diff --git a/gilda/generate_terms.py b/gilda/generate_terms.py index 63cdf3d..77a4a79 100644 --- a/gilda/generate_terms.py +++ b/gilda/generate_terms.py @@ -336,13 +336,13 @@ def generate_uniprot_terms(download=False, organisms=None): organisms = popular_organisms path = os.path.join(resource_dir, 'up_synonyms.tsv') if not os.path.exists(path) or download: + # Columns according to the new API, comments for old API columns = [ - 'accession', # id - 'gene_primary', # genes(PREFERRED) - #'gene_names', # genes(PREFERRED) - 'gene_synonym', # genes(ALTERNATIVE)' - 'protein_name', # protein names - 'organism_id', # organism-id + 'accession', # id + 'gene_primary', # genes(PREFERRED) + 'gene_synonym', # genes(ALTERNATIVE)' + 'protein_name', # protein names + 'organism_id', # organism-id ] org_filter_str = '+OR+'.join(f'(taxonomy_id:{org})' for org in organisms) query = f'reviewed:true+AND+({org_filter_str})'