{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T03:07:07Z","timestamp":1781147227941,"version":"3.54.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2023,3,10]],"date-time":"2023-03-10T00:00:00Z","timestamp":1678406400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Genome Canada\/G\u00e9nome Qu\u00e9bec","award":["249333"],"award-info":[{"award-number":["249333"]}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,4,3]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>Large-scale sharing of genomic quantification data requires standardized access interfaces. In this Global Alliance for Genomics and Health project, we developed RNAget, an API for secure access to genomic quantification data in matrix form. RNAget provides for slicing matrices to extract desired subsets of data and is applicable to all expression matrix-format data, including RNA sequencing and microarrays. Further, it generalizes to quantification matrices of other sequence-based genomics such as ATAC-seq and ChIP-seq.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>https:\/\/ga4gh-rnaseq.github.io\/schema\/docs\/index.html.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad126","type":"journal-article","created":{"date-parts":[[2023,3,9]],"date-time":"2023-03-09T16:58:17Z","timestamp":1678381097000},"source":"Crossref","is-referenced-by-count":4,"title":["RNAget: an API to securely retrieve RNA quantifications"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3119-8975","authenticated-orcid":false,"given":"Sean","family":"Upchurch","sequence":"first","affiliation":[{"name":"Biology and Biomedical Engineering, California Institute of Technology , Pasadena, CA 91125, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emilio","family":"Palumbo","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology , Barcelona, Catalonia 08003, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeremy","family":"Adams","sequence":"additional","affiliation":[{"name":"Ontario Institute for Cancer Research , Toronto, ON M5G 0A3, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Bujold","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, McGill University , Montreal, QC H3A 0G4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3933-9656","authenticated-orcid":false,"given":"Guillaume","family":"Bourque","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, McGill University , Montreal, QC H3A 0G4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jared","family":"Nedzel","sequence":"additional","affiliation":[{"name":"Broad Institute , Cambridge, MA 02142, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keenan","family":"Graham","sequence":"additional","affiliation":[{"name":"Department of Genetics, Stanford University , Stanford, CA 94305, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meenakshi S","family":"Kagda","sequence":"additional","affiliation":[{"name":"Department of Genetics, Stanford University , Stanford, CA 94305, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pedro","family":"Assis","sequence":"additional","affiliation":[{"name":"Department of Genetics, Stanford University , Stanford, CA 94305, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3361-3594","authenticated-orcid":false,"given":"Benjamin","family":"Hitz","sequence":"additional","affiliation":[{"name":"Department of Genetics, Stanford University , Stanford, CA 94305, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emilio","family":"Righi","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology , Barcelona, Catalonia 08003, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roderic","family":"Guig\u00f3","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology , Barcelona, Catalonia 08003, Spain"},{"name":"Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF) , Barcelona, Catalonia 08002, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barbara J","family":"Wold","sequence":"additional","affiliation":[{"name":"Biology and Biomedical Engineering, California Institute of Technology , Pasadena, CA 91125, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"GA4GH RNA-Seq Task Team","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeremy","family":"Adams","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alvis","family":"Brazma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Bujold","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia","family":"Burchard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joe","family":"Capka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Cherry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Clarke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian","family":"Craft","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manolis","family":"Dermitzakis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Diekhans","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Dursi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael Sean","family":"Fitzsimons","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zac","family":"Flaming","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Romina","family":"Garrido","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alfred","family":"Gil","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Godden","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matt","family":"Green","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roderic","family":"Guigo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mitch","family":"Guttman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian","family":"Haas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Max","family":"Haeussler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin","family":"Hitz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sten","family":"Linnarsson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam","family":"Lipski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simonne","family":"Longerich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Lougheed","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan","family":"Manning","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Marioni","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Meyer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen","family":"Montgomery","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alyssa","family":"Morrow","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alfonso","family":"Munoz-Power Fuentes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jared","family":"Nedzel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Nguyen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin","family":"Osborn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francis","family":"Ouellette","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emilio","family":"Palumbo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Irene","family":"Papatheodorou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dmitri","family":"Pervouchine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arun","family":"Ramani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jordi","family":"Rambla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bashir","family":"Sadjad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Steinberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeremiah","family":"Talkar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy","family":"Tickle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathy","family":"Tzeng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sean","family":"Upchurch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saman","family":"Vaisipour","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sean","family":"Watford","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barbara","family":"Wold","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhenyu","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,3,10]]},"reference":[{"key":"2023040719575036700_","author":"Birney","year":"2017"},{"key":"2023040719575036700_","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1016\/j.cels.2016.10.019","article-title":"The International Human Epigenome Consortium data portal","volume":"3","author":"Bujold","year":"2016","journal-title":"Cell Syst"},{"key":"2023040719575036700_","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/s13073-017-0467-4","article-title":"A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications","volume":"9","author":"Haque","year":"2017","journal-title":"Genome Med"},{"key":"2023040719575036700_","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nmeth.1226","article-title":"Mapping and quantifying mammalian transcriptomes by RNA-Seq","volume":"5","author":"Mortazavi","year":"2008","journal-title":"Nat Methods"},{"key":"2023040719575036700_","doi-asserted-by":"crossref","first-page":"100029","DOI":"10.1016\/j.xgen.2021.100029","article-title":"GA4GH: International policies and standards for data sharing across genomic research and healthcare","volume":"1","author":"Rehm","year":"2021","journal-title":"Cell Genomics"},{"key":"2023040719575036700_","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s13059-017-1382-0","article-title":"SCANPY: Large-scale single-cell gene expression data analysis","volume":"19","author":"Wolf","year":"2018","journal-title":"Genome Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad126\/49501924\/btad126.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/4\/btad126\/49798692\/btad126.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/4\/btad126\/49798692\/btad126.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,8]],"date-time":"2023-12-08T16:38:22Z","timestamp":1702053502000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad126\/7075541"}},"subtitle":[],"editor":[{"given":"Valentina","family":"Boeva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,3,10]]},"references-count":6,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2023,4,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad126","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,4,1]]},"published":{"date-parts":[[2023,3,10]]},"article-number":"btad126"}}