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Package Definition

A Poseidon package is defined as a directory with specific files:

  • a POSEIDON.yml file, which gives important meta-information for the package, like author, version and file paths
  • Genotype data in PLINK or EIGENSTRAT format
  • An optional (but strongly recommended) so-called .janno file, which lists meta-data for each individual in a tab-separated table
  • an optional bibliography file formatted as BibTeX
  • an optional README file
  • an optional CHANGELOG file

The precise definitions of each of these files is detailed in our schema-repository.

Here is an example of the files in a typical package:

Switzerland_LNBA_Roswita/POSEIDON.yml
Switzerland_LNBA_Roswita/Switzerland_LNBA.plink.bed
Switzerland_LNBA_Roswita/Switzerland_LNBA.plink.bim
Switzerland_LNBA_Roswita/Switzerland_LNBA.plink.fam
Switzerland_LNBA_Roswita/Switzerland_LNBA.janno
Switzerland_LNBA_Roswita/Switzerland_LNBA.bib
Switzerland_LNBA_Roswita/README.txt
Switzerland_LNBA_Roswita/CHANGELOG.txt

And here a fitting POSEIDON.yml file. It lists relative file paths and metainformation in a standardized, machine-readable format.

poseidonVersion: 2.4.0
title: Switzerland_LNBA_Roswita
description: LNBA Switzerland genetic data not yet published
contributor:
  - name: Roswita Malone
    email: [email protected]
  - name: Paul Panther
    email: [email protected]
packageVersion: 1.1.2
lastModified: 2021-04-28
genotypeData:
  format: PLINK	
  genoFile: Switzerland_LNBA_Roswita.bed
  snpFile: Switzerland_LNBA_Roswita.bim
  indFile: Switzerland_LNBA_Roswita.fam
  snpSet: 1240K
jannoFile: Switzerland_LNBA_Roswita.janno
bibFile: sources.bib
readmeFile: README.txt
changelogFile: CHANGELOG.txt

When a package is modified in any way (e.g. 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.

For the key elements in a package, see the pages for genotype data and the .janno file.