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).
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 multiplexed experiments.Values include single cell, reference, bridge, carrier, empty, quality control sample,
and various control types. This column replaces older per-template role columns.
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 | Anatomical part of the organism from which sample was derived | |
|
Anatomical part of the organism from which sample was derived
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[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 experimental samples from cont... | |
|
Classification of the sample role in the experiment. Distinguishes experimental samples 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)
single cell, reference, bridge, carrier, pooled, empty, quality control sample, negative control
|
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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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