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Ingests that use symmetric edge_labels (like interacts_with) should assert edge in both directions

Open justaddcoffee opened this issue 3 years ago • 1 comments

Describe the bug

Some ingests like IntAct and STRING use symmetric edge labels like interacts_with. These should assert in both directions: if ingest asserts: A interacts_with B it should also assert: B interacts with A

To Reproduce

Example, STRING has this edge: ENSEMBL:ENSP00000256935 biolink:interacts_with ENSEMBL:ENSP00000439601 RO:0002434

So it should also have: ENSEMBL:ENSP00000439601 biolink:interacts_with ENSEMBL:ENSP00000256935 RO:0002434

Expected behavior

See above

Version

Example above is for the Aug 17 build

justaddcoffee avatar Sep 03 '20 17:09 justaddcoffee

This applies to at least 7 ingests currently:

grep -l interacts_with `find data/transformed/ -name "*edge*tsv" `
data/transformed//ttd/edges.tsv
data/transformed//drug_central/edges.tsv
data/transformed//pharmgkb/edges.tsv
data/transformed//zhou_host_proteins/edges.tsv
data/transformed//ChEMBL/edges.tsv
data/transformed//STRING/edges.tsv
data/transformed//intact/edges.tsv

Possibly would be worth considering adding this enhancement to KGX instead of adding this to each of the above ingests (I could help with this)

justaddcoffee avatar Sep 03 '20 20:09 justaddcoffee