{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T21:46:58Z","timestamp":1775252818129,"version":"3.50.1"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2023,4,13]],"date-time":"2023-04-13T00:00:00Z","timestamp":1681344000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32200545"],"award-info":[{"award-number":["32200545"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,5,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Many ophthalmic disease biomarkers have been identified through comprehensive multiomics profiling, and hold significant potential in advancing the diagnosis, prognosis, and management of diseases. Meanwhile, the eye itself serves as a natural biomarker for several systemic diseases including neurological, renal, and cardiovascular systems. We aimed to collect and standardize this eye biomarkers information and construct the eye biomarker database (EBD) to provide ophthalmologists with a platform to search, analyze, and download these eye biomarker data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this study, we present the EBD &amp;lt;http:\/\/www.eyeseeworld.com\/ebd\/index.html&amp;gt;, a world-first online compilation comprising 889 biomarkers for 26 ocular diseases and 939 eye biomarkers for 181 systemic diseases. The EBD also includes the information of 78 \u201cnonbiomarkers\u201d\u2014the objects that have been proven cannot be biomarkers. Biological function and network analysis were conducted for these ocular disease biomarkers, and several hub pathways and common network topology characteristics were newly identified, which may promote future ocular disease biomarker discovery and characterizes the landscape of biomarkers for eye diseases at the pathway and network level. The EBD is expected to yield broader utility among developmental biologists and clinical scientists in and outside of the eye field by assisting in the identification of biomarkers linked to eye disorders and related systemic diseases.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>EBD is available at http:\/\/www.eyeseeworld.com\/ebd\/index.html.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad194","type":"journal-article","created":{"date-parts":[[2023,4,13]],"date-time":"2023-04-13T15:35:52Z","timestamp":1681400152000},"source":"Crossref","is-referenced-by-count":8,"title":["EBD: an eye biomarker database"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5963-9261","authenticated-orcid":false,"given":"Xueli","family":"Zhang","sequence":"first","affiliation":[{"name":"Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People\u2019s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University , No. 106 Zhongshan Second Road , Guangzhou 510080, China"},{"name":"Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University , No. 106 Zhongshan Second Road , Guangzhou 510080, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3607-1532","authenticated-orcid":false,"given":"Lingcong","family":"Kong","sequence":"additional","affiliation":[{"name":"Medical Big Data Center, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University , No. 106 Zhongshan Second Road , Guangzhou 510080, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shunming","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People\u2019s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University , No. 106 Zhongshan Second Road , Guangzhou 510080, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiayin","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People\u2019s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University , No. 106 Zhongshan Second Road , Guangzhou 510080, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xianwen","family":"Shang","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People\u2019s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University , No. 106 Zhongshan Second Road , Guangzhou 510080, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhuoting","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People\u2019s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University , No. 106 Zhongshan Second Road , Guangzhou 510080, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People\u2019s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University , No. 106 Zhongshan Second Road , Guangzhou 510080, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuo","family":"Ma","sequence":"additional","affiliation":[{"name":"Medical Big Data Center, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University , No. 106 Zhongshan Second Road , Guangzhou 510080, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ha","family":"Jason","sequence":"additional","affiliation":[{"name":"Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital , 32 Gisborne Street , East Melbourne, VIC 3002, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katerina V","family":"Kiburg","sequence":"additional","affiliation":[{"name":"Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital , 32 Gisborne Street , East Melbourne, VIC 3002, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chunwen","family":"Zheng","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People\u2019s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University , No. 106 Zhongshan Second Road , Guangzhou 510080, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yunyan","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People\u2019s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University , No. 106 Zhongshan Second Road , Guangzhou 510080, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cong","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People\u2019s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University , No. 106 Zhongshan Second Road , Guangzhou 510080, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guanrong","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People\u2019s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University , No. 106 Zhongshan Second Road , Guangzhou 510080, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yingying","family":"Liang","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People\u2019s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University , No. 106 Zhongshan Second Road , Guangzhou 510080, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mengxia","family":"He","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People\u2019s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University , No. 106 Zhongshan Second Road , Guangzhou 510080, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yan","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People\u2019s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University , No. 106 Zhongshan Second Road , Guangzhou 510080, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaohe","family":"Bai","sequence":"additional","affiliation":[{"name":"Department of Mathematics, University of California , 9500 Gilman Dr, La Jolla , San Diego, CA 92093, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6094-137X","authenticated-orcid":false,"given":"Danli","family":"Shi","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University , No. 54 Xianlie South Road , Guangzhou 510060, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University , No. 54 Xianlie South Road , Guangzhou 510060, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chi","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Otolaryngology, Guangzhou Women and Children's Medical Centre , No. 9 Jinsui Road , Guangzhou 510623, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ke","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Radiology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University , No. 106 Zhongshan Second Road , Guangzhou 510080, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haining","family":"Yuan","sequence":"additional","affiliation":[{"name":"HangZhou Medical College , No. 8 Jikang Street, Lin'an District , Hangzhou 311399, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8754-1541","authenticated-orcid":false,"given":"Guang","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Center for Systems Biology, School of Biology and Basic Medical Sciences, Soochow University , No. 199 Ren'ai Road, Suzhou Industrial Park , Suzhou 215123, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yijun","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People\u2019s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University , No. 106 Zhongshan Second Road , Guangzhou 510080, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huiying","family":"Liang","sequence":"additional","affiliation":[{"name":"Medical Big Data Center, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University , No. 106 Zhongshan Second Road , Guangzhou 510080, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Honghua","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People\u2019s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University , No. 106 Zhongshan Second Road , Guangzhou 510080, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2343-084X","authenticated-orcid":false,"given":"Lei","family":"Zhang","sequence":"additional","affiliation":[{"name":"Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital , 32 Gisborne Street , East Melbourne, VIC 3002, Australia"},{"name":"China-Australia Joint Research Center for Infectious Diseases, School of Public Health, Xi'an Jiaotong University Health Science Center , No.76 Yanta West Road , Xi'an 710061, China"},{"name":"Artificial Intelligence and Modelling in Epidemiology Program, Melbourne Sexual Health Centre, Alfred Health , 55 Commercial Rd , Melbourne, VIC 3004, Australia"},{"name":"Central Clinical School, Faculty of Medicine, Monash University , 27 Rainforest Walk , Melbourne, Clayton VIC 3800, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mingguang","family":"He","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People\u2019s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University , No. 106 Zhongshan Second Road , Guangzhou 510080, China"},{"name":"Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital , 32 Gisborne Street , East Melbourne, VIC 3002, Australia"},{"name":"State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University , No. 54 Xianlie South Road , Guangzhou 510060, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,4,13]]},"reference":[{"key":"2023050917375016000_btad194-B1","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1126\/science.1173299","article-title":"Scale-free networks: a decade and beyond","volume":"325","author":"Barab\u00e1si","year":"2009","journal-title":"Science"},{"key":"2023050917375016000_btad194-B2","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1093\/bfgp\/els036","article-title":"Protein-protein interaction networks: unraveling the wiring of molecular machines within the cell","volume":"11","author":"De las Rivas","year":"2012","journal-title":"Brief Funct Genomics"},{"key":"2023050917375016000_btad194-B3","doi-asserted-by":"crossref","first-page":"e1221","DOI":"10.1016\/S2214-109X(17)30393-5","article-title":"Global causes of blindness and distance vision impairment 1990\u20132020: a systematic review and meta-analysis","volume":"5","author":"Flaxman","year":"2017","journal-title":"Lancet