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

Fellows Yates, J. A., Andrades Valtueña, A., Vågene, A. J., Cribdon, B., Velsko, I. M., Borry, M., et al. (2021). Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Scientific Data, 8(1): 31, pp. 1-8. doi:10.1038/s41597-021-00816-y.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0007-7A46-2 Version Permalink: http://hdl.handle.net/21.11116/0000-0008-0EA0-4
Genre: Journal Article

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Code for validation of the dataset (Supplementary material)
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(with version 1 used for the first release of AncientMetagenomeDir). - (last checked Nov. 2020)
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R notebooks (Supplementary material)
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(last checked: Nov. 2020)

Creators

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 Creators:
Fellows Yates, James A.1, Author              
Andrades Valtueña, Aida1, Author              
Vågene, Ashild J., Author
Cribdon, Becky, Author
Velsko, Irina M.1, Author              
Borry, Maxime1, Author              
Bravo-López, Miriam J., Author
Fernandez-Guerra, Antonio, Author              
Green, Eleanor J., Author
Ramachandran, Shreya L., Author
Heintzman, Peter D., Author
Spyrou, Maria A.1, Author              
Hübner, Alexander1, Author              
Gancz, Abigail S., Author
Hider, Jessica, Author
Allshouse, Aurora F., Author
Warinner, Christina1, 2, Author              
Affiliations:
1Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2074310              
2Kostbare Kulturen, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2591692              

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Free keywords: Data publication and archiving, Genetic databases, Metagenomics
 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.

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Language(s): eng - English
 Dates: 2021-01-26
 Publication Status: Published online
 Pages: 8
 Publishing info: -
 Table of Contents: Background & Summary
Methods
- Repository Structure
- Data Acquisition
- Data Validation
Data Records
Technical Validation
Usage Notes
 Rev. Type: Peer
 Identifiers: DOI: 10.1038/s41597-021-00816-y
DOI: 10.1101/2020.09.02.279570
Other: shh2777
 Degree: -

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Project information

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Project name : PALEoRIDER
Grant ID : 771234
Funding program : Horizon 2020 (H2020)
Funding organization : European Commission (EC)

Source 1

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Title: Scientific Data
  Abbreviation : Sci. Data
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: London, United Kingdom : Nature Publishing Group
Pages: - Volume / Issue: 8 (1) Sequence Number: 31 Start / End Page: 1 - 8 Identifier: ISSN: 2052-4463
CoNE: https://pure.mpg.de/cone/journals/resource/2052-4463

Source 2

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Title: bioRxiv
Source Genre: Journal
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Publ. Info: Cold Spring Harbor : Cold Spring Harbor Laboratory
Pages: - Volume / Issue: - Sequence Number: 279570 Start / End Page: - Identifier: URI: https://www.biorxiv.org/