preferred_term`	`string`	single	required	Organism name (e.g., "Escherichia coli")
`term`	`OrganismTerm`	single	optional	NCBITaxon identifier
`scoped_to_variant`	`string`	single	optional	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.
`gtdb_term`	`GTDBTerm`	single	optional	GTDB genome or lineage identifier (alternative to NCBITaxon)
`genome_assembly_id`	`string`	list	optional	Genome assembly accession(s) for this organism, complementing gtdb_term. Accepts RefSeq (GCF_), GenBank (GCA_), or BioSample (SAMN) identifiers.
`strain`	`string`	single	optional	Specific strain designation (e.g., "K-12", "MG1655")
`growth_phase`	`GrowthPhaseEnum`	single	optional	Target growth phase (e.g., "exponential", "stationary")
`growth_metrics`	`GrowthMetrics`	list	optional	Quantitative growth measurements observed for this organism on this medium
`community_role`	`CommunityOrganismRoleEnum`	list	optional	Functional role in microbial community (e.g., PRIMARY_DEGRADER, SYNERGIST, COMMENSAL, COMPETITOR).
`target_abundance`	`float`	single	optional	Target relative abundance in community (0.0-1.0)
`community_function`	`string`	list	optional	Specific functional contribution to community
`cofactor_requirements`	`CofactorRequirement`	list	optional	Cofactors required by this organism
`transporters`	`TransporterAnnotation`	list	optional	Annotated transport systems
`evidence`	`EvidenceItem`	list	optional	Evidence supporting growth on this medium
`strain_modifications`	`StrainModification`	list	optional	Genotype/phenotype modifications relative to the wild-type or type strain. Strain-level (carries across observations) and distinct from per-observation `growth_metrics[].perturbations`.

`SourceEnvironmentDescriptor`

Environment from which target organisms originate or for which the medium is designed. Enables environment-based discovery and cross-repository linking with CommunityMech.

Attribute	Range	Cardinality	Status	Description
`preferred_term`	`string`	single	required	Human-readable environment name (e.g., "peatland", "marine", "soil")
`term`	`EnvironmentTerm`	single	recommended	ENVO ontology term for the environment
`notes`	`string`	single	optional	Additional environmental context, conditions, or specificity

`CofactorDescriptor`

A cofactor or coenzyme required for enzymatic activity

Attribute	Range	Cardinality	Status	Description
`preferred_term`	`string`	single	required	Human-readable cofactor name (e.g., "Thiamine pyrophosphate", "NAD")
`term`	`ChemicalEntityTerm`	single	recommended	CHEBI term for the cofactor
`category`	`CofactorCategoryEnum`	single	recommended	High-level classification
`precursor`	`string`	single	optional	Precursor molecule (e.g., thiamine → TPP)
`precursor_term`	`ChemicalEntityTerm`	single	optional	CHEBI term for precursor
`ec_associations`	`string`	list	optional	EC numbers of enzymes using this cofactor
`kegg_pathways`	`string`	list	optional	KEGG pathway IDs for biosynthesis
`enzyme_examples`	`string`	list	optional	Example enzymes requiring this cofactor
`biosynthesis_genes`	`string`	list	optional	Genes involved in cofactor biosynthesis
`bioavailability`	`string`	single	optional	Uptake and availability characteristics
`notes`	`string`	single	optional	Additional information about the cofactor

`SourceReference`

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).

Attribute	Range	Cardinality	Status	Description
`database`	`string`	single	required	Source database/repository name (e.g. CultureBotHT, MediaDive).
`database_id`	`string`	single	optional	Identifier or name in the source database.
`url`	`string`	single	optional	Direct URL to the source record.

`IngredientSynonym`

An alternate name for an ingredient (e.g. brand name, abbreviation).

Attribute	Range	Cardinality	Status	Description
`synonym_text`	`string`	single	required	The alternate name string.
`synonym_type`	`SynonymTypeEnum`	single	optional	Synonym match type (e.g. EXACT, RELATED, BROAD).

`IngredientCurationMetadata`

Structured metadata describing how an ingredient mapping was produced (mapping quality, confidence, source). Populated by curation pipelines.

Attribute	Range	Cardinality	Status	Description
`mapping_quality`	`string`	single	optional	Quality tier of the mapping (e.g. EXACT, LLM_ASSISTED, KG_FALLBACK).
`confidence_score`	`float`	single	optional	Confidence score for the mapping (0.0-1.0).
`curation_date`	`string`	single	optional	When the curation was performed (ISO-8601).
`ontology_source`	`string`	single	optional	Ontology used as the mapping target (e.g. CHEBI).

