Add 2024_Antonio_HighMobility

[Tlkhi]

PR Checklist for a new package submission

• The package does not exist already in the community archive, also not with a different name.
• The package title in the POSEIDON.yml conforms to the general title structure suggested here: <Year>_<Last name of first author>_<Region, time period or special feature of the paper>, e.g. 2021_Zegarac_SoutheasternEurope, 2021_SeguinOrlando_BellBeaker or 2021_Kivisild_MedievalEstonia.
• The package is stored in a directory that is named like the package title.

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• Samples that already have been published previously, and got re-analysed (e.g. re-sequenced) for the now packaged publication, have a modified Poseidon_ID of the form <Original Poseidon_ID>_<Initials of the main author>_<Year>. Re-analysed versions of I1685 (Lazaridis et al. 2016) should, for example, be assigned the IDs I1685_IL22 (Lazaridis et al. 2022) and I1685_IL25 (Lazaridis et al. 2025).

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• The package is complete and features the following elements:
  • Genotype data in binary PLINK format (not EIGENSTRAT format).
  • Genotype has been provided by the original authors of the publication describing the data.
  • A POSEIDON.yml file with not just the file-referencing fields, but also the following meta-information fields present and filled: poseidonVersion, title, description, contributor, packageVersion, lastModified (see here for their definition)
  • A reasonably filled .janno file (for a list of available fields look here and here for more detailed documentation about them).
  • A .bib file with the necessary literature references for each sample in the .janno file.
• Every file in the submission is correctly referenced in the POSEIDON.yml file and there are no additional, supplementary files in the submission that are not documented there.
• Genotype data, .janno and .bib file are all named after the package title and only differ in the file extension.
• The package version in the POSEIDON.yml file is 1.0.0.
• The poseidonVersion of the package in the POSEIDON.yml file is set to the latest version of the Poseidon schema.
• The POSEIDON.yml file contains the corresponding checksums for the fields genoFile, snpFile, indFile, jannoFile and bibFile.
• There is either no CHANGELOG file or one with a single entry for version 1.0.0.

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• The Publication column in the .janno file is filled and the respective .bib file has complete entries for the listed mentioned keys.
• The .janno file does not include any empty columns or columns only filled with n/a.
• The order of columns in the .janno file adheres to the standard order as defined in the Poseidon schema here.
• The .janno and the .ssf files are not fully quoted, so they only use single- or double quotes ("...", '...') to enclose text fields where it is strictly necessary (i.e. their entry includes a TAB).

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• The package passes a validation with trident validate --fullGeno.

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• Large genotype data files are properly tracked with Git LFS and not directly pushed to the repository. For an instruction on how to set up Git LFS please look here. If you accidentally pushed the files the wrong way you can fix it with git lfs migrate import --no-rewrite path/to/file.bed (see here).

[nevrome]

Nice! I'll try to find a reviewer asap 👍

[nevrome]

Thankfully, @denisazlamalova has agreed to review this package submission! Please see the review guide here: https://www.poseidon-adna.org/#/archive_reviewer_guide

By now there are also a lot of other PRs that may serve as a reference, e.g. #299 or #275.

[denisazlamalova]

Thank you @Tlkhi for you submission! I have gone through the files and only have some minor comments regarding the .janno file.

1. In column called Relation_Note, you only have n/a values. Maybe the whole column could be removed?

2. According to the Overview table of the columns in the .janno file, values in Source_Tissue for bones should follow this format: bone_type, in the case of petrous bone it should be bone_petrous

3. I noticed one potentially missing entry regarding the identical individuals. To make the table symmetrical, individuals R11553.SG and R11554.SG should also have an identical relationship to R11555.SG, so columns Relation_To, Relation_Degree and Relation_Type should be modified for these two individuals.

Other than that, the rest of the files and their content look good to me.

[nevrome]

Thanks for the review, @denisazlamalova. Maybe you could address 1. and 3., @Tlkhi. 2. is not so important - we'll adjust how this is done in Poseidon v3.0.0 anyway. I'll have a final look when you're done 👍

[nevrome]

I'm sorry that it took me so long to get back to this. I implemented the suggested changes myself now and will merge the package.