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Sub Classes#

address #

Address pydantic-model #

Bases: BaseModel

Address object comparable to schema.org PostalAddress.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

Validators:

  • _check_values

addressCountry: str | None = None pydantic-field #

Name of the country

addressCountryIso: CountryAlpha2 | None = None pydantic-field #

Country ISO code, see ISO 3166-1 alpha-2

addressLocality: str | None = None pydantic-field #

Locality within the region

addressRegion: str | None = None pydantic-field #

Region within the country

streetAddress: str | None = None pydantic-field #

Name of the street and number within street

application #

Application pydantic-model #

Bases: BaseModel

Application of the strain.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

application: str pydantic-field #

Name of the application or patent

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

biosafety #

BioSafety pydantic-model #

Bases: BaseModel

Biosafety classification.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

classification: str | None = None pydantic-field #

Classification Agency or Country, e.g. 'WHO' or 'German classification'

riskgroup: str pydantic-field #

In most cases a number system 1-4

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

url: HttpUrl | None = None pydantic-field #

Uniform Resource Locator of a resource on the Internet

chemicalsubstance #

CellWall pydantic-model #

Bases: ChemicalSubstance

Cell Wall constituent - ChemSubstance + percent of CellWall.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

Validators:

  • _check_values

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

ChemicalSubstance pydantic-model #

Bases: BaseModel

Chemical Substance base class.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

alternateName: list[str] pydantic-field #

List of alternative names for this substance

name: str | None = None pydantic-field #

Valid scientific name

FattyAcid pydantic-model #

Bases: ChemicalSubstance

Single Fatty Acid - used in Fatty Acid Profile.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

Validators:

  • _check_values

Halophil pydantic-model #

Bases: ChemicalSubstance

Halophily abilities of a Strain.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

Validators:

  • _check_values

maximal: float | None = None pydantic-field #

Single optimal growth value

minimal: float | None = None pydantic-field #

Single optimal growth value

optimal: float | None = None pydantic-field #

Single optimal growth value

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

tests: list[GrowthRange] pydantic-field #

List of tests and if the strain grows in tested ranges

Metabolite pydantic-model #

Bases: ChemicalSubstance

Information about tested Metabolites.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

Validators:

  • _check_values

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

tests: list[MetaboliteTest] pydantic-field #

List of performed tests on this metabolite

country #

Country pydantic-model #

Bases: BaseModel

Country information, mostly on nagoya protocol.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

Validators:

  • _ensure_country_not_empty

iso_3166_2: CountryAlpha2 | CountryHistoricalAlpha2 | CountryOtherCodes | None = None pydantic-field #

Country code, see ISO 3166-1 alpha-2

name: str | None = None pydantic-field #

Full name of the country

cultivationmedia #

CultivationMedia pydantic-model #

Bases: BaseModel

Cultivation media, use links to Media Dive or other resources.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

relatedData: list[RelationLink] pydantic-field #

JSON paths to relation object

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

enums #

ColonyColor #

Bases: str, Enum

Valid colors for colonies.

Attributes:

Name Type Description
white

white
cream

cream
yellowish

yellowish
orange

orange
pink

pink
red

red
buff

buff
darkbrown

darkbrown
reyish

reyish
tannish

tannish
beige

beige
brownish

brownish

ConcentrationUnit #

Bases: str, Enum

Valid concentration units for solutions.

Attributes:

Name Type Description
gram_per_liter

g/L
mol_per_liter

mol/L
mass_percent

g/g%
volume_percent

v/v%

CountryHistoricalAlpha2 #

Bases: str, Enum

WARNING: This list was generated by ChatGPT no human verification has been done so far.

Attributes:

Name Type Description
CS

Czechoslovakia
DD

German Democratic Republic (East Germany)
DY

Dahomey
FQ

French Southern and Antarctic Territories
GE

Gilbert and Ellice Islands
HV

Upper Volta
JT

Johnston Island
MI

Midway Islands
NH

New Hebrides
RH

Southern Rhodesia
SU

Soviet Union
TP

East Timor
UK

United Kingdom
VD

North Vietnam
YU

Yugoslavia
ZR

Zaire
BU

Burma
AN

Netherlands Antilles

CountryOtherCodes #

Bases: str, Enum

Other allowed Values in case of non-country origin.

Attributes:

Name Type Description
international

International Waters
other

Other

CurationMode #

Bases: str, Enum

Curation mode options.

Attributes:

Name Type Description
manual

manual
automated

automated
unknown

unknown

FlagellumArrangement #

Bases: str, Enum

Valid flagellum arrangement options.

