decoupler.get_resource

decoupler.get_resource(name: str, organism: str | int = 'human', genesymbol_resource: Literal['uniprot', 'ensembl'] | dict[str, set[str]] | bool | None = None, **kwargs) → DataFrame

Wrapper to access resources inside Omnipath.

This wrapper allows to easly query different prior knowledge resources. To check available resources run decoupler.show_resources(). For more information visit the official website for [Omnipath](https://omnipathdb.org/).

Parameters:

namestr

Name of the resource to query.

organismint | str

The organism of interest: either NCBI Taxonomy ID, common name, latin name or Ensembl name. Organisms other than human will be translated from human data by orthology.

genesymbol_resourcestr

Resource to query for Gene Symbols. Either “uniprot” or “ensembl”, or a dictionary with UniProt IDs as keys and sets of Gene Symbols as values. If None, the Gene Symbols provided by the web service will be left intact. If False, the Gene Symbols will be dropped and UniProt IDs will be used instead.

kwargs

Passed to omnipath.requests.Annotations.get.

Returns:

dfDataFrame

Dataframe in long format relating genes to biological entities.