ID

39055

Description

SBP is the national coordination platform for human and non-human biobanks. The dataset covers the different biobanking processes from sampling to retrieval and propose a common language to describe preanalytical attributes of samples. It also includes some health related data required for initial searches of suitable samples. Finally, it covers fields related to quality of biobanking processes. More information can be found at https://swissbiobanking.ch

Link

https://swissbiobanking.ch

Keywords

Versions (1)
  1. 11/25/19 11/25/19 -
Copyright Holder

Swiss Biobanking Platform (SBP)

Uploaded on

November 25, 2019

DOI

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License

Creative Commons BY-NC 3.0
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Swiss Biobanking Platform (SBP)

English

Data Dictionary Liquid

1 forms  
  1. StudyEvent: ODM
    1. Data Dictionary Liquid
Patient related data
Description

Patient related data

Alias
UMLS CUI-1
C2707520
Unique identifier of patient
Description

Specific to each Institute / institution

Data type

text

Alias
UMLS CUI [1,1]
C0030705
UMLS CUI [1,2]
C0600091
Unique patient identifier generated by the biobank
Description

Externalisable without compromising patient identity

Data type

text

Alias
UMLS CUI [1,1]
C0030705
UMLS CUI [1,2]
C0600091
UMLS CUI [1,3]
C0205276
Unique identifier of patient at the Swiss level
Description

Corresponds to H code of Patholink

Data type

text

Alias
UMLS CUI [1,1]
C0030705
UMLS CUI [1,2]
C0600091
UMLS CUI [1,3]
C2348867
Sex of the subject
Description

Source: Administrative HL-7

Data type

text

Alias
UMLS CUI [1]
C0150831
Data related to case
Description

Data related to case

Alias
UMLS CUI-1
C1511726
UMLS CUI-2
C2585021
UMLS CUI-3
C1698493
Unique identifier of case (may include different sample types) specific to each institute
Description

ID_case

Data type

text

Alias
UMLS CUI [1,1]
C1698493
UMLS CUI [1,2]
C0600091
Type of consent signed by the patient allowing sampling and use of specimen
Description

consent_type

Data type

integer

Alias
UMLS CUI [1,1]
C0009797
UMLS CUI [1,2]
C4288222
UMLS CUI [1,3]
C0030705
Last answer of the patient to the selected type of consent
Description

consent_answer

Data type

integer

Alias
UMLS CUI [1,1]
C0021430
UMLS CUI [1,2]
C1517741
UMLS CUI [1,3]
C1706817
Is the date of the last update of the consent decision known?
Description

consent_date

Data type

integer

Alias
UMLS CUI [1,1]
C0205309
UMLS CUI [1,2]
C0011008
UMLS CUI [1,3]
C1519814
UMLS CUI [1,4]
C0021430
If the date of the last update of the consent decision is reported, please fill in:
Description

consent_date

Data type

date

Alias
UMLS CUI [1,1]
C0011008
UMLS CUI [1,2]
C1519814
UMLS CUI [1,3]
C0021430
Is the patient's age at collection known?
Description

Calculation of (patient age) - (collection time)

Data type

integer

Alias
UMLS CUI [1,1]
C4698447
UMLS CUI [1,2]
C0205309
If patient age at collection is known, please fill in:
Description

Calculation of (patient age) - (collection time)

Data type

integer

Alias
UMLS CUI [1,1]
C4698447
UMLS CUI [1,2]
C0205309
Unit for patient age at collection
Description

patient_age_unit

Data type

integer

Alias
UMLS CUI [1,1]
C4698447
UMLS CUI [1,2]
C0439148
Primary disease diagnosis
Description

patient_prim_disease

Data type

integer

Alias
UMLS CUI [1,1]
C0277554
UMLS CUI [1,2]
C0011900
If "Known" selected, please specify:
Description

Ontology based on ICD-10

Data type

text

Alias
UMLS CUI [1,1]
C0277554
UMLS CUI [1,2]
C0011900
Are other diseases, different from primary disease, known?
Description

Can be multiple. Ontology based on ICD-10

Data type

integer

Alias
UMLS CUI [1,1]
C2359476
UMLS CUI [1,2]
C1137110
If "Yes" selected, please specify which other diseases
Description

Ontology based on ICD-10 - can be multiple

Data type

text

Alias
UMLS CUI [1,1]
C2359476
UMLS CUI [1,2]
C1137110
Collection of the specimen
Description

Collection of the specimen

Alias
UMLS CUI-1
C0200345
UMLS CUI-2
C1511726
UMLS CUI-3
C2585021
UMLS CUI-4
C2347026
Localisation of specimen source
Description

= code of the Institution Global Local Number = GS + GLN: https://www.gs1.org/standards/id-keys/gln

