Main Class

Bases: BaseModel

Microbe - main class of the new microbial data standard

Parameters:

Name	Type	Description	Default
organism_type	OrganismType		required
morph_type	Morph | None	Applicable and required for fungi only	None
unified_type_strain	bool | None	Is this strain type for unified species	None
unified_taxon	Taxon | None	Evaluated and updated taxonomy	None
type_strain	list[TypeStrain]		required
taxon	list[TaxonWithSource]		required
sample	list[Sample]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
isolation	list[Isolation]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
legal	list[Legal]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
cell_shape	list[CellShape]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
oxygen_relation	list[OxygenRelation]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
multi_cell_complex_forming	list[MultiCell]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
cell_size	list[CellSize]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
motility	list[Motility]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
colony	list[Colony]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
spore_formation	list[Spore]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
temperature	list[Growth[Literal[C]]]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
ph	list[Growth[Literal[pH]]]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
identifier	list[IdentifierStrain]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
connected_persons	list[ConnectedPerson]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
pathogenicity	list[Pathogen]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
bio_safety	list[BioSafety]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
sequences	list[Sequence]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
gc_content	list[GCContent]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
literature	list[Literature]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
wall_constituents	list[CellWall]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
fatty_acid_profiles	list[FattyAcidProfile]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
stainings	list[Staining]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
hemolysis	list[Hemolysis]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
cultivation_media	list[CultivationMedia]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
halophily	list[Halophil]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
tolerances	list[Tolerance]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
enzymes	list[Enzyme]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
metabolites	list[Metabolite]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
known_applications	list[Application]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
collections	list[Collection]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
other_media	list[OtherMedia]	Built-in mutable sequence. If no argument is given, the constructor creates a new empty list. The argument must be an iterable if specified.	<dynamic>
sources	list[Union[Literature, Organization, Person]]		required

Source code in src/microbial_strain_data_model/microbe.py

class Microbe(BaseModel):
    """Microbe - main class of the new microbial data standard"""

    # single data points

    organism_type: OrganismType = Field(
        title="Organism Type", alias="organismType", description="", frozen=True
    )

    morph_type: Morph | None = Field(
        default=None,
        title="Morph Type",
        alias="morphType",
        description="Applicable and required for fungi only",
        frozen=True,
    )

    unified_type_strain: bool | None = Field(
        default=None,
        title="Unified Type Strain",
        alias="unifiedTypeStrain",
        description="Is this strain type for unified species",
        frozen=True,
    )

    unified_taxon: Taxon | None = Field(
        default=None,
        title="Unified Taxon",
        alias="unifiedTaxon",
        description="Evaluated and updated taxonomy",
    )

    # lists of data objects

    type_strain: list[TypeStrain] = Field(
        title="Type Strain", alias="typeStrain", description=""
    )

    taxon: list[TaxonWithSource] = Field(title="Taxon", alias="taxon", description="")

    sample: list[Sample] = Field(
        default_factory=list, title="Sample", alias="sample", description=""
    )

    isolation: list[Isolation] = Field(
        default_factory=list, title="Isolation", alias="isolation", description=""
    )

    legal: list[Legal] = Field(
        default_factory=list, title="Legal", alias="legal", description=""
    )

    cell_shape: list[CellShape] = Field(
        default_factory=list, title="Cell Shape", alias="cellShape", description=""
    )

    oxygen_relation: list[OxygenRelation] = Field(
        default_factory=list,
        title="Oxygen Relation",
        alias="oxygenRelation",
        description="",
    )

    multi_cell_complex_forming: list[MultiCell] = Field(
        default_factory=list,
        title="Multi Cell Complex Forming",
        alias="multiCellComplexForming",
        description="",
    )

    cell_size: list[CellSize] = Field(
        default_factory=list, title="Cell Size", alias="cellSize", description=""
    )

    motility: list[Motility] = Field(
        default_factory=list, title="Motility", alias="motility", description=""
    )

    colony: list[Colony] = Field(
        default_factory=list, title="Colony", alias="colony", description=""
    )

    spore_formation: list[Spore] = Field(
        default_factory=list,
        title="Spore Formation",
        alias="sporeFormation",
        description="",
    )

    temperature: list[Growth[CelsiusUnit]] = Field(
        default_factory=list, title="Temperature", alias="temperature", description=""
    )

    ph: list[Growth[PHUnit]] = Field(
        default_factory=list, title="pH", alias="pH", description=""
    )

    identifier: list[IdentifierStrain] = Field(
        default_factory=list, title="Identifier", alias="identifier", description=""
    )

    connected_persons: list[ConnectedPerson] = Field(
        default_factory=list,
        title="Connected Persons",
        alias="connectedPersons",
        description="",
    )

    pathogenicity: list[Pathogen] = Field(
        default_factory=list, title="pathogenicity", alias="pathogenicity", description=""
    )

    bio_safety: list[BioSafety] = Field(
        default_factory=list, title="Bio Safety", alias="bioSafety", description=""
    )

    sequences: list[Sequence] = Field(
        default_factory=list, title="Sequences", alias="sequences", description=""
    )

    gc_content: list[GCContent] = Field(
        default_factory=list, title="GC Content", alias="gcContent", description=""
    )

    literature: list[Literature] = Field(
        default_factory=list, title="Literature", alias="literature", description=""
    )

    wall_constituents: list[CellWall] = Field(
        default_factory=list,
        title="Wall Constituents",
        alias="wallConstituents",
        description="",
    )

    fatty_acid_profiles: list[FattyAcidProfile] = Field(
        default_factory=list,
        title="Fatty Acid Profile",
        alias="fattyAcidProfiles",
        description="",
    )

    stainings: list[Staining] = Field(
        default_factory=list, title="Stainings", alias="stainings", description=""
    )

    hemolysis: list[Hemolysis] = Field(
        default_factory=list, title="Hemolysis", alias="hemolysis", description=""
    )

    cultivation_media: list[CultivationMedia] = Field(
        default_factory=list,
        title="Cultivation Media",
        alias="cultivationMedia",
        description="",
    )

    halophily: list[Halophil] = Field(
        default_factory=list, title="Halophily", alias="halophily", description=""
    )

    tolerances: list[Tolerance] = Field(
        default_factory=list, title="Tolerances", alias="tolerances", description=""
    )

    enzymes: list[Enzyme] = Field(
        default_factory=list, title="Enzymes", alias="enzymes", description=""
    )
    metabolites: list[Metabolite] = Field(
        default_factory=list, title="Metabolites", alias="metabolites", description=""
    )

    known_applications: list[Application] = Field(
        default_factory=list,
        title="Known Applications",
        alias="knownApplications",
        description="",
    )

    collections: list[Collection] = Field(
        default_factory=list, title="Collections", alias="collections", description=""
    )

    other_media: list[OtherMedia] = Field(
        default_factory=list, title="Other Media", alias="otherMedia", description=""
    )

    sources: list[Literature | Organization | Person] = Field(
        title="Source", alias="sources", description=""
    )

    model_config = ConfigDict(
        strict=True,
        extra="forbid",
        revalidate_instances="always",
        str_strip_whitespace=True,
    )