Remapping organism names in BioGRID identifiers dump

README.md

BioGRID Identifiers Problem, Solved

The file I included here has a set of organisms in the BioGRID identifiers download (version 3.5.184), latest as of time of writing on 2020-04-17) whose ORGANISM_OFFICIAL_NAME is not correct. I went and mapped these all with a mixture of synonym search on NCBITaxon and manual intervention. Each has the taxonomy identifier, so it can be used to get the most up-to-date information.

I would highly suggest including a taxonomy ID in this dump as well as the name, so it can be programatically mapped for anyone trying to integrate this data with other sources

biogrid_organism_remapping.py

taxonomy_remapping = {  # correct name in comment after
    "Canis familiaris": "9615",  # Canis lupus familiaris
    "Human Herpesvirus 1": "10298",  # Human alphaherpesvirus 1
    "Human Herpesvirus 3": "10335",  # Human alphaherpesvirus 3
    "Murid Herpesvirus 1": "10366",  # Murid betaherpesvirus 1
    "Human Herpesvirus 4": "10376",  # Human gammaherpesvirus 4
    "Hepatitus C Virus": "11103",  # Hepacivirus C
    "Human Immunodeficiency Virus 1": "11676",  # Human immunodeficiency virus 1
    "Human Immunodeficiency Virus 2": "11709",  # Human immunodeficiency virus 2
    "Human Herpesvirus 2": "10310",  # Human alphaherpesvirus 2
    "Human Herpesvirus 5": "10359",  # Human betaherpesvirus 5
    "Human Herpesvirus 6A": "32603",  # Human betaherpesvirus 6A
    "Human Herpesvirus 6B": "32604",  # Human betaherpesvirus 6B
    "Human Herpesvirus 7": "10372",  # Human betaherpesvirus 7
    "Human Herpesvirus 8": "37296",  # Human gammaherpesvirus 8
    "Emericella nidulans": "162425",  # Aspergillus nidulans
    "Bassica campestris": "145471",  # Brassica rapa subsp. oleifera (was a typo)
    "Tarsius syrichta": "1868482",  # Carlito syrichta
    "Felis Catus": "9685",  # Felis catus
    "Vaccinia Virus": "10245",  # Vaccinia virus
    "Simian Virus 40": "1891767",  # Macaca mulatta polyomavirus 1
    "Simian Immunodeficiency Virus": "11723",  # Simian immunodeficiency virus
    "Tobacco Mosaic Virus": "12242",  # Tobacco mosaic virus
}