GENE_CONFIGURATION

GENE_CONFIGURATION = Configuration(name='SeMRA Gene Mappings Database', key='gene', description='Analyze the landscape of gene nomenclature resources, species-agnostic.', creators=[NormalizedNamableReference(prefix='orcid', identifier='0000-0003-4423-4370', name='Charles Tapley Hoyt')], inputs=[Input(source='pyobo', prefix='hgnc', confidence=0.99, extras={}), Input(source='pyobo', prefix='mgi', confidence=0.99, extras={}), Input(source='pyobo', prefix='rgd', confidence=0.99, extras={}), Input(source='pyobo', prefix='cgnc', confidence=0.99, extras={}), Input(source='pyobo', prefix='sgd', confidence=0.99, extras={}), Input(source='pyobo', prefix='civic.gid', confidence=0.99, extras={}), Input(source='pyobo', prefix='flybase', confidence=0.99, extras={}), Input(source='custom', prefix='ncit_hgnc', confidence=0.99, extras={}), Input(source='custom', prefix='omim_gene', confidence=0.99, extras={}), Input(source='wikidata', prefix='ncbigene', confidence=0.99, extras={}), Input(source='wikidata', prefix='civic.gid', confidence=0.99, extras={}), Input(source='wikidata', prefix='ensembl', confidence=0.99, extras={}), Input(source='wikidata', prefix='hgnc', confidence=0.99, extras={}), Input(source='wikidata', prefix='omim', confidence=0.99, extras={}), Input(source='wikidata', prefix='umls', confidence=0.99, extras={})], negative_inputs=[Input(source='biomappings', prefix='negative', confidence=1.0, extras={})], priority=['ncbigene', 'hgnc', 'mgi', 'rgd', 'cgnc', 'wormbase', 'flybase', 'sgd', 'omim', 'civic.gid', 'umls', 'ncit', 'wikidata'], mutations=[Mutation(source='umls', target=None, confidence=0.8, old=NormalizedNamableReference(prefix='oboinowl', identifier='hasDbXref', name='has database cross-reference'), new=NormalizedNamableReference(prefix='skos', identifier='exactMatch', name='exact match')), Mutation(source='ncit', target=None, confidence=0.8, old=NormalizedNamableReference(prefix='oboinowl', identifier='hasDbXref', name='has database cross-reference'), new=NormalizedNamableReference(prefix='skos', identifier='exactMatch', name='exact match'))], subsets={'umls': [NormalizedNamableReference(prefix='umls', identifier='C0017337', name=None)], 'ncit': [NormalizedNamableReference(prefix='ncit', identifier='C16612', name=None)]}, exclude_pairs=[], remove_prefixes=None, keep_prefixes=None, post_remove_prefixes=None, post_keep_prefixes=None, remove_imprecise=False, validate_raw=False, directory=PosixPath('/home/docs/.data/semra/case-studies/gene'), write_raw_neo4j=False, neo4j_gzip='during', add_labels=True, zenodo_record=11092012)

Configuration for the gene mappings database