▶ source name
required
base Unique identifier for the biological sample
Description
Unique identifier for the biological sample
▶ assay name
required
base Unique identifier for the data acquisition run
Description
Unique identifier for the data acquisition run
▶ technology type
required
base Type of technology used
Description
Type of technology used
Validators
single_cardinality_validator
values
— values: proteomic profiling by mass spectrometry, protein expression profiling by antibody array, protein expression profiling by aptamer array
▶ comment[technical replicate]
required
base Identifier for the technical replicate (integer starting from 1)
Description
Identifier for the technical replicate (integer starting from 1)
▶ comment[data file]
required
base Name of the raw data file
Description
Name of the raw data file
▶ characteristics[organism]
required
sample-metadata Species of the sample using NCBI Taxonomy
Description
Species of the sample using NCBI Taxonomy
Validators
ontology
— ontologies: ncbitaxon
The organism should be a valid NCBI Taxonomy term
Examples
homo sapiens, mus musculus, rattus norvegicus, saccharomyces cerevisiae
▶ characteristics[organism part]
required
sample-metadata Main normalized anatomical term for the sample
Description
Main normalized anatomical term for the sample
Properties
allows N/A
allows not available
multiple cardinality
Validators
ontology
— ontologies: uberon, bto
The organism part should be a valid UBERON or BTO term
Examples
liver, brain, heart, blood
▶ characteristics[biological replicate]
required
sample-metadata Identifier for the biological replicate (integer starting from 1, or 'pooled' for pooled samples)
Description
Identifier for the biological replicate (integer starting from 1, or 'pooled' for pooled samples)
Validators
pattern
— pattern:
^\d+$|^pooled$
Biological replicate should be an integer or 'pooled' for pooled reference samples
▶ characteristics[disease]
required
vertebrates Disease state of the sample
Description
Disease state of the sample
Properties
allows N/A
allows not available
Validators
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.
Examples
normal, breast cancer, infection, metabolic disease
▶ characteristics[developmental stage]
required
vertebrates Developmental stage of the organism
Description
Developmental stage of the organism
Properties
allows N/A
allows not available
Validators
ontology
— ontologies: efo
The developmental stage should be a valid EFO ontology term
Examples
adult, embryo, juvenile, larval stage
▶ comment[sdrf version]
recommended
base Version of the SDRF-Proteomics specification used to annotate this file
Description
Version of the SDRF-Proteomics specification used to annotate this file
Validators
semver
SDRF specification version
Examples
v1.1.0, v2.0.0-dev
▶ characteristics[cell type]
recommended
sample-metadata Cell type of the sample
Description
Cell type of the sample
Properties
allows N/A
allows not available
multiple cardinality
Validators
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
Examples
hepatocyte, neuron, fibroblast, T cell
▶ characteristics[strain or breed]
recommended
vertebrates Strain or breed of the organism
Description
Strain or breed of the organism
Properties
allows N/A
allows not available
Validators
ontology
— ontologies: ncbitaxon
The strain or breed should be documented
Examples
C57BL/6, Sprague-Dawley, BALB/c, Wistar
▶ characteristics[sex]
recommended
vertebrates Biological sex of the organism
Description
Biological sex of the organism
Properties
allows N/A
allows not available
Validators
values
— values:
male,
female,
hermaphrodite
Sex should be one of the allowed values
▶ comment[sdrf template]
optional
base Template name and version used for annotation. Two formats are supported - key=value format (NT=t...
Description
Template name and version used for annotation. Two formats are supported - key=value format (NT=template_name;VV=vX.Y.Z) or simple format (template_name vX.Y.Z). Multiple templates can be specified using multiple columns.
Properties
allows not available
multiple cardinality
Validators
pattern
— pattern:
^(NT=[\w-]+;VV=v\d+\.\d+\.\d+(-[\w.]+)?|[\w-]+ v\d+\.\d+\.\d+(-[\w.]+)?)$
Template can be specified as 'NT=name;VV=vX.Y.Z' or 'name vX.Y.Z'
Examples
NT=human;VV=v1.1.0, human v1.1.0, NT=ms-proteomics;VV=v1.1.0, ms-proteomics v1.1.0
▶ comment[sdrf annotation tool]
optional
base Software tool or method used to generate or annotate the SDRF file. Two formats are supported - k...
Description
Software tool or method used to generate or annotate the SDRF file. Two formats are supported - key=value format (NT=tool_name;VV=vX.Y.Z) or simple format (tool_name vX.Y.Z).
