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Fellows Yates JA, Andrades Valtueña A, Vågene ÅJ, et al. Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Sci Data. 2021;8(1):31doi: 10.1038/s41597-021-00816-y.
Fellows Yates, J. A., Andrades Valtueña, A., Vågene, �. �. J., Cribdon, B., Velsko, I. M., Borry, M., Bravo-Lopez, M. J., Fernandez-Guerra, A., Green, E. J., Ramachandran, S. L., Heintzman, P. D., Spyrou, M. A., Hübner, A., Gancz, A. S., Hider, J., Allshouse, A. F., Zaro, V., & Warinner, C. (2021). Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Scientific data, 8(1), 31. https://doi.org/10.1038/s41597-021-00816-y
Fellows Yates, James A, et al. "Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir." Scientific data vol. 8,1 (2021): 31. doi: https://doi.org/10.1038/s41597-021-00816-y
Fellows Yates JA, Andrades Valtueña A, Vågene ÅJ, Cribdon B, Velsko IM, Borry M, Bravo-Lopez MJ, Fernandez-Guerra A, Green EJ, Ramachandran SL, Heintzman PD, Spyrou MA, Hübner A, Gancz AS, Hider J, Allshouse AF, Zaro V, Warinner C. Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Sci Data. 2021 Jan 26;8(1):31. doi: 10.1038/s41597-021-00816-y. PMID: 33500403; PMCID: PMC7838265.
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Sci Data. 2021 Jan 26;8(1):31. doi: 10.1038/s41597-021-00816-y.

Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir.

Scientific data

James A Fellows Yates, Aida Andrades Valtueña, Åshild J Vågene, Becky Cribdon, Irina M Velsko, Maxime Borry, Miriam J Bravo-Lopez, Antonio Fernandez-Guerra, Eleanor J Green, Shreya L Ramachandran, Peter D Heintzman, Maria A Spyrou, Alexander Hübner, Abigail S Gancz, Jessica Hider, Aurora F Allshouse, Valentina Zaro, Christina Warinner

Affiliations

  1. Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany. [email protected].
  2. Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, München, 80539, Germany. [email protected].
  3. Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany.
  4. Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1350, Denmark.
  5. School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom.
  6. International Laboratory for Human Genome Research, National Autonomous University of Mexico, Queretaro, 76230, Mexico.
  7. Section for GeoGenetics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1350, Denmark.
  8. Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany.
  9. BioArCh, Department of Archaeology, University of York, York, YO10 5DD, United Kingdom.
  10. Department of Earth Sciences, Natural History Museum, London, SW7 5BD, United Kingdom.
  11. Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
  12. The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, 9037, Norway.
  13. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany.
  14. Department of Anthropology, Pennsylvania State University, Pennsylvania, PA, 16802, USA.
  15. Department of Anthropology, McMaster University, Hamilton, L8S4L9, Canada.
  16. McMaster Ancient DNA Centre, McMaster University, Hamilton, L8S4L10, Canada.
  17. Department of Anthropology, Harvard University, Cambridge, MA, 02138, USA.
  18. Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA, 02138, USA.
  19. Department of Biology, Università degli Studi di Firenze, Florence, 50122, Italy.
  20. Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany. [email protected].
  21. Department of Anthropology, Harvard University, Cambridge, MA, 02138, USA. [email protected].

PMID: 33500403 PMCID: PMC7838265 DOI: 10.1038/s41597-021-00816-y

Abstract

Ancient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is particularly important for large-scale ecological and evolutionary studies of individual taxa and communities of both microbes and eukaryotes. AncientMetagenomeDir (archived at https://doi.org/10.5281/zenodo.3980833 ) is a collection of annotated metagenomic sample lists derived from published studies that provide basic, standardised metadata and accession numbers to allow rapid data retrieval from online repositories. These tables are community-curated and span multiple sub-disciplines to ensure adequate breadth and consensus in metadata definitions, as well as longevity of the database. Internal guidelines and automated checks facilitate compatibility with established sequence-read archives and term-ontologies, and ensure consistency and interoperability for future meta-analyses. This collection will also assist in standardising metadata reporting for future ancient metagenomic studies.

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