Taxon constraint: GO:0019853 L-ascorbic acid biosynthetic process

[ValWood]

Please provide as much information as you can:

• GO term ID label: taxon restrict GO:0019853    L-ascorbic acid biosynthetic process for yeast to block

UniProtKB:P38235 | YBR053C | involved_in | GO:0019853    L-ascorbic acid biosynthetic process | ECO:0000318   IBA | GO_REF:0000033 | MGI:MGI:108024 more... | 559292 Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

I'm surprised that mice can make vitamin C? I wanted to check it but the page in the xref is giving an error @LiNiMGI do you know why?

• Request to add a taxon constraint:

• • only in taxon:
• • never in taxon:

• Request to remove a taxon constraint: Please specify

• Supporting evidence if available (e.g PMID):

[LiNiMGI]

@ValWood Hi Val, I am not sure what you meant by "the page in the xref is giving an error", in MGI, the reference for the annotation is PMID:16585534 (https://pubmed.ncbi.nlm.nih.gov/16585534/). thanks! Li

[ValWood]

Hi @LiNiMGI go to https://www.ebi.ac.uk/QuickGO/annotations?geneProductId=P38235&aspect=molecular_function and follow the links to MGI from the "with" field (I think it happens for quite a lot of the MGI links from "with fields", I have seen it a few times).

~I wonder if the Alliance bug that I reported retrieving GO data from MGI is related to this? I can't see how, but it seems odd to have 2 GO-related bugs that only affect MGI ?~ off topic

[ValWood]

Actually, I see what's causing this; I'm sure I reported this way back. Is it because of the MGI:MIGI:prefix? Could this be causing the Alliance problems too?

[LiNiMGI]

@ValWood Hi Val, I don't see this problem in alliance page, could this be a quick GO issuer? https://www.alliancegenome.org/gene/SGD:S000000257

[LiNiMGI]

@ValWood MGI:MGI:108024 Quick GO link to: https://www.informatics.jax.org/accession/MGI Alliance link to: https://www.informatics.jax.org/marker/MGI:108024

[cmungall]

• vitamin C is synthesized in mice - no action required
• uniprot, quickgo, amigo, and alliance all show an IBA propagation from various extant species, including mouse - no action required
• as far as I can tell there is no software or UI or data or prefix errors - no action required

Although it's not directly the subject of this ticket:

• vitamin C is not synthesized in human - action: we should add a taxon constraint

• we should also add basic textbook biochemistry taxon constraints - e.g essential amino acids in mammals see https://github.com/geneontology/go-ontology/issues/28894

[ValWood]

The Alliance issue is probably unrelated, it's that MGI GO EXP annotations are not retrieved using the ortholog feature. We can ignore that. maybe this is a QuickGO issue.

[ValWood]

There is definitely a problem accessing MGI from the QuickGO "with" field.

[ValWood]

Actions from this ticket Add
GO:0019853 L-ascorbic acid biosynthetic process never in yeast never in human

[deustp01]

• vitamin C is not synthesized in human

Also not in guinea pigs. Don't know about chimpanzees and gorillas. I think (too overloaded to research properly) that for humans, a single enzyme step in a synthetic pathway that is well-conserved in mammals, so one could look at a sequence alignment of that enzyme sequence over mammalian taxa to figure out how broad the "never in taxon" constraint should be.