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

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

doi:10.1016/j.xgen.2021.100029

Cited by 125 publications

(116 citation statements)

References 113 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The RO-Crate community is strongly engaged with the European-wide biology/bioinformatics collaborative e-Infrastructure ELIXIR [34], along with European Open Science Cloud 40 (EOSC) projects including EOSC-Life, 41 FAIRplus, 42 CS3MESH4EOSC 43 and BY-COVID. 44 RO-Crate has also es- tablished collaborations with Bioschemas [58], GA4GH [99], OpenAIRE [100] and multiple H2020 projects.…”

Section: Peoplementioning

confidence: 99%

See 1 more Smart Citation

Packaging research artefacts with RO-Crate

Soiland‐Reyes

Sefton

Crosas

et al. 2022

View full text Add to dashboard Cite

An increasing number of researchers support reproducibility by including pointers to and descriptions of datasets, software and methods in their publications. However, scientific articles may be ambiguous, incomplete and difficult to process by automated systems. In this paper we introduce RO-Crate, an open, community-driven, and lightweight approach to packaging research artefacts along with their metadata in a machine readable manner. RO-Crate is based on Schema.org annotations in JSON-LD, aiming to establish best practices to formally describe metadata in an accessible and practical way for their use in a wide variety of situations. An RO-Crate is a structured archive of all the items that contributed to a research outcome, including their identifiers, provenance, relations and annotations. As a general purpose packaging approach for data and their metadata, RO-Crate is used across multiple areas, including bioinformatics, digital humanities and regulatory sciences. By applying “just enough” Linked Data standards, RO-Crate simplifies the process of making research outputs FAIR while also enhancing research reproducibility. An RO-Crate for this article11 https://w3id.org/ro/doi/10.5281/zenodo.5146227 is archived at https://doi.org/10.5281/zenodo.5146227.

show abstract

Section: Peoplementioning

confidence: 99%

“…This work has received funding from the European Commission's Horizon 2020 research and innovation programme for projects BioExcel-2 99 Ana Trisovic is funded by the Alfred P. Sloan Foundation (grant number P-2020-13988). 106 Harvard Data Commons is supported by an award from Harvard University Information Technology (HUIT).…”

Section: Acknowledgementsmentioning

confidence: 99%

Packaging research artefacts with RO-Crate

Soiland‐Reyes

Sefton

Crosas

et al. 2022

View full text Add to dashboard Cite

show abstract

“…These national initiatives will generate genomic datasets for tens of millions of individual people as part of routine healthcare. 1 Connecting this wealth of data internationally offers great potential to advance our understanding of and our ability to address disease. Genomic and health-related data are sensitive, however, implicating the privacy of sequenced individuals and their families and typically attracting legal restrictions on disclosure and potentially also international transfer.…”

Section: Introductionmentioning

confidence: 99%

“…The Global Alliance for Genomics and Health (GA4GH) is a standards-setting body established to promote the international sharing of genomic and health-related data. 1 It supports diverse models for sharing genomic and health-related data with authorized users while also protecting competing interests. These models span central databases to networks of distributed databases connected by common infrastructure.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

International federation of genomic medicine databases using GA4GH standards

et al. 2021

Self Cite

View full text Add to dashboard Cite

We promote a shared vision and guide for how and when to federate genomic and health-related data sharing, enabling connections and insights across independent, secure databases. The GA4GH encourages a federated approach wherein data providers have the mandate and resources to share, but where data cannot move for legal or technical reasons. We recommend a federated approach to connect national genomics initiatives into a global network and precision medicine resource.

show abstract