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Record W3213819329 · doi:10.1016/j.xgen.2021.100029

GA4GH: International policies and standards for data sharing across genomic research and healthcare

2021· article· en· W3213819329 on OpenAlexafffund
Heidi L. Rehm, Angela Page, Lindsay Smith, Jeremy Adams, Gil Alterovitz, Lawrence Babb, Maxmillian P. Barkley, Michael Baudis, Michael J. S. Beauvais, Tim Beck, J. Beckmann, Sergi Beltrán, David L. Bernick, Alexander Bernier, James Bonfield, Tiffany Boughtwood, Guillaume Bourque, Sarion R. Bowers, Anthony J. Brookes, Michael Brudno, Matthew Brush, David Bujold, Tony Burdett, Orion J. Buske, Moran N. Cabili, Daniel Cameron, Robert J. Carroll, Esmeralda Casas-Silva, Debyani Chakravarty, Bimal P. Chaudhari, Shu Hui Chen, J. Michael Cherry, Justina Chung, Melissa Cline, Hayley Clissold, Robert Cook‐Deegan, Mélanie Courtot, Fiona Cunningham, Miro Cupak, Robert M. Davies, Danielle Denisko, Megan Doerr, Lena Dolman, Edward S. Dove, Lewis Jonathan Dursi, Stephanie O. M. Dyke, James A. Eddy, Karen Eilbeck, Kyle Ellrott, Susan Fairley, Khalid A. Fakhro, Helen V. Firth, Michael Fitzsimons, Marc Fiume, Paul Flicek, Ian Fore, Mallory Freeberg, Robert R. Freimuth, Lauren A. Fromont, Jonathan Fuerth, Clara Gaff, Weiniu Gan, Elena M. Ghanaim, David Glazer, Robert C. Green, Malachi Griffith, Obi L. Griffith, Robert L. Grossman, Tudor Groza, Jaime M. Guidry Auvil, Roderic Guigó, Dipayan Gupta, Melissa Haendel, Ada Hamosh, David Hansen, Reece K. Hart, Dean M. Hartley, David Haussler, Rachele Hendricks‐Sturrup, Calvin Wai-Loon Ho, Ashley E. Hobb, Michael M. Hoffman, Oliver Hofmann, Petr Holub, Jacob Shujui Hsu, Jean‐Pierre Hubaux, Sarah Hunt, Ammar Husami, Julius O.B. Jacobsen, Saumya S. Jamuar, Elizabeth Janes, Francis Jeanson, Aina Jené, Amber L. Johns, Yann Joly, Steven J.M. Jones, Alexander Kanitz, Yoshihiro Kato, Thomas Keane, Kristina Kekesi-Lafrance, Jerome Kelleher, Giselle Kerry, Seik‐Soon Khor, Bartha Maria Knoppers, Melissa Konopko, Kenjiro Kosaki, Martin Kuba, Jonathan Lawson, Rasko Leinonen, Stephanie Li, Michael Lin, Mikael Lindén, Xianglin Liu, Isuru Liyanage, Javier Ferreiros, Anneke Lucassen, Michael Lukowski, Alice Mann, John Marshall, Michele Mattioni, Alejandro Metke‐Jimenez, Anna Middleton, Richard Milne, Fruzsina Molnár‐Gábor, Nicola Mulder, Mónica Muñoz-Torres, Rishi Nag, Hidewaki Nakagawa, Jamal Nasir, Arcadi Navarro, Tristan Nelson, Ania Niewielska, Amy Nisselle, Jeffrey Niu, Tommi Nyrönen, Brian D. O’Connor, Sabine Oesterle, Soichi Ogishima, Vivian Ota Wang, Laura A.D. Paglione, Emilio Palumbo, Helen Parkinson, Anthony Philippakis, Angel Pizarro, Andreas Prlić, Jordi Rambla, Augusto Rendon, Renee Rider, Peter N. Robinson, Kurt W. Rodarmer, Laura Lyman Rodriguez, Alan F. Rubin, Manuel Rueda, Gregory A. Rushton, Rosalyn Ryan, Gary Saunders, Helen Schuilenburg, Torsten Schwede, Serena Scollen, Alexander Senf, Nathan C. Sheffield, Neerjah Skantharajah, Albert V. Smith, Heidi J. Sofia, Dylan Spalding, Amanda B. Spurdle, Zornitza Stark, Lincoln Stein, Makoto Suematsu, Patrick Tan, Jonathan Tedds, Alastair Thomson, Adrian Thorogood, Timothy L. Tickle, Katsushi Tokunaga, Juha Törnroos, David Torrents, Sean Upchurch, Alfonso Valencia, Roman Valls Guimerà, Jessica Vamathevan, S.D. Varma, Danya F. Vears, Coby Viner, Craig Voisin, Alex H. Wagner, Susan Wallace, Brian Walsh, Marc S. Williams, Eva C. Winkler, B Wold, Grant M. Wood, Jessica Woolley, Chisato Yamasaki, Andrew Yates, Christina K. Yung, Lyndon Zass, Ksenia Zaytseva, Junjun Zhang, Peter Goodhand, Kathryn N. North, Ewan Birney