Attributes:

Name Type Description
polar

Polar
peritrichous

Peritrichous
monotrichous_polar

Monotrichous polar

GCMethod #

Bases: str, Enum

Methods for GC measurement.

Attributes:

Name Type Description
experimental

experimental
genomeSequence

genome sequence

HemolysisBlood #

Bases: str, Enum

Valid blood types.

Attributes:

Name Type Description
sheep

sheep
horse

horse
unknown

unknown

HemolysisType #

Bases: str, Enum

Valid hemolysis types.

Attributes:

Name Type Description
alpha

alpha
beta

beta
gamma

gamma

Host #

Bases: str, Enum

Valid host types.

Attributes:

Name Type Description
plant

plant
animal

animal
invertebrates

invertebrates
vertebrates

vertebrates
mammals

mammals
primates

non-human primates
human

human
fungi

fungi

KindOfUtilization #

Bases: str, Enum

Types of utilization.

Attributes:

Name Type Description
assimilation

assimilation
buildsAcidFrom

builds acid from
degradation

degradation
energySource

energy source
fermentation

fermentation
hydrolysis

hydrolysis
reduction

reduction

MetaboliteTestType #

Bases: str, Enum

Valid metabolite test types.

Attributes:

Name Type Description
utilization

Utilization
production

Production

Morph #

Bases: str, Enum

Valid morph types for fungi.

Attributes:

Name Type Description
yeast

yeast
filamentous

filamentous

NagoyaRestrictions #

Bases: str, Enum

Valid values of Nagoya protocol information.

Attributes:

Name Type Description
no_restrictions

No known restrictions under the Nagoya protocol
documents_available

Documents providing proof of legal access and terms of use available at the collection
contact_collection

Strain probably in scope, please contact the culture collection

OrganismType #

Bases: str, Enum

Valid organism types.

Attributes:

Name Type Description
algae

Algae
archaea

Archaea
bacteria

Bacteria
fungi

Fungi
protist

Protist

OxygenTolerance #

Bases: str, Enum

How does the strain tolerate Oxygen.

Attributes:

Name Type Description
aerobe

aerobe
aerotolerant

aerotolerant
anaerobe

anaerobe
facultativeAerobe

facultative aerobe
facultativeAnaerobe

facultative anaerobe
microaerophile

microaerophile
microaerotolerant

microaerotolerant
obligateAerobe

obligate aerobe
obligateAnaerobe

obligate anaerobe

PathogenLevel #

Bases: str, Enum

Valid pathogen levels.

Attributes:

Name Type Description
no

no pathogen
opportunistic

opportunistic
obligate

obligate

Restriction #

Bases: str, Enum

Valid supply forms.

Attributes:

Name Type Description
no_restrictions

no known restrictions apply
no_commercial

only for non-commercial purposes
agreement

for commercial development a special agreement is requested

SequenceLevel #

Bases: str, Enum

Valid sequence level categories.

Attributes:

Name Type Description
genome

genome
id_sequence

identifier sequence
gene

gene
artificial

artificial
other

other

SequenceType #

Bases: str, Enum

Valid sequence types.

Attributes:

Name Type Description
nucleotide

Nucleotide
protein

Protein

SizeUnit #

Bases: str, Enum

Valid size options for microbes.

Attributes:

Name Type Description
µm

µm
mm

mm

SourceType #

Bases: str, Enum

Source type options.

Attributes:

Name Type Description
literature

literature
website

website
dataset

dataset

SporeType #

Bases: str, Enum

Valid spore types.

Attributes:

Name Type Description
spore

spore
endospore

endospore

StainingValue #

Bases: str, Enum

Valid staining test results.

Attributes:

Name Type Description
pos

positive
neg

negative
var

variable

SupplyForm #

Bases: str, Enum

Valid supply forms.

Attributes:

Name Type Description
agar

Agar
cryo

Cryo
dry

Dry ice
liquid

Liquid medium
lyo

Lyophilization
oil

Oil
water

Water
dna

DNA

TaxonRank #

Bases: str, Enum

Valid ranks of taxonomy.

Attributes:

Name Type Description
subspecies

subspecies
species

species
section

section
genus

genus
family

family
order

order
tax_class

class
phylum

phylum
domain

domain

TaxonStatus #

Bases: str, Enum

Valid taxon status.

Attributes:

Name Type Description
proposed

Proposed
valid

Validly published
valid_synonym

Validly published synonym

ToleranceReaction #

Bases: str, Enum

Valid tolerance reactions.