`IngredientReference`

Reference to canonical ingredient

Attribute	Range	Cardinality	Status	Description
`preferred_term`	`string`	single	required	Name of parent ingredient
`mediaingredientmech_id`	`string`	single	optional	MediaIngredientMech ID

`ConcentrationValue`

Quantified concentration with units

Attribute	Range	Cardinality	Status	Description
`value`	`string`	single	required	Numeric value or range
`unit`	`ConcentrationUnitEnum`	single	required	Concentration unit
`per_volume`	`string`	single	optional	Volume basis (e.g., "per liter", "per 100 mL")

`ConcentrationCandidate`

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.

Attribute	Range	Cardinality	Status	Description
`value`	`string`	single	required	Numeric value or range, as the evidence gives it.
`unit`	`ConcentrationUnitEnum`	single	required	Concentration unit
`basis`	`ConcentrationBasisEnum`	single	required	What kind of claim this is — how the value was arrived at.
`support`	`string`	single	recommended	The evidence, stated so it can be re-checked, e.g. "10 of 11 MediaDive media citing this stock add it at this volume".
`counterevidence`	`string`	single	optional	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.
`source`	`string`	single	recommended	Citation or URL the support was read from.
`proposed_by`	`string`	single	optional	Script or curator that proposed the value.
`proposed_on`	`string`	single	optional	ISO-8601 date the proposal was made.

`GrowthMetrics`

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.

Attribute	Range	Cardinality	Status	Description
`max_od600`	`float`	single	optional	Maximum optical density observed (default wavelength 600 nm)
`max_od_wavelength_nm`	`integer`	single	optional	Wavelength at which OD was measured, in nanometers (default 600)
`doubling_time_minutes`	`float`	single	optional	Population doubling time in minutes
`growth_rate_per_hour`	`float`	single	optional	Specific growth rate μ in h⁻¹ (inverse hours)
`temperature_celsius`	`float`	single	optional	Temperature at which the measurement was taken, in degrees Celsius
`ph_at_measurement`	`float`	single	optional	Medium pH at the time of measurement
`measurement_conditions`	`string`	single	optional	Free-text description of measurement context (e.g., "shake flask, 200 rpm", "microtiter plate, 96-well, plate reader Tecan Spark")
`evidence`	`EvidenceItem`	list	required	Literature evidence supporting these growth measurements
`is_max_attainment`	`boolean`	single	optional	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".
`growth_mode`	`GrowthModeEnum`	single	optional	Cultivation mode under which the metric was measured.
`perturbations`	`PerturbationContext`	list	optional	Applied stresses, modifications, or non-default conditions that accompanied this growth observation. When non-empty, `is_max_attainment` should typically be FALSE.
`nutrient_overrides`	`NutrientOverride`	list	optional	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").

`PerturbationContext`

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).

Attribute	Range	Cardinality	Status	Description
`perturbation_type`	`PerturbationTypeEnum`	single	required	Class of perturbation applied during the observation.
`descriptor`	`string`	single	optional	Free-text description (e.g. "Cr(VI) at 10 mg/L", "magnetosome-deficient strain", "cellulose-adapted", "induced at OD600=0.6").
`target`	`string`	single	optional	Subject of the perturbation — gene/locus for genetic, stressor compound for chemical, limiting nutrient for nutritional, substrate for adaptation.
`level`	`float`	single	optional	Quantitative level of the perturbation (e.g. 10.0 for 10 mg/L Cr(VI), 4.0 for 4 °C).
`level_unit`	`string`	single	optional	Unit for `level` (e.g. "mg/L", "mM", "%", "°C", "µmol·m⁻²·s⁻¹").
`ontology_id`	`string`	single	optional	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 `<provenance>_id` convention used for bare-string CURIEs elsewhere in the schema. The typed-Term-object convention is `<provenance>_term`.
`evidence`	`EvidenceItem`	list	optional	Literature evidence supporting the perturbation claim.

`StrainModification`

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.

Attribute	Range	Cardinality	Status	Description
`modification_type`	`StrainModificationTypeEnum`	single	required	Class of modification applied to the strain.
`target`	`string`	single	optional	Gene/locus name, phenotype label, or substrate the modification targets (e.g. "magnetosome operon", "spo0A", "cellulose utilization").
`description`	`string`	single	optional	Curator free-text describing the modification.
`ontology_id`	`string`	single	optional	Optional CURIE — NCIT:C120956 (Knockout), NCIT:C17026 (Genetic Modification), PATO:0015009 (mutant), etc. Renamed from `ontology_term` (G13) to align with the `<provenance>_id` convention used for bare-string CURIEs.
`evidence`	`EvidenceItem`	list	optional	Literature evidence supporting the modification claim.

`NutrientOverride`

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.

