IngredientRecord

Name

IngredientRecord

Description

Core record for a media ingredient with ontology mapping, synonyms, and curation history. Represents either a mapped ingredient (with a primary ontology, registry, or local identity CURIE) or an unmapped ingredient (placeholder identifier, awaits curation). Can serve as root element for individual YAML files or as elements in IngredientCollection.

From schema

https://w3id.org/mediaingredientmech

Attributes

Identifier

Name: identifier
Description: Semantic identifier for the record and its LinkML identifier slot, but not a guaranteed unique document address: reviewed duplicate families may share a CURIE. For mapped ingredients this is the primary ontology, registry, or local identity (e.g. `CHEBI:26710`, `cas:247167-54-0`, `kgmicrobe.compound:aburamycin_a`); for unmapped ingredients it is a generated `UNMAPPED_NNNN` placeholder. The nested `ontology_mapping.ontology_id` is a grounding target: it equals `identifier` when the identifier itself names the grounded ontology term, but registry or local identities may legitimately differ from the ontology target at any evidence-backed mapping quality.
From schema: https://w3id.org/mediaingredientmech
Identifier: True
Required: True

Preferred term

Name: preferred_term
Description: Canonical name for this ingredient
From schema: https://w3id.org/mediaingredientmech
Required: True

Ontology mapping

Name

ontology_mapping

Description

Ontology term mapping (CHEBI/FOODON)

From schema

https://w3id.org/mediaingredientmech

Range

OntologyMapping

Bindings

Obligation level
REQUIRED
Binds value of
ontology_id

Synonyms

Name: synonyms
Description: Alternative names and raw text variants
From schema: https://w3id.org/mediaingredientmech
Range: IngredientSynonym
Multivalued: True
Inlined as list: True

Mapping status

Name: mapping_status
Description: Current mapping status
From schema: https://w3id.org/mediaingredientmech
Range: MappingStatusEnum
Required: True

Occurrence statistics

Name: occurrence_statistics
Description: Usage statistics across media recipes
From schema: https://w3id.org/mediaingredientmech
Range: OccurrenceStats

Curation history

Name: curation_history
Description: Audit trail of all curation actions
From schema: https://w3id.org/mediaingredientmech
Range: CurationEvent
Multivalued: True
Inlined as list: True

Notes

Name: notes
Description: Free-text curation notes
From schema: https://w3id.org/mediaingredientmech

Community organism roles

Name: community_organism_roles
Description: Role(s) this organism plays in a microbial community (e.g., PRIMARY_DEGRADER, SYNERGIST, COMPETITOR). Formerly `cellular_roles`; renamed to disambiguate from ingredient-level cellular metabolic roles.
From schema: https://w3id.org/mediaingredientmech
Range: CommunityOrganismRoleAssignment
Multivalued: True
Inlined as list: True

Nutritional roles

Name: nutritional_roles
Description: What element or macronutrient this ingredient supplies to the medium (e.g., CARBON_SOURCE, SULFUR_SOURCE, VITAMIN_SOURCE). Facet 1 of 3 orthogonal ingredient-role facets — a single ingredient may carry multiple values (e.g., L-cysteine → AMINO_ACID_SOURCE + SULFUR_SOURCE).
From schema: https://w3id.org/mediaingredientmech
Range: NutritionalRoleAssignment
Multivalued: True
Inlined as list: True

Physicochemical roles

Name: physicochemical_roles
Description: Chemical or physical function this ingredient performs in the medium (e.g., BUFFER, CHELATOR, REDUCING_AGENT). Facet 2 of 3 orthogonal ingredient-role facets — independent of what element the ingredient supplies.
From schema: https://w3id.org/mediaingredientmech
Range: PhysicochemicalRoleAssignment
Multivalued: True
Inlined as list: True

Cellular metabolic roles

Name: cellular_metabolic_roles
Description: Role of this ingredient inside/on the cultured microbe (e.g., SUBSTRATE, ELECTRON_DONOR, COFACTOR). Facet 3 of 3 orthogonal ingredient-role facets — often organism-conditional (e.g., ELECTRON_DONOR applies only for organisms that oxidize the compound for energy).
From schema: https://w3id.org/mediaingredientmech
Range: CellularMetabolicRoleAssignment
Multivalued: True
Inlined as list: True

Solution type

Name: solution_type
Description: Type of solution if this is a stock/pre-mix rather than individual chemical
From schema: https://w3id.org/mediaingredientmech
Range: SolutionTypeEnum

Chemical properties

Name: chemical_properties
Description: Chemical structure and properties (for CHEBI-mapped ingredients only)
From schema: https://w3id.org/mediaingredientmech
Range: ChemicalProperties

Supplied form

Name: supplied_form
Description: The material actually ordered and delivered for this ingredient — the thing on the shelf, as distinct from the substance the record denotes. Multivalued because one ingredient is legitimately buyable in several forms (anhydrous vs a hydrate, free acid vs sodium salt) and a recipe may not say which. Keeps procurement detail OUT of the identity: the `identifier` optimises for how the node reads in the knowledge graph, and this slot carries what you would put on a purchase order.
From schema: https://w3id.org/mediaingredientmech
Range: SuppliedForm
Multivalued: True
Inlined as list: True

