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AssociationSetFactory does not handle associations from multiple relations for a subject #370

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deepakunni3 opened this issue Sep 14, 2019 · 1 comment · May be fixed by #384
Open

AssociationSetFactory does not handle associations from multiple relations for a subject #370

deepakunni3 opened this issue Sep 14, 2019 · 1 comment · May be fixed by #384

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@deepakunni3
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deepakunni3 commented Sep 14, 2019 •
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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

for a in assocs:
rel = a['relation']
subj = a['subject']
subject_label_map[subj] = a['subject_label']
amap[subj] = a['objects']

@cmungall FYI
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cmungall commented Oct 4, 2019

It should not overwrite, that's a bug. The default behavior should be to take the union.

The ASset model is a simple entity-termset one by design. Making it truly relation aware is non trivial as you want to include inference.

If clients want to do separate analyses for separate ASsets, then the client can create multiple ASets, with different relation filtering parameters each time.

@deepakunni3 deepakunni3 linked a pull request Oct 4, 2019 that will close this issue
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Handle associations from multiple relations by taking their union deepakunni3/ontobio
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@cmungall @deepakunni3