The carbohydrate-extension from pdbxmmcifwg

carbohydrate-extension's Introduction

Branched Chain Entity Extension Dictionary

The documents in this repository include content extension definitions and example data files for the upcoming Carbohydrate Remediation Project at PDB.

A description of the project
Branched Chain Entity Dictionary Extension (text) (markdown)
Chemical Component Dictionary Extension (text) (markdown)
Examples

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carbohydrate-extension's Issues

No 'SNFG CARB SYMBOL' type for UAP in 2HYV-carb.cif

Hi, there is no 'SNFG CARB SYMBOL' _pdbx_chem_comp_identifier.type in examples/models/2HYV-carb.cif. Is that intentional or is it missing?

On a related note, there is also no 'COMMON NAME' type in that file but in the other examples there is.

Ending of carbohydrate-extension/dict/chem_comp-extension.txt

Should it be .dic?

Distinction between oligosaccharide and polysaccharide

Hi,

PDBj has received a comment on wwPDB carbohydrate remediation proposal from a carbohydrate expert in Japan.

Oligosaccharides differ polysaccharides in many aspects, such as glycosidic linkage (alpha or beta), metabolism, biosynthesis, and their function (protein modification or storing energy) so that glycan researchers focus on one or the other. Therefore, the distinction between oligosaccharides and polysaccharides is strictly applied in the glycan research field. Term “glycan” or “carbohydrate” in general are a broader concept that includes oligosaccharides and polysaccharide.
Please refer to ontology established by international community of glycan research: https://bioportal.bioontology.org/ontologies/GLYCO

As shown in the Glycomics Ontology, the polysaccharide is classified into separate category from the oligosaccharide. But, the first figure in the proposal may be misleading. The footer “Polysaccharides”, next to "Proteins/Nucleotide", is to be replaced with “Carbohydrates” solely or "Oligosaccharides/Polysaccharides”.

To clear the distinction further, entity.type data item in current dictionary for carbohydrate remediation can have polysaccharide as well as oligosaccharide, which is the only defined enumeration at present. The extension of entity.type can provide more useful information for the glycan researchers if we add “N-glycan oligosaccharide” and “O-glycan oligosaccharide” for glycoprotein case.

loop_
_item_enumeration.value
_item_enumeration.details
  oligosaccharide .
  polysaccharide .
# candidates for additional enumerations
  “N-glycan oligosaccharide” .
  “O-glycan oligosaccharide” .

I am also confusing whether all non-branched carbohydrates such as disaccharides, or polysaccharide, incorporated into the carbohydrate remediation or not.

Thank you,

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