"NADP biosynthetic process" logical definition

[ukemi]

If I create a construct of 'biosynthetic process' has_primary_output some NADP+ in a GO-CAM, it is not inferred to be an NADP biosynthetic process. Based on the definition this term refers to both the biosynthesis of NADP+ and NADPH. The ontology group needs to check the differentia of the logical definition.

[sjm41]

Hi @ukemi

The LD has:
has_primary_output CHEBI:58349 ! NADP(3-)

That looks right - did you use CHEBI:58349 in your model?

[ukemi]

@sjm41 Thanks for checking this! No, I used [CHEBI:18009] NADP(+), my bad. I corrected this now, but it's still not consistent with the textual def, don't you think?

[sjm41]

Is it possible to have a LD that says:
has_primary_output CHEBI:58349 ! NADP(3-) OR CHEBI:57783 ! NADPH(4-)

??

Looking at the current terms, I'm guessing LDs including 'or' are not possible, and it looks like there was a decision to standardize on just stating the oxidized form in the LDs for the NAD/NADP BP terms.

Here's the essential bits of the current entry for the record:

id: GO:0006741
name: NADP biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; biosynthesis may be of either the oxidized form, NADP+, or the reduced form, NADPH." [GOC:mah]
intersection_of: GO:0009058 ! biosynthetic process
intersection_of: has_primary_output CHEBI:58349 ! NADP(3-)

[ukemi]

Or ask ChEBI for 'NADP(H) anion'? or have NADP(H) only refer to the ph7.3 forms?

[cmungall]

Here's the CHEBI subgraph:

The conjugate relations (⊕⇌⊖ -- lmk if this glyph makes sense) are treated like is-a due to the biochebi gcis - is this not what we want?

[sjm41]

Thanks @cmungall

The conjugate relations looks fine.

The issue is that while ChEBI has the concept of NAD(P), NAD(P)H and NAD(P)+, i.e. to cover both phosphorylated/unphosphorylated NAD, it doesn't have the concept of NADP(H), which would cover both oxidized and reduced forms of NAD.

The text def of GO:0006741 NADP biosynthetic process (and related terms) say it covers both NADP+ and NADPH synthesis, so ideally the ChEBI in the LD would match that.

I don't see ChEBI making a single term for NADP(3-)/NADPH(4-).
So is it legal to have a LD like "has_primary_output CHEBI:58349 ! NADP(3-) OR CHEBI:57783 ! NADPH(4-)"?