Data type

text

Alias
UMLS CUI [1,1]
C2347026
UMLS CUI [1,2]
C0449416
UMLS CUI [1,3]
C0450429
Department where specimen is collected
Description

collection_departement

Data type

text

Alias
UMLS CUI [1,1]
C2347027
UMLS CUI [1,2]
C1704729
Service/ward where specimen is collected
Description

collection_service

Data type

text

Alias
UMLS CUI [1,1]
C2347027
UMLS CUI [1,2]
C0557854
Forname and surname of the person who collect the specimen
Description

collection_person

Data type

text

Alias
UMLS CUI [1,1]
C2347027
UMLS CUI [1,2]
C1522390
UMLS CUI [1,3]
C1999110
UMLS CUI [1,4]
C0027365
Date and time of sampling
Description

collection_time

Data type

datetime

Alias
UMLS CUI [1,1]
C2347027
UMLS CUI [1,2]
C1264639
Year of sampling, calculated from collection_time (no need to document)
Description

collection_year

Data type

integer

Alias
UMLS CUI [1,1]
C2347027
UMLS CUI [1,2]
C0439234
Unique Identifier of specimen (primary sample)
Description

specimen_ID

Data type

text

Alias
UMLS CUI [1,1]
C2347026
UMLS CUI [1,2]
C4071975
Type of specimen collected
Description

Source: SPREC 3.0 Type of sample

Data type

text

Alias
UMLS CUI [1]
C2347029
Type of primary container in which the specimen is collected
Description

Source: SPREC 3.0 Type of primary container

Data type

text

Alias
UMLS CUI [1,1]
C0205225
UMLS CUI [1,2]
C0183391
UMLS CUI [1,3]
C0332307
Volume of primary container in which specimen is collected
Description

primary_container_volume

Data type

float

Measurement units
  • mL
Alias
UMLS CUI [1,1]
C0449468
UMLS CUI [1,2]
C0205225
UMLS CUI [1,3]
C0183391
mL
Volume of specimen (primary sample)
Description

specimen_volume

Data type

float

Measurement units
  • mL
Alias
UMLS CUI [1,1]
C0205225
UMLS CUI [1,2]
C2347026
UMLS CUI [1,3]
C0449468
mL
Additives or specific conditions applied
Description

collection_special_conditions

Data type

integer

Alias
UMLS CUI [1,1]
C2347026
UMLS CUI [1,2]
C0442796
UMLS CUI [1,3]
C4048755
UMLS CUI [2,1]
C2347026
UMLS CUI [2,2]
C0205369
UMLS CUI [2,3]
C0348080
If "Other" selected: Description of special conditions
Description

collection_special_conditions_text

Data type

text

Alias
UMLS CUI [1,1]
C0205369
UMLS CUI [1,2]
C0348080
UMLS CUI [1,3]
C0205394
Metabolic status of patient
Description

Yes = patient has not eaten overnight

Data type

integer

Alias
UMLS CUI [1,1]
C0311400
UMLS CUI [1,2]
C0449438
UMLS CUI [1,3]
C0030705
Temperature conditions before transport
Description

RT = room temperature:18-28 °C LN = either vapor or liquid phase (this information should be documented in the Biobank's SOP) To calculate SPREC 3.0 Precentrifugation (delay between collection and processing)

Data type

integer

Alias
UMLS CUI [1,1]
C0039476
UMLS CUI [1,2]
C0348080
UMLS CUI [1,3]
C0332152
UMLS CUI [1,4]
C0040756
Transport of the specimen
Description

Transport of the specimen

Alias
UMLS CUI-1
C2347026
UMLS CUI-2
C0040756
UMLS CUI-3
C1511726
UMLS CUI-4
C2585021
UMLS CUI-5
C2347026
For internal use only - precision if transported item is the unprocessed specimen or if specimen has already been processed (=sample)
Description

transport_sample_type

Data type

integer

Alias
UMLS CUI [1,1]
C2347026
UMLS CUI [1,2]
C1522240
UMLS CUI [1,3]
C0332307
Forename and surname of person who transports specimen (or sample)
Description

transport_person

Data type

text

Alias
UMLS CUI [1,1]
C2347026
UMLS CUI [1,2]
C0040756
UMLS CUI [1,3]
C1522390
UMLS CUI [1,4]
C199911
UMLS CUI [1,5]
C0027365
Transport mode - migth be important depending on the application
Description

transport_mode

Data type

integer

Alias
UMLS CUI [1,1]
C1550400
UMLS CUI [1,2]
C2347026
Date & time when transport starts
Description

transport_time

Data type

integer

Alias
UMLS CUI [1,1]
C2347026
UMLS CUI [1,2]
C1273722
UMLS CUI [1,3]
C0808070
UMLS CUI [1,4]
C0040223
If date & time when transport starts is known, please fill in:
Description

transport_time_specify

Data type

datetime

Alias
UMLS CUI [1,1]
C2347026
UMLS CUI [1,2]
C1273722
UMLS CUI [1,3]
C0808070
UMLS CUI [1,4]
C0040223
Temperature conditions during transport
Description