Attribute	Range	Cardinality	Status	Description
`role`	`NutritionalRoleEnum`	single	required	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.
`source`	`string`	single	required	e.g. "succinate", "L-phenylalanine", "acetate".
`ontology_id`	`string`	single	optional	Preferred CHEBI / FOODON CURIE for the source compound.
`is_sole_source`	`boolean`	single	optional	TRUE when this is the only source for that role in the experiment.
`evidence`	`EvidenceItem`	list	optional	Literature evidence supporting the nutrient-override claim.

`TemperatureValue`

Temperature with units

Attribute	Range	Cardinality	Status	Description
`value`	`float`	single	required	Numeric temperature value
`unit`	`TemperatureUnitEnum`	single	required	Temperature unit

`PhRange`

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).

Attribute	Range	Cardinality	Status	Description
`min`	`float`	single	optional	Lower bound of the acceptable pH range (inclusive).
`max`	`float`	single	optional	Upper bound of the acceptable pH range (inclusive).
`notes`	`string`	single	optional	Free-text qualifier or the original unparseable value (e.g. "varies by species", "alkaline 9-10 for halophiles").

`PreparationStep`

A step in medium preparation

Attribute	Range	Cardinality	Status	Description
`step_number`	`integer`	single	required	Sequential order
`action`	`PreparationActionEnum`	single	required	Action type
`description`	`string`	single	required	Detailed instruction
`temperature`	`TemperatureValue`	single	optional	Temperature for this step
`duration`	`string`	single	optional	Time duration (e.g., "15 minutes", "overnight")
`equipment`	`string`	single	optional	Required equipment (e.g., "autoclave", "magnetic stirrer")
`notes`	`string`	single	optional	Additional tips or warnings

`SterilizationDescriptor`

Sterilization method and parameters

Attribute	Range	Cardinality	Status	Description
`method`	`SterilizationMethodEnum`	single	required	Sterilization technique
`temperature`	`TemperatureValue`	single	optional	Temperature setting
`pressure`	`float`	single	optional	Pressure in psi or kPa (for autoclaving)
`duration`	`string`	single	optional	Sterilization duration
`notes`	`string`	single	optional	Special instructions (e.g., "Filter-sterilize heat-labile components separately")

`StorageConditions`

Storage requirements for prepared medium

Attribute	Range	Cardinality	Status	Description
`temperature`	`TemperatureValue`	single	required	Storage temperature
`light_condition`	`LightConditionEnum`	single	optional	Light exposure requirement
`shelf_life`	`string`	single	optional	Duration of stability
`container_type`	`string`	single	optional	Recommended container (e.g., "glass bottle", "polypropylene tube")
`notes`	`string`	single	optional	Additional storage tips

`MediaVariant`

A variant or modification of the base recipe

Attribute	Range	Cardinality	Status	Description
`name`	`string`	single	required	Variant name (e.g., "Low Salt LB", "LB + Ampicillin")
`relationship`	`MediaVariantRelationshipEnum`	single	recommended	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.
`description`	`string`	single	optional	Purpose and context
`modifications`	`string`	list	optional	What differs from base recipe
`purpose`	`string`	single	optional	Why this variant exists
`supplier_info`	`SupplierInfo`	single	optional	Commercial supplier if premix
`evidence`	`EvidenceItem`	list	optional	Evidence supporting the variant

`MediaRecipeReference`

Reference to another CultureMech media recipe record

Attribute	Range	Cardinality	Status	Description
`id`	`string`	single	optional	Stable CultureMech identifier for the referenced media record
`name`	`string`	single	optional	Referenced media recipe name
`path`	`string`	single	optional	Repository-relative YAML path for the referenced media record
`relationship`	`MediaVariantRelationshipEnum`	single	optional	Parent-child relationship type for this link
`notes`	`string`	single	optional	Curator notes about the relationship or unresolved mapping
`evidence`	`EvidenceItem`	list	optional	Evidence supporting the media parent-child relationship

`SupplierInfo`

Commercial supplier information

Attribute	Range	Cardinality	Status	Description
`supplier_name`	`string`	single	required	Vendor name (e.g., "Sigma-Aldrich", "Thermo Fisher")
`catalog_number`	`string`	single	optional	Product catalog number
`product_url`	`uri`	single	optional	Direct product link
`notes`	`string`	single	optional	Additional sourcing notes

`PublicationReference`

Literature reference

Attribute	Range	Cardinality	Status	Description
`reference`	`string`	single	required	Citation (PMID, DOI, or historical reference)
`title`	`string`	single	optional	Publication title
`authors`	`string`	single	optional	Author list
`year`	`integer`	single	optional	Publication year
`notes`	`string`	single	optional	Additional context about the reference

