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Cited by 99

The DOI matches its Crossref record; 23 of the 23 references it cites were found in a registry or an index.

Standards recommendations for the Earth BioGenome Project

Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark L., Marques Bonet, Tomas, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, Lopez, Jose Victor, Myers, Eugene W., Pettersson, Olga Vinnere, Phillippy, Adam M., Poelchau, Monica F., Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Françoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen·2022·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.2115639118PMC PMC8795494
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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.

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Figures

Fig. 1. An example of the documentation that should occur as a sample is being processed. The SPECIMEN_ID (the Natural History Museum, London [NHMUK] barcode under the fly) is photographed alongside the specimen and the barcoded tubes into which different samples of that specimen will be placed. The metadata tracking sheet would have three entries for this fly, where collection-related information would be identical, but tissue type and tissue size would vary (e.g., head, thorax, and abdomen, each in a separate tube). Image credit: M.K.N.L.
Fig. 1. An example of the documentation that should occur as a sample is being processed. The SPECIMEN_ID (the Natural History Museum, London [NHMUK] barcode under the fly) is photographed alongside the specimen and the barcoded tubes into which different samples of that specimen will be placed. The metadata tracking sheet would have three entries for this fly, where collection-related information would be identical, but tissue type and tissue size would vary (e.g., head, thorax, and abdomen, each in a separate tube). Image credit: M.K.N.L.CC BY-NC-ND · PubMed Central
Fig. 2. Recommended EBP INSDC assembly BioProject submission structure. Alternatives on this theme could include maternal assembly and paternal assembly at the DataBioProject levels, when complete genome assemblies are generated for both haplotypes of a diploid sexually reproducing species. “Your Project” represents a project sequencing multiple genomes, such as the VGP or DToL.
Fig. 2. Recommended EBP INSDC assembly BioProject submission structure. Alternatives on this theme could include maternal assembly and paternal assembly at the DataBioProject levels, when complete genome assemblies are generated for both haplotypes of a diploid sexually reproducing species. “Your Project” represents a project sequencing multiple genomes, such as the VGP or DToL.CC BY-NC-ND · PubMed Central
Fig. 3. Recommended future EBP data service portal. Researchers would easily apply for the hardware resources that are shared by the EBP affiliated project networks.
Fig. 3. Recommended future EBP data service portal. Researchers would easily apply for the hardware resources that are shared by the EBP affiliated project networks.CC BY-NC-ND · PubMed Central

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Research works printed but not linked: 1

  1. F. Shaw , COPO-linked open infrastructure for plant data, in Semantic Web Applications and Tools for Life Science (SWAT4LS, 2015), pp 181–182.

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Metadata

Authors
Lawniczak, M. K. N., Durbin, R., Flicek, P., Lindblad-Toh, K., Wei, X., Archibald, J. M., Baker, W. J., Belov, K., Blaxter, M. L., Marques Bonet, T., Childers, A. K., Coddington, J. A., Crandall, K. A., Crawford, A. J., Davey, R. P., Di Palma, F., Fang, Q., Haerty, W., Hall, N., Hoff, K. J., Howe, K., Jarvis, E. D., Johnson, W. E., Johnson, R. N., Kersey, P. J., Liu, X., Lopez, J. V., Myers, E. W., Pettersson, O. V., Phillippy, A. M., Poelchau, M. F., Pruitt, K. D., Rhie, A., Castilla-Rubio, J. C., Sahu, S. K., Salmon, N. A., Soltis, P. S., Swarbreck, D., Thibaud-Nissen, F., Wang, S., Wegrzyn, J. L., Zhang, G., Zhang, H., Lewin, H. A., & Richards, S.
Affiliations
  • Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
  • Broad Institute of MIT and Harvard, Cambridge, MA 02142
  • China National GeneBank, Shenzhen 518120, China
  • Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
  • Department of Accelerated Taxonomy, Royal Botanic Gardens, Kew, Surrey TW9 3AE, United Kingdom
  • School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, NSW 2006, Australia
  • Institute of Evolutionary Biology, Consejo Superior de Investigaciones Científicas-Universitat Pompeau Fabra, Parc de Rechercha Biomédica Barcelona 08003 Barcelona, Spain
  • Bee Research Laboratory, Beltsville Agricultural Research Center, US Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705
  • Smithsonian Institution, National Museum of Natural History, Washington, DC 20560‐0105
  • Computational Biology Institute and Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052
  • Department of Biological Sciences, Universidad de los Andes 111711 Bogotá, Colombia
  • Engineering Biology, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
  • Genome British Columbia, Vancouver, BC V5Z 0C4, Canada
  • BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
  • Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
  • Institute of Mathematics and Computer Science, Center for Functional Genomics of Microbes, University of Greifswald 17489 Greifswald, Germany
  • Vertebrate Genomes Lab, The Rockefeller University, New York, NY 10065
  • Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630
  • European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, United Kingdom
  • Halmos College of Arts and Sciences, Guy Harvey Oceanographic Center, Nova Southeastern University, Dania Beach, FL 33004
  • Department of Systems Biology, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
  • Science for Life Laboratory in Uppsala, Uppsala University 75123 Uppsala, Sweden
  • Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20894
  • National Agricultural Library, USDA Agricultural Research Service, Beltsville, MD 20705
  • National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894
  • Spacetime Ventures, São Paulo 05449-050, Brazil
  • Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
  • Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269
  • Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen 1165 Copenhagen, Denmark
  • BGI-Qingdao, BGI-Shenzhen 266555 Qingdao, China
  • University of California Davis Genome Center, University of California, Davis, CA 95616
ORCID
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2022-01-18
Volume
119
Issue
4
ISSN
  • 0027-8424
  • 1091-6490
DOI
10.1073/pnas.2115639118
PMC
PMC8795494
Cited by
99
References
23
Language
en
Licence
creativecommons.org/licenses/by-nc-nd/4.0/ (vor, 181 d)
Funders
  • Wellcome (WT108749/Z/15/Z)
  • National Science Foundation (DBI:IIBR:CAREER #1943371)

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