RT = room temperature:18-28 °C LN = either vapor or liquid phase (this information should be documented in the Biobank's SOP) To calculate SPREC 3.0 Precentrifugation (delay between collection and processing) Standard PREanalytical Code Version 3.0 Betsou et al. Biopreserv Biobank. 2018 Jan 29. doi: 10.1089/bio.2017.0109 Temperature ranges from Table 1: Precentrifugation (delay between collection and processing)

Data type

integer

Alias
UMLS CUI [1,1]
C2347026
UMLS CUI [1,2]
C1273722
UMLS CUI [1,3]
C0039476
Reception of the specimen
Description

Reception of the specimen

Alias
UMLS CUI-1
C2347026
UMLS CUI-2
C0544683
UMLS CUI-3
C1511726
UMLS CUI-4
C2585021
UMLS CUI-5
C2347026
Forename and surname of person who receives specimen (or sample)
Description

reception_person

Data type

text

Alias
UMLS CUI [1,1]
C0544683
UMLS CUI [1,2]
C2347026
UMLS CUI [1,3]
C1522390
UMLS CUI [1,4]
C199911
UMLS CUI [1,5]
C0027365
Date & time when specimen (or sample) arrives at reception
Description

reception_time

Data type

integer

Alias
UMLS CUI [1,1]
C2347026
UMLS CUI [1,2]
C0544683
UMLS CUI [1,3]
C1264639
If date & time when specimen (or sample) arrives at reception is known, please fill in:
Description

reception_time_specify

Data type

datetime

Alias
UMLS CUI [1,1]
C2347026
UMLS CUI [1,2]
C0544683
UMLS CUI [1,3]
C1264639
Is the person from which the specimen was extracted infected?
Description

Y = person from which specimen was extracted is infected

Data type

integer

Alias
UMLS CUI [1,1]
C2347026
UMLS CUI [1,2]
C0013018
UMLS CUI [1,3]
C0517627
If the specimen is know to be infected (specimen_infectious Y), precision of type of infection
Description

specimen_infectious_details

Data type

integer

Alias
UMLS CUI [1,1]
C2347026
UMLS CUI [1,2]
C0013018
UMLS CUI [1,3]
C0457463
If "Other" selected: Precision of type of infection
Description

specimen_infectious_details_text

Data type

text

Alias
UMLS CUI [1,1]
C2347026
UMLS CUI [1,2]
C0013018
UMLS CUI [1,3]
C0205394
UMLS CUI [1,4]
C0457463
Sample processing
Description

Sample processing

Alias
UMLS CUI-1
C0037793
UMLS CUI-2
C1511726
UMLS CUI-3
C2585021
UMLS CUI-4
C0370003
Forename and surename of person who processes specimen
Description

If not done by a single person, it should be documented who does what / when

Data type

text

Alias
UMLS CUI [1,1]
C1709694
UMLS CUI [1,2]
C2347026
UMLS CUI [1,3]
C0027361
Date & time when processing starts
Description

Correspons to start time of first centrifuation if specimen is centrifuged To calculate SPREC 3.0 Precentrifugation (delay between collection and processing)

Data type

integer

Alias
UMLS CUI [1,1]
C1709694
UMLS CUI [1,2]
C2347026
UMLS CUI [1,3]
C0808070
UMLS CUI [1,4]
C0040223
If "Yes" selected, please fill in the date & time when processing started
Description

Correspons to start time of first centrifuation if specimen is centrifuged To calculate SPREC 3.0 Precentrifugation (delay between collection and processing)

Data type

datetime

Alias
UMLS CUI [1,1]
C1709694
UMLS CUI [1,2]
C2347026
UMLS CUI [1,3]
C0808070
UMLS CUI [1,4]
C0040223
Temperature conditions during processing = temperature before centrifugation (if applicable)
Description

RT = room temperature:18-28 °C LN = either vapor or liquid phase (this information should be documented in the Biobank's SOP) To calculate SPREC 3.0 Precentrifugation (delay between collection and processing)

Data type

integer

Alias
UMLS CUI [1,1]
C1709694
UMLS CUI [1,2]
C2347026
UMLS CUI [1,3]
C0039476
Special conditions during processing
Description

processing_special_conditions

Data type

integer

Alias
UMLS CUI [1,1]
C1709694
UMLS CUI [1,2]
C2347026
UMLS CUI [1,3]
C0205555
UMLS CUI [1,4]
C0348080
If "Other" selected: Description of special conditions
Description

processing_special_conditions_text

Data type

text

Alias
UMLS CUI [1,1]
C1709694
UMLS CUI [1,2]
C2347026
UMLS CUI [1,3]
C0205555
UMLS CUI [1,4]
C0348080
UMLS CUI [1,5]
C0205394
Force of first centrifugation
Description

