Clean-up of term names specifying NAD+/NADH or NADP+/NADPH as cofactor.

[sjm41]

Following on from discussion in #27136: I looked at all current GO term names that include the string '(NAD' (=187 terms) to check for instances of:

• just 'NAD', when NAD+/NADH or NADP+/NADPH or NAD(P)+/NAD(P)H should be specified => 15 cases found
• 'NAD-dependent' instead of the preferred format of "NAD+" etc. => 6 cases
• 'NAD+/NADP+/NAD(P)+' where it should be 'NADH/NADPH/NAD(P)H - these can be spotted fairly easily since term names of the format "[susbstrate} dehydrogenase" should include 'NAD+/NADP+/NAD(P)+' whereas those of the format "[susbstrate} reductase" should include 'NADH/NADPH/NAD(P)H' => 14 cases

Proposed changes are below. (These were all verified by checking the reaction and EC name, where available)

CURRENT NAME	NEW NAME
name: mevaldate reductase (NAD+) activity	name: mevaldate reductase (NADH) activity
name: L-xylulose reductase (NAD+) activity	name: L-xylulose reductase (NADH) activity
name: glyoxylate reductase (NAD+) activity	name: glyoxylate reductase (NADH) activity
name: trans-2-enoyl-CoA reductase (NAD+) activity	name: trans-2-enoyl-CoA reductase (NADH) activity
name: dihydroorotate dehydrogenase (NADH) activity	name: dihydroorotate dehydrogenase (NAD+) activity
name: indolelactate dehydrogenase (NADH) activity	name: indolelactate dehydrogenase (NAD+) activity
name: glyoxylate reductase (NADP+) activity	name: glyoxylate reductase (NADPH) activity
name: 2-alkenal reductase (NADP+) activity	name: 2-alkenal reductase (NADPH) activity
name: acryloyl-CoA reductase (NADP+) activity	name: acryloyl-CoA reductase (NADPH) activity
name: L-xylulose reductase (NADP+) activity	name: L-xylulose reductase (NADPH) activity
name: biliverdin reductase (NADP+) activity	name: biliverdin reductase (NADPH) activity
name: (R)-4-hydroxyphenyllactate dehydrogenase (NADPH) activity	name: (R)-4-hydroxyphenyllactate dehydrogenase (NADP+) activity
name: dihydroorotate dehydrogenase (NADPH) activity	name: dihydroorotate dehydrogenase (NADP+) activity
name: biliverdin reductase (NAD(P)+) activity	name: biliverdin reductase (NAD(P)H) activity
name: aryl-aldehyde dehydrogenase (NAD) activity	name: aryl-aldehyde dehydrogenase (NAD+) activity
name: valine dehydrogenase (NAD) activity	name: valine dehydrogenase (NAD+) activity
name: D-xylose 1-dehydrogenase (NAD) activity	name: D-xylose 1-dehydrogenase (NAD+) activity
name: (3R)-hydroxyacyl-CoA dehydrogenase (NAD) activity	name: (3R)-hydroxyacyl-CoA dehydrogenase (NAD+) activity
name: RNA NAD-cap (NAD-forming) hydrolase activity	name: RNA NAD+-cap (NAD+-forming) hydrolase activity
name: aldo-keto reductase (NADP) activity	name: aldo-keto reductase (NADPH) activity
name: glutathione-disulfide reductase (NADP) activity	name: glutathione-disulfide reductase (NADPH) activity
name: thioredoxin-disulfide reductase (NADP) activity	name: thioredoxin-disulfide reductase (NADPH) activity
name: trypanothione-disulfide reductase (NADP) activity	name: trypanothione-disulfide reductase (NADPH) activity
name: glyceraldehyde dehydrogenase (NADP) activity	name: glyceraldehyde dehydrogenase (NADP+) activity
name: valine dehydrogenase (NADP) activity	name: valine dehydrogenase (NADP+) activity
name: CoA-disulfide reductase (NADP) activity	name: CoA-disulfide reductase (NADPH) activity
name: CoA-glutathione reductase (NADP) activity	name: CoA-glutathione reductase (NADPH) activity
name: selenodiglutathione-disulfide reductase (NADP) activity	name: selenodiglutathione-disulfide reductase (NADPH) activity
name: protein-disulfide reductase (NAD(P)) activity	name: protein-disulfide reductase (NAD(P)H) activity
name: L-idonate 5-dehydrogenase activity (NAD-dependent)	name: L-idonate 5-dehydrogenase (NAD+) activity
name: choline monooxygenase activity (NADP-dependent)	name: choline monooxygenase (NADP+) activity
name: methylglyoxal reductase (NADH-dependent) activity	name: methylglyoxal reductase (NADH) activity
name: methylglyoxal reductase (NADPH-dependent) activity	name: methylglyoxal reductase (NADPH) activity
name: methylglyoxal reductase (NADPH-dependent, acetol producing)	name: methylglyoxal reductase (NADPH) (acetol producing) activity
name: nitric oxide reductase activity (NAD(P)H-dependent) activity	name: nitric oxide reductase (NAD(P)H) activity

[pgaudet]

~Fixed parents:~

• ~'GO:0141152 glycerol-3-phosphate dehydrogenase (NAD+) activity' >> add is_a 'GO:0047952 glycerol-3-phosphate dehydrogenase (NAD(P)+) activity'~
• ~'GO:0141153 glycerol-3-phosphate dehydrogenase (NADP+) activity' >> add is_a 'GO:0047952 glycerol-3-phosphate dehydrogenase (NAD(P)+) activity'~ 

Interesting ! This is not possible because of disjoint taxon constraints.

[pgaudet]

- GO:0035798 2-alkenal reductase (NADPH) activity: add xref EC:1.3.1.102 and RHEA:13737

- GO:0032440 2-alkenal reductase (NAD(P)H) activity add xref: RHEA:13737 {source="skos:narrowMatch"} and xref: RHEA:36731 {source="skos:narrowMatch"}

- GO:0047881 estradiol 17-alpha-dehydrogenase (NAD(P)+) activity add RHEA:16701 {source="skos:narrowMatch"} and xref: RHEA:16705 {source="skos:narrowMatch"}

[pgaudet]

IUBMB writes NAD(P) in brackets, to avoid double parentheses. I've added this to the documentation:

https://wiki.geneontology.org/Guidelines_for_new_Molecular_Functions#Meaning_of_NAD%28P%29H_in_GO_and_in_IUBMB