SDRF-Proteomics

1. Status

Status: Released

Version: 1.1.0 - 2026-01

2. Abstract

The plants template provides standardized metadata fields for plant proteomics experiments. This includes model organisms like Arabidopsis thaliana, as well as crop species, trees, and other plant systems.

This template is appropriate for:

  • Arabidopsis proteomics studies

  • Crop proteomics (rice, maize, wheat, soybean)

  • Plant stress response studies

  • Agricultural and plant biology research

3. Template Hierarchy

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

The plants template extends the base template, adding disease annotation and plant-specific fields.

Important

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

  • ms-proteomics + plants - For MS-based proteomics of plant samples

  • affinity-proteomics + plants - For affinity proteomics of plant 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. Plants-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 plant Plant Ontology (PO), EFO seedling stage, flowering stage, rosette growth stage, senescent stage
characteristics[strain/breed] OPTIONAL Cultivar, ecotype, or accession of the plant — Col-0, Ler-0, Nipponbare, B73
characteristics[growth conditions] OPTIONAL Growth conditions for the plant — long day (16h light/8h dark), short day (8h light/16h dark), continuous light, greenhouse
characteristics[treatment] OPTIONAL Treatment applied to the plant EFO, ChEBI drought stress, salt stress, pathogen infection, hormone treatment

5. Common Plant Organisms

Common Name Scientific Name NCBITaxon ID Common Ecotypes/Cultivars

Arabidopsis

Arabidopsis thaliana

NCBITaxon:3702

Col-0, Ler-0, Ws-0, C24

Rice

Oryza sativa

NCBITaxon:4530

Nipponbare, IR64, Kasalath

Maize

Zea mays

NCBITaxon:4577

B73, Mo17, W22

Wheat

Triticum aestivum

NCBITaxon:4565

Chinese Spring

Soybean

Glycine max

NCBITaxon:3847

Williams 82

Tomato

Solanum lycopersicum

NCBITaxon:4081

M82, Micro-Tom

6. Developmental Stages

Common developmental stages from the Plant Ontology (PO):

Stage PO Term Description

seedling stage

PO:0007131

Plant after germination before mature vegetative growth

rosette growth stage

PO:0007113

Arabidopsis-specific rosette development

vegetative growth stage

PO:0007134

Mature vegetative plant

reproductive growth stage

PO:0007130

Flowering and fruiting

flowering stage

PO:0007616

Active flowering

fruit formation stage

PO:0007042

Fruit/seed development

senescent stage

PO:0025337

Aging and senescence

7. Plant Organism Parts

Common plant tissue/organ terms:

Organ/Tissue Ontology Term Description

leaf

PO:0025034

Photosynthetic organ

root

PO:0009005

Underground organ

stem

PO:0009047

Main axis

flower

PO:0009046

Reproductive structure

seed

PO:0009010

Mature ovule

fruit

PO:0009001

Mature ovary

shoot

PO:0009006

Aerial part

whole plant

PO:0000003

Entire organism

8. Growth Conditions

Document growth conditions using standard descriptions:

Condition Format Example

Photoperiod

{light}h light/{dark}h dark

16h light/8h dark

Temperature

{temp}°C

22°C

Light intensity

{value} μmol m⁻² s⁻¹

120 μmol m⁻² s⁻¹

Growth medium

{medium name}

1/2 MS medium

9. Common Plant Treatments

Treatment Type Example Values Ontology

Abiotic stress

drought stress, salt stress, cold stress, heat stress

EFO

Biotic stress

pathogen infection, herbivore attack

EFO

Hormone treatment

auxin treatment, ABA treatment, jasmonic acid

ChEBI

Nutrient stress

nitrogen starvation, phosphate starvation

EFO

10. Validation

Validate SDRF files using sdrf-pipelines:

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

11. Examples

11.1. Arabidopsis Stress Study Example

source name characteristics[organism] characteristics[organism part] characteristics[disease] characteristics[developmental stage] characteristics[strain/breed] characteristics[growth conditions] characteristics[treatment] characteristics[biological replicate]
sample_1 arabidopsis thaliana leaf normal rosette growth stage Col-0 long day (16h light/8h dark) control 1
sample_2 arabidopsis thaliana leaf normal rosette growth stage Col-0 long day (16h light/8h dark) control 2
sample_3 arabidopsis thaliana leaf normal rosette growth stage Col-0 long day (16h light/8h dark) drought stress 1
sample_4 arabidopsis thaliana leaf normal rosette growth stage Col-0 long day (16h light/8h dark) drought stress 2
Sample metadata

11.2. Rice Proteomics Example

source name characteristics[organism] characteristics[organism part] characteristics[disease] characteristics[developmental stage] characteristics[strain/breed] characteristics[biological replicate]
sample_1 oryza sativa leaf normal seedling stage Nipponbare 1
sample_2 oryza sativa leaf normal seedling stage Nipponbare 2
sample_3 oryza sativa root normal seedling stage Nipponbare 1
sample_4 oryza sativa root normal seedling stage Nipponbare 2
Sample metadata