Matrix: ero1b prdx4 amino acid metabolism/protein folding

ValWood commented 5 years ago

4-hydroxyproline metabolic process

I think this is protein folding or isomerization upstream of collagen modification, but isn't part of the amino-acid derivative biosyntheis

above should be fixed by pipeline

Prdx4 peroxiredoxin 4 4-hydroxyproline metabolic process MGI Mus musculus IGI MGI:MGI:1354385 MGI:MGI:1914725 thioredoxin peroxidase pthr10681 protein MGI:MGI:5461404 PMID:22981861 20140120

ValWood commented 5 years ago

If the modification is the term you need, then its:

peptidyl-proline hydroxylation to 4-hydroxy-L-proline

which will still create a violation right now but will be fixed by: https://github.com/geneontology/go-ontology/issues/17518

ValWood commented 5 years ago

Same issue with

ValWood commented 5 years ago

pdi-2 | | | peptidyl-proline hydroxylation to 4-hydroxy-L-proline | | WB | Caenorhabditis elegans | IDA | | | gene | | PMID:18276589WB_REF:WBPaper00031524 | 20120112

or am I wrong here?

ValWood commented 5 years ago

This does seem to act directly on collagens so maybe these terms should be merged (or this one obsoleted)? The appear to mean the same thing?

gthayman commented 5 years ago

The first 3 are from MGD.

ValWood commented 5 years ago

yup: https://en.wikipedia.org/wiki/Hydroxyproline Hydroxyproline is produced by hydroxylation of the amino acid proline by the enzyme prolyl hydroxylase following protein synthesis (as a post-translational modification). T

hdrabkin commented 5 years ago

@ValWood , Looking the close this; I see the MGI lines crossed out. What does this mean? Are we good?

hdrabkin commented 5 years ago

looking at the paper for the one not crossed out, (the IGI), I see it is actually that ascorbic acid biosynthesis is getting hit; Ascorbic acid is a required co-factor for any collagen proline hydroxylase. So it's a bit further along 'Compromised ER disulfide relay thus exposes protein thiols to competing for oxidation to sulfenic acid, resulting in depletion of ascorbic acid, impaired procollagen proline 4-hydroxylation,"

ValWood commented 5 years ago

HI HArold,

I think the prdx4 issue will be fixed by changing the parentage of https://github.com/geneontology/go-ontology/issues/17518 so it is not an amino acid metabolic process (its a modification)

17518 is assigned to you too, ~you could close this one....~ I see there are others too

ValWood commented 5 years ago

I was referring to prdx4 in my comment. I will edit to make this clear

ValWood commented 5 years ago

you could also fix the pedx4 issue for this annotation by moving to peptidyl-proline hydroxylation to 4-hydroxy-L-proline (I think?)

ValWood commented 5 years ago

...I'm a bit confused...

hdrabkin commented 5 years ago

So to fix this annotation, it should be to the peptidyl term. not the term that could be interpreted as acting on free proline (however, I am not aware of hydroxylation of free proline anyway.)

ValWood commented 5 years ago

Yes, I agree. I think the other term should probably not exist...that is what the ontology tracker ticket is about.

I got confused by the ascorbic acid part....

hdrabkin commented 5 years ago

| GO:0018401 peptidyl-proline hydroxylation to 4-hydroxy-L-proline Done; THIS ticket can be closed now; looking at the ontology ticket now

vanaukenk commented 5 years ago

@ValWood - Is there anything I need to do for the WB annotation here? Is it that the annotation okay, but the ontology parentage needs to be updated?

hdrabkin commented 5 years ago

quickly looking at the wb paper; I think it's fine. The paper talks about the activity on peptides.

ValWood commented 5 years ago

@vanaukenk yes, the ontology fix will fix yours.

hdrabkin commented 5 years ago

And also found 2 more mis-annotations (same paper; IGI will always include at least two genes).

geneontology / go-annotation

Matrix: ero1b prdx4 amino acid metabolism/protein folding #2423

4-hydroxyproline metabolic process