{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T15:42:23Z","timestamp":1774626143512,"version":"3.50.1"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2018,12,7]],"date-time":"2018-12-07T00:00:00Z","timestamp":1544140800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Database Integration and Coordination Program"},{"DOI":"10.13039\/501100004696","name":"National Bioscience Database Center","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004696","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004696","name":"NBDC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004696","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002241","name":"Japan Science and Technology Agency","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002241","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001695","name":"JST","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001695","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Glycans are biomolecules that take an important role in the biological processes of living organisms. They form diverse, complicated structures such as branched and cyclic forms. Web3 Unique Representation of Carbohydrate Structures (WURCS) was proposed as a new linear notation for uniquely representing glycans during the GlyTouCan project. WURCS defines rules for complex glycan structures that other text formats did not support, and so it is possible to represent a wide variety glycans. However, WURCS uses a complicated nomenclature, so it is not human-readable. Therefore, we aimed to support the interpretation of WURCS by converting WURCS to the most basic and widely used format IUPAC.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this study, we developed GlycanFormatConverter and succeeded in converting WURCS to the three kinds of IUPAC formats (IUPAC-Extended, IUPAC-Condensed and IUPAC-Short). Furthermore, we have implemented functionality to import IUPAC-Extended, KEGG Chemical Function (KCF) and LinearCode formats and to export WURCS. We have thoroughly tested our GlycanFormatConverter and were able to show that it was possible to convert all the glycans registered in the GlyTouCan repository, with exceptions owing only to the limitations of the original format. The source code for this conversion tool has been released as an open source tool.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/glycoinfo\/GlycanFormatConverter.git<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty990","type":"journal-article","created":{"date-parts":[[2018,12,6]],"date-time":"2018-12-06T22:37:40Z","timestamp":1544135860000},"page":"2434-2440","source":"Crossref","is-referenced-by-count":31,"title":["GlycanFormatConverter: a conversion tool for translating the complexities of glycans"],"prefix":"10.1093","volume":"35","author":[{"given":"Shinichiro","family":"Tsuchiya","sequence":"first","affiliation":[{"name":"Graduate School of Engineering, Soka University, Hachioji, Tokyo, Japan"}]},{"given":"Issaku","family":"Yamada","sequence":"additional","affiliation":[{"name":"The Noguchi Institute, Itabashi, Tokyo, Japan"}]},{"given":"Kiyoko F","family":"Aoki-Kinoshita","sequence":"additional","affiliation":[{"name":"Graduate School of Engineering, Soka University, Hachioji, Tokyo, Japan"},{"name":"Faculty of Science and Engineering, Soka University, Hachioji, Tokyo, Japan"}]}],"member":"286","published-online":{"date-parts":[[2018,12,7]]},"reference":[{"key":"2023062712301286400_bty990-B1","volume-title":"Glycome Informatics: Methods and Applications","author":"Aoki-Kinoshita","year":"2010"},{"key":"2023062712301286400_bty990-B2","doi-asserted-by":"crossref","first-page":"D1237","DOI":"10.1093\/nar\/gkv1041","article-title":"GlyTouCan 1.0\u2014the international glycan structure repository","volume":"44","author":"Aoki-Kinoshita","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023062712301286400_bty990-B3","doi-asserted-by":"crossref","first-page":"W597","DOI":"10.1093\/nar\/gks400","article-title":"ExPASy: SIB bioinformatics resource portal","volume":"40","author":"Artimo","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023062712301286400_bty990-B4","doi-asserted-by":"crossref","first-page":"127","DOI":"10.4052\/tigg.14.127","article-title":"A novel linear code nomenclature for complex carbohydrates","volume":"14","author":"Banin","year":"2002","journal-title":"Trends Glycosci. Glycotechnol"},{"key":"2023062712301286400_bty990-B5","doi-asserted-by":"crossref","first-page":"D215","DOI":"10.1093\/nar\/gkt1128","article-title":"UniCarbKB: building a knowledge platform for glycoproteomics","volume":"42","author":"Campbell","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023062712301286400_bty990-B6","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1016\/0968-0004(89)90175-8","article-title":"The complex carbohydrate structure database","volume":"14","author":"Doubet","year":"1989","journal-title":"Trends Biochem. Sci"},{"key":"2023062712301286400_bty990-B7","doi-asserted-by":"crossref","first-page":"63R","DOI":"10.1093\/glycob\/cwj010","article-title":"KEGG as a glycome informatics resource","volume":"16","author":"Hashimoto","year":"2006","journal-title":"Glycobiolotgy"},{"key":"2023062712301286400_bty990-B8","doi-asserted-by":"crossref","first-page":"11853","DOI":"10.1021\/ja036030u","article-title":"Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways","volume":"125","author":"Hattori","year":"2003","journal-title":"J. Am. Chem. Soc"},{"key":"2023062712301286400_bty990-B9","doi-asserted-by":"crossref","first-page":"2162","DOI":"10.1016\/j.carres.2008.03.011","article-title":"GlycoCT\u2014a unifying sequence format for carbohydrates","volume":"343","author":"Herget","year":"2008","journal-title":"Carbohydrate Res"},{"key":"2023062712301286400_bty990-B10","doi-asserted-by":"crossref","first-page":"2849","DOI":"10.1093\/bioinformatics\/bts516","article-title":"The GlycomeAtlas tool for visualizing and querying glycome data","volume":"28","author":"Konishi","year":"2012","journal-title":"Bioinformatics"},{"key":"2023062712301286400_bty990-B11","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1093\/glycob\/cwq188","article-title":"EUROCarbDB: an open-access platform for glycoinformatics","volume":"21","author":"Lieth","year":"2010","journal-title":"Glycobiology"},{"key":"2023062712301286400_bty990-B12","doi-asserted-by":"crossref","first-page":"632","DOI":"10.1021\/acs.jcim.6b00650","article-title":"WURCS 2.0 update to encapsulate ambiguous carbohydrate structures","volume":"57","author":"Matsubara","year":"2017","journal-title":"J. Chem.Inf. Model"},{"key":"2023062712301286400_bty990-B13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0008-6215(97)83449-0","article-title":"Nomenclature of carbohydrates","volume":"297","author":"McNaught","year":"1997","journal-title":"Carbohydrate Res"},{"key":"2023062712301286400_bty990-B14","volume-title":"Oligosaccharides and Polysaccharides. Essentials of Glycobiology","author":"Packer","year":"2017","edition":"3"},{"key":"2023062712301286400_bty990-B15","doi-asserted-by":"crossref","first-page":"82R","DOI":"10.1093\/glycob\/cwj080","article-title":"Advancing glycomics: implementation strategies at the Consortium for Functional Glycomics","volume":"16","author":"Raman","year":"2006","journal-title":"Glycobiology"},{"key":"2023062712301286400_bty990-B16","doi-asserted-by":"crossref","first-page":"384.","DOI":"10.1186\/1471-2105-9-384","article-title":"GlycomeDB\u2014integration of open-access carbohydrate structure databases","volume":"9","author":"Ranzinger","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023062712301286400_bty990-B17","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1007\/BF01049370","article-title":"IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature of glycoproteins, glycopeptides and peptidoglycans","volume":"3","author":"Sharon","year":"1986","journal-title":"Glycoconjugate J"},{"key":"2023062712301286400_bty990-B18","doi-asserted-by":"crossref","first-page":"1558","DOI":"10.1021\/ci400571e","article-title":"WURCS: the Web3 unique representation of carbohydrate structures","volume":"54","author":"Tanaka","year":"2014","journal-title":"J. Chem. Inf. Model"},{"key":"2023062712301286400_bty990-B19","volume-title":"Structural Basis of Glycan Diversity. Essentials of Glycobiology","author":"Varki","year":"2009","edition":"2"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/14\/2434\/50720371\/bioinformatics_35_14_2434.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/14\/2434\/50720371\/bioinformatics_35_14_2434.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,27]],"date-time":"2023-06-27T12:30:44Z","timestamp":1687869044000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/14\/2434\/5233002"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,12,7]]},"references-count":19,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2019,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty990","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,7]]},"published":{"date-parts":[[2018,12,7]]}}}