cell-lines

v1.1.0 experiment

SDRF template for cell line samples with Cellosaurus-based annotation. Cell lines can originate from any organism - combine with appropriate organism template (human for HeLa, vertebrates for NIH 3T3, invertebrates for Sf9).

Key Guidance

The cell-lines template provides standardized annotation for cultured cell lines using

Cellosaurus as the primary reference database.

Required combination: technology template + organism template (based on cell line origin).

Example: HeLa study = cell-lines + human + ms-proteomics. The same sample-layer

combination can also be paired with ms-metabolomics when the experiment is metabolomics.

Key guidance:

characteristics[cellosaurus accession]: Required. Look up accessions at

https://www.cellosaurus.org/. Format: CVCL_XXXX (e.g., CVCL_0030 for HeLa).

characteristics[cell line]: Required. Use standard cell line names from CLO/BTO/EFO.
characteristics[disease]: Required. The disease of the donor tissue from which the

cell line was originally derived. Use normal for non-disease-derived cell lines.

characteristics[tissue supergroup]: Optional broader anatomical bucket inherited from

sample-metadata for higher-level grouping of tissue of origin.

characteristics[sampling site]: Preserve the original Cellosaurus source term, local

provenance, or finer tissue-of-origin context. It can be equal to

characteristics[organism part] when no better distinction exists.

characteristics[passage number]: Recommended. Document passage for reproducibility.

Passage drift can significantly affect proteomics results.

characteristics[culture medium]: Recommended. Use NCIT terms (DMEM, RPMI 1640).
characteristics[cell line authentication]: Optional but encouraged. STR profiling

is the gold standard for human cell lines.

Inheritance

base → sample-metadata → cell-lines

Combination Rules

Requires a technology layer template.
Requires a sample layer template.

