# SDRF Templates

> Versioned SDRF template definitions for proteomics and related omics, including inheritance rules, column metadata, and the generated manifest used by downstream tooling.

Use this repository when you need the canonical YAML template definitions for SDRF sample
metadata and acquisition metadata. Start with the README for repository structure, then consult
the generated manifest and the specific template YAML files you need. Template inheritance is
important: most concrete templates extend shared layers such as `base` and `sample-metadata`.

When interpreting `comment[sdrf template]`, prefer the most specific leaf templates instead of
repeating every inherited parent. Downstream validators should resolve inheritance transitively.

## Core files

- [README](https://raw.githubusercontent.com/bigbio/sdrf-templates/dev/README.md): Repository overview, structure, manifest usage, and inheritance model.
- [Manifest](https://raw.githubusercontent.com/bigbio/sdrf-templates/dev/templates.yaml): Generated index of all templates, versions, and inheritance metadata.
- [Schema](https://raw.githubusercontent.com/bigbio/sdrf-templates/dev/sdrf-template.schema.json): JSON schema describing the YAML template structure.
- [Manifest generator](https://raw.githubusercontent.com/bigbio/sdrf-templates/dev/scripts/generate_manifest.py): Script that discovers templates and regenerates `templates.yaml`.

## Shared template layers

- [base](https://raw.githubusercontent.com/bigbio/sdrf-templates/dev/base/1.1.0/base.yaml): Core SDRF infrastructure columns such as source name, assay name, technology type, and template declarations.
- [sample-metadata](https://raw.githubusercontent.com/bigbio/sdrf-templates/dev/sample-metadata/1.0.0/sample-metadata.yaml): Shared biological sample metadata layer used by organism and technology templates.
- [clinical-metadata](https://raw.githubusercontent.com/bigbio/sdrf-templates/dev/clinical-metadata/1.0.0/clinical-metadata.yaml): Shared clinical annotation layer for treatment, demographics, and provenance.
- [oncology-metadata](https://raw.githubusercontent.com/bigbio/sdrf-templates/dev/oncology-metadata/1.0.0/oncology-metadata.yaml): Cancer-focused extension of the clinical layer.

## Technology templates

- [ms-proteomics](https://raw.githubusercontent.com/bigbio/sdrf-templates/dev/ms-proteomics/1.1.0/ms-proteomics.yaml): Mass-spectrometry proteomics template.
- [dia-acquisition](https://raw.githubusercontent.com/bigbio/sdrf-templates/dev/dia-acquisition/1.1.0/dia-acquisition.yaml): DIA-specific extension of `ms-proteomics`.
- [affinity-proteomics](https://raw.githubusercontent.com/bigbio/sdrf-templates/dev/affinity-proteomics/1.0.0/affinity-proteomics.yaml): Affinity assay template family.
- [ms-metabolomics](https://raw.githubusercontent.com/bigbio/sdrf-templates/dev/ms-metabolomics/1.0.0-dev/ms-metabolomics.yaml): Shared mass-spectrometry metabolomics layer.
- [lc-ms-metabolomics](https://raw.githubusercontent.com/bigbio/sdrf-templates/dev/lc-ms-metabolomics/1.0.0-dev/lc-ms-metabolomics.yaml): LC-MS metabolomics specialization.
- [gc-ms-metabolomics](https://raw.githubusercontent.com/bigbio/sdrf-templates/dev/gc-ms-metabolomics/1.0.0-dev/gc-ms-metabolomics.yaml): GC-MS metabolomics specialization.

## Organism and sample-context templates

- [human](https://raw.githubusercontent.com/bigbio/sdrf-templates/dev/human/1.1.0/human.yaml): Human-specific sample annotations.
- [vertebrates](https://raw.githubusercontent.com/bigbio/sdrf-templates/dev/vertebrates/1.1.0/vertebrates.yaml): Non-human vertebrate sample annotations.
- [invertebrates](https://raw.githubusercontent.com/bigbio/sdrf-templates/dev/invertebrates/1.1.0/invertebrates.yaml): Invertebrate sample annotations.
- [plants](https://raw.githubusercontent.com/bigbio/sdrf-templates/dev/plants/1.1.0/plants.yaml): Plant-specific sample annotations.
- [cell-lines](https://raw.githubusercontent.com/bigbio/sdrf-templates/dev/cell-lines/1.1.0/cell-lines.yaml): Cell line metadata built on top of the shared sample layer.

## Related repositories

- [proteomics-sample-metadata](https://github.com/bigbio/proteomics-sample-metadata): SDRF specification and end-user documentation.
- [sdrf-pipelines](https://github.com/bigbio/sdrf-pipelines): Validation, parsing, and automation pipelines that consume these templates.
