SDRF template with shared sample metadata columns (organism, tissue, disease). This is an internal construction layer inherited by technology and organism templates - not used directly.
The sample-metadata template is the shared biological layer inherited by all technology
and organism templates. It defines the core sample identity and biology columns.
Key columns and guidance:
characteristics[organism]: Use NCBI Taxonomy names in lowercase (e.g., homo sapiens).characteristics[organism part]: Use UBERON or BTO terms. Supports multiple cardinalityfor mixed-tissue samples (add multiple columns with the same header). This is the main
normalized anatomy field used for integration across studies.
characteristics[tissue supergroup]: Optional broader anatomical bucket (for exampleheart, liver, brain, or a higher-level system such as gastrointestinal tract)
used alongside characteristics[organism part] when higher-level grouping is useful.
characteristics[disease]: Use normal (PATO:0000461) for healthy/control samples.Organism templates (human, vertebrates, etc.) override this to required.
characteristics[biological replicate]: Integer starting from 1. Use pooled forpooled reference samples only.
characteristics[sample type]: Classifies the sample's role in the experiment.Use study sample for biological samples under investigation. Control wells use
PRIDE control terms (e.g. negative control, positive control, calibrator, plate control,
quality control sample). Multiplexed or plate-normalization roles include reference,
bridge, carrier, pooled, and empty.
characteristics[biosample accession number]: Link to BioSample record (SAMN/SAMEA/SAMD).| Column | Requirement | Source | Description | |
|---|---|---|---|---|
| characteristics[organism] | required | sample-metadata | Species of the sample using NCBI Taxonomy | |
|
Species of the sample using NCBI Taxonomy
ontology
— ontologies: ncbitaxon
The organism should be a valid NCBI Taxonomy term
homo sapiens, mus musculus, rattus norvegicus, saccharomyces cerevisiae
|
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| characteristics[organism part] | required | sample-metadata | Main normalized anatomical term for the sample | |
|
Main normalized anatomical term for the sample
ontology
— ontologies: uberon, bto
The organism part should be a valid UBERON or BTO term
liver, brain, heart, blood
|
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| characteristics[biological replicate] | required | sample-metadata | Identifier for the biological replicate (integer starting from 1, or 'pooled' for pooled samples) | |
|
Identifier for the biological replicate (integer starting from 1, or 'pooled' for pooled samples)
pattern
— pattern:
^\d+$|^pooled$
Biological replicate should be an integer or 'pooled' for pooled reference samples
1, 2, pooled
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| characteristics[cell type] | recommended | sample-metadata | Cell type of the sample | |
|
Cell type of the sample
ontology
— ontologies: cl, bto, clo
The cell type should be a valid Cell Ontology (CL), BRENDA Tissue Ontology (BTO), or Cell Line Ontology (CLO) term
hepatocyte, neuron, fibroblast, T cell
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| characteristics[disease] | recommended | sample-metadata | Disease state of the sample | |
|
Disease state of the sample
ontology
— ontologies: mondo, efo, doid, ncit, pato
The disease should be a valid MONDO, EFO, DOID, NCIT, or PATO ontology term. Use 'normal' (PATO:0000461) for healthy samples.
normal, breast cancer, infection, metabolic disease
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| characteristics[tissue supergroup] | optional | sample-metadata | Broader anatomical grouping or system-level bucket for the sample, used alongside the organism pa... | |
|
Broader anatomical grouping or system-level bucket for the sample, used alongside the organism part for higher-level grouping
ontology
— ontologies: uberon, bto
Tissue supergroup should be a valid UBERON or BTO anatomy term such as heart, liver, brain, or gastrointestinal tract when possible
heart, liver, brain, gastrointestinal tract
|
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| characteristics[pooled sample] | optional | sample-metadata | Whether the sample is a pooled sample combining material from multiple biological sources. Use 'n... | |
|
Whether the sample is a pooled sample combining material from multiple biological sources. Use 'not pooled' for individual samples, 'pooled' when sources are unknown, or 'SN=sample1;SN=sample2' to list source names.
