move MetaCyc:CODH-PWY from acetate biosynthetic process from carbon monoxide to carbon fixation by acetyl-CoA pathway

[cmungall]

https://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=CODH-PWY

id: GO:0019415
name: acetate biosynthetic process from carbon monoxide
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of acetate from other compounds, including carbon monoxide." [GOC:go_curators]
synonym: "acetate anabolism from carbon monoxide" EXACT []
synonym: "acetate formation from carbon monoxide" EXACT []
synonym: "acetate synthesis from carbon monoxide" EXACT []
synonym: "carbon monoxide dehydrogenase pathway" EXACT []
xref: MetaCyc:CODH-PWY
intersection_of: GO:0009058 ! biosynthetic process
intersection_of: has_primary_input CHEBI:17245 ! carbon monoxide
intersection_of: has_primary_output CHEBI:30089 ! acetate

should be here:

id: GO:0030634
name: carbon fixation by acetyl-CoA pathway
namespace: biological_process
def: "A pathway of carbon dioxide fixation in which one molecule of acetyl-CoA is completely synthesized from two molecules of carbon dioxide (CO2)." [PMID:11607093]
synonym: "Ljungdahl-Wood pathway" EXACT []
xref: MIPS_funcat:01.05.01.05.07
xref: Wikipedia:Wood–Ljungdahl_pathway
is_a: GO:0006085 ! acetyl-CoA biosynthetic process
is_a: GO:0015977 ! carbon fixation

[cmungall]

I guess this is not totally straightforward. The LW pathway is sometimes extended to acetate as in here:

(from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC262307/)

here GO:0030634 would be a part of the LW pathway (see above)

in other cases it stops at acetyl-CoA (MetaCyc has the acetyle-CoA to acetate part as a separate pathway). Here GO:0030634 would overlap LW/

The fact that different pathway databases consider different start/endpoints is well known, but we should pick one and be very clear on our starts/ends.

I think GO:0019415 may be a candidate for obsoletion

Note all annotations are ISS http://amigo.geneontology.org/amigo/term/GO:0019415

(we should have a rule that no term should have ONLY ISS annotations)

Some of the ISS annotations are from orthology with https://www.ebi.ac.uk/QuickGO/annotations?geneProductId=P31897 others from a tigrfam

It's not clear the reaction this enzyme catalyzes is part of the GO:0019415 pathway

[ValWood]

(we should have a rule that no term should have ONLY ISS annotations)

I would love that we have such a rule. This has been proposed for a long time. However ,historically it was not mandatory that the annotation exists. I have often used SGD when an annotation should be obvious, but does not always exist. Usually I would mail SGD but I can't always be sure that I did, or that it was added, and for some from the past couple of years I am still waiting for the paper to be curated. This would be a good way to check these, but it doen't necessarily mean that the annotation should not exist.

It would really help us to also identify annotations which used to exist but have been deleted. We have no way to identify these at present except by chance.

I'll open a ticket for this.

[ukemi]

From the GOC naming convention and definition, this pathway would end at acetate and it should be the primary output.

[pgaudet]

@ukemi You have a PR for this - can it be merged and closed ?

[ValWood]

@ukemi You have a PR for this - can it be merged and closed ?