RTX-KG2 issues with predicate-remap.yaml regarding qualifiers

in predicate-remap.yaml, shouldn't this line actually be upregulated, which is more specific and a closer map to the source predicate GO:positively_regulated_by?

https://github.com/RTXteam/RTX-KG2/blob/bbb3366dbeff8e3cf6dd1faf492184af4a14a56f/predicate-remap.yaml#L2547C1-L2547C1

Jun 29 '23 21:06 saramsey

Same goes for this one: https://github.com/RTXteam/RTX-KG2/blob/bbb3366dbeff8e3cf6dd1faf492184af4a14a56f/predicate-remap.yaml#L2553

Jun 29 '23 21:06 saramsey

Tagging @amykglen for her concurrence

Jun 29 '23 21:06 saramsey

These two entries in predicate-remap.yaml also need object aspect qualifiers, do they not?

https://github.com/RTXteam/RTX-KG2/blob/bbb3366dbeff8e3cf6dd1faf492184af4a14a56f/predicate-remap.yaml#L4860C1-L4871C32

Jun 29 '23 21:06 saramsey

Lili I think the last two commits should fix it. Please have a look and let me know if you see any issues. Thanks.

Jun 30 '23 00:06 saramsey

Note, I also fixed a bunch of other issues with predicate-remap.yaml including use of predicates that are now mixins.

Jun 30 '23 00:06 saramsey

This is the only relation with a qualified_predicate that is not biolink:affects. Overall, this looks a little weird, so we are going to get rid of it.

https://github.com/RTXteam/RTX-KG2/blob/34f2b4a03eb2b855eb41af783ea03b0a72401b48/predicate-remap.yaml#L1590-L1595

Jun 30 '23 02:06 ecwood

@ecwood by "get rid of it", do you mean convert it to:

GOREL:0002003: 
   operation: keep 
   core_predicate: biolink:affects

Jun 30 '23 20:06 saramsey

@saramsey I deleted the qualified_predicate line, but kept the qualifiers. I'm not sure if that is valid:

https://github.com/RTXteam/RTX-KG2/blob/9aa895416f9ff7abbae5fb699869244ea908a2c0/predicate-remap.yaml#L1590-L1594

Jun 30 '23 20:06 ecwood