AssociationSetFactory does not handle associations from multiple relations for a subject #370
Description
When fetching associations, say gene to phenotype associations, AssociationSetFactory populates an association map for each subject.
But this code does not handle associations with multiple relations.
For example, HGNC:6764 has two sets of associations:
# objects from association with relation RO:0002200
'HP:0000238', 'HP:0100587', 'HP:0000364', 'HP:0000864', 'HP:0000130', 'HP:0006501', 'HP:0008678', 'HP:0001392', 'HP:0000047', 'HP:0001903', 'HP:0007400', 'HP:0007565', 'HP:0000582', 'HP:0005522', 'HP:0003220', 'HP:0006824', 'HP:0000252', 'HP:0001639', 'HP:0002997', 'HP:0001873', 'HP:0001199', 'HP:0001631', 'HP:0001347', 'HP:0100542', 'HP:0001636', 'HP:0001562', 'HP:0000483', 'HP:0000268', 'HP:0000813', 'HP:0002863', 'HP:0000286', 'HP:0000508', 'HP:0010293', 'HP:0002245', 'HP:0001679', 'HP:0000175', 'HP:0002827', 'HP:0004322', 'HP:0000486', 'HP:0000453', 'HP:0001871', 'HP:0002007', 'HP:0001510', 'HP:0002251', 'HP:0100760', 'HP:0001643', 'HP:0002023', 'HP:0000010', 'HP:0100026', 'HP:0000135', 'HP:0006254', 'HP:0002664', 'HP:0000324', 'HP:0007874', 'HP:0000027', 'HP:0000365', 'HP:0001882', 'HP:0001053', 'HP:0001000', 'HP:0001511', 'HP:0004209', 'HP:0002575', 'HP:0010469', 'HP:0004349', 'HP:0000520', 'HP:0000083', 'HP:0001824', 'HP:0001671', 'HP:0000340', 'HP:0000316', 'HP:0002823', 'HP:0001646', 'HP:0012745', 'HP:0000072', 'HP:0008572', 'HP:0006101', 'HP:0000568', 'HP:0000218', 'HP:0001537', 'HP:0002817', 'HP:0000478', 'HP:0012041', 'HP:0000505', 'HP:0012639', 'HP:0000504', 'HP:0006265', 'HP:0005528', 'HP:0008053', 'HP:0012210', 'HP:0100867', 'HP:0005344', 'HP:0001875', 'HP:0001263', 'HP:0001763', 'HP:0000079', 'HP:0002414', 'HP:0001770', 'HP:0000518', 'HP:0000035', 'HP:0001760', 'HP:0003022', 'HP:0000347', 'HP:0002650', 'HP:0000639', 'HP:0000492', 'HP:0001249', 'HP:0001172', 'HP:0002119', 'HP:0000028'
and
# objects from association with relation RO:0003304
'EFO:0004340', 'EFO:0004765'
When populating the association map, the earlier entry is overwritten because the keys used in association map does not take relation into account. This yields an incorrect representation of associations fetched and analyses performed downstream with this association set.
Block of code where this is happening:
ontobio/ontobio/assoc_factory.py
Lines 72 to 76 in c1864a8
@cmungall FYI