UniProt API

Wrapper function for the UniProt API.

UniProt_API.uniprot_domains(protein_names, species='human', n_cores=1)

Uses the UniProt API (https://www.uniprot.org/) to look up the annotated domains and regions for a list of protein names/gene names. The domains will only contain the ones from PROSITE, the regions also other annotations. Only entries that are reviewed are considered. Also, the proteins must exist like that in UniProt, aliases are not mapped. CARE: The UniProt API is unreliable, time-outs, random mal-formatted JSONs, empty results etc.

Parameters:

  • protein_names – List of protein names or gene names that should be queried.

  • species – Species. Check their website for available options.

  • n_cores – Cores for parallelization. For large list it can take quite long, it has to be batched to not exceed character limits.

Returns:

  • protein_domains: Dictionary of {protein: set(domains)} with the PROSITE domains. Can be empty.

  • protein_regions: Dictionary of {protein: set(regions)}. Can be empty.

  • missed_proteins: Set of proteins where no matching entry was found in UniProt.

  • failed_requests: Dictionary of {batch number: {Failure information}} in cases the request didn’t work or where the JSON from the API was malformatted, not sure why and when this happens.

Return type:

tuple

import UniProt_API
# Look up the annotated domains and regions of three examples.
protein_domains, protein_regions, missed_proteins, failed_requests = UniProt_API.uniprot_domains(protein_names=['KDM6A', 'DNMT3A', 'STAT2'], species='human', n_cores=1)
print(protein_domains)
print(protein_regions)

{'KDM6A': {'JmjC'}, 'DNMT3A': {'ADD', 'PWWP', 'SAM-dependent MTase C5-type'}, 'STAT2': {'SH2'}}

{'KDM6A': {'Interaction with SUPT6H', 'Disordered'}, 'DNMT3A': {'Interaction with the PRC2/EED-EZH2 complex', 'Interaction with DNMT1 and DNMT3B', 'Disordered'}, 'STAT2': {'Interaction with SFTSV virus NSs', 'Interaction with heartland virus NSs', 'Mediates interaction with USP18'}}