Attributes:

Name Type Description
Sensitive

No tolerance
Resistant

High tolerance
Intermediate

Not assignable

enzyme #

Enzyme pydantic-model #

Bases: BaseModel

Information about one enzyme.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

active: bool | None = None pydantic-field #

Is this enzyme active

hasECNumber: str pydantic-field #

An EC number defined by the Enzyme Commission

relatedData: list[RelationLink] pydantic-field #

JSON paths to relation object

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

fattyacidprofile #

FattyAcidProfile pydantic-model #

Bases: BaseModel

Full Fatty Acid Profile.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

Validators:

  • _ensure_list_not_empty

library: str | None = None pydantic-field #

The used library

profile: list[FattyAcid] pydantic-field #

List of fatty acids and their percentages

relatedData: list[RelationLink] pydantic-field #

JSON paths to relation object

software: str | None = None pydantic-field #

The used software

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

gccontent #

GCContent pydantic-model #

Bases: BaseModel

GC content of the microorganism.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

method: GCMethod | None = None pydantic-field #

Name of the method used to measure the GC content

noteMethod: str | None = None pydantic-field #

Note about the used method

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

growthcondition #

GrowthCondition pydantic-model #

Bases: BaseModel

Optimal and tested information about growing a Strain.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

maximalPh: float | None = None pydantic-field #

Known maximal growth pH value

maximalTemperature: float | None = None pydantic-field #

Known maximal growth temperature value in celsius

minimalPh: float | None = None pydantic-field #

Known minimal growth pH value

minimalTemperature: float | None = None pydantic-field #

Known minimal growth temperature value in celsius

optimalPh: float | None = None pydantic-field #

Single optimal growth pH value

optimalTemperature: float | None = None pydantic-field #

Single optimal growth temperature value in celsius

oxygenRelation: OxygenTolerance | None = None pydantic-field #

Aerobic, anaerobic etc.

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

testsPh: list[GrowthRange] pydantic-field #

List of tests and if the strain grows in tested ranges

testsTemperature: list[GrowthRange] pydantic-field #

List of tests and if the strain grows in tested ranges

GrowthRange pydantic-model #

Bases: BaseModel

Single grow condition test.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

growth: bool pydantic-field #

Does the strain grow within this range?

maximal: float | None = None pydantic-field #

Maximal value of tested range

minimal: float | None = None pydantic-field #

Minimal value of tested range

relatedData: list[RelationLink] pydantic-field #

JSON paths to relation object

hemolysis #

Hemolysis pydantic-model #

Bases: BaseModel

Hemolysis of bloods.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

blood: HemolysisBlood pydantic-field #

Type of blood used for the test

hemolysisType: HemolysisType pydantic-field #

Type of hemolysis that the strain is capable of

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

identifier #

Identifier pydantic-model #

Bases: BaseModel

Identifier of every Kind, compare to schema.org PropertyValue class.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...)

name: str pydantic-field #

Name of the identifier

propertyID: str | None = None pydantic-field #

See schema.org/propertyID

url: HttpUrl | None = None pydantic-field #

Uniform Resource Locator of a resource on the Internet

value: str pydantic-field #

Value of the identifier (can also be a URL)

IdentifierStrain pydantic-model #

Bases: Identifier

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

isolationtag #

IsolationTag pydantic-model #

Bases: BaseModel

Isolation tag system, original used by BacDive.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

  • level1 (str)
  • level2 (str | None)
  • level3 (str | None)

Validators:

  • _check_isolation_tag

legal #

Legal pydantic-model #

Bases: BaseModel

Legal information of the strain.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

gmo: bool | None = None pydantic-field #

Is this strain genetically modified

gmoInformation: str | None = None pydantic-field #

What was genetically modified

gras: bool | None = None pydantic-field #

Status of 'Generally Recognized As Safe' by FDA - USA

nagoyaRestrictions: NagoyaRestrictions pydantic-field #

Are there any known Nagoya restrictions in place for this strain

otherRestrictions: list[Restriction] pydantic-field #

List of restrictions in place for this strain

qps: bool | None = None pydantic-field #

Status of 'Qualified presumption of safety' by EFSA - European Union

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

Restriction pydantic-model #

Bases: BaseModel

Restriction information.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

authority: str | None = None pydantic-field #

The responsible authority

country: Country | None = None pydantic-field #

Country that put the restriction in place

name: str pydantic-field #

Name of the restriction

url: HttpUrl | None = None pydantic-field #

Link to the restriction documents

value: str pydantic-field #

What is the restriction

literature #

Literature pydantic-model #

Bases: LiteratureSource

Connected Literature.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

Validators:

  • _check_if_name_or_url_is_set

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

LiteratureSource pydantic-model #

Bases: BaseModel

Literature used in Source.

