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Report to structure errors to GlyTouCan + Yamada #544

Open ReneRanzinger opened 1 year ago

ReneRanzinger commented 1 year ago

@edwardsnj will report the structure errors to GlyTouCan (with copy to Rene) and we will hope they clean this up.

edwardsnj commented 1 year ago

Email sent to support@glytoucan.org with a Cc to Kiyoko, Issaku, and @ReneRanzinger.

ReneRanzinger commented 1 year ago

Hi Kiyoko, Issaku,

Rene identified the following structures that have problematic carbon-bond linkage positions.

It would be nice for these specific accessions to be archived if you agree they are problematic. We presume these got past your validity checker at some point.

If possible, it would be great to have the validity checker updated to catch these cases and to archive any others that are found not to be valid.

G26481RZ - Methyl substituent with bond-position 1, on the reducing end monosaccharide.

G62400VU - WURCS has the carbon bond position of the NeuAc end of then linkage as 1, which doesn't make sense. The GlyTouCan image is quite wrong - it shows just one monosaccharide (GalNAc) at the reducing end. Note at GlyCosmos, this is shown as a match to the Tn antigen motif, which implies the GalNAc is considered to be at the reducing end, but the WURCS sequence shows the NeuAc as the first monosaccharide. My code for WURCS parsing puts the GalNAc at the reducing end to try to resolve the issue with the bond-position 1 linkage (which affects generated GlycoCT and IUPAC sequences at GlyGen).

G89097YO - 3-linked mannose has bond-position linkage as 2. Should be 1 of course.

Thank you!