Properties
allows not available
Validators
pattern
— pattern:
^(NT=[\w-]+;VV=v[\d.]+[\w.-]*|[\w-]+ v[\d.]+[\w.-]*|manual curation)$
Annotation tool can be specified as 'NT=name;VV=vX.Y.Z' or 'name vX.Y.Z' or 'manual curation'
Examples
NT=lesSDRF;VV=v0.1.0, lesSDRF v0.1.0, NT=sdrf-pipelines;VV=v1.0.0, sdrf-pipelines v1.0.0, manual curation
▶ comment[sdrf validation hash]
optional
base Hash value for SDRF validation integrity checking
Description
Hash value for SDRF validation integrity checking
Properties
allows N/A
allows not available
Validators
pattern
— pattern:
^.+$
Validation hash string
▶ characteristics[tissue supergroup]
optional
sample-metadata Broader anatomical grouping or system-level bucket for the sample, used alongside the organism pa...
Description
Broader anatomical grouping or system-level bucket for the sample, used alongside the organism part for higher-level grouping
Properties
allows N/A
allows not available
Validators
ontology
— ontologies: uberon, bto
Tissue supergroup should be a valid broad UBERON or BTO anatomy term when possible
Examples
digestive system, nervous system, cardiovascular system, gastrointestinal tract
▶ characteristics[pooled sample]
optional
sample-metadata Whether the sample is a pooled sample combining material from multiple biological sources. Use 'n...
Description
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.
Properties
allows N/A
allows not available
Validators
values
— values: not pooled, pooled
pattern
— pattern:
^(not pooled|pooled|SN=.+(;SN=.+)*)$
Use 'not pooled', 'pooled', or list sample IDs with SN= prefix
Examples
SN=sample1;SN=sample2
▶ characteristics[sample type]
optional
sample-metadata Classification of the sample role in the experiment. Distinguishes experimental samples from cont...
Description
Classification of the sample role in the experiment. Distinguishes experimental samples from controls, references, and other roles in multiplexed or plate-based experiments.
Properties
allows N/A
allows not available
Validators
ontology
— ontologies: pride
Sample type should be a child of PRIDE:0000895 (sample type)
Examples
single cell, reference, bridge, carrier, pooled, empty, quality control sample, negative control
▶ characteristics[material type]
optional
sample-metadata Type of biological material being analyzed
Description
Type of biological material being analyzed
Properties
allows N/A
allows not available
Validators
values
— values:
tissue,
cell,
cell line,
organism part,
whole organism,
synthetic
Material type
▶ characteristics[tissue mass]
optional
sample-metadata Mass of tissue used for extraction
Description
Mass of tissue used for extraction
Properties
allows N/A
allows not available
Validators
number_with_unit
Tissue mass with unit
Examples
50 mg, 1 g, 500 ug
▶ characteristics[biosample accession number]
optional
sample-metadata BioSample accession number for the sample (e.g., SAMN or SAMEA identifiers)
Description
BioSample accession number for the sample (e.g., SAMN or SAMEA identifiers)
Properties
allows N/A
allows not available
Validators
accession
BioSample accession
Examples
SAMN12345678, SAMEA12345678, SAMD1234567
▶ characteristics[sampling time]
optional
sample-metadata Time at which the sample was collected (for longitudinal or time-course studies)
Description
Time at which the sample was collected (for longitudinal or time-course studies)
Properties
allows N/A
allows not available
Validators
number_with_unit
Sampling time with unit
Examples
0 hour, 24 hour, 7 day, 3 month
▶ characteristics[treatment]
optional
sample-metadata Treatment or perturbation applied to the sample (drug, stimulus, environmental stress)
Description
Treatment or perturbation applied to the sample (drug, stimulus, environmental stress)
Properties
allows N/A
allows not available
Validators
ontology
— ontologies: ncit, efo
Treatment should be a valid ontology term. Use 'untreated' for controls.
Examples
untreated, LPS stimulation, doxorubicin treatment, drought stress, salt stress
▶ characteristics[synthetic peptide]
optional
sample-metadata Whether the sample is a synthetic peptide library or biological material
Description
Whether the sample is a synthetic peptide library or biological material
Validators
values
— values:
synthetic,
not synthetic
Synthetic peptide status
▶ characteristics[spiked compound]
optional
sample-metadata Spiked-in compound details using key-value format (CT=compound type, QY=quantity, PS=peptide sequ...
Description
Spiked-in compound details using key-value format (CT=compound type, QY=quantity, PS=peptide sequence, AC=UniProt accession, CN=compound name, CV=vendor)
Properties
allows N/A
allows not available
multiple cardinality
Validators
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)
Examples
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
▶ characteristics[enrichment process]
optional
sample-metadata Enrichment strategy applied to the sample (e.g., phosphopeptide enrichment, crosslinked peptide e...
Description
Enrichment strategy applied to the sample (e.g., phosphopeptide enrichment, crosslinked peptide enrichment, glycopeptide enrichment)
Properties
allows N/A
allows not available
Validators
ontology
— ontologies: pride, efo
Enrichment type should be a child term of EFO:0009090 (enrichment process)
Examples
enrichment of cross-linked peptides, enrichment of phosphorylated protein, enrichment of glycopeptides, enrichment of ubiquitinated proteins