Fields:

Validators:

  • _check_if_name_or_url_is_set

location #

GeoPoint pydantic-model #

Bases: BaseModel

Geopoint / Coordinate object.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

latitude: Latitude pydantic-field #

Should be a float value between -90 and 90

longitude: Longitude pydantic-field #

Should be a float value between -180 and 180

Location pydantic-model #

Bases: BaseModel

Location object.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

Validators:

  • _check_values

description: str | None = None pydantic-field #

Description of the location

geo: GeoPoint | None = None pydantic-field #

Precise location coordinates

name: str | None = None pydantic-field #

Name of the location, e.g. 'Lake Como'

metabolitetest #

MetaboliteTest pydantic-model #

Bases: BaseModel

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

active: bool | None = None pydantic-field #

Is the metabolite utilization or production active

kindOfUtilization: KindOfUtilization | None = None pydantic-field #

Only relevant if the type is utilization, as there are multiple kinds of utilization

protocol: str | None = None pydantic-field #

What test was used

relatedData: list[RelationLink] pydantic-field #

JSON paths to relation object

type: MetaboliteTestType pydantic-field #

The type of metabolic test, can be utilization or production

morphology #

Morphology pydantic-model #

Bases: BaseModel

Morphology of a cell.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

Validators:

  • _check_values

cellLength: Size | None = None pydantic-field #

Length of a cell

cellShape: str | None = None pydantic-field #

The shape type the cells

cellWidth: Size | None = None pydantic-field #

Width of a cell

colonyColor: ColonyColor | None = None pydantic-field #

Color of the colony on the

flagellum: bool | None = None pydantic-field #

Do the cells have flagella

flagellumArrangement: FlagellumArrangement | None = None pydantic-field #

How are the flagella arranged

gliding: bool | None = None pydantic-field #

Cells can be motile by gliding instead of having flagella

motile: bool | None = None pydantic-field #

Are the cells of this strain are motile

multiCellComplexForming: bool | None = None pydantic-field #

Do the cells form complexes

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

organization #

Collection pydantic-model #

Bases: Organization

Information about one culture collection.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

absFile: HttpUrl | None = None pydantic-field #

Link to ABS file

available: bool | None = None pydantic-field #

Is the strain in the current catalog

axenicCulture: bool | None = None pydantic-field #

Is the culture pure or mixed with other microbes

catalogUrl: HttpUrl | None = None pydantic-field #

Link to catalog

depositedAs: str | None = None pydantic-field #

The CCNO or designation before deposition

depositionDate: Annotated[str, StringConstraints(strip_whitespace=True, to_upper=True, pattern='^(?:\\d{4}[-\\._]?\\d{0,2}[-\\._]?\\d{0,2})?/?(?:\\d{4}[-\\._]?\\d{0,2}[-\\._]?\\d{0,2})?$')] | None = None pydantic-field #

Date of Deposition, using date range format of dublin core: 'YYYY-MM-DD/YYYY-MM-DD' ether side can be empty defining an open ended range, only the year is mandatory, e.g. '/1978' means before 1978

depositor: Person | None = None pydantic-field #

Person who deposited the strain at this collection

history: str | None = None pydantic-field #

Exchange history of the strain

mtaFile: HttpUrl | None = None pydantic-field #

Link to MTA file

policyUrl: HttpUrl | None = None pydantic-field #

Link to collections policy

registeredCollection: bool | None = None pydantic-field #

Registered collection status of this collection

resourceNumber: str pydantic-field #

The CCNO of the strain at this collection

restrictionsOnUse: Restriction | None = None pydantic-field #

Restrictions of use by the collection

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

supplyForms: list[SupplyForm] pydantic-field #

How the strain are available

Organization pydantic-model #

Bases: BaseModel

Individual Entity of a Organization.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

address: Address | None = None pydantic-field #

Address of the organization

email: EmailStr | None = None pydantic-field #

Contact email

identifier: list[Identifier] pydantic-field #

Identifiers of the organization, e.g. ROR

legalName: str | None = None pydantic-field #

Full legal name of the organization

Link to logo

name: str pydantic-field #

Short name of the organization

url: HttpUrl | None = None pydantic-field #

Link to homepage

origin #

Origin pydantic-model #

Bases: BaseModel

Isolation event information.

