TY - JOUR
T1 - A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)
AU - Kellman, Benjamin P.
AU - Zhang, Yujie
AU - Logomasini, Emma
AU - Meinhardt, Eric
AU - Chiang, Austin W. T.
AU - Sorrentino, James T.
AU - Liang, Chenguang
AU - Bao, Bokan
AU - Zhou, Yusen
AU - Akase, Sachiko
AU - Sogabe, Isami
AU - Kouka, Thukaa
AU - Wilson, Iain B.H.
AU - Campbell, Matthew P.
AU - Neelamegham, Sriram
AU - Krambeck, Frederick J.
AU - Aoki-Kinoshita, Kiyoko F.
AU - Lewis, Nathan E.
PY - 2020
Y1 - 2020
N2 - 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.
AB - 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.
UR - http://dx.doi.org/10.3762/bjoc.16.215
U2 - 10.1101/2020.05.31.126623
DO - 10.1101/2020.05.31.126623
M3 - Article
SN - 1860-5397
JO - Beilstein Journal of Organic Chemistry
JF - Beilstein Journal of Organic Chemistry
ER -