{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:48:37Z","timestamp":1753876117098,"version":"3.41.2"},"reference-count":137,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2019,11,18]],"date-time":"2019-11-18T00:00:00Z","timestamp":1574035200000},"content-version":"vor","delay-in-days":321,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["5 R24 OD011883"],"award-info":[{"award-number":["5 R24 OD011883"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>While abnormalities related to carbohydrates (glycans) are frequent for patients with rare and undiagnosed diseases as well as in many common diseases, these glycan-related phenotypes (glycophenotypes) are not well represented in knowledge bases (KBs). If glycan-related diseases were more robustly represented and curated with glycophenotypes, these could be used for molecular phenotyping to help to realize the goals of precision medicine. Diagnosis of rare diseases by computational cross-species comparison of genotype\u2013phenotype data has been facilitated by leveraging ontological representations of clinical phenotypes, using Human Phenotype Ontology (HPO), and model organism ontologies such as Mammalian Phenotype Ontology (MP) in the context of the Monarch Initiative. In this article, we discuss the importance and complexity of glycobiology and review the structure of glycan-related content from existing KBs and biological ontologies. We show how semantically structuring knowledge about the annotation of glycophenotypes could enhance disease diagnosis, and propose a solution to integrate glycophenotypes and related diseases into the Unified Phenotype Ontology (uPheno), HPO, Monarch and other KBs. We encourage the community to practice good identifier hygiene for glycans in support of semantic analysis, and clinicians to add glycomics to their diagnostic analyses of rare diseases.<\/jats:p>","DOI":"10.1093\/database\/baz114","type":"journal-article","created":{"date-parts":[[2019,9,5]],"date-time":"2019-09-05T11:41:59Z","timestamp":1567683719000},"source":"Crossref","is-referenced-by-count":7,"title":["Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery"],"prefix":"10.1093","volume":"2019","author":[{"given":"Jean-Philippe F","family":"Gourdine","sequence":"first","affiliation":[{"name":"Oregon Clinical & Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA"},{"name":"OHSU Library, Oregon Health & Science University Library, Portland, OR 97239, USA"},{"name":"Monarch Initiative, monarchinitiative.org"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew H","family":"Brush","sequence":"additional","affiliation":[{"name":"Oregon Clinical & Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA"},{"name":"Monarch Initiative, monarchinitiative.org"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicole A","family":"Vasilevsky","sequence":"additional","affiliation":[{"name":"Oregon Clinical & Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA"},{"name":"Monarch Initiative, monarchinitiative.org"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kent","family":"Shefchek","sequence":"additional","affiliation":[{"name":"Monarch Initiative, monarchinitiative.org"},{"name":"Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sebastian","family":"K\u00f6hler","sequence":"additional","affiliation":[{"name":"Monarch Initiative, monarchinitiative.org"},{"name":"Charit\u00e9 Centrum f\u00fcr Therapieforschung, Charit\u00e9-Universit\u00e4tsmedizin Berlin Corporate Member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin and Berlin Institute of Health, Berlin 10117, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicolas","family":"Matentzoglu","sequence":"additional","affiliation":[{"name":"Monarch Initiative, monarchinitiative.org"},{"name":"European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Monica C","family":"Munoz-Torres","sequence":"additional","affiliation":[{"name":"Monarch Initiative, monarchinitiative.org"},{"name":"Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julie A","family":"McMurry","sequence":"additional","affiliation":[{"name":"Monarch Initiative, monarchinitiative.org"},{"name":"Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xingmin Aaron","family":"Zhang","sequence":"additional","affiliation":[{"name":"Monarch Initiative, monarchinitiative.org"},{"name":"The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter N","family":"Robinson","sequence":"additional","affiliation":[{"name":"Monarch Initiative, monarchinitiative.org"},{"name":"The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Melissa A","family":"Haendel","sequence":"additional","affiliation":[{"name":"Oregon Clinical & Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA"},{"name":"Monarch Initiative, monarchinitiative.org"},{"name":"Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,11,18]]},"reference":[{"key":"2019111800401843500_ref1","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1111\/j.1600-0420.1997.tb00792.x","article-title":"The eye and its diseases in ancient Egypt","volume":"75","author":"Andersen","year":"1997","journal-title":"Acta Ophthalmol. 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