Notes
  • Sample = The material probe in which the strain was found
  • Isolation = Isolation of the strain from the sample

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

country: Country | None = None pydantic-field #

Country where the sample material originated from

description: str | None = None pydantic-field #

Description of the sample

isolatedAt: Organization | None = None pydantic-field #

Institute where the strain was isolated from the sample

isolationDate: Annotated[str, StringConstraints(strip_whitespace=True, to_upper=True, pattern='^(?:\\d{4}[-\\._]?\\d{0,2}[-\\._]?\\d{0,2})?/?(?:\\d{4}[-\\._]?\\d{0,2}[-\\._]?\\d{0,2})?$')] | None = None pydantic-field #

Date of isolation from the sample material, using date range format of dublin core:'YYYY-MM-DD/YYYY-MM-DD' ether side can be empty defining an open ended range, only the year is mandatory, e.g. '/1978' means before 1978

isolator: Person | None = None pydantic-field #

Person that isolated the strain from the sample

locationCreated: Location | None = None pydantic-field #

Location where the sample was taken

sampleDate: Annotated[str, StringConstraints(strip_whitespace=True, to_upper=True, pattern='^(?:\\d{4}[-\\._]?\\d{0,2}[-\\._]?\\d{0,2})?/?(?:\\d{4}[-\\._]?\\d{0,2}[-\\._]?\\d{0,2})?$')] | None = None pydantic-field #

Date of sampling, using date range format of dublin core: 'YYYY-MM-DD/YYYY-MM-DD' ether side can be empty defining an open ended range, only the year is mandatory, e.g. '/1978' means before 1978

sampler: Person | None = None pydantic-field #

Person that sampled the material

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

othermedia #

OtherMedia pydantic-model #

Bases: BaseModel

A Media object e.g. Photo, Video, Document, etc.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

Validators:

  • _check_values

description: str | None = None pydantic-field #

Description of the medium and the content in the medium

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

url: HttpUrl | None = None pydantic-field #

Link to medium

usageInfo: str | None = None pydantic-field #

License or other information on usage

pathogen #

Pathogen pydantic-model #

Bases: BaseModel

Pathogen, defining Host, pathogenicity and under what classification.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

classification: str | None = None pydantic-field #

Type of classification, e.g. German classification or WHO classification

host: Host pydantic-field #

Organism or group of organisms that can be infected

pathogen: PathogenLevel pydantic-field #

Frequency of pathogenicity: no pathogen, opportunistic or obligate

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

url: HttpUrl | None = None pydantic-field #

Link to classification document

person #

Person pydantic-model #

Bases: BaseModel

Person.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

identifier: list[Identifier] pydantic-field #

Person identifiers like ORCID

name: str pydantic-field #

Name of the person, preferable: Last, First

relateddata #

RelatedData pydantic-model #

Bases: BaseModel

RelatedData.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

relation: str pydantic-field #

The kind or type of relation of the data points, e.g. growthCondition, testCondition, API20

source: SourceLink pydantic-field #

JSON path to source object

sequence #

Sequence pydantic-model #

Bases: BaseModel

Information on a Sequence.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

size #

Size pydantic-model #

Bases: BaseModel

Size object, use only for micro and millimeter.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

  • minimal (PositiveFloat)
  • maximal (PositiveFloat)
  • unit (SizeUnit)

source #

Source pydantic-model #

Bases: BaseModel

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

Validators:

  • _check_if_name_or_url_is_set

mode: CurationMode pydantic-field #

Mode of curation

sourceType: SourceType pydantic-field #

Source Type

spore #

Spore pydantic-model #

Bases: BaseModel

Spore information about one Strain.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

relatedData: list[RelationLink] pydantic-field #

JSON paths to relation object

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

staining #

Staining pydantic-model #

Bases: BaseModel

Stainings tested on the strain.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

taxon #

ScientificName pydantic-model #

Bases: BaseModel

Scientific name.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

Taxon pydantic-model #

Bases: BaseModel

Aggregates taxon data for the new microbial standard.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

TaxonWithSource pydantic-model #

Bases: Taxon

Taxon class with source information.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

TypeStrain pydantic-model #

Bases: BaseModel

Information if a strain is the type strain of its species.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

tolerance #

Tolerance pydantic-model #

Bases: ChemicalSubstance

Tolerance information - e.g. antibiotic resistance.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

mic: str | None = None pydantic-field #

The minimal inhibitory concentration

source: list[SourceLink] pydantic-field #

List of JSON paths to source object

ToleranceTest pydantic-model #

Bases: BaseModel

Tested tolerance of compound.

Config:

  • strict: True
  • extra: forbid
  • revalidate_instances: always
  • str_strip_whitespace: True

Fields:

concentration: float | None = None pydantic-field #

Concentration value

relatedData: list[RelationLink] pydantic-field #

JSON paths to relation object

unit: ConcentrationUnit pydantic-field #

Unit of concentration e.g. g/ml