omnipath.requests.Annotations.get

classmethod Annotations.get(proteins=None, resources=None, force_full_download=False, wide=False, **kwargs)[source]

Import annotations from [OmniPath].

Retrieves protein annotations about function, localization, expression, structure and other properties of proteins from OmniPath.

Parameters:

  • proteins (Union[str, Iterable[str], None]) –

    Genes or proteins for which annotations will be retrieved (UniProt IDs, HGNC Gene Symbols or miRBase IDs).

    In order to download annotations for proteins complexes, write ‘COMPLEX:’ before the gene symbols of the genes integrating the complex.

    If None, fetch annotations for all available genes or proteins.

  • resources (Union[str, Iterable[str], None]) – Load the annotations only from these databases. See resources() for available options. If None, use all available resources.

  • force_full_download (bool) – Force the download of the entire annotations dataset. The full size of the data is ~1GB. We recommend to retrieve the annotations for a set of proteins or only from a few resources, depending on your interest.

  • wide (bool) – Pivot the annotations from a long to a wide dataframe format, reconstituting the format of the original resource.

  • kwargs – Additional query parameters.

Returns:

A dataframe containing different molecule (protein, complex, gene, miRNA, small molecule) annotations. If wide is True and the result contains more than one resource, a dict of dataframes will be returned, one for each resource.

Return type:

pandas.DataFrame

Notes

There might be also a few miRNAs and small molecules annotated. A vast majority of protein complex annotations are inferred from the annotations of the members: if all members carry the same annotation the complex inherits.