A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)
| Autor: | Matthew Paul Campbell, Sriram Neelamegham, Karla P. Godinez-Macias, Isami Sogabe, Yujie Zhang, Thukaa Kouka, James T. Sorrentino, Yusen Zhou, Iain B. H. Wilson, Eric Meinhardt, Austin W. T. Chiang, Frederick J. Krambeck, Benjamin P. Kellman, Kiyoko F. Aoki-Kinoshita, Elizabeth A. Winzeler, Nathan E. Lewis, Chenguang Liang, Emma Logomasini, Sachiko Akase, Bokan Bao |
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| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Structure (mathematical logic)
0303 health sciences Syntax (programming languages) Programming language Chemistry 030302 biochemistry & molecular biology Interoperability Organic Chemistry Extension (predicate logic) computer.software_genre Linear code lcsh:QD241-441 03 medical and health sciences glycoinformatics lcsh:Organic chemistry systems glycobiology Code (cryptography) Glycoinformatics linear code lcsh:Q Representation (mathematics) lcsh:Science computer 030304 developmental biology |
| Zdroj: | Beilstein Journal of Organic Chemistry, Vol 16, Iss 1, Pp 2645-2662 (2020) Beilstein journal of organic chemistry, vol 16, iss 1 |
| ISSN: | 1860-5397 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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