Bibliographic record

VenueCell Genomics · 2021
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicCancer Genomics and Diagnostics
Canadian institutionsIndoc ResearchGoogle (Canada)Vector InstituteUniversity of TorontoUniversity Health NetworkMcGill UniversityOntario Institute for Cancer ResearchCanada's Michael Smith Genome Sciences CentreUniversity of WaterlooGenome CanadaOntario Genomics
FundersInstitute of GeneticsU.S. National Library of MedicineNational Cancer InstituteNational Human Genome Research InstituteNational Heart, Lung, and Blood InstituteHorizon 2020Instituto de Salud Carlos IIIMedical Research CouncilNatural Sciences and Engineering Research Council of CanadaCanadian Institutes of Health ResearchNational Health and Medical Research CouncilResearch Institute, Nationwide Children's HospitalCompute CanadaInnovative Medicines InitiativeNovo Nordisk FondenTerry Fox Research InstituteBayer FundEidgenössische Technische Hochschule ZürichAcademy of FinlandGovernment of OntarioNational Taiwan UniversityInstitut National de la Santé et de la Recherche MédicaleMicrosoftNational University of SingaporeInstitute for Research in BiomedicineGovernment of CanadaAdditional VenturesNational Center for Advancing Translational SciencesSeventh Framework ProgrammeSwiss Institute of BioinformaticsInvitaeInternational Business Machines CorporationCanada Research ChairsCotton Research and Development CorporationVirginia Marine Resources CommissionGoogleEOSC-LifeChan Zuckerberg InitiativeWellcome TrustRobertson FoundationNovo NordiskGenome CanadaEuropean Molecular Biology LaboratoryCanarieBroad InstituteState Government of VictoriaCenter for Individualized Medicine, Mayo ClinicDeutsche ForschungsgemeinschaftJapan Agency for Medical Research and DevelopmentNovartisAgency for Science, Technology and ResearchAmazon Web ServicesHoward Hughes Medical InstituteNational Institute on Handicapped ResearchFoundation MedicineMayo ClinicVanderbilt UniversityIntel CorporationStaatssekretariat für Bildung, Forschung und Innovation“la Caixa” FoundationNational Institutes of HealthVanderbilt-Ingram Cancer CenterNational Institute of General Medical SciencesOntario Genomics InstituteCanada Foundation for InnovationNationwide Children's Hospital
KeywordsInteroperabilityData sharingSuiteData scienceHealth careGenomicsBig dataKey (lock)AllianceKnowledge managementComputer scienceBusinessGenomeWorld Wide WebPolitical scienceMedicineComputer securityBiologyData mining

Abstract

fetched live from OpenAlex

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

How this classification was reachedexpand

Full frame machine prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.

metaresearch head score (Codex)0.178
metaresearch head score (Gemma)0.225
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesScholarly communication, Open science
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: none
GenreCandidate signal: Methods · Consensus signal: Methods
Teacher disagreement score0.988
Threshold uncertainty score0.942

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.1780.225
Meta-epidemiology (narrow)0.0020.002
Meta-epidemiology (broad)0.0020.003
Bibliometrics0.0090.015
Science and technology studies0.0050.010
Scholarly communication0.0220.022
Open science0.0120.022
Research integrity0.0150.015
Insufficient payload (model declined to judge)0.0080.011

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.100
GPT teacher head0.420
Teacher spread0.319 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.

Study designNot applicable
Domainnot available
GenreMethods

How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".

Quick stats

Citations294
Published2021
Admission routes2
Has abstractyes

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