To calculate SPREC 3.0 Centrifugation

Data type

integer

Alias
UMLS CUI [1,1]
C0205435
UMLS CUI [1,2]
C0007703
UMLS CUI [1,3]
C0441722
If the force of first centrifugation is known, please fill in:
Description

To calculate SPREC 3.0 Centrifugation

Data type

integer

Measurement units
  • g/dl
Alias
UMLS CUI [1,1]
C0205435
UMLS CUI [1,2]
C0007703
UMLS CUI [1,3]
C0441722
g/dl
Temperature conditions during first centrifugation
Description

RT = room temperature:18-28 °C To calculate SPREC 3.0 Centrifugation

Data type

integer

Alias
UMLS CUI [1,1]
C0205435
UMLS CUI [1,2]
C0007703
UMLS CUI [1,3]
C0039476
Duration of first centrifugation
Description

To calculate SPREC 3.0 Centrifugation

Data type

integer

Alias
UMLS CUI [1,1]
C0205435
UMLS CUI [1,2]
C0007703
UMLS CUI [1,3]
C0449238
If the duration of first centrifugation is known, please fill in:
Description

To calculate SPREC 3.0 Centrifugation

Data type

integer

Measurement units
  • min
Alias
UMLS CUI [1,1]
C0205435
UMLS CUI [1,2]
C0007703
UMLS CUI [1,3]
C0449238
min
Is the brake on during decelaration?
Description

"With braking" = brake is on during decelaration To calculate SPREC 3.0 Centrifugation

Data type

integer

Alias
UMLS CUI [1,1]
C0205435
UMLS CUI [1,2]
C0007703
UMLS CUI [1,3]
C0011100
UMLS CUI [1,4]
C0337108
Force of second centrifugation
Description

To calculate SPREC 3.0 Second centrifugation

Data type

integer

Alias
UMLS CUI [1,1]
C0205436
UMLS CUI [1,2]
C0007703
UMLS CUI [1,3]
C0441722
If the force of second centrifugation is known, please fill in:
Description

To calculate SPREC 3.0 Second centrifugation

Data type

text

Measurement units
  • g
Alias
UMLS CUI [1,1]
C0205436
UMLS CUI [1,2]
C0007703
UMLS CUI [1,3]
C0441722
g
Temperature conditions during second centrifugation
Description

RT = room temperature:18-28 °C To calculate SPREC 3.0 Second centrifugation Standard PREanalytical Code Version 3.0 Betsou et al. Biopreserv Biobank. 2018 Jan 29. doi: 10.1089/bio.2017.0109 Temperature ranges from Table 1: Postcentrifugation delay

Data type

integer

Alias
UMLS CUI [1,1]
C0205436
UMLS CUI [1,2]
C0007703
UMLS CUI [1,3]
C0039476
Duration of second centrifugation
Description

To calculate SPREC 3.0 Second centrifugation

Data type

integer

Alias
UMLS CUI [1,1]
C0205436
UMLS CUI [1,2]
C0007703
UMLS CUI [1,3]
C2926735
Is the brake on during decelaration?
Description

"With braking" = brake is on during decelaration To calculate SPREC 3.0 Second centrifugatio

Data type

integer

Alias
UMLS CUI [1,1]
C0205436
UMLS CUI [1,2]
C0007703
UMLS CUI [1,3]
C0011100
UMLS CUI [1,4]
C0337108
Temperature conditions during processing after centrifugation
Description

RT = room temperature:18-28 °C To calculate SPREC 3.0 Postcentrifugation delay Standard PREanalytical Code Version 3.0 Betsou et al. Biopreserv Biobank. 2018 Jan 29. doi: 10.1089/bio.2017.0109 Temperature ranges from Table 1: Postcentrifugation delay

Data type

integer

Alias
UMLS CUI [1,1]
C0687676
UMLS CUI [1,2]
C0007703
UMLS CUI [1,3]
C0039476
Date & time when processing stops. Can be similar as free freezing_time
Description

To calculate SPREC 3.0 Postcentrifugation delay

Data type

integer

Alias
UMLS CUI [1,1]
C1709694
UMLS CUI [1,2]
C2347026
UMLS CUI [1,3]
C0806020
UMLS CUI [1,4]
C1522314
If date & time when processing stops is known, please fill in:
Description

To calculate SPREC 3.0 Postcentrifugation delay

Data type

datetime

Alias
UMLS CUI [1,1]
C1709694
UMLS CUI [1,2]
C2347026
UMLS CUI [1,3]
C0806020
UMLS CUI [1,4]
C1522314
Unique Identifier of sample
Description

sample_ID

Data type

text

Alias
UMLS CUI [1]
C1299222
Type of samples
Description

Source: SPREC 3.0 Type of sample "Standard PREanalytical Code Version 3.0 Betsou et al. Biopreserv Biobank. 2018 Jan 29. doi: 10.1089/bio.2017.0109 Table 1: Type of sample Addition of DNA & RNA

