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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

  • Quick Start section with minimal example, key concepts, format requirements, and scope clarification.
  • Format Requirements documenting core SDRF rules (tab-delimited, column structure, row semantics).
  • Scope clarification: SDRF captures sample-to-data relationships but not downstream analysis parameters (FDR, p-values, etc.).
  • Styled HTML tables for SDRF examples with color-coded columns (blue=sample, green=data, orange=factor values) and PDF fallback.
  • Ontology table with direct links to OLS for each ontology, organized by category.
  • Disease annotation guidelines (link:metadata-guidelines/sample-metadata.adoc#disease-annotation): clarifying normal vs healthy vs control terminology.
  • Pooled reference sample handling: use pooled value for biological replicate, age, sex, and other individual-specific fields.
  • DEVELOPMENT.md: documentation for building the website locally and contributing.
  • Experiment-specific templates with YAML validation schemas:
    • Affinity proteomics (Olink, SomaScan)
    • Cell lines (Cellosaurus integration)
    • Crosslinking mass spectrometry (XL-MS)
    • DDA acquisition parameters
    • DIA acquisition parameters
    • Immunopeptidomics (MHC/HLA)
    • Metaproteomics (environmental samples)
    • Single-cell proteomics
  • Core templates in YAML format for validation: ms-proteomics, human, vertebrates, invertebrates, plants.
  • Metadata guidelines documentation:
    • Sample metadata guidelines (sample-metadata.adoc)
    • Human-specific metadata guidelines (templates/human/README.adoc)
    • MS data file metadata (in ms-proteomics template)
    • SDRF terms reference (sdrf-terms.tsv)
  • Website infrastructure (site/): homepage, SDRF explorer, terms reference, search functionality, CSS styling.
  • PDF generation workflow with custom theme for specification documents.
  • File-level metadata support using dedicated columns (comment[sdrf version], comment[sdrf template], comment[sdrf annotation tool]) for capturing SDRF version, template, and provenance information.
  • Row uniqueness requirements documentation (renamed to "Additional SDRF Rules"):
    • Error-level: source name + assay name + comment[label] must be unique.
    • Warning-level: source name + assay name should be unique.
  • Validation of 256+ annotated projects.
  • Abbreviated SDRF examples use ... columns to indicate omitted columns.

Changed

  • Version bump to v1.1.0.
  • Specification restructured with clearer organization: Quick Start → Validation → Specification Structure → Notational Conventions → Sample Metadata → Data File Metadata → Templates → Factor Values.
  • Column naming: fileformat changed to file_format for consistency with underscore convention.
  • Ontology recommendations: added NCIT and PRIDE to general purpose; added PATO for healthy samples (normal = PATO:0000461).
  • BioSamples section shortened with citation added.
  • Replicates section simplified with clearer examples.
  • Pooled samples section simplified; added simple pooled value option alongside detailed SN= format.
  • Standardized proteomics data acquisition method terms across all annotated projects.
  • Updated enzyme.tsv file; removed enzyme regular expression requirement.
  • Small changes in typos and grammar throughout the specification.

Removed

  • Outdated readthedocs link and configuration (.readthedocs.yaml).
  • Verbose/redundant sections consolidated into metadata guidelines documents.

[1.0.0] - 2023-05-24

Added

  • First release of the project.
  • First version of the SDRF specification document (psi-document/SDRF_Proteomics_Specification_v1.0.0.docx).
  • First projects annotated in the SDRF format.

Fixed

  • Nothing fixed.

Changed

  • Nothing changed.

Removed

  • Nothing removed.