Representative

Name: representative
Description: `identifier` of the representative record if this record has been merged. Only set when mapping_status is REJECTED due to merge. Points to the canonical record representing this ingredient. (No pattern constraint: the merge-tracking feature is currently unused — when revived, point at the schema's canonical identifier format.)
From schema: https://w3id.org/mediaingredientmech

Merged

Name: merged
Description: List of record `identifier`s merged into this representative. Only set on records serving as merge targets. Tracks all records consolidated into this canonical representation. (No pattern constraint: see `representative` above.)
From schema: https://w3id.org/mediaingredientmech
Multivalued: True

Ingredient type

Name: ingredient_type
Description: Classification of entry type: single chemical ingredient vs whole named medium. SINGLE_INGREDIENT: Pure chemical (NaCl, agar, glucose). NAMED_MEDIUM: A complete, named medium formulation/recipe (R2A agar, LB broth) -- "defined" = record granularity (a whole named medium), NOT "chemically defined"; undefined components are expected. UNDEFINED_MIXTURE: Complex mixture of unknown composition (yeast extract, peptone). STOCK_SOLUTION: Pre-mixed solution of defined ingredients.
From schema: https://w3id.org/mediaingredientmech
Range: IngredientTypeEnum

Components

Name: components
Description: A has-part decomposition for a STOCK_SOLUTION, NAMED_MEDIUM, or UNDEFINED_MIXTURE: the list of component ingredients (with concentration where known). This is ingredient/mixture partonomy, not an identity mapping, a complete culturing recipe, or a relationship among chemical forms. It may transcribe a combination label. Populate only from verifiable evidence; omit the slot when no constituent is known. When present, component_assertion records how the decomposition was made and its evidence.
From schema: https://w3id.org/mediaingredientmech
Range: StockComponent
Multivalued: True
Inlined as list: True

Component assertion

Name: component_assertion
Description: Method and structured evidence for the record-level has-part claim carried by components. Required whenever components is non-empty and forbidden when components is absent; the corpus-level partonomy validator enforces that cross-field invariant.
From schema: https://w3id.org/mediaingredientmech
Range: ComponentAssertion
Inlined: True

Culturemech reference

Name: culturemech_reference
Description: Typed, stable link to a CultureMech recipe. Replaces the former `culturemech_medium_name`, which held a display string and no relationship semantics, so it could not distinguish the same formulation from a variant or a merely similar composition (#447). CultureMech remains authoritative for the recipe body and for recipe family/variant structure; this records only which recipe a record answers to and how.
From schema: https://w3id.org/mediaingredientmech
Range: CultureMechReference

Kg microbe node id

Name: kg_microbe_node_id
Description: KG-Microbe node ID for this ingredient when found in the KG exactly. Populated when the ingredient is present as a named node in the KG-Microbe mediadive graph (i.e. used as an ingredient in at least one KG-Microbe medium solution). The node ID is a CURIE using whichever scheme the KG-Microbe graph stores the entity under — most often `CHEBI:`, but also `mesh:`, `NCIT:`, `FOODON:`, `ENVO:`, or one of the kg-microbe registry prefixes (`kgmicrobe.compound:`, `kgmicrobe.ingredient:`).
From schema: https://w3id.org/mediaingredientmech
Required: False
Pattern: ^[A-Za-z][A-Za-z0-9.]*:[A-Za-z0-9][A-Za-z0-9._~-]*$

Environmental context

Name

environmental_context

Description

Environmental contexts where this ingredient is relevant. Each entry pairs an ENVO term with a relevance qualifier explaining the association (natural source, selective agent, environment mimic, etc.). Enables cross-repository environment-driven queries with CommunityMech (`environment_term`) and CultureMech (`source_environment`). Optional; ubiquitous ingredients (water, glucose) typically have no entries.

From schema

https://w3id.org/mediaingredientmech

Range

EnvironmentContext

Bindings

Obligation level
REQUIRED
Binds value of
environment_term

Required

False

Multivalued

True

Inlined as list

True

Discussions

Name: discussions
Description: Open questions, knowledge gaps, controversies, and curation todos attached to this ingredient (shared Discussion supertype; anchor `attaches_to` into e.g. `ontology_mapping#<term>`).
From schema: https://w3id.org/mediaingredientmech
Range: Discussion
Multivalued: True
Inlined as list: True

Datasets

Name: datasets
Description: Public datasets (omics/sequence/phenotype) relevant to this ingredient.
From schema: https://w3id.org/mediaingredientmech
Range: Dataset
Multivalued: True
Inlined as list: True

Tree root

True

Rules

Preconditions
Slot conditions
Components
Name
components
Value presence
PRESENT
Postconditions
Slot conditions
Component assertion
Name
component_assertion
Value presence
PRESENT
Bidirectional
True
Preconditions
Slot conditions
Components
Name
components
Value presence
PRESENT
Postconditions
Slot conditions
Ingredient type
Name
ingredient_type
Equals string in
STOCK_SOLUTION
NAMED_MEDIUM
UNDEFINED_MIXTURE