Glob Health"},{"key":"2023050917375016000_btad194-B4","doi-asserted-by":"crossref","first-page":"4534","DOI":"10.1093\/bioinformatics\/btab470","article-title":"HFBD: a biomarker knowledge database for heart failure heterogeneity and personalized applications","volume":"37","author":"He","year":"2021","journal-title":"Bioinformatics"},{"key":"2023050917375016000_btad194-B5","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nrneurol.2012.227","article-title":"The retina as a window to the brain - from eye research to CNS disorders","volume":"9","author":"London","year":"2013","journal-title":"Nat Rev Neurol"},{"key":"2023050917375016000_btad194-B6","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1097\/COH.0b013e32833ed177","article-title":"What are biomarkers?","volume":"5","author":"Strimbu","year":"2010","journal-title":"Curr Opin HIV AIDS"},{"key":"2023050917375016000_btad194-B7","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1007\/s11095-019-2569-8","article-title":"Review of biomarkers in ocular matrices: challenges and opportunities","volume":"36","author":"Tamhane","year":"2019","journal-title":"Pharm Res"},{"key":"2023050917375016000_btad194-B9","doi-asserted-by":"crossref","first-page":"2081","DOI":"10.1016\/j.ophtha.2014.05.013","article-title":"Global prevalence of glaucoma and projections of glaucoma burden through 2040: a systematic review and meta-analysis","volume":"121","author":"Tham","year":"2014","journal-title":"Ophthalmology"},{"key":"2023050917375016000_btad194-B10","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1038\/s41433-022-02056-9","article-title":"Optical coherence tomography as retinal imaging biomarker of neuroinflammation\/neurodegeneration in systemic disorders in adults and children","volume":"37","author":"Vujosevic","year":"2023","journal-title":"Eye (Lond)"},{"key":"2023050917375016000_btad194-B11","doi-asserted-by":"crossref","first-page":"110286","DOI":"10.1016\/j.ygeno.2022.110286","article-title":"The human eye transcriptome atlas: a searchable comparative transcriptome database for healthy and diseased human eye tissue","volume":"114","author":"Wolf","year":"2022","journal-title":"Genomics"},{"key":"2023050917375016000_btad194-B12","doi-asserted-by":"crossref","first-page":"1290","DOI":"10.1038\/ki.2013.491","article-title":"Kidney and eye diseases: common risk factors, etiological mechanisms, and pathways","volume":"85","author":"Wong","year":"2014","journal-title":"Kidney Int"},{"key":"2023050917375016000_btad194-B13","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1001\/jama.293.1.63","article-title":"Retinopathy and risk of congestive heart failure","volume":"293","author":"Wong","year":"2005","journal-title":"JAMA"},{"key":"2023050917375016000_btad194-B14","doi-asserted-by":"crossref","first-page":"e106","DOI":"10.1016\/S2214-109X(13)70145-1","article-title":"Global prevalence of age-related macular degeneration and disease burden projection for 2020 and 2040: a systematic review and meta-analysis","volume":"2","author":"Wong","year":"2014","journal-title":"Lancet Glob Health"},{"key":"2023050917375016000_btad194-B15","volume-title":"World Report on Vision","author":"World Health Organization","year":"2019"},{"key":"2023050917375016000_btad194-B16","doi-asserted-by":"crossref","first-page":"D455","DOI":"10.1093\/nar\/gkm925","article-title":"IDBD: infectious disease biomarker database","volume":"36","author":"Yang","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2023050917375016000_btad194-B17","doi-asserted-by":"crossref","first-page":"iqab050","DOI":"10.1093\/nargab\/lqab050","article-title":"EyeDiseases: an integrated resource for dedicating to genetic variants, gene expression and epigenetic factors of human eye diseases","volume":"3","author":"Yuan","year":"2021","journal-title":"NAR Genom Bioinform"},{"key":"2023050917375016000_btad194-B18","doi-asserted-by":"crossref","first-page":"bay046","DOI":"10.1093\/database\/bay046","article-title":"CBD: a biomarker database for colorectal cancer","volume":"2018","author":"Zhang","year":"2018","journal-title":"Database"},{"key":"2023050917375016000_btad194-B19","doi-asserted-by":"crossref","first-page":"172","DOI":"10.3390\/cancers11020172","article-title":"Potential applications of DNA, RNA and protein biomarkers in diagnosis, therapy and prognosis for colorectal cancer: a study from databases to AI-assisted verification","volume":"11","author":"Zhang","year":"2019","journal-title":"Cancers (Basel)"},{"key":"2023050917375016000_btad194-B20","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1136\/bjophthalmol-2021-319807","article-title":"Retinal age gap as a predictive biomarker for mortality risk","volume":"107","author":"Zhu","year":"2023","journal-title":"Br J Ophthalmol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad194\/49880148\/btad194.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/5\/btad194\/50259524\/btad194.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/5\/btad194\/50259524\/btad194.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,11]],"date-time":"2023-05-11T03:01:31Z","timestamp":1683774091000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad194\/7117545"}},"subtitle":[],"editor":[{"given":"Christina","family":"Kendziorski","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2023,4,13]]},"references-count":19,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2023,5,4]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad194","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,5,1]]},"published":{"date-parts":[[2023,4,13]]},"article-number":"btad194"}}