Skip to content

Biosamples

Term Description Type Properties Example Enum
biosampleStatus Ontology value from Experimental Factor Ontology (EFO) Material Entity term (BFO:0000040). Classification of the sample in abnormal sample (EFO:0009655) or reference sample (EFO:0009654). object id, label [{"id": "EFO:0009654", "label": "reference sample"}, {"id": "EFO:0009655", "label": "abnormal sample"}, {"id": "EFO:0009656", "label": "neoplastic sample"}, {"id": "EFO:0010941", "label": "metastasis sample"}, {"id": "EFO:0010942", "label": "primary tumor sample"}, {"id": "EFO:0010943", "label": "recurrent tumor sample"}] NA
collectionDate Date of biosample collection in ISO8601 format. string NA 2021-04-23 NA
collectionMoment Individual's or cell cullture age at the time of sample collection in the ISO8601 duration format P[n]Y[n]M[n]DT[n]H[n]M[n]S. string NA P32Y6M1D, P7D NA
diagnosticMarkers NA array id, label NA NA
histologicalDiagnosis Disease diagnosis that was inferred from the histological examination. RECOMMENDED. object id, label [{"id": "NCIT:C3778", "label": "Serous Cystadenocarcinoma"}] NA
id Biosample identifier (external accession or internal ID). string NA S0001 NA
individualId Reference to the individual from which that sample was obtained. string NA P0001 NA
info Placeholder to allow the Beacon to return any additional information that is necessary or could be of interest in relation to the query or the entry returned. It is recommended to encapsulate additional informations in this attribute instead of directly adding attributes at the same level than the others in order to avoid collision in the names of attributes in future versions of the specification. object NA NA NA
measurements Definition of a measurement class. Provenance: GA4GH Phenopackets v2 Measurement array assayCode, date, measurementValue, notes, observationMoment, procedure NA NA
notes Any relevant info about the biosample that does not fit into any other field in the schema. string NA Some free text NA
obtentionProcedure Ontology value from NCIT Intervention or Procedure ontology term (NCIT:C25218) describing the procedure for sample obtention, e.g. NCIT:C15189 (biopsy). object ageAtProcedure, bodySite, dateOfProcedure, procedureCode [{"code": {"id": "NCIT:C15189", "label": "biopsy"}}, {"code": {"id": "NCIT:C157179", "label": "FGFR1 Mutation Analysis"}}] NA
pathologicalStage Pathological stage, if applicable, preferably as subclass of NCIT:C28108 - Disease Stage Qualifier. RECOMMENDED. object id, label [{"id": "NCIT:C27977", "label": "Stage IIIA"}] NA
pathologicalTnmFinding NA array id, label [{"id": "NCIT:C48725", "label": "T2a Stage Finding"}, {"id": "NCIT:C48709", "label": "N1c Stage Finding"}, {"id": "NCIT:C48699", "label": "M0 Stage Finding"}] NA
phenotypicFeatures Used to describe a phenotype that characterizes the subject or biosample. array evidence, excluded, featureType, modifiers, notes, onset, resolution, severity NA NA
sampleOriginDetail Tissue from which the sample was taken or sample origin matching the category set in 'sampleOriginType'. Value from Uber-anatomy ontology (UBERON) or BRENDA tissue / enzyme source (BTO), Ontology for Biomedical Investigations (OBI) or Cell Line Ontology (CLO), e.g. 'cerebellar vermis' (UBERON:0004720), 'HEK-293T cell' (BTO:0002181), 'nasopharyngeal swab specimen' (OBI:0002606), 'cerebrospinal fluid specimen' (OBI:0002502). object id, label [{"id": "UBERON:0000474", "label": "female reproductive system"}, {"id": "BTO:0002181", "label": "HEK-293T cell"}, {"id": "OBI:0002606", "label": "nasopharyngeal swab specimen"}] NA
sampleOriginType Category of sample origin. Value from Ontology for Biomedical Investigations (OBI) material entity (BFO:0000040) ontology, e.g. 'specimen from organism' (OBI:0001479),'xenograft' (OBI:0100058), 'cell culture' (OBI:0001876) object id, label [{"id": "OBI:0001479", "label": "specimen from organism"}, {"id": "OBI:0001876", "label": "cell culture"}, {"id": "OBI:0100058", "label": "xenograft"}] NA
sampleProcessing Status of how the specimen was processed,e.g. a child term of EFO:0009091. object id, label [{"id": "EFO:0009129", "label": "mechanical dissociation"}] NA
sampleStorage Status of how the specimen was stored. object id, label NA
tumorGrade Term representing the tumor grade. Child term of NCIT:C28076 (Disease Grade Qualifier) or equivalent. object id, label [{"id": "NCIT:C28080", "label": "Grade 3a"}] NA
tumorProgression Tumor progression category indicating primary, metastatic or recurrent progression. Ontology value from Neoplasm by Special Category ontology (NCIT:C7062), e.g. NCIT:C84509 (Primary Malignant Neoplasm). object id, label [{"id": "NCIT:C84509", "label": "Primary Malignant Neoplasm"}, {"id": "NCIT:C4813", "label": "Recurrent Malignant Neoplasm"}] NA

Examples

These are examples extracted directly from the GitHub repository.

{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "biosampleStatus": {
        "id": "EFO:0009655",
        "label": "abnormal sample"
    },
    "id": "sample-example-0001",
    "sampleOriginType": {
        "id": "UBERON:0000474",
        "label": "female reproductive system"
    }
}
{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "biosampleStatus": {
        "id": "EFO:0009655",
        "label": "abnormal sample"
    },
    "collectionDate": "2020-09-11",
    "collectionMoment": "P32Y6M1D",
    "id": "sample-example-0001",
    "obtentionProcedure": {
        "procedureCode": {
            "id": "OBI:0002654",
            "label": "needle biopsy"
        }
    },
    "sampleOriginType": {
        "id": "UBERON:0000992",
        "label": "ovary"
    }
}