liana.rs.get_hcop_orthologs

liana.rs.get_hcop_orthologs(target_organism='mouse', url=None, filename=None, min_evidence=3, columns=None)

Download the HCOP orthology file and filter it by minimum evidence.

Parameters:

target_organism str (default: 'mouse')

Target organism for orthology mapping. Default is "mouse". Supported values: anole_lizard, c.elegans, cat, cattle, chicken, chimpanzee, dog, fruitfly, horse, macaque, mouse, opossum, pig, platypus, rat, s.cerevisiae, s.pombe, xenopus, zebrafish. The target-organism column in the returned DataFrame follows the pattern {target_organism}_symbol (e.g. mouse_symbol, rat_symbol).

url str | None (default: None)

Override the download URL. If None (default), the URL is constructed from target_organism using the HGNC Google Cloud Storage bucket.

filename str | Path | None (default: None)

Local filename to save the downloaded file. Derived from the URL if None.

min_evidence int (default: 3)

Minimum number of orthology resources that must support an interaction.

columns list[str] | None (default: None)

Columns to keep in the final DataFrame. If None, all columns are kept.

Return type:

DataFrame

Returns:

mapping DataFrame with the HCOP mapping.

Notes

HCOP is a composite database combining data from various orthology resources. It provides a comprehensive set of human orthologs across many species.

If you use this function, please reference the original HCOP papers: - Eyre, T.A., Wright, M.W., Lush, M.J. and Bruford, E.A., 2007. HCOP: a searchable database of human orthology predictions. Briefings in bioinformatics, 8(1), pp.2-5. - Yates, B., Gray, K.A., Jones, T.E. and Bruford, E.A., 2021. Updates to HCOP: the HGNC comparison of orthology predictions tool. Briefings in Bioinformatics, 22(6), p.bbab155.

For more information, please visit the HCOP website: https://www.genenames.org/tools/hcop/

Examples

This function downloads from HCOP, so it is not run here. A typical call keeps only the two symbol columns needed by liana.rs.translate_resource():

map_df = get_hcop_orthologs(
    target_organism="mouse",
    columns=["human_symbol", "mouse_symbol"],
    min_evidence=3,
).rename(columns={"human_symbol": "source", "mouse_symbol": "target"})