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

View ORCID ProfileJames A. Fellows Yates, View ORCID ProfileAida Andrades Valtueña, View ORCID ProfileAshild J. Vågene, View ORCID ProfileBecky Cribdon, View ORCID ProfileIrina M. Velsko, View ORCID ProfileMaxime Borry, View ORCID ProfileMiriam J. Bravo-López, View ORCID ProfileAntonio Fernandez-Guerra, View ORCID ProfileEleanor J. Green, View ORCID ProfileShreya L. Ramachandran, View ORCID ProfilePeter D. Heintzman, View ORCID ProfileMaria A. Spyrou, View ORCID ProfileAlexander Hübner, Abigail S. Gancz, View ORCID ProfileJessica Hider, Aurora F. Allshouse, View ORCID ProfileChristina Warinner
doi: https://doi.org/10.1101/2020.09.02.279570
James A. Fellows Yates
1Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany
2Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig Maximilian University, München, 80539, Germany
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  • ORCID record for James A. Fellows Yates
  • For correspondence: fellows@shh.mpg.de warinner@shh.mpg.de
Aida Andrades Valtueña
1Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany
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Ashild J. Vågene
3Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1350, Denmark
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  • ORCID record for Ashild J. Vågene
Becky Cribdon
4School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
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Irina M. Velsko
1Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany
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Maxime Borry
1Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany
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Miriam J. Bravo-López
5International Laboratory for Human Genome Research, National Autonomous University of Mexico, Queretaro, 76230, Mexico
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Antonio Fernandez-Guerra
6Section for GeoGenetics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1350, Denmark
7Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
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Eleanor J. Green
8BioArCh, Department of Archaeology, University of York, York, YO10 5DD, United Kingdom
9Department of Earth Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
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Shreya L. Ramachandran
10Human Genetics, University of Chicago, Chicago IL, 60637, USA
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Peter D. Heintzman
11The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, 9037, Norway
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Maria A. Spyrou
1Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany
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Alexander Hübner
1Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany
12Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
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Abigail S. Gancz
13Department of Anthropology, Pennsylvania State University, Pennsylvania PA, 16802, USA
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Jessica Hider
14Department of Anthropology, McMaster University, Hamilton, L8S4L9, Canada
15McMaster Ancient DNA Centre, McMaster University, Hamilton, L8S4L10, Canada
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Aurora F. Allshouse
16Department of Anthropology, Harvard University, Cambridge MA, 02138, USA
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Christina Warinner
1Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany
16Department of Anthropology, Harvard University, Cambridge MA, 02138, USA
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  • ORCID record for Christina Warinner
  • For correspondence: fellows@shh.mpg.de warinner@shh.mpg.de
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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 microbial taxa, microbial communities, and metagenomic assemblages. AncientMetagenomeDir (archived at https://doi.org/10.5281/zenodo.3980833) is a collection of indices of published genetic data deriving from ancient microbial samples that provides basic, standardised metadata and accession numbers to allow rapid data retrieval from online repositories. These collections are community-curated and span multiple sub-disciplines in order to ensure adequate breadth and consensus in metadata definitions, as well as longevity of the database. Internal guidelines and automated checks to facilitate compatibility with established sequence-read archives and term-ontologies ensure consistency and interoperability for future meta-analyses. This collection will also assist in standardising metadata reporting for future ancient metagenomic studies.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/SPAAM-workshop/AncientMetagenomeDir/

  • https://doi.org/10.5281/zenodo.4011751

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir
James A. Fellows Yates, Aida Andrades Valtueña, Ashild J. Vågene, Becky Cribdon, Irina M. Velsko, Maxime Borry, Miriam J. Bravo-López, 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, Christina Warinner
bioRxiv 2020.09.02.279570; doi: https://doi.org/10.1101/2020.09.02.279570
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Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir
James A. Fellows Yates, Aida Andrades Valtueña, Ashild J. Vågene, Becky Cribdon, Irina M. Velsko, Maxime Borry, Miriam J. Bravo-López, 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, Christina Warinner
bioRxiv 2020.09.02.279570; doi: https://doi.org/10.1101/2020.09.02.279570

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