A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)

• Published in: Beilstein journal of organic chemistry Vol. 16; no. 1; pp. 2645 - 2662
• Main Authors: Kellman, Benjamin P, Zhang, Yujie, Logomasini, Emma, Meinhardt, Eric, Godinez-Macias, Karla P, Chiang, Austin W T, Sorrentino, James T, Liang, Chenguang, Bao, Bokan, Zhou, Yusen, Akase, Sachiko, Sogabe, Isami, Kouka, Thukaa, Winzeler, Elizabeth A, Wilson, Iain B H, Campbell, Matthew P, Neelamegham, Sriram, Krambeck, Frederick J, Aoki-Kinoshita, Kiyoko F, Lewis, Nathan E
• Format: Journal Article
• Language: English
• Published: Trakehner Str. 7-9, 60487 Frankfurt am Main, Germany Beilstein-Institut 27.10.2020
• Subjects: Chemistry; glycoinformatics; linear code; systems glycobiology
• ISSN: 1860-5397; 1860-5397
• DOI: 10.3762/bjoc.16.215

Systems glycobiology aims to provide models and analysis tools that account for the biosynthesis, regulation, and interactions with glycoconjugates. To facilitate these methods, there is a need for a clear glycan representation accessible to both computers and humans. Linear Code, a linearized and readily parsable glycan structure representation, is such a language. For this reason, Linear Code was adapted to represent reaction rules, but the syntax has drifted from its original description to accommodate new and originally unforeseen challenges. Here, we delineate the consensuses and inconsistencies that have arisen through this adaptation. We recommend options for a consensus-based extension of Linear Code that can be used for reaction rule specification going forward. Through this extension and specification of Linear Code to reaction rules, we aim to minimize inconsistent symbology thereby making glycan database queries easier. With a clear guide for generating reaction rule descriptions, glycan synthesis models will be more interoperable and reproducible thereby moving glycoinformatics closer to compliance with FAIR standards. Here, we present Linear Code for Reaction Rules (LiCoRR), version 1.0, an unambiguous representation for describing glycosylation reactions in both literature and code.