values
— values:
not pooled, pooled
pattern
— pattern:
^(not pooled|pooled|SN=.+(;SN=.+)*)$
Use 'not pooled', 'pooled', or list sample IDs with SN= prefix
SN=sample1;SN=sample2
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| characteristics[sample type] | optional | sample-metadata | Classification of the sample role in the experiment. Distinguishes study samples under investigat... | |
|
Classification of the sample role in the experiment. Distinguishes study samples under investigation from controls, references, and other roles in multiplexed or plate-based experiments.
ontology
— ontologies: pride
Sample type should be a child of PRIDE:0000895 (sample type)
study sample, single cell, environmental sample, reference, bridge, carrier, pooled, empty
|
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| characteristics[material type] | optional | sample-metadata | Type of biological material being analyzed | |
|
Type of biological material being analyzed
values
— values:
tissue, cell, cell line, organism part, whole organism, synthetic
Material type
|
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| characteristics[tissue mass] | optional | sample-metadata | Mass of tissue used for extraction | |
|
Mass of tissue used for extraction
number_with_unit
Tissue mass with unit
50 mg, 1 g, 500 ug
|
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| characteristics[biosample accession number] | optional | sample-metadata | BioSample accession number for the sample (e.g., SAMN or SAMEA identifiers) | |
|
BioSample accession number for the sample (e.g., SAMN or SAMEA identifiers)
accession
BioSample accession
SAMN12345678, SAMEA12345678, SAMD1234567
|
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| characteristics[sampling time] | optional | sample-metadata | Time at which the sample was collected (for longitudinal or time-course studies) | |
|
Time at which the sample was collected (for longitudinal or time-course studies)
number_with_unit
Sampling time with unit
0 hour, 24 hour, 7 day, 3 month
|
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| characteristics[treatment] | optional | sample-metadata | Treatment or perturbation applied to the sample (drug, stimulus, environmental stress) | |
|
Treatment or perturbation applied to the sample (drug, stimulus, environmental stress)
ontology
— ontologies: ncit, efo
Treatment should be a valid ontology term. Use 'untreated' for controls.
untreated, LPS stimulation, doxorubicin treatment, drought stress, salt stress
|
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| characteristics[synthetic peptide] | optional | sample-metadata | Whether the sample is a synthetic peptide library or biological material | |
|
Whether the sample is a synthetic peptide library or biological material
values
— values:
synthetic, not synthetic
Synthetic peptide status
|
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| characteristics[spiked compound] | optional | sample-metadata | Spiked-in compound details using key-value format (CT=compound type, QY=quantity, PS=peptide sequ... | |
|
Spiked-in compound details using key-value format (CT=compound type, QY=quantity, PS=peptide sequence, AC=UniProt accession, CN=compound name, CV=vendor)
pattern
— pattern:
^CT=.+(;(QY|PS|AC|CN|CV|SP)=.+)*$
Key-value format for spiked compound details (CT=type, SP=species, QY=quantity, PS=sequence, AC=accession, CN=name, CV=vendor)
CT=peptide;PS=PEPTIDESEQ;QY=10 fmol, CT=protein;AC=A9WZ33;QY=20 nmol, CT=protein;SP=Homo sapiens;QY=1 pmol;AC=P37840, CT=mixture;CN=iRT mixture;CV=Biognosys;QY=1 pmol
|
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| characteristics[enrichment process] | optional | sample-metadata | Enrichment strategy applied to the sample (e.g., phosphopeptide enrichment, crosslinked peptide e... | |
|
Enrichment strategy applied to the sample (e.g., phosphopeptide enrichment, crosslinked peptide enrichment, glycopeptide enrichment)
ontology
— ontologies: pride, efo
Enrichment type should be a child term of EFO:0009090 (enrichment process)
enrichment of cross-linked peptides, enrichment of phosphorylated protein, enrichment of glycopeptides, enrichment of ubiquitinated proteins
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