{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,18]],"date-time":"2025-12-18T14:28:55Z","timestamp":1766068135709,"version":"3.41.2"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:00:00Z","timestamp":1740182400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000943","name":"CSIRO","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000943","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Enabling clinicians and researchers to directly interact with global genomic data resources by removing technological barriers is vital for medical genomics. AskBeacon enables large language models (LLMs) to be applied to securely shared cohorts via the Global Alliance for Genomics and Health Beacon protocol. By simply \u201casking\u201d Beacon, actionable insights can be gained, analyzed, and made publication-ready.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In the Parkinson's Progression Markers Initiative (PPMI), we use natural language to ask whether the sex-differences observed in Parkinson's disease are due to X-linked or autosomal markers. AskBeacon returns a publication-ready visualization showing that for PPMI the autosomal marker occurred 1.4 times more often in males with Parkinson\u2019s disease than females, compared to no differences for the X-linked marker. We evaluate commercial and open-weight LLM models, as well as different architectures to identify the best strategy for translating research questions to Beacon queries. AskBeacon implements extensive safety guardrails to ensure that genomic data is not exposed to the LLM directly, and that generated code for data extraction, analysis and visualization process is sanitized and hallucination resistant, so data cannot be leaked or falsified.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>AskBeacon is available at https:\/\/github.com\/aehrc\/AskBeacon.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf079","type":"journal-article","created":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T15:14:31Z","timestamp":1740237271000},"source":"Crossref","is-referenced-by-count":1,"title":["AskBeacon\u2014performing genomic data exchange and analytics with natural language"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4160-5965","authenticated-orcid":false,"given":"Anuradha","family":"Wickramarachchi","sequence":"first","affiliation":[{"name":"Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation , Adelaide, SA 5000,","place":["Australia"]}]},{"given":"Shakila","family":"Tonni","sequence":"additional","affiliation":[{"name":"Data61, Commonwealth Scientific and Industrial Research Organisation , Sydney, NSW 2015,","place":["Australia"]}]},{"given":"Sonali","family":"Majumdar","sequence":"additional","affiliation":[{"name":"Data61, Commonwealth Scientific and Industrial Research Organisation , Sydney, NSW 2015,","place":["Australia"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4927-3937","authenticated-orcid":false,"given":"Sarvnaz","family":"Karimi","sequence":"additional","affiliation":[{"name":"Data61, Commonwealth Scientific and Industrial Research Organisation , Sydney, NSW 2015,","place":["Australia"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6087-6643","authenticated-orcid":false,"given":"Sulev","family":"K\u00f5ks","sequence":"additional","affiliation":[{"name":"Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University , Perth, WA 6150,","place":["Australia"]},{"name":"Perron Institute for Neurological and Translational Science , Perth, WA 6009,","place":["Australia"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4018-2489","authenticated-orcid":false,"given":"Brendan","family":"Hosking","sequence":"additional","affiliation":[{"name":"Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation , Sydney, NSW 2145,","place":["Australia"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9091-257X","authenticated-orcid":false,"given":"Jordi","family":"Rambla","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology , Barcelona, Ciutat Vella 08003,","place":["Spain"]},{"name":"Department of Medicine and Life Sciences, Universitat Pompeu Fabra, PRBB , Barcelona 08003,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2051-8275","authenticated-orcid":false,"given":"Natalie A","family":"Twine","sequence":"additional","affiliation":[{"name":"Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation , Sydney, NSW 2145,","place":["Australia"]},{"name":"Faculty of Science and Engineering, Applied BioSciences, Macquarie University , Macquarie Park, NSW 2109,","place":["Australia"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0556-6586","authenticated-orcid":false,"given":"Yatish","family":"Jain","sequence":"additional","affiliation":[{"name":"Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation , Sydney, NSW 2145,","place":["Australia"]},{"name":"Faculty of Science and Engineering, Applied BioSciences, Macquarie University , Macquarie Park, NSW 2109,","place":["Australia"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8033-9810","authenticated-orcid":false,"given":"Denis C","family":"Bauer","sequence":"additional","affiliation":[{"name":"Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation , Adelaide, SA 5000,","place":["Australia"]},{"name":"Faculty of Science and Engineering, Applied BioSciences, Macquarie University , Macquarie Park, NSW 2109,","place":["Australia"]},{"name":"Department of Biomedical Informatics and Digital Health, School of Medical Sciences, University of Sydney , Sydney, NSW 2006,","place":["Australia"]}]}],"member":"286","published-online":{"date-parts":[[2025,2,22]]},"reference":[{"year":"2023","author":"Achiam","key":"2025030810265636000_btaf079-B1"},{"key":"2025030810265636000_btaf079-B2","doi-asserted-by":"publisher","first-page":"123091","DOI":"10.1016\/j.jns.2024.123091","article-title":"Unraveling 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