Knowledge-Graph-Hub / kg-covid-19

An instance of KG Hub to produce a knowledge graph for COVID-19 response.
https://github.com/Knowledge-Graph-Hub/kg-covid-19/wiki
BSD 3-Clause "New" or "Revised" License
80 stars 26 forks source link

Ingests that use symmetric edge_labels (like interacts_with) should assert edge in both directions #328

Open justaddcoffee opened 4 years ago

justaddcoffee commented 4 years ago

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 commented 4 years ago

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)