oncology-metadata

v1.0.0 sample

SDRF template for cancer/oncology study samples with tumor staging, grading, and clinical outcome metadata. Extends clinical-metadata with oncology-specific columns. Combine with organism template (human, vertebrates) and technology template (ms-proteomics, affinity-proteomics).

Key Guidance

The oncology-metadata template extends clinical-metadata with cancer-specific staging,

grading, and outcome columns. It supports multiple standardized staging systems.

Key guidance:

characteristics[disease staging]: General disease stage (stage I-IV). Use NCIT or

EFO terms.

characteristics[tumor stage]: TNM notation (e.g., T2N1M0). Prefix with p for

pathological or c for clinical staging.

Specialized staging systems (use the appropriate column for the cancer type):
characteristics[dukes stage]: Colorectal cancer (A, B, C, D).
characteristics[ann arbor stage]: Lymphoma (I-IV with A/B/E/S suffix).
characteristics[gleason score]: Prostate cancer (sum or components: 3+4, 4+3).
characteristics[weiss grade]: Adrenal cortical carcinoma (low, high).
characteristics[histologic subtype]: Molecular/histologic classification (luminal A,

triple-negative, adenocarcinoma, squamous cell carcinoma).

characteristics[survival time] / characteristics[last follow up]: Time with unit

for clinical outcome tracking.

characteristics[metastasis site] / characteristics[biopsy site]: UBERON/BTO terms

for anatomical locations.

Inherits all clinical-metadata columns (compound, dose, treatment, demographics).

