{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T14:34:17Z","timestamp":1782830057506,"version":"3.54.5"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2020,7,7]],"date-time":"2020-07-07T00:00:00Z","timestamp":1594080000000},"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\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["693174"],"award-info":[{"award-number":["693174"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Data-Driven Genomic Computing"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>With the spreading of biological and clinical uses of next-generation sequencing (NGS) data, many laboratories and health organizations are facing the need of sharing NGS data resources and easily accessing and processing comprehensively shared genomic data; in most cases, primary and secondary data management of NGS data is done at sequencing stations, and sharing applies to processed data. Based on the previous single-instance GMQL system architecture, here we review the model, language and architectural extensions that make the GMQL centralized system innovatively open to federated computing.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>A well-designed extension of a centralized system architecture to support federated data sharing and query processing. Data is federated thanks to simple data sharing instructions. Queries are assigned to execution nodes; they are translated into an intermediate representation, whose computation drives data and processing distributions. The approach allows writing federated applications according to classical styles: centralized, distributed or externalized.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability<\/jats:title>\n                  <jats:p>The federated genomic data management system is freely available for non-commercial use as an open source project at http:\/\/www.bioinformatics.deib.polimi.it\/FederatedGMQLsystem\/<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Contact<\/jats:title>\n                  <jats:p>{arif.canakoglu, pietro.pinoli}@polimi.it<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n               <\/jats:sec>","DOI":"10.1093\/bib\/bbaa091","type":"journal-article","created":{"date-parts":[[2020,4,29]],"date-time":"2020-04-29T19:17:43Z","timestamp":1588187863000},"source":"Crossref","is-referenced-by-count":8,"title":["Federated sharing and processing of genomic datasets for tertiary data analysis"],"prefix":"10.1093","volume":"22","author":[{"given":"Arif","family":"Canakoglu","sequence":"first","affiliation":[{"name":"Politecnico di Milano"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pietro","family":"Pinoli","sequence":"additional","affiliation":[{"name":"Computational Biology at Politecnico di Milano"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Gulino","sequence":"additional","affiliation":[{"name":"Computer Science and Engineering at Politecnico di Milano"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luca","family":"Nanni","sequence":"additional","affiliation":[{"name":"Computer Science and Engineering at Politecnico di Milano"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Masseroli","sequence":"additional","affiliation":[{"name":"Politecnico di Milano"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefano","family":"Ceri","sequence":"additional","affiliation":[{"name":"Politecnico di Milano"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,7,7]]},"reference":[{"key":"2021052109495295300_ref1","author":"Beacon Network"},{"key":"2021052109495295300_ref2","author":"AllOfUs"},{"key":"2021052109495295300_ref3","author":"CanDIG"},{"key":"2021052109495295300_ref4","author":"Docker"},{"key":"2021052109495295300_ref5","author":"FinnGen"},{"key":"2021052109495295300_ref6","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/j.jbi.2015.05.022","article-title":"Privacy preserving processing of genomic data: a survey","volume":"56","author":"Mete Akg\u00fcn","year":"2015","journal-title":"J Biomed Inform"},{"key":"2021052109495295300_ref7","first-page":"1","volume-title":"11th Int. 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