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resolve NAD(P) rhea problems #19648

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hdrabkin opened this issue Jun 22, 2020 · 4 comments
Open

resolve NAD(P) rhea problems #19648

hdrabkin opened this issue Jun 22, 2020 · 4 comments
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enzymes go2rhea Issues related to the mapping GO-Rhea
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Ontology jamboree January 2023

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@hdrabkin
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hdrabkin commented Jun 22, 2020 •
edited

During applying RHEAs in bulk we came across problems mapping to terms in GO that have "NAD(P) in their defs. RHEA only does NAD or separate term NADP.
We know of 35 instances either already in GO with RHEA, or just added with our bulk addition that have NAD(P) in def.
total RHEA NAD(P).txt

There are 15 in the bulk set. i will work on these as I can. Essentially any NAD(P) term should have two children with two separate RHEAs.
Rhea automapped to NAD(P)s.txt

See this pull request
Add proposed RHEA mappings which have no logical conflicts. #19609
@hdrabkin hdrabkin added the go2rhea Issues related to the mapping GO-Rhea label Jun 22, 2020
@hdrabkin hdrabkin self-assigned this Jun 22, 2020
@hdrabkin
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RHEA:64576 2 [Fe(III)-cytochrome b5] + NADPH = 2 [Fe(II)-cytochrome b5] + H+ + NADP+
This will be added as term def for new term when it goes public.

@hdrabkin
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RHEA:64576 not public yet as of today

@hdrabkin
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hdrabkin commented Feb 1, 2021

RHEA:64576 now public and added to GO:0090523

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hdrabkin commented Feb 2, 2021

PROBLEM:
GO:0050578 two rehas for ec; both with NADP and ec and rhea does not match GO DEF; there is no sulfo anything in the xrefs

GO:0102564 ec has one rhea to nadh make term using
Metacyc maps to EC:1.1.1.394
RHEA:48730 and RHEA:48720

@pgaudet pgaudet added this to To do in Ontology jamboree January 2023 via automation Jan 17, 2023
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enzymes go2rhea Issues related to the mapping GO-Rhea
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Ontology jamboree January 2023
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