SDRF-Proteomics

1. Status

Status: Released

Version: 1.1.0 - 2026-01

2. Abstract

The invertebrates template provides standardized metadata fields for invertebrate proteomics experiments. This includes model organisms like Drosophila melanogaster and Caenorhabditis elegans, as well as other insects, worms, and invertebrate species.

This template is appropriate for:

  • Drosophila (fruit fly) proteomics studies

  • C. elegans proteomics studies

  • Insect proteomics (bees, mosquitoes, etc.)

  • Marine invertebrate studies

3. Template Hierarchy

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

The invertebrates template extends the base template, adding disease annotation and invertebrate-specific fields.

Important

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

  • ms-proteomics + invertebrates - For MS-based proteomics of invertebrate samples

  • affinity-proteomics + invertebrates - For affinity proteomics of invertebrate 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. Invertebrates-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 FBdv (Drosophila), WBls (C. elegans), EFO, UBERON adult stage, larval stage, pupal stage, embryonic stage
characteristics[strain/breed] OPTIONAL Strain of the organism NCBITaxon Oregon-R, w1118, N2, Canton-S
characteristics[genotype] OPTIONAL Genotype of the organism — wild type, daf-2(e1370), w[*]; P{GAL4}

5. Common Invertebrate Organisms

Common Name Scientific Name NCBITaxon ID Common Strains Developmental Stage Ontology

Fruit fly

Drosophila melanogaster

NCBITaxon:7227

Oregon-R, Canton-S, w1118

FBdv

Nematode

Caenorhabditis elegans

NCBITaxon:6239

N2, CB4856

WBls

Honey bee

Apis mellifera

NCBITaxon:7460

—

—

Mosquito

Anopheles gambiae

NCBITaxon:7165

—

—

6. Developmental Stages

6.1. Drosophila Stages (FBdv)

Stage FBdv Term Description

embryonic stage

FBdv:00005289

Embryo development

larval stage

FBdv:00005336

Larval instar stages (L1, L2, L3)

pupal stage

FBdv:00005349

Metamorphosis

adult stage

FBdv:00005369

Sexually mature adult

6.2. C. elegans Stages (WBls)

Stage WBls Term Description

embryo Ce

WBls:0000003

Embryonic development

L1 larva Ce

WBls:0000024

First larval stage

L2 larva Ce

WBls:0000027

Second larval stage

L3 larva Ce

WBls:0000035

Third larval stage

L4 larva Ce

WBls:0000038

Fourth larval stage

dauer larva Ce

WBls:0000032

Dauer stage

adult Ce

WBls:0000041

Adult stage

7. Genotype Notation

7.1. Drosophila Genotype Format

Drosophila genotypes follow a specific notation:

# Wild type
wild type

# Single mutation
w[1118]

# Multiple alleles with GAL4/UAS system
w[*]; P{GAL4-da.G32}

7.2. C. elegans Genotype Format

  1. elegans genotypes use allele notation:

# Wild type
wild type

# Single mutation (gene-allele format)
daf-2(e1370)

# Multiple mutations
daf-2(e1370); daf-16(mgDf50)

8. Validation

Validate SDRF files using sdrf-pipelines:

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

9. Examples

9.1. Drosophila Study Example

source name characteristics[organism] characteristics[organism part] characteristics[disease] characteristics[developmental stage] characteristics[strain/breed] characteristics[genotype] characteristics[biological replicate]
sample_1 drosophila melanogaster whole organism normal adult stage Oregon-R wild type 1
sample_2 drosophila melanogaster whole organism normal adult stage Oregon-R wild type 2
sample_3 drosophila melanogaster whole organism normal adult stage w1118 w[1118] 1
Sample metadata

9.2. C. elegans Study Example

source name characteristics[organism] characteristics[organism part] characteristics[disease] characteristics[developmental stage] characteristics[strain/breed] characteristics[genotype] characteristics[biological replicate]
sample_1 caenorhabditis elegans whole organism normal adult Ce N2 wild type 1
sample_2 caenorhabditis elegans whole organism normal adult Ce N2 wild type 2
sample_3 caenorhabditis elegans whole organism normal adult Ce CB1370 daf-2(e1370) 1
Sample metadata