bionty.CellMarker#

class bionty.CellMarker(species='human', source=None, version=None, **kwargs)#

Cell markers.

1. Cell Marker Ontology Edits of terms are coordinated and reviewed on: http://bio-bigdata.hrbmu.edu.cn/CellMarker/

Parameters:

species – name of Species entity.
source – The key of the source in the local.yml versions file. Get all available databases with bionty.display_available_sources.
version – The version of the ontology. Typically a date or an actual version. Get available versions with bionty.display_available_sources.

Attributes

version :class:`~<class 'property'>`#: The name of version entity Bionty.

Methods

curate(df, column=None, reference_id='name')#

Curate index of passed DataFrame to conform with default identifier.

In addition to the .curate() in base class, this also performs alias mapping.

column: If column is None, checks the existing index for compliance with

the default identifier.

If column denotes an entity identifier, tries to map that identifier: to the default identifier.

reference_id: The type of identifier for mapping.

Return type:: DataFrame
Returns:: The input DataFrame with the curated index and a boolean __curated__ column that indicates compliance with the default identifier.

df()#

DataFrame.