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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

Added

  • Added all versions of the Array templates (reside within ega-metadata-schema/templates/array-based-metadata/deprecated_versions). Taken from their previous location.
  • Added docs folder [PR#26]
  • Added metadata model diagram [PR#26]
  • Added markdown documentation (json_browser) explaining the schemas (see README) [PR#26]
  • Added titles and descriptions to several constraints within the schemas (for the markdowns to have a better explanation) [PR#26]
  • Added examples and meta:enum keywords within the schemas for them to appear in the markdowns. [PR#26]
  • Added sample and individual JSON schemas [PR#27]
  • Added object-set schema to contain grouped objects in sets [PR#30].
  • Added remaining schemas (some empty for the moment) [PR#30].
  • Added PR and issue templates [PR#40].
  • Added example XML to JSON documents (see README.md) [PR#35].
  • Added contributing documentation [PR#41]
  • Added GH workflow to lint code and documentation of the repository [PR#42].
  • Added GH workflow to validate JSON examples automatically on PRs [PR#42].
  • Added GH workflow to generate automatically the JSON browser's markdown documentation when changes are pushed to "main" (a PR is closed) [PR#42].
  • Added GH workflow diagram [PR#42].
  • Added new attributes to samples and individuals, aligning with phenopackets but with the least overlapping fields [PR#45].
  • Added "resources" (ontologies) property to the submission object to handle ontology versions [PR#48].

Modified

  • star2xml - Moved tool star2xml to its own repository: "https://github.com/EGA-archive/star2xml".
  • JSON schemas - improved drafted JSON schemas for AF (Array Format) Array and Experiment metadata.
  • Modified the relationships node so that the target and source are of type object_core_id (being able to reference non-registered objects). [PR#26]
  • Updated markdown documentation of the schemas (see README) [PR#27]
  • Updated JSON schemas (common definitions, ArrayAssay and ArrayExperiment) [PR#27]
  • Removed Jupyter-notebook for validation and added instructions in README.md to validate through AJV [PR#30].
  • Replaced ArrayAssay with Assay, fusing "Run" object (from previous model) and Array Assays [PR#34]
  • Added the Experiment object, and fused ArrayExperiment with it, removing the latter [PR#34]
  • Added the Analysis object [PR#34]
  • Added loci descriptor node to common definitions (inherited by other objects) [PR#34]
  • Updated protocols object [PR#34]
  • Added folder controlled_vocabulary_schemas with JSON documents containing controlled vocabulary for specific fields. These are inherited in the common definitions mainly [PR#34]
  • All external accessions are now required to follow a CURIE format (e.g. ncbigene:100010) [PR#34]
  • Updated JSON markdowns [PR#34]
  • Added example XML to JSON documents (see README.md) [PR#35].
  • Modified relationship nodes so that only one end of the relationship is allowed [PR#39].
  • Modified relationship nodes to accept only specific combinations per object [PR#39].
  • Moved and renamed the validation examples from schemas/validation_tests to examples/json_validation_tests [PR#42].
  • Changed cross-schema absolute references to relative ones PR#44]
  • Modified all JSON schema pointers ($ids) for them to point to the raw text version of each file PR#46].
  • Transformed the protocols properties of experiments and analyses into an object on its own PR#47].

[0.0.0] - 2021-04-26

Added [2021-04-26]

  • ega-metadata-schema/README.md - Main README of the project with all its related information.
  • LICENSE - License applied to the ega-metadata-schema project.
  • Descriptive XMLs - Folder containing (at least) one descriptive XML (with instructions on what information corresponds to which nodes of the XML) for each metadata object.
  • True XMLs - Folder containing (at least) one "true" XML (with fabricated values an little to no comments to see what an XML ready to be submitted would look like) for each metadata object.
  • EGA_Array_based_Format_V4.3.xlsx - Spreadsheet used as template to store and submit Array Format (AF) metadata.
  • EGA_metadata_submission_template_v1.xlsx - Spreadsheet used as template to store metadata related to Sequence data. Such spreadsheet can be used as input of the star2xml tool.