Madison2023 #1123

DianaSpurite · 2023-10-09T18:58:04Z

Adding Maddison2023 samples

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): 10.1371/journal.pone.0291540

This is to close #1116

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: Madison_enums_sample_host.json #1121

Adding Maddison2023 samples

github-actions · 2023-10-09T19:00:28Z

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

Invalid dataset ancientmetagenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Dataset Parsing Error	ancientmetagenome-hostassociated_samples.tsv	-	-	Error tokenizing data. C error: Expected 16 fields in line 1403, saw 17

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

adding Madoson2023 libraries

github-actions · 2023-10-09T19:12:22Z

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

Invalid dataset ancientmetagenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Dataset Parsing Error	ancientmetagenome-hostassociated_samples.tsv	-	-	Error tokenizing data. C error: Expected 16 fields in line 1403, saw 17

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

Added Madison 2023

github-actions · 2023-10-09T19:17:55Z

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

Invalid dataset ancientmetagenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Dataset Parsing Error	ancientmetagenome-hostassociated_samples.tsv	-	-	Error tokenizing data. C error: Expected 16 fields in line 1403, saw 17

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

DianaSpurite · 2023-10-09T19:21:40Z

As I understood the library protocol the authors used is this: https://www.neb.com/en/-/media/nebus/files/manuals/manuale7103-e7645.pdf?rev=de09eaf8fcdf45e0ac8a66bf6fee75fb&hash=FC51B96E7568B4482CF1B5217EF04E31

I didn't find anything familiar to library polymerase there

removed an unnecessary space

github-actions · 2023-10-09T19:26:05Z

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

Invalid dataset ancientmetagenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Schema Validation Error	Lithobates pipiens	sample_host	1403	'Lithobates pipiens' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Lithobates pipiens	sample_host	1404	'Lithobates pipiens' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Lithobates pipiens	sample_host	1405	'Lithobates pipiens' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Lithobates pipiens	sample_host	1406	'Lithobates pipiens' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Lithobates pipiens	sample_host	1407	'Lithobates pipiens' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Lithobates pipiens	sample_host	1408	'Lithobates pipiens' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Lithobates pipiens	sample_host	1409	'Lithobates pipiens' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Lithobates pipiens	sample_host	1410	'Lithobates pipiens' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Lithobates pipiens	sample_host	1411	'Lithobates pipiens' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Lithobates pipiens	sample_host	1412	'Lithobates pipiens' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Lithobates pipiens	sample_host	1413	'Lithobates pipiens' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.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

DianaSpurite · 2023-10-10T12:27:12Z

Quick comment

the host species are updated to a newer genus, so Lithobates pipiens instead of Rana pipiens :Madison_enums_sample_host.json #1121
validation checks should pass then, once that PR is merged into master

rerun after merging enums

github-actions · 2023-11-30T14:22:49Z

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

…enomeDir into Madison2023

github-actions · 2023-11-30T16:02:42Z

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 · 2023-11-30T16:07:19Z

Hi @jfy133,
I have reviewed the PR and made some changes to it. Mainly, I have added two samples that were previously missing for a reason I am not aware.
So maybe you just briefly check whether these changes look correct to you and then I merge the PR into the master branch.

DianaSpurite · 2023-11-30T18:06:20Z

I have added two samples that were previously missing for a reason I am not aware.

I think those were very modern samples, if I'm not wrong.

alexhbnr · 2023-11-30T20:50:51Z

Thanks @DianaSpurite, I will check that.

alexhbnr · 2023-11-30T21:24:32Z

You are right @DianaSpurite , these samples were only sampled in 1993 and 2012. I guess we can discard these two samples.
Any objections @jfy133 ?

jfy133 · 2023-12-01T05:01:08Z

No, that's how we've done it for young samples in other publications, so discarding is fine.

The only exception is the environmental samples when you have distinct/defined sequence.

github-actions · 2023-12-01T11:16:47Z

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

Update ancientmetagenome-hostassociated_samples.tsv

8cd97a3

Adding Maddison2023 samples

DianaSpurite changed the title ~~Update ancientmetagenome-hostassociated_samples.tsv~~ Madison2023 Oct 9, 2023

Update ancientmetagenome-hostassociated_libraries.tsv

864d65f

adding Madoson2023 libraries

Update CHANGELOG.md

6f9e2a6

Added Madison 2023

Update ancientmetagenome-hostassociated_samples.tsv

1c348c7

removed an unnecessary space

DianaSpurite requested review from jfy133 and alexhbnr October 10, 2023 09:06

Update ancientmetagenome-hostassociated_samples.tsv

dfd3cec

rerun after merging enums

alexhbnr added 3 commits November 30, 2023 15:41

Add missing two samples and round lat and long

0547c22

Add two missing samples and add lib polymerase

2e171e6

Merge branch 'Madison2023' of github.com:SPAAM-community/AncientMetag…

d086f49

…enomeDir into Madison2023

Remove the two youngest samples after discussing with Diana and James

8459e31

alexhbnr approved these changes Dec 1, 2023

View reviewed changes

alexhbnr merged commit 09a0f38 into master Dec 1, 2023
1 check passed

alexhbnr deleted the Madison2023 branch December 1, 2023 11:22

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Madison2023 #1123

Madison2023 #1123

DianaSpurite commented Oct 9, 2023 •

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Madison2023 #1123

Madison2023 #1123

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DianaSpurite commented Oct 9, 2023 • edited Loading

Pull Request

New Publication

Publication Information

Checklist

github-actions bot commented Oct 9, 2023

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

github-actions bot commented Oct 9, 2023

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

github-actions bot commented Oct 9, 2023

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

DianaSpurite commented Oct 9, 2023

github-actions bot commented Oct 9, 2023

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

DianaSpurite commented Oct 10, 2023

github-actions bot commented Nov 30, 2023

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

github-actions bot commented Nov 30, 2023

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

alexhbnr commented Nov 30, 2023

DianaSpurite commented Nov 30, 2023

alexhbnr commented Nov 30, 2023

alexhbnr commented Nov 30, 2023

jfy133 commented Dec 1, 2023 • edited Loading

github-actions bot commented Dec 1, 2023

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

DianaSpurite commented Oct 9, 2023 •

edited

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jfy133 commented Dec 1, 2023 •

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