`EvidenceItem`

Evidence supporting a claim about media formulation or performance

Attribute	Range	Cardinality	Status	Description
`reference`	`string`	single	required	Citation (PMID, DOI, or historical reference)
`supports`	`EvidenceItemSupportEnum`	single	required	Level of support
`snippet`	`string`	single	optional	Exact quote from paper (if PMID/DOI available)
`explanation`	`string`	single	required	Why this evidence supports the claim

`CurationEvent`

Audit trail entry for curation

Attribute	Range	Cardinality	Status	Description
`timestamp`	`string`	single	required	ISO 8601 timestamp with a plausible 21st-century curation year
`curator`	`string`	single	required	Name or identifier of curator
`action`	`string`	single	required	Action taken (created, updated, validated, etc.)
`notes`	`string`	single	optional	Additional context
`changes`	`string`	single	optional	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)`).
`source`	`string`	single	optional	Source attribution for this curation event (e.g. a source PDF, a sibling CultureMech recipe, an external dataset).

`SourceData`

Provenance information for imported records

Attribute	Range	Cardinality	Status	Description
`origin`	`string`	single	required	Source repository name
`community_ids`	`string`	list	optional	List of CommunityMech IDs this recipe was derived from
`import_date`	`string`	single	optional	Date of import (ISO 8601)
`evidence`	`EvidenceItem`	list	optional	Evidence records from source repository
`notes`	`string`	single	optional	Import notes and additional context
`mediaingredientmech_id`	`string`	single	optional	MediaIngredientMech identifier for this imported solution record (carried when origin is `MediaIngredientMech`). Format `UNMAPPED_NNNN` or `MediaIngredientMech:NNNNNN`.

`CofactorRequirement`

Cofactor requirement for an organism

Attribute	Range	Cardinality	Status	Description
`cofactor`	`CofactorDescriptor`	single	required	Required cofactor
`can_biosynthesize`	`boolean`	single	required	Whether organism can synthesize this cofactor
`confidence`	`float`	single	optional	Confidence level (0.0-1.0) based on genome annotation
`evidence`	`EvidenceItem`	list	optional	Supporting evidence for requirement
`genes`	`string`	list	optional	Genes related to biosynthesis or utilization

`TransporterAnnotation`

Annotation of a transporter or transport system

Attribute	Range	Cardinality	Status	Description
`name`	`string`	single	required	Transporter name or gene name
`transporter_type`	`TransporterTypeEnum`	single	required	Classification of transporter
`substrates`	`string`	list	optional	Transported substrates
`substrate_terms`	`ChemicalEntityTerm`	list	optional	CHEBI terms for substrates
`direction`	`string`	single	optional	Transport direction (import, export, bidirectional)
`genes`	`string`	list	optional	Gene names or locus tags
`ec_number`	`string`	single	optional	EC number if enzymatic
`notes`	`string`	single	optional	Additional functional notes

`ChemicalEntityTerm`

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.

No inline attributes.

`ChebiTerm`

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.

No inline attributes.

`OrganismTerm`

An NCBITaxon term representing an organism

No inline attributes.

`GTDBTerm`

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;...)

No inline attributes.

`MediaDatabaseTerm`

Identifier from authoritative media database

No inline attributes.

`MediaIngredientMechTerm`

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.

No inline attributes.

`MediaIngredientMechChebiTerm`

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.

No inline attributes.

`CultureMechTerm`

A CultureMech identifier for a media recipe used as component

No inline attributes.

`EnvironmentTerm`

An ENVO term representing an environmental system or biome

No inline attributes.

`ImportMetadata`

Tracking information for imported media records. Enables versioning, provenance tracking, and reproducible updates.

Attribute	Range	Cardinality	Status	Description
`source_database`	`SourceDatabaseEnum`	single	required	Source database from which this medium was imported
`source_id`	`string`	single	required	Original identifier in source database (e.g., "Medium 1234", "M3205"). Preserved for traceability and update tracking.
`import_version`	`string`	single	required	Import version following format vMAJOR.MINOR.PATCH_YYYY-MM-DD. Example: v1.0.0_2026-01-27
`import_date`	`string`	single	required	ISO 8601 timestamp when this record was imported
`import_skill`	`string`	single	optional	Name of the skill or script that performed the import. Example: "import-mediadive", "import-togo-skill"
`last_updated`	`string`	single	optional	ISO 8601 timestamp of most recent update
`update_history`	`UpdateEvent`	list	optional	Chronological log of all updates applied to this record. Enables full audit trail from initial import to present.

`UpdateEvent`

Record of a single update to an imported media recipe. Captures what changed, when, and why.

