{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T07:53:49Z","timestamp":1778226829529,"version":"3.51.4"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2022,1,19]],"date-time":"2022-01-19T00:00:00Z","timestamp":1642550400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31871302"],"award-info":[{"award-number":["31871302"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Overseas Natural Science of China","award":["31829002"],"award-info":[{"award-number":["31829002"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The increasing volume of ribosome profiling (Ribo-seq) data, computational complexity of its data processing and operational handicap of related analytical procedures present a daunting set of informatics challenges. These impose a substantial barrier to researchers particularly with no or limited bioinformatics expertise in analyzing and decoding translation information from Ribo-seq data, thus driving the need for a new research paradigm for data computation and information extraction. In this knowledge base, we herein present a novel interactive web platform, RiboChat (https:\/\/db.cngb.org\/ribobench\/chat.html), for direct analyzing and annotating Ribo-seq data in the form of a chat conversation. It consists of a user-friendly web interface and a backend cloud-computing service. When typing a data analysis question into the chat window, the object-text detection module will be run to recognize relevant keywords from the input text. Based on the features identified in the input, individual analytics modules are then scored to find the perfect-matching candidate. The corresponding analytics module will be further executed after checking the completion status of the uploading of datasets and configured parameters. Overall, RiboChat represents an important step forward in the emerging direction of next-generation data analytics and will enable the broad research community to conveniently decipher translation information embedded within Ribo-seq data.<\/jats:p>","DOI":"10.1093\/bib\/bbab559","type":"journal-article","created":{"date-parts":[[2021,12,9]],"date-time":"2021-12-09T12:23:14Z","timestamp":1639052594000},"source":"Crossref","is-referenced-by-count":5,"title":["RiboChat: a chat-style web interface for analysis and annotation of ribosome profiling data"],"prefix":"10.1093","volume":"23","author":[{"given":"Mingzhe","family":"Xie","sequence":"first","affiliation":[{"name":"State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ludong","family":"Yang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gennong","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yan","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5589-4836","authenticated-orcid":false,"given":"Zhi","family":"Xie","sequence":"additional","affiliation":[{"name":"Bioinformatics at Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3581-8892","authenticated-orcid":false,"given":"Hongwei","family":"Wang","sequence":"additional","affiliation":[{"name":"Bioinformatics at Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,1,19]]},"reference":[{"key":"2022031506263428700_ref1","doi-asserted-by":"crossref","first-page":"1534","DOI":"10.1038\/nprot.2012.086","article-title":"The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments","volume":"7","author":"Ingolia","year":"2012","journal-title":"Nat Protoc"},{"key":"2022031506263428700_ref2","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1126\/science.1168978","article-title":"Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling","volume":"324","author":"Ingolia","year":"2009","journal-title":"Science"},{"key":"2022031506263428700_ref3","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1146\/annurev-virology-100114-054854","article-title":"Ribosome profiling as a tool to decipher viral 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