Gancz2023

[LooseGoose99]

Pull Request

This PR is for a

• New Publication(s)
• Correction

For the following list(s):

• ancientmetagenome-environmental (README)
• ancientmetagenome-hostassociated (README)
• ancientsinglegenome-hostassociated (README)

New Publication

Publication Information

This pull request is to add samples from the following publication(s): 10.1038/s41564-023-01527-3

This is to close

Checklist

• Publication is published (preprints currently not accepted)?
• Checked the publication is not already in the database?
• Checked samples in this publication are not previously published data (newly re-sequenced metagenomes are OK!)?
• Samples are shotgun metagenomes (hostassociated-singlegenome may also contain whole-genome enriched data)?
• Checked the list follows conventions as described in the corresponding sample type's README file (e.g. using ERS/SRS accession codes for ENA/SRA)?
• Changelog is updated to include the publication under 'Added'?
• Pull request has passed validation checks (see automated comment from github-bot)?
• Review requested from @SPAAM-community/ancientmetagenomedir?
• (If applicable) Made a separate PR to add new categories to controlled lists (stored under /assets/enums, e.g. material or archive)? If so the corresponding PR is here:

[github-actions]

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

Invalid dataset ancientmetagenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Schema Validation Error	Scotland	geo_loc_name	1414	'Scotland' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error	Scotland	geo_loc_name	1415	'Scotland' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

[github-actions]

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

[alexhbnr]

Hi @LooseGoose99,

Thanks for adding your samples. There are a few minor things that need to changed before I can approve the merging:

• the entries in the sample age column should be rounded to the nearest 100 (see https://github.com/SPAAM-community/AncientMetagenomeDir/tree/master/ancientmetagenome-hostassociated/samples#sample_age)
• I couldn't find any information on the longitude/latitude of the individual cementeries so I guess this is internal knowledge. However, we have the rule that longitude/latitude Can be searched in wider literature, rough location is acceptable but use fewer decimals. In case, your coordinates point to rough estimates, I would suggest to reduce the precision of longitude/latitude to two decimals.

Is there already an update on uploading the unmerged sequencing data to ENA?