Attribute	Range	Cardinality	Status	Description
`timestamp`	`string`	single	required	ISO 8601 timestamp when update was applied
`import_version`	`string`	single	required	Import version that applied this update
`action`	`UpdateActionEnum`	single	required	Type of update action performed
`fields_changed`	`string`	list	optional	List of field names that were modified in this update. Example: ["ingredients", "ph_value", "description"]
`notes`	`string`	single	optional	Human-readable explanation of the update. Why was this change made? What was the context?

Enumerations (33)

`RecordKindEnum`

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 Value	Meaning / Term	Description
`MEDIUM`		A growth medium.
`SOLUTION`		A standalone stock solution (trace elements, vitamins, buffers). Excluded from media-level audits and from the deep-research ranking.

`MediumTypeEnum`

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 Value	Meaning / Term	Description
`DEFINED`	`NCIT:C64372`	Chemically defined medium with known composition. Migrates to composition_type=DEFINED.
`COMPLEX`	`NCIT:C64371`	Medium with undefined components (e.g., yeast extract). Migrates to composition_type=UNDEFINED.
`SELECTIVE`		Medium that selects for specific organisms. Migrates to functional_role=[SELECTIVE].
`DIFFERENTIAL`		Medium that differentiates organism types. Migrates to functional_role=[DIFFERENTIAL].
`ENRICHMENT`		Medium that enriches for specific organisms. Migrates to functional_role=[ENRICHMENT].
`MINIMAL`		Medium with minimal nutrients required for growth. Migrates to nutritional_class=MINIMAL.
`BUFFER`		Buffer solution (e.g. PBS) — not a growth medium per se but stored alongside media for context.
`NEGATIVE_CONTROL`		Negative-control "medium" used as an experimental baseline (e.g. distilled water).

`MediumCompositionTypeEnum`

Composition axis: how chemically defined the medium is. Single-valued and orthogonal to nutritional level (MediumNutritionalClassEnum) and functional role (MediumFunctionalRoleEnum).

Permissible Value	Meaning / Term	Description
`DEFINED`	`NCIT:C64372`	Chemically defined (synthetic) medium; every component and its exact quantity is known. Synonyms —synthetic.
`UNDEFINED`	`NCIT:C64371`	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.
`SEMI_DEFINED`		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`

Nutritional-level axis: how nutrient-rich the medium is. Single-valued and orthogonal to composition (MediumCompositionTypeEnum) and functional role (MediumFunctionalRoleEnum).

Permissible Value	Meaning / Term	Description
`MINIMAL`		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`		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`		Standard nutrient level for routine cultivation — neither deliberately minimal nor deliberately enriched. Use when a medium is not clearly MINIMAL or RICH.

`MediumFunctionalRoleEnum`

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 Value	Meaning / Term	Description
`GENERAL_PURPOSE`		Non-selective, non-differential medium for routine growth of a broad range of organisms. Synonyms —non-selective, basal.
`SELECTIVE`		Suppresses or prevents growth of unwanted organisms (via antibiotics, dyes, bile salts, NaCl, pH, etc.) to favor a target group.
`DIFFERENTIAL`		Distinguishes organism types by a visible biochemical reaction (e.g. color change from fermentation, or hemolysis) without necessarily inhibiting growth.
`ENRICHMENT`		Promotes growth of a target organism to detectable numbers from a mixed population, typically prior to isolation.
`TRANSPORT`		Maintains organism viability without significant multiplication during transport or storage.
`ASSAY`		Standardized medium for a specific assay (e.g. antibiotic potency, vitamin or growth-factor bioassay).
`ENUMERATION`		Supports viable-count / colony enumeration (e.g. heterotrophic plate count media such as R2A).

`PhysicalStateEnum`

Physical form of the medium

Permissible Value	Meaning / Term	Description
`LIQUID`		Liquid broth medium
`SOLID_AGAR`		Solidified with agar
`SEMISOLID`		Reduced agar concentration for motility testing
`BIPHASIC`		Both liquid and solid phases

`ConcentrationBasisEnum`

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 Value	Meaning / Term	Description
`READ_FROM_THIS_MEDIUM`		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`		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`		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`		A conventional value for this class of stock, with no per-medium evidence at all. The weakest basis; recorded only to be checked.

