{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T00:32:44Z","timestamp":1761611564095,"version":"3.41.2"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,12,20]],"date-time":"2024-12-20T00:00:00Z","timestamp":1734652800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>With the recent advancement in single-cell RNA-sequencing technologies and the increased availability of integrative tools, challenges arise in easy and fast access to large collections of cell atlas. Existing cell atlas portals rarely are open sourced and adaptable, and do not support meta-analysis at cell level. Here, we present an open source, highly optimized and scalable architecture, named Scope+, to allow quick access, meta-analysis and cell-level selection of the atlas data. We applied this architecture to our well-curated 5 million COVID-19 blood and immune cells, as a portal called Covidscope. We achieved efficient access to atlas-scale data via three strategies, such as cell-as-unit data modelling, novel database optimization techniques and innovative software architectural design. Scope+ serves as an open source architecture for researchers to build on with their own atlas.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The COVID-19 web portal, data and meta-analysis are available on Covidscope (https:\/\/covidsc.d24h.hk\/). User tutorials on how to implement Scope+ architecture with their atlases can be found at https:\/\/hiyin.github.io\/scopeplus-user-tutorial\/. Scope+ source code can be found at https:\/\/doi.org\/10.5281\/zenodo.14174632 and https:\/\/github.com\/hiyin\/scopeplus.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae727","type":"journal-article","created":{"date-parts":[[2024,12,20]],"date-time":"2024-12-20T18:01:33Z","timestamp":1734717693000},"source":"Crossref","is-referenced-by-count":2,"title":["Scope+: an open source generalizable architecture for single-cell RNA-seq atlases at sample and cell levels"],"prefix":"10.1093","volume":"41","author":[{"given":"Danqing","family":"Yin","sequence":"first","affiliation":[{"name":"Laboratory of Data Discovery for Health Limited (D24H), Pak Shek Kok, Hong Kong SAR, 999077,","place":["China"]},{"name":"School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, 999077,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2356-4031","authenticated-orcid":false,"given":"Yue","family":"Cao","sequence":"additional","affiliation":[{"name":"Laboratory of Data Discovery for Health Limited (D24H), Pak Shek Kok, Hong Kong SAR, 999077,","place":["China"]},{"name":"Charles Perkins Centre, University of Sydney, Camperdown, NSW, 2006,","place":["Australia"]},{"name":"School of Mathematics and Statistics, University of Sydney, Camperdown, NSW, 2006,","place":["Australia"]},{"name":"Sydney Precision Data Science Centre, University of Sydney, Camperdown, NSW, 2006,","place":["Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9992-7273","authenticated-orcid":false,"given":"Junyi","family":"Chen","sequence":"additional","affiliation":[{"name":"Laboratory of Data Discovery for Health Limited (D24H), Pak Shek Kok, Hong Kong SAR, 999077,","place":["China"]},{"name":"School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, 999077,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Candice L Y","family":"Mak","sequence":"additional","affiliation":[{"name":"Laboratory of Data Discovery for Health Limited (D24H), Pak Shek Kok, Hong Kong SAR, 999077,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ken H O","family":"Yu","sequence":"additional","affiliation":[{"name":"Laboratory of Data Discovery for Health Limited (D24H), Pak Shek Kok, Hong Kong SAR, 999077,","place":["China"]},{"name":"School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, 999077,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiaxuan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Guangzhou National Laboratory, Guangzhou International Bio Island , Guangzhou, Guangdong Province 510005,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-7116-9296","authenticated-orcid":false,"given":"Jia","family":"Li","sequence":"additional","affiliation":[{"name":"Guangzhou National Laboratory, Guangzhou International Bio Island , Guangzhou, Guangdong Province 510005,","place":["China"]},{"name":"State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, 510005,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yingxin","family":"Lin","sequence":"additional","affiliation":[{"name":"Laboratory of Data Discovery for Health Limited (D24H), Pak Shek Kok, Hong Kong SAR, 999077,","place":["China"]},{"name":"Charles Perkins Centre, 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