Inheritance

base → sample-metadata → clinical-metadata → oncology-metadata

Columns

17 own + 39 inherited = 56 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	Anatomical part of the organism from which sample was derived
Description Anatomical part of the organism from which sample was derived 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	clinical-metadata	Disease state of the sample
Description Disease state of the sample Ontology EFO:0000408 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`
▶	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`
▶	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: `^.+$` Validation hash string
▶	characteristics[pooled sample]	optional	sample-metadata	Whether the sample is a pooled sample combining material from multiple biological sources. Use 'n...
Description Whether the sample is a pooled sample combining material from multiple biological sources. Use 'not pooled' for individual samples, 'pooled' when sources are unknown, or 'SN=sample1;SN=sample2' to list source names. Ontology NCIT:C165587 Properties allows N/A allows not available Validators values — values: `not pooled`, `pooled` pattern — pattern: `^(not pooled\|pooled\|SN=.+(;SN=.+)*)$` 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[compound]	optional	clinical-metadata	Chemical compound or drug applied to sample
Description Chemical compound or drug applied to sample Ontology CHEBI:24431 Properties allows N/A allows not available Validators ontology — ontologies: chebi, ncit, efo The compound should be a valid ChEBI, NCIT, or EFO term Examples `doxorubicin`, `cisplatin`, `tamoxifen`, `metformin`
▶	characteristics[dose]	optional	clinical-metadata	Dose or concentration of compound treatment
Description Dose or concentration of compound treatment Ontology NCIT:C25488 Properties allows N/A allows not available Validators number_with_unit Dose with unit Examples `10 mg/kg`, `50 uM`, `100 nM`, `5 mg`
▶	characteristics[exposure duration]	optional	clinical-metadata	Duration of treatment exposure
Description Duration of treatment exposure Ontology NCIT:C83280 Properties allows N/A allows not available Validators number_with_unit Exposure duration with time unit Examples `24 hour`, `5 day`, `30 minute`, `2 week`
▶	characteristics[treatment status]	optional	clinical-metadata	Treatment status at time of sampling
Description Treatment status at time of sampling Ontology NCIT:C45501 Properties allows N/A allows not available Validators values — values: `pre-treatment`, `on treatment`, `post-treatment`, `treatment naive` Treatment status
▶	characteristics[treatment response]	optional	clinical-metadata	Response to treatment (for studies measuring therapeutic outcomes)
Description Response to treatment (for studies measuring therapeutic outcomes) Ontology NCIT:C50995 Properties allows N/A allows not available Validators ontology — ontologies: ncit Treatment response should be a valid NCIT term Examples `complete response`, `partial response`, `progressive disease`, `stable disease`
▶	characteristics[pre-existing condition]	optional	clinical-metadata	Pre-existing medical conditions or comorbidities
Description Pre-existing medical conditions or comorbidities Ontology NCIT:C54056 Properties allows N/A allows not available Validators ontology — ontologies: mondo, efo, doid Pre-existing condition should be a valid MONDO, EFO, or DOID term Examples `diabetes mellitus`, `hypertension`, `obesity`
▶	characteristics[body mass index]	optional	clinical-metadata	Body mass index (BMI) in kg/m^2
Description Body mass index (BMI) in kg/m^2 Ontology EFO:0004340 Properties allows N/A allows not available Validators pattern — pattern: `^[\d.]+$` Numeric BMI value Examples `24.5`, `31.2`, `18.7`
▶	characteristics[smoking status]	optional	clinical-metadata	Patient smoking status
Description Patient smoking status Ontology NCIT:C19796 Properties allows N/A allows not available Validators ontology — ontologies: ncit Smoking status should be a child term of NCIT:C19796 Examples `never smoker`, `former smoker`, `current smoker`
▶	characteristics[menopausal status]	optional	clinical-metadata	Menopausal status for female patients
Description Menopausal status for female patients Ontology NCIT:C16151 Properties allows N/A allows not available Validators values — values: `pre-menopausal`, `peri-menopausal`, `post-menopausal` Menopausal status
▶	characteristics[genetic modification]	optional	clinical-metadata	Method of genetic modification (knockout, knockdown, overexpression, transduction)
Description Method of genetic modification (knockout, knockdown, overexpression, transduction) Ontology EFO:0000510 Properties allows N/A allows not available Validators ontology — ontologies: efo Genetic modification method should be a valid EFO term Examples `knockout`, `knockdown`, `overexpression`, `transduction`, `CRISPR-Cas9`
▶	characteristics[phenotype]	optional	clinical-metadata	Observable characteristics or traits (drug sensitivity, molecular markers, expression phenotypes)
Description Observable characteristics or traits (drug sensitivity, molecular markers, expression phenotypes) Ontology EFO:0000651 Properties allows N/A allows not available Validators ontology — ontologies: pato, efo Phenotype should be a valid PATO or EFO term, or free text Examples `drug resistant`, `HER2-positive`, `high expresser`, `wild-type phenotype`
▶	characteristics[weight]	optional	clinical-metadata	Body weight of the subject
Description Body weight of the subject Ontology EFO:0004324 Properties allows N/A allows not available Validators number_with_unit Weight with unit Examples `70 kg`, `55 kg`, `154 lb`
▶	characteristics[height]	optional	clinical-metadata	Height of the subject
Description Height of the subject Ontology EFO:0004339 Properties allows N/A allows not available Validators number_with_unit Height with unit Examples `175 cm`, `1.75 m`, `160 cm`
▶	characteristics[sampling site]	optional	clinical-metadata	Specific anatomical location or context of sampling within the organism part
Description Specific anatomical location or context of sampling within the organism part Ontology EFO:0000688 Properties allows N/A allows not available Validators ontology — ontologies: uberon, bto Sampling site should be a valid UBERON or BTO term, or a descriptive term Examples `tumor`, `normal tissue adjacent to tumor`, `left ventricle`, `frontal cortex`
▶	characteristics[genotype]	optional	clinical-metadata	Known genetic variant, mutation, or genotype of the subject
