Standards recommendations for the Earth BioGenome Project-Reference-Cited by-同舟云学术

Standards recommendations for the Earth BioGenome Project

Published:2022-01-18 Issue:4 Volume:119 Page:
ISSN:0027-8424
Container-title:Proceedings of the National Academy of Sciences
language:en
Short-container-title:Proc. Natl. Acad. Sci. U.S.A.

Author:

Lawniczak Mara K. N.¹,Durbin Richard¹²,Flicek Paul¹³,Lindblad-Toh Kerstin⁴⁵^ORCID,Wei Xiaofeng⁶,Archibald John M.⁷^ORCID,Baker William J.⁸^ORCID,Belov Katherine⁹,Blaxter Mark L.¹,Marques Bonet Tomas¹⁰¹¹¹²¹³^ORCID,Childers Anna K.¹⁴^ORCID,Coddington Jonathan A.¹⁵^ORCID,Crandall Keith A.¹⁶^ORCID,Crawford Andrew J.¹⁷,Davey Robert P.¹⁸,Di Palma Federica¹⁹,Fang Qi²⁰^ORCID,Haerty Wilfried²¹,Hall Neil¹⁹²¹^ORCID,Hoff Katharina J.²²^ORCID,Howe Kerstin¹^ORCID,Jarvis Erich D.²³²⁴,Johnson Warren E.²⁵²⁶,Johnson Rebecca N.¹⁵^ORCID,Kersey Paul J.²⁷^ORCID,Liu Xin⁶,Lopez Jose Victor²⁸^ORCID,Myers Eugene W.²⁹^ORCID,Pettersson Olga Vinnere³⁰^ORCID,Phillippy Adam M.³¹^ORCID,Poelchau Monica F.³²^ORCID,Pruitt Kim D.³³,Rhie Arang³¹^ORCID,Castilla-Rubio Juan Carlos³⁴,Sahu Sunil Kumar⁶²⁰^ORCID,Salmon Nicholas A.¹,Soltis Pamela S.³⁵^ORCID,Swarbreck David²¹^ORCID,Thibaud-Nissen Françoise³³,Wang Sibo⁶,Wegrzyn Jill L.³⁶³⁷^ORCID,Zhang Guojie³⁸³⁹⁴⁰⁴¹^ORCID,Zhang He⁴²,Lewin Harris A.⁴³⁴⁴^ORCID,Richards Stephen⁴³^ORCID

Affiliation:

1. Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom

2. Department of Genetics, University of Cambridge, Cambridge CB3 0DH, United Kingdom

3. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom

4. Broad Institute of MIT and Harvard, Cambridge, MA 02142

5. Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University 751 23 Uppsala, Sweden

6. China National GeneBank, Shenzhen 518120, China

7. Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada

8. Department of Accelerated Taxonomy, Royal Botanic Gardens, Kew, Surrey TW9 3AE, United Kingdom

9. School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, NSW 2006, Australia

10. Institute of Evolutionary Biology, Consejo Superior de Investigaciones Científicas-Universitat Pompeau Fabra, Parc de Rechercha Biomédica Barcelona 08003 Barcelona, Spain

11. Catalan Institution of Research and Advanced Studies 08010 Barcelona, Spain

12. Centre Nacional d’Anàlisi Geonòmica - Centre for Genomic Regulation, Barcelona Institute of Science and Technology 08028 Barcelona, Spain

13. Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona 08193 Barcelona, Spain

14. Bee Research Laboratory, Beltsville Agricultural Research Center, US Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705

15. Smithsonian Institution, National Museum of Natural History, Washington, DC 20560‐0105

16. Computational Biology Institute and Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052

17. Department of Biological Sciences, Universidad de los Andes 111711 Bogotá, Colombia

18. Engineering Biology, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom

19. Genome British Columbia, Vancouver, BC V5Z 0C4, Canada

20. BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China

21. Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom

22. Institute of Mathematics and Computer Science, Center for Functional Genomics of Microbes, University of Greifswald 17489 Greifswald, Germany

23. Vertebrate Genomes Lab, The Rockefeller University, New York, NY 10065

24. HHMI, Chevy Chase, MD 20815

25. Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630

26. The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD 20746-2863

27. European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, United Kingdom

28. Halmos College of Arts and Sciences, Guy Harvey Oceanographic Center, Nova Southeastern University, Dania Beach, FL 33004

29. Department of Systems Biology, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany

30. Science for Life Laboratory in Uppsala, Uppsala University 75123 Uppsala, Sweden

31. Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20894

32. National Agricultural Library, USDA Agricultural Research Service, Beltsville, MD 20705

33. National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894

34. Spacetime Ventures, São Paulo 05449-050, Brazil

35. Florida Museum of Natural History, University of Florida, Gainesville, FL 32611

36. Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269

37. Institute for Systems Genomics, Computational Biology Core, University of Connecticut, Storrs, CT 06269

38. Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen 1165 Copenhagen, Denmark

39. China National Genebank, BGI-Shenzhen 518083 Shenzhen, China

40. State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences 650223 Kunming, China

41. Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences 650223 Kunming, China

42. BGI-Qingdao, BGI-Shenzhen 266555 Qingdao, China

43. University of California Davis Genome Center, University of California, Davis, CA 95616

44. Department of Evolution and Ecology, University of California, Davis, CA 95616

Abstract

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Funder

Wellcome

National Science Foundation

Publisher

Proceedings of the National Academy of Sciences

Subject

Multidisciplinary

Link

https://pnas.org/doi/pdf/10.1073/pnas.2115639118

Reference23 articles.

1. The Earth BioGenome Project 2020: Starting the clock

2. Earth BioGenome Project: Sequencing life for the future of life