AncientMetagenomeDir is a community curated resource of lists of all published shotgun-sequenced ancient metagenome samples. It is primarily meant to act as a reference guide to help point researchers toward any relevent public data for comparative analysis. It is hoped it will help researchers track growth and development of the field of ancient metagenomics over time.
These lists contain information such as publication, sample name, sample type, geographic location, dates and DOIs and other accession numbers to samples in establised sequencing data databases. We define here 'metagenome' in a broad sense, primarily focusing any data where the whole DNA content is analysed and explored. Examples for this are (but not limited to) ancient microbiomes (host associated metagenome), ancient sedimentary DNA (environmental) and also samples used for ancient pathogen screening (single genomes). See the README of each list for more detailed descriptions of the contents of each list. Further modification and expansion of these categories can be proposed to the SPAAM community for further consideration.
The purpose of this repository is not meant to be a comprehensive set of all metadata about every ancient metagenome, but the aim is to have a lightweight set of minimal information but with sufficient links to original sources of detailed information. Keeping the repository simple and lightweight will promote continual updating of the lists over a long period of time. That said, we will design lists as far as possible to follow larger database metadata specifications e.g. MIxS for compatibility.
Finally, we aim to make releases of this at regular intervals, and assign each release a citeable DOI. Each release will also include a changelog to record all additions and any corrections or modifications. Therefore researchers are free to use the information in their own publications, as per the CC-BY 4.0 licence.
Please download the .tsv file stored in the metagenome type of interest.
For citations use the Zenodo DOI listed in the badge at the top of this page. To cite a specific release, click on the Zenodo badge and find the corresponding DOI under the 'Versions' box on the righthand side of the Zenodo webpage.
The AncientMetagenomeDir community curates this data on a voluntary basis, and therefore provides no warranty or completeness or accuracy of the data. If in doubt, refer to the original publication of a given sample.
If you are not familiar with Git(Hub), quick start step-by-step guides can be found in the following:
- Adding samples to a list via pull request here or in PDF format here
- Performing a pull request review here or in PDF format here
More detailed versions with more tips and tricks can be seen on our wiki:
Samples must be from published studies, and should only include sample level information. Preprints often have not made data avaliable at this point, and we make the assumption that peer-review has correctly evaluated any submitted metagenome is valid. Included papers should generally have uploaded their own data, however in certain cases may see exceptions (such as retrieval of bacterial genomes from off-target reads from human population studies). If unsure, please consult the AncientMetagenomeDir community on slack.
Samples must also have been accessible on public databases (e.g. EBI ENA or NCBI SRA).
Important: we do not currently record sequencing data information, due to different uploading strategies by different groups.
Contributing a new publication's sample information consists of the following:
- check under the
issues tab if
the paper is already listed (if not, make one!)
- check whether the issue has already been closed
- if it listed, check to see if there is already a pull request linked to it
- assign yourself to the issue
- check if site/samples have been published before (i.e. to ensure the same names are used for any new samples)
- making your own fork or branch of the repository
- update the given list (e.g. in spreadsheet program, R etc.)
- generally you will be copying direct from a publication's supplementary information
- some columns have standard pre-defined categories, check a lists's README if in doubt!
- if you need to add a category please request one by mentioning
@ancientmetagenomedir-coreteam in your PR, or update the enums in JSON files
under
assets/enumsyourself
- making a pull-request
- receive a review to check your additions follow current conventions
- have your PR merged
- close the issue
All contributions are attributed through Git's in-built recording of the author of each commit and pull request. These will be displayed publically in the future.
In addition to researchers adding their own publications, we will also maintain lists of published but not-yet-added studies using github issues.
Therefore researchers who wish to contribute who do not yet have their own publications, can 'assign' themselves to specific 'issues' (papers), and reduce the risk of duplicates.
Contribution of these publications follow as above.
To ensure efficient and consistent searching, we include guidelines on how to record and format information. Adherence to these guidelines is enforced by 'pull request' review by members of the SPAAM community and other contributors. Furthermore, each category of metagenome will have their own 'special' fields, which will be defined in each specific context.
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