Description Known genetic variant, mutation, or genotype of the subject Ontology EFO:0000513 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Genotype as free text (gene name + variant) Examples `BRCA1 mutation carrier`, `KRAS G12D mutant`, `wild type`, `TP53 R175H`
▶	characteristics[disease staging]	optional	oncology-metadata	Disease progression stage (stage I-IV, chronic phase, end stage)
Description Disease progression stage (stage I-IV, chronic phase, end stage) Ontology EFO:0000410 Properties allows N/A allows not available Validators ontology — ontologies: ncit, efo Disease staging should be a valid NCIT or EFO term Examples `stage I`, `stage II`, `stage III`, `stage IV`, `chronic phase`, `end stage`
▶	characteristics[tumor grading]	optional	oncology-metadata	Histological tumor grade (describes how abnormal cells look)
Description Histological tumor grade (describes how abnormal cells look) Ontology OBI:0600002 Properties allows N/A allows not available Validators ontology — ontologies: ncit Tumor grading should be a valid NCIT term Examples `grade 1`, `grade 2`, `grade 3`, `grade 4`, `high grade`, `low grade`
▶	characteristics[tumor stage]	optional	oncology-metadata	TNM staging notation (describes extent of cancer spread)
Description TNM staging notation (describes extent of cancer spread) Ontology EFO:0004925 Properties allows N/A allows not available Validators ontology — ontologies: ncit Tumor stage in TNM notation Examples `T2N1M0`, `T3N0M0`, `T1N0M0`, `T4N2M1`
▶	characteristics[tumor size]	optional	oncology-metadata	Tumor size measurement
Description Tumor size measurement Ontology EFO:0004134 Properties allows N/A allows not available Validators number_with_unit Tumor size with unit Examples `2.5 cm`, `15 mm`, `0.8 cm`
▶	characteristics[tumor mass]	optional	oncology-metadata	Tumor mass/weight measurement
Description Tumor mass/weight measurement Ontology EFO:0007062 Properties allows N/A allows not available Validators number_with_unit Tumor mass with unit Examples `15 g`, `250 mg`
▶	characteristics[histologic subtype]	optional	oncology-metadata	Cancer molecular or histologic subtype
Description Cancer molecular or histologic subtype Ontology NCIT:C19790 Properties allows N/A allows not available Validators ontology — ontologies: ncit Histologic subtype should be a valid NCIT term Examples `luminal A`, `luminal B`, `HER2-enriched`, `triple-negative`, `adenocarcinoma`, `squamous cell carcinoma`
▶	characteristics[metastasis site]	optional	oncology-metadata	Location where cancer has spread from primary site
Description Location where cancer has spread from primary site Ontology NCIT:C172233 Properties allows N/A allows not available Validators ontology — ontologies: uberon, bto Metastasis site should be a valid UBERON or BTO term Examples `liver`, `lung`, `bone`, `brain`
▶	characteristics[biopsy site]	optional	oncology-metadata	Specific anatomical location of biopsy
Description Specific anatomical location of biopsy Ontology EFO:0000288 Properties allows N/A allows not available Validators ontology — ontologies: uberon, bto Biopsy site should be a valid UBERON or BTO term Examples `breast`, `colon`, `prostate`, `lung`
▶	characteristics[clinical data]	optional	oncology-metadata	Free-text clinical details (receptor status, treatment history, surgical details)
Description Free-text clinical details (receptor status, treatment history, surgical details) Ontology EFO:0030083 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Free-text clinical data Examples `ER+/PR+/HER2-`, `prior chemotherapy with doxorubicin`, `surgical resection performed`
▶	characteristics[clinical history]	optional	oncology-metadata	Relevant medical history information for the patient
Description Relevant medical history information for the patient Ontology EFO:0000352 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Free-text clinical history Examples `family history of breast cancer`, `previous radiation therapy`, `no significant medical history`
▶	characteristics[survival time]	optional	oncology-metadata	Patient survival time for survival analysis studies
Description Patient survival time for survival analysis studies Ontology EFO:0000714 Properties allows N/A allows not available Validators number_with_unit Survival time with unit Examples `24 month`, `3 year`, `180 day`
▶	characteristics[last follow up]	optional	oncology-metadata	Time of last clinical follow-up for longitudinal studies
Description Time of last clinical follow-up for longitudinal studies Ontology EFO:0007058 Properties allows N/A allows not available Validators number_with_unit Last follow-up time with unit Examples `36 month`, `5 year`, `365 day`
▶	characteristics[mitotic rate]	optional	oncology-metadata	Number of mitoses per high-power field (indicator of tumor proliferation)
Description Number of mitoses per high-power field (indicator of tumor proliferation) Ontology NCIT:C62401 Properties allows N/A allows not available Validators pattern — pattern: `^[\d]+(/\d+\s*HPF)?$` Mitotic rate as count or count per HPF Examples `5`, `12/10 HPF`, `3/10 HPF`
▶	characteristics[dukes stage]	optional	oncology-metadata	Dukes staging for colorectal cancer (A, B, C, D)
Description Dukes staging for colorectal cancer (A, B, C, D) Ontology NCIT:C16475 Properties allows N/A allows not available Validators values — values: `A`, `B`, `C`, `D` Dukes stage (A-D)
▶	characteristics[ann arbor stage]	optional	oncology-metadata	Ann Arbor staging for lymphoma (I, II, III, IV with optional A/B suffix)
Description Ann Arbor staging for lymphoma (I, II, III, IV with optional A/B suffix) Ontology NCIT:C16282 Properties allows N/A allows not available Validators pattern — pattern: `^(I\|II\|III\|IV)[AB]?[ES]?$` Ann Arbor stage (I-IV with optional A/B suffix for symptoms, E for extranodal, S for spleen) Examples `IA`, `IIB`, `IIIA`, `IVB`, `IIE`
▶	characteristics[gleason score]	optional	oncology-metadata	Gleason score for prostate cancer grading (sum of two pattern grades, range 2-10)
Description Gleason score for prostate cancer grading (sum of two pattern grades, range 2-10) Ontology NCIT:C28091 Properties allows N/A allows not available Validators pattern — pattern: `^\d+(\+\d+)?$` Gleason score as sum (e.g., 7) or component pattern (e.g., 3+4) Examples `7`, `3+4`, `4+3`, `9`, `5+4`
▶	characteristics[weiss grade]	optional	oncology-metadata	Weiss scoring system for adrenal cortical carcinoma (low or high)
Description Weiss scoring system for adrenal cortical carcinoma (low or high) Ontology NCIT:C160679 Properties allows N/A allows not available Validators values — values: `low`, `high` Weiss grade (low or high)

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