DISEASE_CONFIGURATION

DISEASE_CONFIGURATION = Configuration(name='SeMRA Disease Mappings Database', key='disease', description='Supports the analysis of the landscape of disease nomenclature resources.', creators=[NormalizedNamableReference(prefix='orcid', identifier='0000-0003-4423-4370', name='Charles Tapley Hoyt')], inputs=[Input(source='biomappings', prefix=None, confidence=1.0, extras={}), Input(source='gilda', prefix=None, confidence=1.0, extras={}), Input(source='bioontologies', prefix='doid', confidence=0.99, extras={}), Input(source='bioontologies', prefix='mondo', confidence=0.99, extras={}), Input(source='bioontologies', prefix='efo', confidence=0.99, extras={}), Input(source='pyobo', prefix='mesh', confidence=0.99, extras={}), Input(source='pyobo', prefix='ncit', confidence=0.85, extras={}), Input(source='pyobo', prefix='umls', confidence=0.9, extras={}), Input(source='bioontologies', prefix='orphanet.ordo', confidence=0.9, extras={})], negative_inputs=[Input(source='biomappings', prefix='negative', confidence=1.0, extras={})], priority=['doid', 'mondo', 'efo', 'mesh', 'ncit', 'orphanet', 'orphanet.ordo', 'umls', 'omim', 'omim.ps', 'gard', 'icd10', 'icd10cm', 'icd10pcs', 'icd11', 'icd11.code', 'icd9', 'icd9cm', 'icdo'], mutations=[Mutation(source='doid', target=None, confidence=0.95, old=NormalizedNamableReference(prefix='oboinowl', identifier='hasDbXref', name='has database cross-reference'), new=NormalizedNamableReference(prefix='skos', identifier='exactMatch', name='exact match')), Mutation(source='mondo', target=None, confidence=0.95, old=NormalizedNamableReference(prefix='oboinowl', identifier='hasDbXref', name='has database cross-reference'), new=NormalizedNamableReference(prefix='skos', identifier='exactMatch', name='exact match')), Mutation(source='efo', target=None, confidence=0.9, 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=0.7, old=NormalizedNamableReference(prefix='oboinowl', identifier='hasDbXref', name='has database cross-reference'), new=NormalizedNamableReference(prefix='skos', identifier='exactMatch', name='exact match')), Mutation(source='umls', target=None, confidence=0.7, old=NormalizedNamableReference(prefix='oboinowl', identifier='hasDbXref', name='has database cross-reference'), new=NormalizedNamableReference(prefix='skos', identifier='exactMatch', name='exact match')), Mutation(source='orphanet.ordo', target=None, confidence=0.7, old=NormalizedNamableReference(prefix='oboinowl', identifier='hasDbXref', name='has database cross-reference'), new=NormalizedNamableReference(prefix='skos', identifier='exactMatch', name='exact match')), Mutation(source='orphanet', target=None, confidence=0.7, old=NormalizedNamableReference(prefix='oboinowl', identifier='hasDbXref', name='has database cross-reference'), new=NormalizedNamableReference(prefix='skos', identifier='exactMatch', name='exact match'))], subsets={'mesh': [NormalizedNamableReference(prefix='mesh', identifier='D007239', name=None), NormalizedNamableReference(prefix='mesh', identifier='D001520', name=None), NormalizedNamableReference(prefix='mesh', identifier='D011579', name=None), NormalizedNamableReference(prefix='mesh', identifier='D001523', name=None), NormalizedNamableReference(prefix='mesh', identifier='D004191', name=None)], 'efo': [NormalizedNamableReference(prefix='efo', identifier='0000408', name=None)], 'ncit': [NormalizedNamableReference(prefix='ncit', identifier='C2991', name=None)], 'umls': [NormalizedNamableReference(prefix='sty', identifier='T049', name=None), NormalizedNamableReference(prefix='sty', identifier='T047', name=None), NormalizedNamableReference(prefix='sty', identifier='T191', name=None), NormalizedNamableReference(prefix='sty', identifier='T050', name=None), NormalizedNamableReference(prefix='sty', identifier='T048', name=None)]}, exclude_pairs=[], remove_prefixes=None, keep_prefixes=['doid', 'mondo', 'efo', 'mesh', 'ncit', 'orphanet', 'orphanet.ordo', 'umls', 'omim', 'omim.ps', 'gard', 'icd10', 'icd10cm', 'icd10pcs', 'icd11', 'icd11.code', 'icd9', 'icd9cm', 'icdo'], post_remove_prefixes=None, post_keep_prefixes=None, remove_imprecise=False, validate_raw=False, directory=PosixPath('/home/docs/.data/semra/case-studies/disease'), write_raw_neo4j=False, neo4j_gzip='during', add_labels=True, zenodo_record=11091885)

Configuration for the disease mappings database