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

MPS-Authors
/persons/resource/persons205371

Fellows Yates,  James A.
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

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Andrades Valtueña,  Aida
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons239673

Velsko,  Irina M.
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons241968

Borry,  Maxime
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons189338

Spyrou,  Maria A.
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons188515

Hübner,  Alexander
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons221103

Warinner,  Christina
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;
Kostbare Kulturen, Max Planck Institute for the Science of Human History, Max Planck Society;

External Ressource

Code for validation of the dataset
(Supplementary material)

R notebooks
(Supplementary material)

Fulltext (public)

shh2777pre.pdf
(Preprint), 2MB

Supplementary Material (public)
There is no public supplementary material available
Citation

Fellows Yates, J. A., Andrades Valtueña, A., Vågene, A. J., Cribdon, B., Velsko, I. M., Borry, M., et al. (2020). Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. bioRxiv, 279570. doi:10.1101/2020.09.02.279570.


Cite as: http://hdl.handle.net/21.11116/0000-0007-7A46-2
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 StatementThe authors have declared no competing interest.