`ConcentrationUnitEnum`

Units for concentration

Permissible Value	Meaning / Term	Description
`G_PER_L`	`UO:0000175`	grams per liter
`MG_PER_L`		milligrams per liter
`MICROG_PER_L`		micrograms per liter
`MOLAR`	`UO:0000062`	moles per liter
`MILLIMOLAR`		millimoles per liter
`MICROMOLAR`		micromoles per liter
`PERCENT_W_V`		percent weight per volume
`PERCENT_W_W`		percent weight per weight
`PERCENT_V_V`		percent volume per volume
`ML_PER_L`		milliliters per liter (for solution/component additions)
`MG_PER_ML`		milligrams per milliliter
`FOLD_DILUTION`		dilution factor expressed as 1:N (e.g. "10-fold dilution")
`L`		liters — used for volume-only entries like "Make up to 1 L" final-volume markers.
`VARIABLE`		variable or unspecified concentration

`TemperatureUnitEnum`

Units for temperature

Permissible Value	Meaning / Term	Description
`CELSIUS`	`UO:0000027`	Degrees Celsius
`FAHRENHEIT`		Degrees Fahrenheit
`KELVIN`	`UO:0000012`	Kelvin

`AtmosphereEnum`

Atmospheric conditions for incubation

Permissible Value	Meaning / Term	Description
`AEROBIC`		Oxygen-rich atmosphere
`ANAEROBIC`		Oxygen-free atmosphere
`MICROAEROPHILIC`		Low oxygen atmosphere (typically 2-10% O2)

`PreparationActionEnum`

Controlled vocabulary for preparation steps

Permissible Value	Meaning / Term	Description
`DISSOLVE`		Dissolve ingredients in solvent
`MIX`		Mix or stir components
`HEAT`		Apply heat
`COOL`		Cool to specified temperature
`AUTOCLAVE`		Steam sterilization under pressure
`FILTER`		Remove solids or particles by filtration
`FILTER_STERILIZE`		Filter through 0.22 μm membrane
`ADJUST_PH`		Adjust pH with acid or base
`ADD_AGAR`		Add agar for solidification
`POUR_PLATES`		Dispense into petri dishes
`ALIQUOT`		Divide into smaller portions
`STORE`		Store under specified conditions

`SterilizationMethodEnum`

Sterilization techniques

Permissible Value	Meaning / Term	Description
`AUTOCLAVE`		Steam sterilization under pressure (121°C, 15 psi, 15-20 min)
`FILTER`		Filtration through 0.22 μm filter
`DRY_HEAT`		Dry heat sterilization (160-180°C)
`TYNDALLIZATION`		Intermittent sterilization for heat-sensitive media
`NONE`		No sterilization (non-sterile media)

`LightConditionEnum`

Light exposure requirements

Permissible Value	Meaning / Term	Description
`DARK`		Store in complete darkness
`LIGHT_PROTECTED`		Protect from light (amber bottle or foil wrap)
`AMBIENT`		Normal laboratory lighting

`ModifierEnum`

Modification type for variants

Permissible Value	Meaning / Term	Description
`INCREASED`		Elevated concentration relative to base recipe
`DECREASED`		Reduced concentration relative to base recipe
`ABSENT`		Ingredient omitted in this variant

`EvidenceItemSupportEnum`

Level of evidence support

Permissible Value	Meaning / Term	Description
`SUPPORT`		Evidence supports the claim
`REFUTE`		Evidence refutes the claim
`PARTIAL`		Evidence partially supports the claim
`NO_EVIDENCE`		No evidence found
`WRONG_STATEMENT`		Statement is incorrect

`CategoryEnum`

Organizational category for media recipes

Permissible Value	Meaning / Term	Description
`bacterial`		Media for bacterial cultivation
`fungal`		Media for fungal cultivation
`archaea`		Media for archaeal cultivation
`specialized`		Specialized or multi-domain media
`algae`		Media for algal cultivation
`imported`		Imported from external sources (to be recategorized)

`OrganismCultureTypeEnum`

Whether the medium targets a pure isolate or a mixed microbial community

Permissible Value	Meaning / Term	Description
`isolate`		Pure culture of one or more specific strains
`community`		Mixed/consortium culture of multiple organisms

`CofactorCategoryEnum`

High-level classification of cofactor types

Permissible Value	Meaning / Term	Description
`VITAMINS`		Vitamins and vitamin-derived cofactors
`METALS`		Metal ions and metal-containing cofactors
`NUCLEOTIDES`		Nucleotide cofactors
`ENERGY_TRANSFER`		Energy transfer and group transfer cofactors
`OTHER_SPECIALIZED`		Specialized cofactors (PQQ, F420, etc.)

