Neumann2023

[DianaSpurite]

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): https://austriaca.at/bronzezeit-pest-in-drasenhofen

This is to close #1092

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

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Schema Validation Error	Neumann 2023	project_name	588	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	publication_doi	588	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	sample_age_doi	588	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	Neumann 2023	project_name	589	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	publication_doi	589	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	sample_age_doi	589	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'

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

Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	Neumann 2023	project_name	2304	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2304	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	Neumann 2023	project_name	2305	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2305	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	Neumann 2023	project_name	2306	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2306	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	Neumann 2023	project_name	2307	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2307	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'

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

Invalid dataset ancientsinglegenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Schema Validation Error	Neumann 2023	project_name	588	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	publication_doi	588	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	sample_age_doi	588	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	Neumann 2023	project_name	589	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	publication_doi	589	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	sample_age_doi	589	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'

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

Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	Neumann 2023	project_name	2304	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2304	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	Neumann 2023	project_name	2305	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2305	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	Neumann 2023	project_name	2306	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2306	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	Neumann 2023	project_name	2307	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2307	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'

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

Invalid dataset ancientsinglegenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	publication_doi	588	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	sample_age_doi	588	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	publication_doi	589	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	sample_age_doi	589	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'

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

Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	Neumann 2023	project_name	2304	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2304	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	Neumann 2023	project_name	2305	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2305	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	Neumann 2023	project_name	2306	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2306	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	Neumann 2023	project_name	2307	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2307	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'

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

Invalid dataset ancientsinglegenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	publication_doi	588	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	sample_age_doi	588	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	publication_doi	589	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	sample_age_doi	589	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'

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

Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2304	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2305	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2306	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2307	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

[DianaSpurite]

1. library_polymerase as always in a different dimension
2. also didn't find a doi

[jfy133]

Library table has the wrong ERS codes assoigned with the sample IDS (e.g. ERS ending in 37 should be with DSH008)

[jfy133]

Bug was due to SPAAM-community/amdirt#125, I've pinned the JSONschema package for you and will keep that temporarily now

[jfy133]

und in eine sequencing library transformiert.12 - > 12 Gansauge et al. 2020. -> Gansauge et al. 2020
M.-T. Gansauge, A. Aximu-Petri, S. Nagel, M. Meyer, Manual
and automated preparation of single-stranded DNA libraries
for the sequencing of DNA from ancient biological remains and
other sources of highly degraded DNA,

Single stranded for the shotgun sequence liraries (2 missing from library list!), and this was with no UDG treatmenment

Also the Gansauge is also cited for the capture libraries so they should also be singlestranded not doublre

Polymerase for Gansauge 2020 is: AccuPrime Pfx DNA

But other than that looks OK (@GUNeumann is also reviewing though :D)

[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

[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

Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	Neumann 2023	project_name	2308	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	Illumina HiSeq 4000 sequencing	instrument_model	2308	'Illumina HiSeq 4000 sequencing' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	Neumann 2023	project_name	2309	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	Illumina HiSeq 4000 sequencing	instrument_model	2309	'Illumina HiSeq 4000 sequencing' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

[DianaSpurite]

Single stranded for the shotgun sequence liraries (2 missing from library list!), and this was with no UDG treatmenment

Added the two libraries

Also the Gansauge is also cited for the capture libraries so they should also be singlestranded not doublre

changed

Polymerase for Gansauge 2020 is: AccuPrime Pfx DNA

added

[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

[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

[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

[jfy133]

I approve on behalf of @GUNeumann as his requested changes overlapped with mine and/or has been addressed as requested