Data type

integer

Alias
UMLS CUI [1]
C2347029
Type of sample additives
Description

sample_additive

Data type

integer

Alias
UMLS CUI [1,1]
C2347029
UMLS CUI [1,2]
C0442796
If "Other" selected: Precision of additive
Description

sample_additive_text

Data type

text

Alias
UMLS CUI [1,1]
C0205394
UMLS CUI [1,2]
C2347029
UMLS CUI [1,3]
C0442796
Volume of sample known?
Description

sample_volume

Data type

integer

Alias
UMLS CUI [1,1]
C2347026
UMLS CUI [1,2]
C0449468
If the volume of sample is known, please fill in:
Description

sample_volume_specify

Data type

integer

Measurement units
  • uL
Alias
UMLS CUI [1,1]
C2347026
UMLS CUI [1,2]
C0449468
uL
Storage container type for long term storage
Description

To calculate SPREC 3.0 Long-term storage

Data type

text

Alias
UMLS CUI [1,1]
C1698986
UMLS CUI [1,2]
C0180098
UMLS CUI [1,3]
C0332307
If "Other" selected, please specify the storage container type for long term storage
Description

To calculate SPREC 3.0 Long-term storage

Data type

text

Alias
UMLS CUI [1,1]
C0205394
UMLS CUI [1,2]
C1698986
UMLS CUI [1,3]
C0180098
UMLS CUI [1,4]
C0332307
Freezing mode of the sample
Description

freezing_mode

Data type

integer

Alias
UMLS CUI [1,1]
C0016701
UMLS CUI [1,2]
C2348146
Date & time of freezing known?
Description

To calculate SPREC Postcentrifugation delay

Data type

integer

Alias
UMLS CUI [1,1]
C1264639
UMLS CUI [1,2]
C0200367
If the date & time of freezing is known, please fill in:
Description

To calculate SPREC Postcentrifugation delay

Data type

datetime

Alias
UMLS CUI [1,1]
C1264639
UMLS CUI [1,2]
C0200367
Is the delay between collection_time and Freezing_time known?
Description

freezing_delay

Data type

integer

Alias
UMLS CUI [1,1]
C0522486
UMLS CUI [1,2]
C0552379
UMLS CUI [1,3]
C0016701
UMLS CUI [1,4]
C0040223
If the delay between collection_time and Freezing_time is known, please fill in:
Description

freezing_delay_specify

Data type

integer

Measurement units
  • min
Alias
UMLS CUI [1,1]
C0522486
UMLS CUI [1,2]
C0552379
UMLS CUI [1,3]
C0016701
UMLS CUI [1,4]
C0040223
min
Number of aliquots: number of identical samples derived from one specimen_ID
Description

aliquot_number

Data type

integer

Alias
UMLS CUI [1,1]
C2347026
UMLS CUI [1,2]
C0237753
UMLS CUI [1,3]
C1510844
Storage of the sample
Description

Storage of the sample

Alias
UMLS CUI-1
C2347026
UMLS CUI-2
C1698986
UMLS CUI-3
C1511726
UMLS CUI-4
C0370003
Date & time when sample is physically stored in the freezer
Description

Can be the same as freezing_time

Data type

integer

Alias
UMLS CUI [1,1]
C1264639
UMLS CUI [1,2]
C0200367
If date & time when sample is physically stored in the freezer is known, please fill in:
Description

Can be the same as freezing_time

Data type

datetime

Alias
UMLS CUI [1,1]
C1264639
UMLS CUI [1,2]
C0200367
Storage temperature
Description

RT = room temperature:18-28 °C LN = either vapor or liquid phase (this information should be documented in the Biobank's SOP) To calculate SPREC 3.0 Long-term storage Standard PREanalytical Code Version 3.0 Betsou et al. Biopreserv Biobank. 2018 Jan 29. doi: 10.1089/bio.2017.0109 Temperature ranges from Table 1: Long-term storage

Data type

integer

Alias
UMLS CUI [1,1]
C1698986
UMLS CUI [1,2]
C0039476
UMLS CUI [1,3]
C0370003
Storage location of sample
Description

Can include building, building number, freezer number, LN tank, Rack ID (level, drawers… ), box ID & position

Data type

text

Alias
UMLS CUI [1,1]
C0337174
UMLS CUI [1,2]
C2347026
Actual sample status
Description

sample_status

Data type

integer

Alias
UMLS CUI [1,1]
C0449438
UMLS CUI [1,2]
C2347026
Is the actual sample status known?
Description

