SDRF-Proteomics

1. Status

Status: Released

Version: 1.1.0 - 2026-01

2. Abstract

The vertebrates template provides standardized metadata fields for non-human vertebrate proteomics experiments. This includes mammals (mouse, rat, etc.), birds, fish, reptiles, and amphibians.

This template is appropriate for:

  • Mouse and rat proteomics studies

  • Model organism research (zebrafish, Xenopus)

  • Livestock and agricultural animal studies

  • Wildlife and comparative proteomics

3. Template Hierarchy

base (construction artifact)
  └── vertebrates (SAMPLE layer - must combine with TECHNOLOGY template)

The vertebrates template extends the base template, adding disease annotation and vertebrate-specific fields.

Important

The vertebrates template cannot be used alone. You must combine it with a technology template:

  • ms-proteomics + vertebrates - For MS-based proteomics of vertebrate samples

  • affinity-proteomics + vertebrates - For affinity proteomics of vertebrate samples

4. Checklist

4.1. Inherited Columns

All columns from the base template are inherited (source name, organism, organism part, biological replicate, assay name, technology type, instrument, technical replicate, data file). Technology-specific columns come from the technology template (ms-proteomics or affinity-proteomics).

4.2. Vertebrates-Specific Columns

ColumnRequirementDescriptionOntologyExample Values
characteristics[disease] REQUIRED Disease state of the sample MONDO, EFO, DOID, PATO normal, breast cancer, diabetes mellitus
characteristics[developmental stage] RECOMMENDED Developmental stage of the organism EFO, UBERON adult, embryo, juvenile, larval stage
characteristics[strain/breed] OPTIONAL Strain or breed of the organism NCBITaxon C57BL/6, Sprague-Dawley, BALB/c
characteristics[sex] OPTIONAL Biological sex of the organism — male, female, hermaphrodite, not available, not applicable

5. Common Vertebrate Organisms

Common Name Scientific Name NCBITaxon ID Common Strains/Breeds

Mouse

Mus musculus

NCBITaxon:10090

C57BL/6, BALB/c, 129S1

Rat

Rattus norvegicus

NCBITaxon:10116

Sprague-Dawley, Wistar, Lewis

Zebrafish

Danio rerio

NCBITaxon:7955

AB, TL, WIK

Pig

Sus scrofa

NCBITaxon:9823

Large White, Duroc

Chicken

Gallus gallus

NCBITaxon:9031

—

Xenopus

Xenopus laevis

NCBITaxon:8355

—

6. Developmental Stages

Common developmental stage terms for vertebrates:

Stage EFO/UBERON Term Description

adult

EFO:0001272

Sexually mature organism

embryo

UBERON:0000068

Organism in early development

juvenile

EFO:0001303

Post-embryonic, pre-adult

neonate

EFO:0001375

Newborn

fetus

UBERON:0000323

Late embryonic stage (mammals)

7. Validation

Validate SDRF files using sdrf-pipelines:

pip install sdrf-pipelines
sdrf_validate --sdrf_file your_file.sdrf.tsv --template vertebrates

8. Examples

8.1. Mouse Study Example

source name characteristics[organism] characteristics[organism part] characteristics[disease] characteristics[developmental stage] characteristics[strain/breed] characteristics[sex] characteristics[biological replicate]
sample_1 mus musculus liver normal adult C57BL/6 male 1
sample_2 mus musculus liver normal adult C57BL/6 male 2
sample_3 mus musculus liver normal adult C57BL/6 female 1
sample_4 mus musculus liver normal adult C57BL/6 female 2
Sample metadata