bridge.core.biotools module#
Auto-generated Pydantic models for the bio.tools schema. Do not edit this file manually — it is generated by scripts/gen_biotools_models.py from the JSON schema at https://raw.githubusercontent.com/bio-tools/biotoolsSchema/refs/heads/v4-dev/biotools.schema.json.
- class bridge.core.biotools.BiotoolsIdType(root=PydanticUndefined, **data)[source]#
Bases:
RootModel[Annotated[str, StringConstraints]]- Parameters:
root (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=None, max_length=None, pattern=^([\--\.0-9A-Z_a-z]*)$)])
- root: constr(pattern='^([\--\.0-9A-Z_a-z]*)$')#
- class bridge.core.biotools.CreditItem(**data)[source]#
Bases:
BaseModel- Parameters:
name (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=1, max_length=100, pattern=None)] | None)
email (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=None, max_length=None, pattern=^([0-9A-Z_a-z]+([\'\+\--\.][0-9A-Z_a-z]+)*@[0-9A-Z_a-z]+([\--\.][0-9A-Z_a-z]+)*\.[0-9A-Z_a-z]+([\--\.][0-9A-Z_a-z]+)*)$)] | None)
url (str | None)
orcidid (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=None, max_length=None, pattern=^(http\://orcid\.org/[0-9]{4,4}\-[0-9]{4,4}\-[0-9]{4,4}\-[0-9]{3,3}[0-9X])$)] | Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=None, max_length=None, pattern=^(https\://orcid\.org/[0-9]{4,4}\-[0-9]{4,4}\-[0-9]{4,4}\-[0-9]{3,3}[0-9X])$)] | None)
gridid (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=None, max_length=None, pattern=^(grid[\w\D][0-9]{4,}[\w\D][0-9a-f]{1,2})$)] | None)
rorid (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=None, max_length=None, pattern=)] | None)
fundrefid (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=None, max_length=None, pattern=)] | None)
typeEntity (TypeEntity | None)
typeRole (List[TypeRoleEnum] | None)
note (TextType | None)
- email: Optional[constr(pattern="^([0-9A-Z_a-z]+([\'\+\--\.][0-9A-Z_a-z]+)*@[0-9A-Z_a-z]+([\--\.][0-9A-Z_a-z]+)*\.[0-9A-Z_a-z]+([\--\.][0-9A-Z_a-z]+)*)$")]#
- fundrefid: Optional[constr(pattern='')]#
- gridid: Optional[constr(pattern='^(grid[\w\D][0-9]{4,}[\w\D][0-9a-f]{1,2})$')]#
- name: Optional[constr(min_length=1, max_length=100)]#
- note: Optional[TextType]#
- orcidid: Optional[Union[constr(pattern='^(http\://orcid\.org/[0-9]{4,4}\-[0-9]{4,4}\-[0-9]{4,4}\-[0-9]{3,3}[0-9X])$'), constr(pattern='^(https\://orcid\.org/[0-9]{4,4}\-[0-9]{4,4}\-[0-9]{4,4}\-[0-9]{3,3}[0-9X])$')]]#
- rorid: Optional[constr(pattern='')]#
- typeEntity: Optional[TypeEntity]#
- typeRole: Optional[List[TypeRoleEnum]]#
- url: Optional[str]#
- class bridge.core.biotools.DataType(**data)[source]#
Bases:
BaseModel- Parameters:
data (EDAMdata)
format (List[EDAMformat] | None)
- data: EDAMdata#
- format: Optional[List[EDAMformat]]#
- class bridge.core.biotools.DocumentationItem(**data)[source]#
Bases:
BaseModel- Parameters:
url (UrlftpType)
type (List[TypeEnum1])
note (TextType | None)
- note: Optional[TextType]#
- type: List[TypeEnum1]#
- url: UrlftpType#
- class bridge.core.biotools.DownloadItem(**data)[source]#
Bases:
BaseModel- Parameters:
url (UrlftpType)
type (Type1)
note (TextType | None)
version (VersionType | None)
- note: Optional[TextType]#
- type: Type1#
- url: UrlftpType#
- version: Optional[VersionType]#
- class bridge.core.biotools.EDAMdata(**data)[source]#
Bases:
BaseModel- Parameters:
term (str | None)
uri (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=None, max_length=None, pattern=^(http\://edamontology\.org/data_[0-9]{4,4})$)] | None)
- term: Optional[str]#
- uri: Optional[constr(pattern='^(http\://edamontology\.org/data_[0-9]{4,4})$')]#
- class bridge.core.biotools.EDAMformat(**data)[source]#
Bases:
BaseModel- Parameters:
term (str | None)
uri (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=None, max_length=None, pattern=^(http\://edamontology\.org/format_[0-9]{4,4})$)] | None)
- term: Optional[str]#
- uri: Optional[constr(pattern='^(http\://edamontology\.org/format_[0-9]{4,4})$')]#
