Update of GlycoRDF: request for comments

[kki...@soka.ac.jp]

Dear GLIC members,

We would like to propose a few new updates to the GlycoRDF ontology.  The current

version is GlycoRDF v1.2.1 (https://bioportal.bioontology.org/ontologies/GLYCORDF) 

and we would like to propose the following.  If there are any objections, please let us

know by the end of this month (Feb 29, 2024).

New classes

• Residue
• Monosaccharide_Residue (subclass of Residue)

 New properties (in relation to classes) underlined below:

 Domain:Saccharide   has_monosaccharide_residue      Range:Monosaccharide_Residue

 Domain:Monosaccharide_Residue    has_anomer      Range:Anomer

 Domain:Monosaccharide_Residue   has_ring_type      Range:Ring_Type

 

We do note that this is already a "has_residue" predicate in the ontology, but the domain

for this is NMR_Spectrum.  We also note that there is a "has_monosaccharide" predicate

for the Monosaccharide class which is a subclass of Saccharide.  However, it is our wish

to make a distinction between Monosaccharides and (Monosaccharide) Residues, where 

the latter implies that it is a member of a larger biomolecule and not a single compound 

on its own.

The GlyTouCan team is working on implementing this to better organize the glycan data in

GlyTouCan.  We plan on releasing a major update later this year, and we'll be sure to let

everyone know when the beta version is available for testing before official release.

Thanks,

Kiyoko

--
Kiyoko F. Aoki-Kinoshita, Ph.D.
Professor
Faculty of Science and Engineering
Soka University
E-mail: kki...@soka.ac.jp