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