- class bridge.core.biotools.FunctionItem(**data)[source]#
Bases:
BaseModel- Parameters:
operation (List[OperationItem])
input (List[InputItem] | None)
output (List[OutputItem] | None)
note (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=10, max_length=1000, pattern=None)] | None)
cmd (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=1, max_length=1000, pattern=None)] | None)
- cmd: Optional[constr(min_length=1, max_length=1000)]#
- input: Optional[List[InputItem]]#
- note: Optional[constr(min_length=10, max_length=1000)]#
- operation: List[OperationItem]#
- output: Optional[List[OutputItem]]#
- class bridge.core.biotools.InputItem(**data)[source]#
Bases:
BaseModel- Parameters:
data (EDAMdata)
format (List[EDAMformat] | None)
- data: EDAMdata#
- format: Optional[List[EDAMformat]]#
- class bridge.core.biotools.LinkItem(**data)[source]#
Bases:
BaseModel- Parameters:
url (UrlftpType)
type (List[TypeEnum])
note (TextType | None)
- note: Optional[TextType]#
- type: List[TypeEnum]#
- url: UrlftpType#
- class bridge.core.biotools.OntologyConcept(**data)[source]#
Bases:
BaseModel- Parameters:
term (List[str] | None)
uri (str | None)
- term: Optional[List[str]]#
- uri: Optional[str]#
- class bridge.core.biotools.OperationItem(**data)[source]#
Bases:
BaseModel- Parameters:
term (str | None)
uri (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=None, max_length=None, pattern=^(http\://edamontology\.org/operation_[0-9]{4,4})$)] | None)
- term: Optional[str]#
- uri: Optional[constr(pattern='^(http\://edamontology\.org/operation_[0-9]{4,4})$')]#
- class bridge.core.biotools.OtherIDItem(**data)[source]#
Bases:
BaseModel- Parameters:
type (Type | None)
value (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=None, max_length=None, pattern=^(10\.[0-9]{4,9}/[\(-\)\--<>A-\[\]_a-z]+)$)] | Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=None, max_length=None, pattern=^((r|r|i|d|RRID)\:[\w\D]+)$)] | Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=None, max_length=None, pattern=^((c|p|e|CPE)\:[\w\D]+)$)] | Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=None, max_length=None, pattern=^((B|I|O|T|O|O|L|S|biotools)\:[\--\.0-9A-Z_a-z]*)$)])
version (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=1, max_length=100, pattern=^([ \(-\)\+-\.0-;A-Z_a-z - ]*)$)] | None)
- type: Optional[Type]#
- value: Union[constr(pattern='^(10\.[0-9]{4,9}/[\(-\)\--<>A-\[\]_a-z]+)$'), constr(pattern='^((r|r|i|d|RRID)\:[\w\D]+)$'), constr(pattern='^((c|p|e|CPE)\:[\w\D]+)$'), constr(pattern='^((B|I|O|T|O|O|L|S|biotools)\:[\--\.0-9A-Z_a-z]*)$')]#
- version: Optional[constr(pattern='^([ \(-\)\+-\.0-;A-Z_a-zxa0u1680u180eu2000-u200au202fu205fu3000]*)$', min_length=1, max_length=100)]#
- class bridge.core.biotools.OutputItem(**data)[source]#
Bases:
BaseModel- Parameters:
data (EDAMdata)
format (List[EDAMformat] | None)
- data: EDAMdata#
- format: Optional[List[EDAMformat]]#
- class bridge.core.biotools.PublicationItem(**data)[source]#
Bases:
BaseModel- Parameters:
doi (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=None, max_length=None, pattern=^(10\.[0-9]{4,9}/[\(-\)\--<>A-\[\]_a-z]+)$)] | None)
pmid (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=None, max_length=None, pattern=^([1-9][0-9]{0,8})$)] | None)
pmcid (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=None, max_length=None, pattern=^((PMC)[1-9][0-9]{0,8})$)] | None)
type (List[TypeEnum2] | None)
note (TextType | None)
version (VersionType | None)
- doi: Optional[constr(pattern='^(10\.[0-9]{4,9}/[\(-\)\--<>A-\[\]_a-z]+)$')]#
- note: Optional[TextType]#
- pmcid: Optional[constr(pattern='^((PMC)[1-9][0-9]{0,8})$')]#
- pmid: Optional[constr(pattern='^([1-9][0-9]{0,8})$')]#
- type: Optional[List[TypeEnum2]]#
- version: Optional[VersionType]#
- class bridge.core.biotools.RelationItem(**data)[source]#
Bases:
BaseModel- Parameters:
type (Type2)
biotoolsID (BiotoolsIdType)
