Skip to content

Sample

Description

A Sample is a limited quantity of something to be used for testing, analysis, inspection, investigation, demonstration, or trial use. It is prepared from a Biospecimen.

Fields

individual

description : The alias of the Individual entity from which this Biospecimen or Sample was derived.
required : True
data type : Individual

name

description : A descriptive name of this Sample (e.g., GHGAS_Blood_Sample1 or GHGAS_PBMC_RNAseq_S1). This property must not include any personally identifiable data.
required : True
data type : string

type

description : The type of the Sample.
required : False
data type : Controlled Vocabulary

Permissible Values
Permissible Values Description
CF_DNA Cell Free (CF), circulating DNA was used for sequencing.
DEPLETED_RNA Depleted RNA was used for sequencing.
DS_DNA_CHIP Double-stranded DNA was used for sequencing.
FFPE_DNA Formalin-fixed, paraffin-embedded DNA was used for sequencing.
FFPE_TOTAL_RNA Formalin-fixed, paraffin-embedded total DNA was used for sequencing.
GENOMIC_DNA Genomic DNA was used for sequencing.
PCR_PRODUCTS PCR products were used for sequencing.
POLY_A_RNA Polyadenylated (polyA) RNA was used for sequencing.
SINGLE_CELL_DNA DNA originating from single cells was used for sequencing.
SINGLE_CELL_RNA RNA originating from single cells was used for sequencing.
SINGLE_CELL_NUCLEI RNA originating from single cell nuclei was used for sequencing.
SMALL_RNA Small RNA was used for sequencing.
TOTAL_RNA Total RNA was used for sequencing.

biological_replicate

description : An integer to indicate the number of a biological replicate.
required : None
data type : integer

description

description : A concise description about the Sample source, the collection method, and the protocol which was followed to process this Sample.
required : True
data type : string

storage

description : Methods by which a Sample is stored.
required : False
data type : Controlled Vocabulary

Permissible Values
Permissible Values Description
REFRIGERATOR The sample / biospecimen was stored in a refrigerator at 2°C to 5°C.
FREEZER The sample / biospecimen was stored in a freezer at -20°C.
ULTRA_LOW_FREEZER The sample / biospecimen was stored in a ultra-low freezer at -80°C.
CRYOGENIC_FREEZER The sample / biospecimen was stored in a cryogenic freezer at -150°C to -190°C.
NONE The sample / biospecimen was not stored.
OTHER The sample / biospecimen was stored with a method differing from the available options.
UNKNOWN The storage method is unknown.

disease_or_healthy

description : Whether a Condition corresponds to a disease or a healthy state.
required : False
data type : Controlled Vocabulary

Permissible Values
Permissible Values Description
DISEASE Disease state.
HEALTHY Healthy state.
NOT_APPLICABLE The distinction is not applicaple.

case_control_status

description : Whether a Condition corresponds to a treatment or a control.
required : True
data type : Controlled Vocabulary

Permissible Values
Permissible Values Description
CASE The participant is a true case for the phenotype under consideration.
CONTROL The participant is a true control for the phenotype under consideration.
OTHER The participant's status is neither case nor control.
UNKNOWN The participant's status is not known.

ega_accession

description : The EGA accession ID of an entity.
required : False
data type : string

xref

description : One or more cross-references for this Sample (e.g., this Sample may have an EBI BioSamples accession ID).
required : False
data type : string

biospecimen_name

description : A descriptive name of this Biospecimen (e.g., GHGAB_caudate_nucleus_biospecimen). This property must not include any personally identifiable data.
required : False
data type : string

biospecimen_type

description : The type of Biospecimen.
required : False
data type : string

biospecimen_description

description : A concise description about the Biospecimen source, the collection method, and the protocol which was followed to process this Biospecimen.
required : False
data type : string

biospecimen_age_at_sampling

description : The age of the Individual at the time of isolating this biospecimen.
required : True
data type : Controlled Vocabulary

Permissible Values
Permissible Values Description
0_TO_5 Age between 0 to 5.
6_TO_10 Age between 6 to 10.
11_TO_15 Age between 11 to 15.
16_TO_20 Age between 16 to 20.
21_TO_25 Age between 21 to 25.
26_TO_30 Age between 26 to 30.
31_TO_35 Age between 31 to 35.
36_TO_40 Age between 36 to 40.
41_TO_45 Age between 41 to 45.
46_TO_50 Age between 46 to 50.
51_TO_55 Age between 51 to 55.
56_TO_60 Age between 56 to 60.
61_TO_65 Age between 61 to 65.
66_TO_70 Age between 66 to 70.
71_TO_75 Age between 71 to 75.
76_TO_80 Age between 76 to 80.
81_OR_OLDER Age above 80.
UNKNOWN Age range unknown.

biospecimen_vital_status_at_sampling

description : Vital Status of the Individual at the time of isolating this biospecimen (e.g., alive).
required : False
data type : Controlled Vocabulary

Permissible Values
Permissible Values Description
ALIVE Showing characteristics of life; displaying signs of life.
DECEASED The cessation of life.
UNKNOWN Vital status is unknown.

biospecimen_tissue_term

description : The tissue this Biospecimen originated from. Should be a term from the BRENDA Tissue Ontology vocabulary (e.g., kidney, blood, melanoma cell).
required : False
data type : string

biospecimen_tissue_id

description : The corresponding ontology ID for the biospecimen_tissue_term (e.g., BTO:0000671, BTO:0000089, BTO:0000848).
required : False
data type : string

biospecimen_isolation

description : Method or device employed for collecting/isolating this Biospecimen.
required : False
data type : Controlled Vocabulary

Permissible Values
Permissible Values Description
BLOOD_DRAW Extraction of a blood specimen.
SURGICAL_REMOVAL Extraction of a sample or part of an organ in a surgical procedure.
SALIVA_COLLECTION Collection of saliva.
BUCCAL_SWAB Sample collection using a buccal swab.

biospecimen_storage

description : Methods by which this Biospecimen is stored.
required : False
data type : Controlled Vocabulary

Permissible Values
Permissible Values Description
REFRIGERATOR The sample / biospecimen was stored in a refrigerator at 2°C to 5°C.
FREEZER The sample / biospecimen was stored in a freezer at -20°C.
ULTRA_LOW_FREEZER The sample / biospecimen was stored in a ultra-low freezer at -80°C.
CRYOGENIC_FREEZER The sample / biospecimen was stored in a cryogenic freezer at -150°C to -190°C.
NONE The sample / biospecimen was not stored.
OTHER The sample / biospecimen was stored with a method differing from the available options.
UNKNOWN The storage method is unknown.

attributes

description : Key/value pairs corresponding to an entity.
required : False
data type : Attribute

alias

description : The alias for an entity at the time of submission.
required : True
data type : string