Sweet! NextMove helps PubChem import UniCarbKB

Sugar CubesLast week, PubChem announced the following:

Structures from UniCarbKB are now available in PubChem. UniCarbKB is an initiative to create an online information storage and search platform for glycomics and glycobiology research. UniCarbKB curates information from the scientific literature on glycoprotein derived glycan structures, building on previous curation efforts by GlycoSuiteDB and continuing the principles of EUROCarbDB to provide an open-access platform for glycoinformatics…

NextMove Software has been collaborating with PubChem on the development of Sugar & Splice, software to handle and interconvert representations of peptides, oligonucleotides and oligosaccharides. The import of UniCarbKB into PubChem is the first large application of the software and requires the conversion to SMILES strings of IUPAC condensed line notation for oligosaccharides (this looks like Fuc(a1-4)GlcNAc).

A nice validation of the software was that it was able to identify a small number of duplicates in the database, as well as some errors in the exported structures (e.g. mismatched brackets). These have been reported back to the database.

Image credit: Michael Allen Smith (INeedCoffee.com on Flickr)

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