`CommunityOrganismRoleEnum`

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 Value	Meaning / Term	Description
`PRIMARY_DEGRADER`		Primary degrader with direct substrate degradation capability (40-60% abundance)
`REDUCTIVE_DEGRADER`		Specialized degrader using reductive pathways
`OXIDATIVE_DEGRADER`		Specialized degrader using oxidative pathways
`BIOTRANSFORMER`		Converts substrates to intermediates without complete degradation
`SYNERGIST`		Provides complementary metabolic functions (15-30% abundance)
`BRIDGE_ORGANISM`		Biosynthesizes and provides essential cofactors to community
`ELECTRON_SHUTTLE`		Facilitates electron transfer between community members
`DETOXIFIER`		Handles and detoxifies metabolic intermediates
`COMMENSAL`		General commensal organism
`COMPETITOR`		Competitive organism

`TransporterTypeEnum`

Classification of membrane transporter systems

Permissible Value	Meaning / Term	Description
`ABC`		ATP-binding cassette transporter
`MFS`		Major facilitator superfamily transporter
`PTS`		Phosphotransferase system
`TONB`		TonB-dependent receptor
`SYMPORTER`		Symporter or co-transporter
`ANTIPORTER`		Antiporter or exchanger
`UNIPORTER`		Uniporter or channel
`PORIN`		Porin or outer membrane protein
`SIDEROPHORE_RECEPTOR`		Siderophore receptor for iron uptake
`DEHALOGENASE`		Dehalogenase enzyme for halogenated compounds
`FLUORIDE_EXPORTER`		Fluoride-specific exporter

`VariantTypeEnum`

Type of chemical variant relationship to parent

Permissible Value	Meaning / Term	Description
`HYDRATE`		Hydrated form of parent chemical
`SALT_FORM`		Different salt form of parent chemical
`ANHYDROUS`		Anhydrous form of parent chemical
`NAMED_HYDRATE`		Named hydrate (monohydrate, heptahydrate, etc.)
`CHEMICAL_VARIANT`		Other chemical variant of parent

`MediaVariantRelationshipEnum`

Type of parent-child relationship between media recipes

Permissible Value	Meaning / Term	Description
`CONCENTRATION_VARIANT`		Same recognizable base medium with one or more concentration changes
`PHYSICAL_STATE_VARIANT`		Same recognizable base medium with broth, agar, semisolid, or biphasic state change
`SUPPLEMENTED_VARIANT`		Parent medium plus added supplement, antibiotic, blood, serum, carbon source, or other component
`OMITTED_COMPONENT_VARIANT`		Parent medium with one or more components omitted
`SUBSTITUTED_COMPONENT_VARIANT`		Parent medium with one or more components substituted
`PH_VARIANT`		Parent medium adjusted to a different pH or pH range
`SALINITY_VARIANT`		Parent medium adjusted to a different salt or salinity level
`STRAIN_SPECIFIC_VARIANT`		Parent medium modified for a specific organism or strain
`SOURCE_DUPLICATE`		Separate source record for the same formulation as the parent
`DERIVED_FROM`		Broad parent-child relationship when a more specific relationship is not yet curated
`UNCERTAIN`		Candidate relationship that requires additional source or formulation review

`MergeReasonEnum`

Reason why recipes were merged together

Permissible Value	Meaning / Term	Description
`EXPLICIT_MERGE_RULE`		Merged due to explicit rule from MediaIngredientMech
`IDENTICAL_FINGERPRINT`		Merged due to identical ingredient fingerprints
`SAME_PARENT_INGREDIENTS`		Merged due to same parent ingredients (aggressive mode)
`HYDRATION_VARIANT_ONLY`		Merged due to only hydration differences (variant-aware mode)
`NO_MATCH`		Not merged - no matching criteria met

`SourceDatabaseEnum`

External databases from which media recipes are imported

Permissible Value	Meaning / Term	Description
`MEDIADIVE`	`https://mediadive.dsmz.de/`	MediaDive (DSMZ) media database
`TOGO`	`http://togodb.org/db/medium/`	TOGO Medium database (Japan)
`KOMODO`		KOMODO media database (Korea)
`MEDIADB`		MediaDB database
`UTEX`	`https://utex.org/`	UTEX Culture Collection of Algae
`CCAP`	`https://www.ccap.ac.uk/`	Culture Collection of Algae and Protozoa
`SAG`	`https://sagdb.uni-goettingen.de/`	Culture Collection of Algae at Göttingen University
`CULTUREBOTHT`		CultureBotHT repository
`COMMUNITYMECH`		CommunityMech (X-Mech) integration
`BACDIVE`	`https://bacdive.dsmz.de/`	BacDive bacterial database
`NBRC`	`https://www.nite.go.jp/nbrc/`	NITE Biological Resource Center
`ATCC`	`https://www.atcc.org/`	American Type Culture Collection
`MANUAL`		Manually curated (not imported from external database)

`UpdateActionEnum`

Type of update action applied to an imported record

Permissible Value	Meaning / Term	Description
`INITIAL_IMPORT`		First import from source database
`ENRICHED`		Additional metadata or enrichment added
`CORRECTED`		Errors or inconsistencies corrected
`MERGED`		Merged with duplicate or related records
`REFRESHED`		Updated from source database refresh
`NORMALIZED`		Format or structure normalized to schema

