biosamples defaultSchema

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.

MINMID

{
    "$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"
    }
}