- biotoolsID: BiotoolsIdType#
- type: Type2#
- class bridge.core.biotools.TextType(root=PydanticUndefined, **data)[source]#
Bases:
RootModel[Annotated[str, StringConstraints]]- Parameters:
root (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=10, max_length=1000, pattern=None)])
- root: constr(min_length=10, max_length=1000)#
- class bridge.core.biotools.ToolModel(**data)[source]#
Bases:
BaseModel- Parameters:
name (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=1, max_length=100, pattern=^([ \(-\)\+-\.0-;A-Z_a-z - ]*)$)])
description (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=10, max_length=1000, pattern=None)])
homepage (UrlftpType)
biotoolsID (BiotoolsIdType | None)
biotoolsCURIE (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=None, max_length=None, pattern=^(biotools\:[\--\.0-9A-Z_a-z]*)$)] | None)
version (List[VersionType] | None)
otherID (List[OtherIDItem] | None)
toolType (List[ToolTypeEnum] | None)
topic (List[TopicItem] | None)
operatingSystem (List[OperatingSystemEnum] | None)
language (List[LanguageEnum] | None)
license (License | None)
collectionID (List[Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=1, max_length=100, pattern=^([ \(-\)\+-\.0-;A-Z_a-z - ]*)$)]] | None)
maturity (Maturity | None)
cost (Cost | None)
accessibility (Accessibility | None)
elixirPlatform (List[ElixirPlatformEnum] | None)
elixirNode (List[ElixirNodeEnum] | None)
elixirCommunity (List[ElixirCommunityEnum] | None)
function (List[FunctionItem] | None)
link (List[LinkItem] | None)
download (List[DownloadItem] | None)
documentation (List[DocumentationItem] | None)
relation (List[RelationItem] | None)
publication (List[PublicationItem] | None)
credit (List[CreditItem] | None)
- accessibility: Optional[Accessibility]#
- biotoolsCURIE: Optional[constr(pattern='^(biotools\:[\--\.0-9A-Z_a-z]*)$')]#
- biotoolsID: Optional[BiotoolsIdType]#
- collectionID: Optional[List[constr(pattern='^([ \(-\)\+-\.0-;A-Z_a-zxa0u1680u180eu2000-u200au202fu205fu3000]*)$', min_length=1, max_length=100)]]#
- cost: Optional[Cost]#
- credit: Optional[List[CreditItem]]#
- description: constr(min_length=10, max_length=1000)#
- documentation: Optional[List[DocumentationItem]]#
- download: Optional[List[DownloadItem]]#
- elixirCommunity: Optional[List[ElixirCommunityEnum]]#
- elixirNode: Optional[List[ElixirNodeEnum]]#
- elixirPlatform: Optional[List[ElixirPlatformEnum]]#
- function: Optional[List[FunctionItem]]#
- homepage: UrlftpType#
- language: Optional[List[LanguageEnum]]#
- license: Optional[License]#
- link: Optional[List[LinkItem]]#
- maturity: Optional[Maturity]#
- name: constr(pattern='^([ \(-\)\+-\.0-;A-Z_a-zxa0u1680u180eu2000-u200au202fu205fu3000]*)$', min_length=1, max_length=100)#
- operatingSystem: Optional[List[OperatingSystemEnum]]#
- otherID: Optional[List[OtherIDItem]]#
- publication: Optional[List[PublicationItem]]#
- relation: Optional[List[RelationItem]]#
- toolType: Optional[List[ToolTypeEnum]]#
- topic: Optional[List[TopicItem]]#
- version: Optional[List[VersionType]]#
- class bridge.core.biotools.TopicItem(**data)[source]#
Bases:
BaseModel- Parameters:
term (str | None)
uri (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=None, max_length=None, pattern=^(http\://edamontology\.org/topic_[0-9]{4,4})$)] | None)
- term: Optional[str]#
- uri: Optional[constr(pattern='^(http\://edamontology\.org/topic_[0-9]{4,4})$')]#
- class bridge.core.biotools.UrlftpType(root=PydanticUndefined, **data)[source]#
Bases:
RootModel[str]- Parameters:
root (str)
- root: str#
- class bridge.core.biotools.VersionType(root=PydanticUndefined, **data)[source]#
Bases:
RootModel[Annotated[str, StringConstraints]]- Parameters:
root (Annotated[str, StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=1, max_length=100, pattern=^([ \(-\)\+-\.0-;A-Z_a-z - ]*)$)])
- root: constr(pattern='^([ \(-\)\+-\.0-;A-Z_a-zxa0u1680u180eu2000-u200au202fu205fu3000]*)$', min_length=1, max_length=100)#