E.g. "2" = defrosted twice

Data type

integer

Alias
UMLS CUI [1,1]
C0449438
UMLS CUI [1,2]
C2347026
UMLS CUI [1,3]
C0205309
If the actual sample status is known, please fill in:
Description

freeze_thaw_cycle_ specify

Data type

integer

Alias
UMLS CUI [1,1]
C0449438
UMLS CUI [1,2]
C2347026
UMLS CUI [1,3]
C0205309
Distribution of the sample
Description

Distribution of the sample

Alias
UMLS CUI-1
C1704711
UMLS CUI-2
C2347026
UMLS CUI-3
C1511726
UMLS CUI-4
C2585021
UMLS CUI-5
C0370003
Date when sample is physically retrieved from storage
Description

retrieval_date

Data type

integer

Alias
UMLS CUI [1,1]
C1514918
UMLS CUI [1,2]
C2347026
UMLS CUI [1,3]
C0011008
If the date when sample is physically retrieved from storage is known, please fill in:
Description

retrieval_date_specify

Data type

date

Alias
UMLS CUI [1,1]
C1514918
UMLS CUI [1,2]
C2347026
UMLS CUI [1,3]
C0011008
Reason why sample is used
Description

retrieval_reason

Data type

integer

Alias
UMLS CUI [1,1]
C3146298
UMLS CUI [1,2]
C2347026
UMLS CUI [1,3]
C1524063
If "Other" selected: Precision of retrieval reason
Description

retrieval_reason_text

Data type

text

Alias
UMLS CUI [1,1]
C1547902
UMLS CUI [1,2]
C1514918
UMLS CUI [1,3]
C0392360
For tracability, precision of project for which sample is retrieved
Description

project_destination

Data type

integer

Alias
UMLS CUI [1,1]
C1547902
UMLS CUI [1,2]
C1709701
UMLS CUI [1,3]
C2347026
If "known" selected: Precision of project for which sample is retrieved
Description

project_destination_specify

Data type

text

Alias
UMLS CUI [1,1]
C1547902
UMLS CUI [1,2]
C1709701
UMLS CUI [1,3]
C2347026
Temperature conditions in shipment container
Description

RT = room temperature:18-28 °C LN = either vapor or liquid phase (this information should be documented in the Biobank's SOP)

Data type

integer

Alias
UMLS CUI [1,1]
C0039476
UMLS CUI [1,2]
C0348080
UMLS CUI [1,3]
C0183391
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Data Dictionary Liquid