Columns

12 own + 24 inherited = 36 total · click a row for details

	Column	Requirement	Source	Description
▶	source name	required	base	Unique identifier for the biological sample
Description Unique identifier for the biological sample Ontology PRIDE:0000623 Properties
▶	assay name	required	base	Unique identifier for the data acquisition run
Description Unique identifier for the data acquisition run Ontology NCIT:C178857 Properties
▶	technology type	required	base	Type of technology used
Description Type of technology used Ontology PRIDE:0000663 Properties 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) Ontology MS:1001808 Properties type: integer
▶	comment[data file]	required	base	Name of the raw data file
Description Name of the raw data file Ontology MS:1003083 Properties
▶	characteristics[organism]	required	sample-metadata	Species of the sample using NCBI Taxonomy
Description Species of the sample using NCBI Taxonomy Ontology COB:0000022 Properties allows N/A 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 Ontology EFO:0000635 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) Ontology MS:1001809 Properties Validators pattern — pattern: `^\d+$\|^pooled$` Biological replicate should be an integer or 'pooled' for pooled reference samples Examples `1`, `2`, `pooled`
▶	characteristics[disease]	required	cell-lines	Disease state of the donor tissue from which the cell line was established
Description Disease state of the donor tissue from which the cell line was established Ontology MONDO:0000001 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[cell line]	required	cell-lines	Name of the cell line
Description Name of the cell line Ontology CLO:0000031 Properties Validators ontology — ontologies: clo, bto, efo The cell line should be a valid Cell Line Ontology (CLO), BTO, or EFO term Examples `HeLa`, `HEK293`, `MCF7`, `A549`
▶	characteristics[cellosaurus accession]	required	cell-lines	Cellosaurus accession number for the cell line
Description Cellosaurus accession number for the cell line Ontology PRIDE:0000835 Properties allows not available Validators accession Cellosaurus accession Examples `CVCL_0030`, `CVCL_0004`
▶	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 Ontology PRIDE:0000839 Properties 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 Ontology EFO:0000324 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[cellosaurus name]	recommended	cell-lines	Official Cellosaurus name for the cell line
Description Official Cellosaurus name for the cell line Ontology PRIDE:0000836 Properties allows not available
▶	characteristics[passage number]	recommended	cell-lines	Passage number of the cell line used in the experiment
Description Passage number of the cell line used in the experiment Ontology EFO:0007061 Properties allows N/A allows not available Validators pattern — pattern: `^\d+(-\d+)?$` Passage number should be an integer or range Examples `10`, `15-20`, `5`
▶	characteristics[culture medium]	recommended	cell-lines	Culture medium used to grow the cell line
Description Culture medium used to grow the cell line Ontology OBI:0000079 Properties allows N/A allows not available Validators ontology — ontologies: ncit The culture medium should be a valid ontology term (NCIT:C85504 Growth Medium hierarchy) Examples `DMEM`, `RPMI 1640`, `MEM`, `Ham's F-12`
▶	characteristics[sample storage temperature]	recommended	cell-lines	Storage temperature of the cell line (in Celsius)
Description Storage temperature of the cell line (in Celsius) Ontology PRIDE:0000705 Properties allows N/A allows not available Validators number_with_unit Storage temperature in Celsius Examples `-80 °C`, `-20 °C`, `4 °C`
▶	comment[sdrf template]	optional	base	Template name and version used for annotation. Two formats are supported - key=value format (NT=t...
Description Template name and version used for annotation. Two formats are supported - key=value format (NT=template_name;VV=vX.Y.Z) or simple format (template_name vX.Y.Z). Multiple templates can be specified using multiple columns. Ontology PRIDE:0000832 Properties allows not available multiple cardinality Validators pattern — pattern: `^(NT=[\w-]+;VV=v\d+\.\d+\.\d+(-[\w.]+)?\|[\w-]+ v\d+\.\d+\.\d+(-[\w.]+)?)$` 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). Ontology PRIDE:0000840 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. Ontology NCIT:C165587 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. Ontology PRIDE:0000895 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 Ontology PRIDE:0000837 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 Ontology OBA:2045411 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) Ontology NCIT:C175889 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) Ontology EFO:0000689 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) Ontology EFO:0000727 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 Ontology PRIDE:0000495 Properties allows N/A 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) Ontology PRIDE:0000496 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) Ontology EFO:0009090 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`
▶	characteristics[sampling site]	optional	cell-lines	Original source term, local provenance, or finer tissue-of-origin context for the cell line
Description Original source term, local provenance, or finer tissue-of-origin context for the cell line Ontology EFO:0000688 Properties allows N/A allows not available Validators ontology — ontologies: uberon, bto The sampling site should be a valid UBERON or BTO term when it is expressed as a normalized anatomy term Examples `cervix`, `kidney`, `breast`
▶	characteristics[biorepository]	optional	cell-lines	BioBank or source from which the cell line was obtained
Description BioBank or source from which the cell line was obtained Ontology NCIT:C48800 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Source of the cell line Examples `ATCC`, `DSMZ`, `ECACC`, `Sigma-Aldrich`
▶	characteristics[cell line authentication]	optional	cell-lines	Method used to authenticate the cell line identity
Description Method used to authenticate the cell line identity Ontology PRIDE:0000955 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Authentication method used Examples `STR profiling`, `SNP fingerprinting`, `cytogenetic analysis`
▶	characteristics[developmental stage]	optional	cell-lines	Developmental stage of the donor from which the cell line was derived
Description Developmental stage of the donor from which the cell line was derived Ontology EFO:0000399 Properties allows N/A allows not available Validators ontology — ontologies: efo The developmental stage should be a valid EFO ontology term Examples `adult`, `embryonic`, `fetal`, `neonatal`
▶	characteristics[ancestry category]	optional	cell-lines	Ancestry category of the cell line donor (if known)
Description Ancestry category of the cell line donor (if known) Ontology HANCESTRO:0004 Properties allows N/A allows not available Validators ontology — ontologies: hancestro The ancestry category should be a valid HANCESTRO term Examples `European`, `African`, `East Asian`, `South Asian`

Contributors

Yasset Perez-Riverol (yperez@ebi.ac.uk) - EMBL-EBI
Deepti Jaiswal Kundu (jaiswal@ebi.ac.uk) - EMBL-EBI
Nithu Sara John (nithu@ebi.ac.uk) - EMBL-EBI
Nandana Madhusoodanan (nandana@ebi.ac.uk) - EMBL-EBI
Asier Larrea (alarre@ebi.ac.uk) - EMBL-EBI
Toan Phung (TPhung001@dundee.ac.uk) - University of Dundee
Timo Sachsenberg (timo.sachsenberg@uni-tuebingen.de) - University of Tübingen