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poseidon-framework / poseidon-schema

An archaeogenetic genotype data organisation file format
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adna ancient-dna data-format standardization

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The Poseidon Standard v2.7.1

Poseidon is a solution for archaeogenetic genotype data organisation. This standard defines the core components of the Poseidon package.

A .pdf version of the latest instance of this document can be downloaded here.

Further details on genotype data, the .janno file and the .ssf file are documented on the Poseidon website.

The website also features a changelog documenting the changes across different schema versions here.

The key words MUST, MUST NOT, REQUIRED, SHALL, SHALL NOT, SHOULD, SHOULD NOT, RECOMMENDED, MAY, and OPTIONAL in this document are to be interpreted as described in RFC 2119.

The Poseidon package structure

A Poseidon package stores genotype data with context information for DNA samples from (ancient) (human) individuals. Packages are defined by the POSEIDON.yml file, which holds relative paths to all other files in a package.

A package therefore MUST contain:

It SHOULD additionally contain:

It MAY also contain:

Here is an example of a package Switzerland_LNBA_Roswita in one directory:

Switzerland_LNBA_Roswita/POSEIDON.yml
Switzerland_LNBA_Roswita/Switzerland_LNBA.bed
Switzerland_LNBA_Roswita/Switzerland_LNBA.bim
Switzerland_LNBA_Roswita/Switzerland_LNBA.fam
Switzerland_LNBA_Roswita/Switzerland_LNBA.janno
Switzerland_LNBA_Roswita/Switzerland_LNBA.ssf
Switzerland_LNBA_Roswita/Switzerland_LNBA.bib
Switzerland_LNBA_Roswita/README.md
Switzerland_LNBA_Roswita/CHANGELOG.md

All text files in the package MUST be UTF-8 encoded.

The POSEIDON.yml file

The POSEIDON.yml file defines Poseidon packages by listing metainformation and relative paths in a standardised, machine-readable format.

Here is an example for a POSEIDON.yml file:

poseidonVersion: 2.7.1
title: Switzerland_LNBA_Roswita
description: LNBA Switzerland genetic data not yet published
contributor:
  - name: Roswita Malone
    email: roswita.malone@example.org
    orcid: 1234-1234-1234-1234
  - name: Paul Panther
    email: paul.panther@example.edu
packageVersion: 1.1.2
lastModified: 2021-01-28
genotypeData:
  format: PLINK
  genoFile: Switzerland_LNBA_Roswita.bed
  genoFileChkSum: 95b093eefacc1d6499afcfe89b15d56c
  snpFile: Switzerland_LNBA_Roswita.bim
  snpFileChkSum: 6771d7c873219039ba3d5bdd96031ce3
  indFile: Switzerland_LNBA_Roswita.fam
  indFileChkSum: f77dc756666dbfef3bb35191ae15a167
  snpSet: 1240K
jannoFile : Switzerland_LNBA_Roswita.janno
jannoFileChkSum: 555d7733135ebcabd032d581381c5d6f
sequencingSourceFile: Switzerland_LNBA_Roswita.ssf
sequencingSourceFileChkSum: 19db1906240ee2f076e1a9659567dca4
bibFile: Switzerland_LNBA_Roswita.bib
bibFileChkSum: 70cd3d5801cee8a93fc2eb40a99c63fa
readmeFile: README.md
changelogFile: CHANGELOG.md

When a package is modified in any way (including updates of the context information in the .janno file), then the packageVersion field SHOULD be incremented and the lastModified field updated to the current date.

Package versioning

The packageVersion field is a mandatory entry of the POSEIDON.yml file. It denotes the version of the individual package, using a three-component versioning system derived from semantic versioning.

Each version number is comprised of three numbers, separated by a .. For example: 0.1.0, 1.0.0 or 2.1.3. The first number gives the Major, the second the Minor and the third the Patch component of the version number. For a Poseidon package these components SHOULD be incremented when the following changes occur:

When the packageVersion is changed, then the lastModified date MUST be updated and an entry to the CHANGELOG.md file SHOULD be added summarising the changes made.

Packages SHOULD start at packageVersion 0.1.0.

Genotype data

Genotype data in Poseidon packages is stored either in (binary) PLINK or EIGENSTRAT format.

PLINK (binary) EIGENSTRAT
genotype file .bed (binary biallelic genotype table) .geno (genotype file)
SNP file .bim (extended MAP file) .snp (snp file)
individual file .fam (sample information) .ind (indiv file)

In addition to these files (and optionally their checksums), the POSEIDON.yml file SHOULD also provide a snpSet entry which determines the shape of the genotype file.

The .janno file

The .janno file is a tab-separated text file with a header line. It holds context information (variables/columns) for each sample (objects/rows) in a package.

The .bib file

A BibTeX file with all references listed in the .janno file. The entry keys MUST fit the ones used in the .janno file.

Example:

@article{CassidyPNAS2015,
    doi = {10.1073/pnas.1518445113},
    url = {https://doi.org/10.1073%2Fpnas.1518445113},
    year = 2015,
    month = {dec},
    publisher = {Proceedings of the National Academy of Sciences},
    volume = {113},
    number = {2},
    pages = {368--373},
    author = {Lara M. Cassidy and Rui Martiniano and Eileen M. Murphy and Matthew D. Teasdale and James Mallory and Barrie Hartwell and Daniel G. Bradley},
    title = {Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome},
    journal = {Proceedings of the National Academy of Sciences}
}

To connect a sample in the package to this particular literature reference, the .janno file column Publication would have to be filled with CassidyPNAS2015.

The README.md file

A simple markdown file with informal, arbitrarily structured information accompanying the package.

Example:

This package contains a rather interesting set of samples relevant for the peopling of the Territory of Christmas Island in the Indian Ocean. We consider this especially relevant, because ...

The CHANGELOG.md file

A markdown file to document changes in the history of a package.

Example:

- V 1.1.1: Fixed a spelling mistake in one site name: "Hosenacker" -> "Rosenacker"
- V 1.1.0: Added mtDNA contamination estimation to the .janno file
- V 1.0.0: Added spatial coordinates and age information to the .janno file and finalized a first stable version of the package
- V 0.2.0: Added previously restricted sample L1337
- V 0.1.0: Creation of the package

The structure with - V X.X.X: at the beginning of each line is not mandatory, but SHOULD be followed for reasons of interoperability.

The .ssf file

The .ssf file is another tab-separated text file with a header line. It stores sequencing source data, so metainformation about the raw sequencing data behind the genotypes in a Poseidon package. The primary entities in this table are sequencing entities, typically corresponding to DNA libraries or even multiple runs/lanes of the same library.