1 forms
  1. StudyEvent: ODM
    1. Data Dictionary Liquid
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
Patient related data
C2707520 (UMLS CUI-1)
ID_patient
Item
Unique identifier of patient
text
C0030705 (UMLS CUI [1,1])
C0600091 (UMLS CUI [1,2])
ID_patient_local
Item
Unique patient identifier generated by the biobank
text
C0030705 (UMLS CUI [1,1])
C0600091 (UMLS CUI [1,2])
C0205276 (UMLS CUI [1,3])
ID_patient_global
Item
Unique identifier of patient at the Swiss level
text
C0030705 (UMLS CUI [1,1])
C0600091 (UMLS CUI [1,2])
C2348867 (UMLS CUI [1,3])
Item
Sex of the subject
text
C0150831 (UMLS CUI [1])
patient_sex
Code List
Sex of the subject
CL Item
ambiguous (A)
CL Item
Female (F)
CL Item
Male (M)
CL Item
Not applicable (N)
CL Item
Other  (O)
CL Item
Unknown (U)
Item Group
Data related to case
C1511726 (UMLS CUI-1)
C2585021 (UMLS CUI-2)
C1698493 (UMLS CUI-3)
ID_case
Item
Unique identifier of case (may include different sample types) specific to each institute
text
C1698493 (UMLS CUI [1,1])
C0600091 (UMLS CUI [1,2])
Item
Type of consent signed by the patient allowing sampling and use of specimen
integer
C0009797 (UMLS CUI [1,1])
C4288222 (UMLS CUI [1,2])
C0030705 (UMLS CUI [1,3])
consent_type
Code List
Type of consent signed by the patient allowing sampling and use of specimen
CL Item
Specific consent (1)
CL Item
General consent (2)
CL Item
NA (No answer?) (3)
CL Item
UNK (Unknown?) (4)
Item
Last answer of the patient to the selected type of consent
integer
C0021430 (UMLS CUI [1,1])
C1517741 (UMLS CUI [1,2])
C1706817 (UMLS CUI [1,3])
consent_answer
Code List
Last answer of the patient to the selected type of consent
CL Item
Yes (1)
CL Item
No (2)
CL Item
Informed (3)
CL Item
Withdrawn (4)
CL Item
Unknown (?) (5)
CL Item
No answer (6)
Item
Is the date of the last update of the consent decision known?
integer
C0205309 (UMLS CUI [1,1])
C0011008 (UMLS CUI [1,2])
C1519814 (UMLS CUI [1,3])
C0021430 (UMLS CUI [1,4])
consent_date
Code List
Is the date of the last update of the consent decision known?
CL Item
Reported (1)
CL Item
No answer (2)
consent_date
Item
If the date of the last update of the consent decision is reported, please fill in:
date
C0011008 (UMLS CUI [1,1])
C1519814 (UMLS CUI [1,2])
C0021430 (UMLS CUI [1,3])
Item
Is the patient's age at collection known?
integer
C4698447 (UMLS CUI [1,1])
C0205309 (UMLS CUI [1,2])
patient_age_at_collection
Code List
Is the patient's age at collection known?
CL Item
Known  (1)
CL Item
Unknown (2)
patient_age_at_collection
Item
If patient age at collection is known, please fill in:
integer
C4698447 (UMLS CUI [1,1])
C0205309 (UMLS CUI [1,2])
Item
Unit for patient age at collection
integer
C4698447 (UMLS CUI [1,1])
C0439148 (UMLS CUI [1,2])
patient_age_unit
Code List
Unit for patient age at collection
CL Item
Years (1)
CL Item
Months (2)
CL Item
Days (3)
CL Item
Unknown (4)
Item
Primary disease diagnosis
integer
C0277554 (UMLS CUI [1,1])
C0011900 (UMLS CUI [1,2])
patient_age_unit
Code List
Primary disease diagnosis
CL Item
Known (1)
CL Item
No disease reported (2)
CL Item
Unknown (3)
patient_prim_disease_specify
Item
If "Known" selected, please specify:
text
C0277554 (UMLS CUI [1,1])
C0011900 (UMLS CUI [1,2])
Item
Are other diseases, different from primary disease, known?
integer
C2359476 (UMLS CUI [1,1])
C1137110 (UMLS CUI [1,2])
patient_sec_disease_specify
Code List
Are other diseases, different from primary disease, known?
CL Item
Yes (1)
CL Item
No disease reported  (2)
CL Item
Unknown (3)
patient_sec_disease
Item
If "Yes" selected, please specify which other diseases
text
C2359476 (UMLS CUI [1,1])
C1137110 (UMLS CUI [1,2])
Item Group
Collection of the specimen
C0200345 (UMLS CUI-1)
C1511726 (UMLS CUI-2)
C2585021 (UMLS CUI-3)
C2347026 (UMLS CUI-4)
collection_institution
Item
Localisation of specimen source
text
C2347026 (UMLS CUI [1,1])
C0449416 (UMLS CUI [1,2])
C0450429 (UMLS CUI [1,3])
collection_departement
Item
Department where specimen is collected
text
C2347027 (UMLS CUI [1,1])
C1704729 (UMLS CUI [1,2])
collection_service
Item
Service/ward where specimen is collected
text
C2347027 (UMLS CUI [1,1])
C0557854 (UMLS CUI [1,2])
collection_person
Item
Forname and surname of the person who collect the specimen
text
C2347027 (UMLS CUI [1,1])
C1522390 (UMLS CUI [1,2])
C1999110 (UMLS CUI [1,3])
C0027365 (UMLS CUI [1,4])
collection_time
Item
Date and time of sampling
datetime
C2347027 (UMLS CUI [1,1])
C1264639 (UMLS CUI [1,2])
collection_year
Item
Year of sampling, calculated from collection_time (no need to document)
integer
C2347027 (UMLS CUI [1,1])
C0439234 (UMLS CUI [1,2])
