Overture: an open-source genomics data platform

doi:10.1093/gigascience/giaf038

2025-04-24

Hardeep K. Nahal-Bose

Aleksandra Pejovic

Samantha Rich

Leonardo Landa Rivera

DOI：10.1093/gigascience/giaf038

原文链接

原文求助

摘要

En 中文

背景下一代测序技术为组织和分发基因组学数据集带来了许多新的技术挑战，这些数据集如今可以常规达到拍字节规模。结合数据密集型人工智能和机器学习应用，可发现、可访问、可互操作和可重用的基因组学数据集的价值前所未有。虽然像Genomics Data Commons、Sequence Reads Archive和European Genome-Phenome Archive等主要档案库提高了研究人员共享和重用数据的能力，而像Zenodo和Figshare这类通用存储库为研究数据发布提供了有价值的平台，但基因组学研究的多样性排除了“一刀切”的方法。在许多情况下，需要定制解决方案，尽管资助机构和期刊越来越强制要求可重用数据实践，研究人员仍缺乏满足数据重用多样化挑战所需的技术支持。成果 Overture通过提供用于构建和部署可定制基因组学数据平台的开源软件填补了这一空白。其架构由模块化微服务组成，每个微服务均具有狭隘的通用职责，这些职责共同组合形成完整的数据管理系统。这些系统使研究人员能够在任何规模上组织、共享和探索他们的基因组学数据。通过Overture，研究人员可以将他们的数据连接到人类和机器，促进可重复性，并通过受控的数据共享和重用来实现新的见解。结论通过免费提供这些工具，我们可以加速研究界可靠基因组数据管理的发展，使其快速、灵活且多尺度化。Overture是一个开源项目，采用AGPLv3.0许可证，所有源代码可从https://github.com/overture-stack公开获取，开发、部署和使用文档可从www.overture.bio获取。

Keyword:

research software

data management

genomics

open-source

open-science

期刊

GigaScience

IF:

3.9

论文数:

1.6K

被引数:

1.2W

机构

Univ Montreal

学者数:

1.5K

论文数: 881

被引数: 282

ontario inst canc res oicr

学者数:

论文数: 2

被引数: 0

Univ Toronto

学者数:

5.3K

论文数: 3.7K

被引数: 1.2K

查看更多机构

引用论文

A pan-African pathogen genomics data sharing platform to support disease outbreaks

NATURE MEDICINE

IF50

2023-05-09

OAAI

Christoffels, Alan; Mboowa, Gerald; van Heusden, Peter; Makhubela, Sello; Githinji, George; Mwangi, Sarah; Onywera, Harris; Nnaemeka, Ndodo; Amoako, Daniel Gyamfi; Olawoye, Idowu; Diallo, Amadou; Mbala-Kingebeni, Placide; Oyola, Samuel O.; Adu, Bright; Mvelase, Christopher; Ondoa, Pascale; Dratibi, Fred Athanasius; Sow, Abdourahmane; Gumede, Nicksy; Tessema, Sofonias K.; Ouma, Ahmed Ogwell; Tebeje, Yenew Kebede

The International Cancer Genome Consortium Data Portal 国际癌症基因组联盟数据门户

NATURE BIOTECHNOLOGY

IF41.7

2019-03-15

338

PREAI

Zhang, Junjun; Bajari, Rosita; Andric, Dusan; Gerthoffert, Francois; Lepsa, Alexandru; Nahal-Bose, Hardeep; Stein, Lincoln D.; Ferretti, Vincent

Big Data: Astronomical or Genomical?大数据: 天文还是基因组？

PLOS Biology

IF0

2015-07-07

OAAI

Zachary D. Stephens; Skylar Y. Lee; Faraz Faghri; Roy H. Campbell; Chengxiang Zhai; Miles J. Efron; Ravishankar Iyer; Michael C. Schatz; Saurabh Sinha; Gene E. Robinson

The views, perspectives, and experiences of academic researchers with data sharing and reuse: A meta-synthesis

PLOS ONE

IF0

2020-02-27

OAAI

Laure Perrier; Erik Blondal; Heather MacDonald

Multi-omics Data Integration, Interpretation, and Its Application 多组学数据整合、解释及其应用

Bioinformatics and Biology Insights

IF0

2020-01-31

OAAI

Indhupriya Subramanian; Srikant Verma; Shiva Kumar; Abhay Jere; Krishanpal Anamika

Practical guide for managing large-scale human genome data in research

Journal of Human Genetics

IF0

2020-10-23

OAAI

Tomoya Tanjo; Yosuke Kawai; Katsushi Tokunaga; Osamu Ogasawara; Masao Nagasaki

GA4GH: International policies and standards for data sharing across genomic research and healthcare GA4GH: 跨基因组研究和医疗保健的数据共享的国际政策和标准

CELL GENOMICS

IF9

2021-11-01

OAAI

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

The EU General Data Protection Regulation (GDPR)

IF0

2020-02-13

OAAI

Best practices for genetic and genomic data archiving

NATURE ECOLOGY & EVOLUTION

IF14.5

2024-05-24

PREAI

Leigh, Deborah M.; Vandergast, Amy G.; Hunter, Margaret E.; Crandall, Eric D.; Funk, W. Chris; Garroway, Colin J.; Hoban, Sean; Oyler-McCance, Sara J.; Rellstab, Christian; Segelbacher, Gernot; Schmidt, Chloe; Vazquez-Dominguez, Ella; Paz-Vinas, Ivan

TIGER: The gene expression regulatory variation landscape of human pancreatic islets 老虎: 人类胰岛的基因表达调控变异景观

CELL REPORTS

IF6.9

2021-10-01

OAAI

Alonso, Lorena; Piron, Anthony; Moran, Ignasi; Guindo-Martinez, Marta; Bonas-Guarch, Silvia; Atla, Goutham; Miguel-Escalada, Irene; Royo, Romina; Puiggros, Montserrat; Garcia-Hurtado, Xavier; Suleiman, Mara; Marselli, Lorella; Esguerra, Jonathan L. S.; Turatsinze, Jean-Valery; Torres, Jason M.; Nylander, Vibe; Chen, Ji; Eliasson, Lena; Defrance, Matthieu; Amela, Ramon; Mulder, Hindrik; Gloyn, Anna L.; Groop, Leif; Marchetti, Piero; Eizirik, Decio L.; Ferrer, Jorge; Mercader, Josep M.; Cnop, Miriam; Torrents, David

查看更多内容