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RTXteam / RTX

Software repo for Team Expander Agent (Oregon State U., Institute for Systems Biology, and Penn State U.)
https://arax.ncats.io/
MIT License
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Is ARAX-connect.py synonymizing node IDs to the "preferred" CURIEs? #2267

Closed saramsey closed 1 month ago

saramsey commented 2 months ago

In the transition from KG2.8.4c to KG2.9.0c, where the preferred CURIE prefix for chemical substances seemed to switch to UNII, we noticed that the regression test test_ARAX_connect.py::test_connect_ulcerative_colitis_to_adalimumab failed, and to fix it, we had to change the drug node's CURIE ID from the old ID (DrugCentral:4904) to the new ID (UNII:FYS6T7F842). https://github.com/RTXteam/RTX/commit/df7c8e1c6b2af9e119343497427f00dd6305591d#diff-747ec5341c314b256f7d29d7239db0b4dceab85de33259046b1fbb813dfdc8b6

This change made the test pass once again. But from inspecting the ARAX logs, it looks like DrugCentral:4904 is supposed to be synonymized to the preferred CURIE UNII:FYS6T7F842. But it looks like the ARAX connect module isn't using synonymization? Can someone please check? Thanks.

dkoslicki commented 2 months ago

@mohsenht Can you look into this? In particular, it will definitely be critical to include synonymization in the ARAX connect module. We can follow up via slack or in person to discuss how to implement this.