CELL_CONFIGURATION

CELL_CONFIGURATION = Configuration(name='SeMRA Cell and Cell Line Mappings Database', key='cell', description='Originally a reproduction of the EFO/Cellosaurus/DepMap/CCLE scenario posed in the Biomappings paper, this configuration imports several different cell and cell line resources and identifies mappings between them.', 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='pyobo', prefix='cellosaurus', confidence=0.99, extras={}), Input(source='bioontologies', prefix='bto', confidence=0.99, extras={}), Input(source='bioontologies', prefix='cl', confidence=0.99, extras={}), Input(source='custom', prefix='clo', confidence=0.65, extras={}), Input(source='pyobo', prefix='efo', confidence=0.99, extras={}), Input(source='pyobo', prefix='depmap', confidence=0.99, extras={'version': '22Q4', 'standardize': True, 'license': 'CC-BY-4.0'}), Input(source='pyobo', prefix='ccle', confidence=0.99, extras={'version': '2019'}), Input(source='pyobo', prefix='ncit', confidence=0.99, extras={}), Input(source='pyobo', prefix='umls', confidence=0.99, extras={})], negative_inputs=[Input(source='biomappings', prefix='negative', confidence=1.0, extras={})], priority=['mesh', 'efo', 'cellosaurus', 'ccle', 'depmap', 'bto', 'cl', 'clo', 'ncit', 'umls'], mutations=[Mutation(source='efo', 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='bto', 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='cl', 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='clo', 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='depmap', 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='ccle', 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='cellosaurus', 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='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'))], subsets={'mesh': [NormalizedNamableReference(prefix='mesh', identifier='D002477', name=None)], 'efo': [NormalizedNamableReference(prefix='efo', identifier='0000324', name=None)], 'ncit': [NormalizedNamableReference(prefix='ncit', identifier='C12508', name=None)], 'umls': [NormalizedNamableReference(prefix='sty', identifier='T025', name=None)]}, exclude_pairs=[], remove_prefixes=None, keep_prefixes=['mesh', 'efo', 'cellosaurus', 'ccle', 'depmap', 'bto', 'cl', 'clo', 'ncit', 'umls'], post_remove_prefixes=None, post_keep_prefixes=None, remove_imprecise=False, validate_raw=False, directory=PosixPath('/home/docs/.data/semra/case-studies/cells'), write_raw_neo4j=False, neo4j_gzip='during', add_labels=True, zenodo_record=11091580)

Configuration for the cell and cell type mappings database