`PerturbationTypeEnum`

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 Value	Meaning / Term	Description
`GENETIC_MODIFICATION`	`NCIT:C17026`	Knockout, deletion, insertion, or point mutation acting at observation time.
`CHEMICAL_STRESS`	`NCIT:C25574`	Heavy metals, antibiotics, oxidative agents, salts at non-default levels.
`TEMPERATURE_STRESS`		Temperature outside the organism's optimum range (heat or cold shock).
`OXIDATIVE_STRESS`		Reactive oxygen species, peroxide, paraquat, etc.
`NUTRIENT_LIMITATION`		Sole-source / depletion / unusual substrate as growth driver.
`ADAPTATION`		Serial passage / experimental evolution to grow on a substrate or condition.
`GROWTH_PHASE`		Slow-growth, lag, or stationary-phase observations distinct from exponential max.
`CULTURE_MODE`		Chemostat, fed-batch, or biofilm vs. standard batch.
`PH_STRESS`		pH outside the organism's optimum.
`OTHER`		Use sparingly; prefer a more specific value above.

`StrainModificationTypeEnum`

Class of genetic or selection-derived modification carried by a strain relative to the wild-type or type strain.

Permissible Value	Meaning / Term	Description
`KNOCKOUT`	`NCIT:C120956`	Targeted gene disruption (most commonly via insertion).
`DELETION`		Targeted gene or operon deletion.
`INSERTION`		Targeted gene or marker insertion.
`POINT_MUTATION`		Single-nucleotide or small-residue substitution.
`OVEREXPRESSION`		Gene placed under stronger promoter / on multi-copy vector.
`COMPLEMENTATION`		Wild-type allele restored on knockout background.
`ADAPTATION`		Serial selection / experimental evolution producing a stable phenotype.
`SELECTION`		Strain isolated by selective pressure (e.g. plate selection, enrichment).
`OTHER`		Use sparingly; prefer a more specific value above.

`GrowthModeEnum`

Cultivation mode under which a growth metric was measured. Distinct from MediaRecipe.culture_vessel which describes the vessel itself.

Permissible Value	Meaning / Term	Description
`BATCH`		Standard closed-system batch culture.
`CHEMOSTAT`		Continuous culture with controlled dilution rate.
`TURBIDOSTAT`		Continuous culture controlled to maintain a target turbidity.
`CONTINUOUS_FLOW`		Other continuous-flow cultivation modes.
`FED_BATCH`		Batch culture with controlled nutrient feed.
`BIOFILM`		Surface-attached / biofilm cultivation.
`SOLID_SURFACE`		Plate / agar / solid-substrate cultivation.
`UNSPECIFIED`		Mode not stated in the source paper.

`MergeModeEnum`

Merge pipeline mode used by `MergeMetadata.merge_mode`.

Permissible Value	Meaning / Term	Description
`CONSERVATIVE`		Only merge on identical fingerprints.
`AGGRESSIVE`		Merge across hydration / parent-ingredient equivalence.
`VARIANT_AWARE`		Use the hierarchy-aware variant fingerprint to merge.

`FingerprintModeEnum`

Algorithm used to compute the ingredient fingerprint.

Permissible Value	Meaning / Term	Description
`ORIGINAL`		Original ingredient set, no hierarchy resolution.
`CHEMICAL`		Parent CHEBI IDs from MediaIngredientMech hierarchy.
`VARIANT`		Parent CHEBI + variant type (HYDRATE / ANHYDROUS / SALT_FORM).

`GrowthPhaseEnum`

Target microbial growth phase for a measurement / inoculum.

Permissible Value	Meaning / Term	Description
`LAG`		Lag phase (no significant net growth).
`EXPONENTIAL`		Exponential / log phase.
`STATIONARY`		Stationary phase.
`DEATH`		Death / decline phase.
`UNSPECIFIED`		Phase not stated by the source.

`TermMatchTypeEnum`

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 Value	Meaning / Term	Description
`exact_match`		Exact label / synonym match.
`kg_fallback`		Inferred from the kg-microbe ingredient graph as a fallback.
`synonym_match_ambiguous`		Multiple equally-good synonym matches; mapping is uncertain.
`manual_curated`		Human curator selected this term.
`automated_expert_mapping`		Produced by an automated expert-mapping pipeline (e.g. LLM-assisted).
`fuzzy`		Fuzzy / approximate string match.
`corpus_consensus`		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`

Type of synonym relationship for an IngredientSynonym.

Permissible Value	Meaning / Term	Description
`EXACT`		Exact synonym.
`RELATED`		Related but not interchangeable.
`BROAD`		Broader concept.
`NARROW`		Narrower concept.
`ABBREVIATION`		Abbreviation or shorthand (e.g. "TSB" for "Tryptic Soy Broth").