specimen_ID
Item
Unique Identifier of specimen (primary sample)
text
C2347026 (UMLS CUI [1,1])
C4071975 (UMLS CUI [1,2])
Item
Type of specimen collected
text
C2347029 (UMLS CUI [1])
specimen_type
Code List
Type of specimen collected
CL Item
Ascites fluid (ASC)
CL Item
Amniotic fluid (AMN)
CL Item
Bronchoalveolar lavage (BAL)
CL Item
Blood (whole) (BLD)
CL Item
Bone marrow aspirate (BMA)
CL Item
Breast milk (BMK)
CL Item
Buccal cells (BUC)
CL Item
Non-density-gradient-centrifugation-separated buffy coat, viable (BUF)
CL Item
Non-density-gradient-centrifugation-separated buffy coat, non-viable (BFF)
CL Item
Density-gradient-centrifugation-separated mononuclear cells, viable (CEL)
CL Item
Fresh cells from non-blood specimen type (CEN)
CL Item
Cells from non blood specimen type(e.g. ascites, amniotic), viable (CLN)
CL Item
Cord blood (CRD)
CL Item
Cerebrospinal fluid (CSF)
CL Item
Enriched (physicochemically) Circulating Tumor Cells (CTC)
CL Item
Dental pulp (PLP)
CL Item
Dried whole blood (e.g. Guthrie cards) (DWB)
CL Item
Nasal washing (NAS)
CL Item
Density-gradient-centrifugation-separated mononuclear cells, non viable (PEL)
CL Item
Cells from non blood specimen type (e.g. ascites, amniotic), non-viable (PEN)
CL Item
Pleural fluid (PFL)
CL Item
Plasma, single spun (PL1)
CL Item
Plasma, double spun (PL2)
CL Item
Red blood cells (RBC)
CL Item
Saliva (SAL)
CL Item
Semen (SEM)
CL Item
Serum (SER)
CL Item
Sputum (SPT)
CL Item
Stool (STL)
CL Item
Synovial fluid (SYN)
CL Item
Tears (TER)
CL Item
24 h urine (U24)
CL Item
Urine, random (“spot”) (URN)
CL Item
Urine, first morning (URM)
CL Item
Urine, timed (URT)
CL Item
Other (ZZZ)
Item
Type of primary container in which the specimen is collected
text
C0205225 (UMLS CUI [1,1])
C0183391 (UMLS CUI [1,2])
C0332307 (UMLS CUI [1,3])
primary_container_type
Code List
Type of primary container in which the specimen is collected
CL Item
Acid citrate dextrose (ACD)
CL Item
Chemical additives / stabilizers (ADD)
CL Item
Serum tube without clot activator (CAT)
CL Item
Citrate phosphate dextrose (CPD)
CL Item
Cell Preparation Tube® citrate (CPT)
CL Item
Cell Preparation Tube® heparin (CPH)
CL Item
Aldehyde-based stabilizer for CTCs (CSV)
CL Item
EDTA and gel (EDG)
CL Item
Physical filtration system (FIL)
CL Item
Glass (GLS)
CL Item
Lithium heparin (HEP)
CL Item
Hirudin (HIR)
CL Item
Lithium heparin and rubber plug (LHB)
CL Item
Lithium heparin and gel (LHG)
CL Item
Oragene collection container or equivalent (ORG)
CL Item
Stool collection container with DNA stabilizer (OMN)
CL Item
PAXgene® blood RNA+ (PAX)
CL Item
Potassium EDTA (PED)
CL Item
Polyethylene tube sterile (PET)
CL Item
S8820 protease inhibitor tablets or equivalent (PI1)
CL Item
Protease inhibitors (PIX)
CL Item
Polypropylene tube sterile (PPS)
CL Item
PAXgene® blood DNA (PXD)
CL Item
PAXgene® bone marrow RNA (PXR)
CL Item
RNA Later® (RNL)
CL Item
Sodium citrate (SC1)
CL Item
Non-aldehyde-based stabilizer for cell-free nucleic acids (SCK)
CL Item
Sodium EDTA (SED)
CL Item
Sodium heparin (SHP)
CL Item
Sodium fluoride/potassium oxalate (SPO)
CL Item
Serum separator tube with clot activator (SST)
CL Item
Tempus® tube (TEM)
CL Item
Trace elements tube (TRC)
CL Item
Unknown (XXX)
CL Item
Other (ZZZ)
primary_container_volume
Item
Volume of primary container in which specimen is collected
float
C0449468 (UMLS CUI [1,1])
C0205225 (UMLS CUI [1,2])
C0183391 (UMLS CUI [1,3])
specimen_volume
Item
Volume of specimen (primary sample)
float
C0205225 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C0449468 (UMLS CUI [1,3])
Item
Additives or specific conditions applied
integer
C2347026 (UMLS CUI [1,1])
C0442796 (UMLS CUI [1,2])
C4048755 (UMLS CUI [1,3])
C2347026 (UMLS CUI [2,1])
C0205369 (UMLS CUI [2,2])
C0348080 (UMLS CUI [2,3])
collection_special_conditions
Code List
Additives or specific conditions applied
CL Item
None (1)
CL Item
Sterile (2)
CL Item
Rnase free (3)
CL Item
Non standard additives (4)
CL Item
Other (5)
collection_special_conditions_text
Item
If "Other" selected: Description of special conditions
text
C0205369 (UMLS CUI [1,1])
C0348080 (UMLS CUI [1,2])
C0205394 (UMLS CUI [1,3])
Item
Metabolic status of patient
integer
C0311400 (UMLS CUI [1,1])
C0449438 (UMLS CUI [1,2])
C0030705 (UMLS CUI [1,3])
patient_fasting_status
Code List
Metabolic status of patient
CL Item
Yes (1)
CL Item
No (2)
CL Item
Unknown (3)
Item
Temperature conditions before transport
integer
C0039476 (UMLS CUI [1,1])
C0348080 (UMLS CUI [1,2])
C0332152 (UMLS CUI [1,3])
C0040756 (UMLS CUI [1,4])
pre_transport_temp
Code List
Temperature conditions before transport
CL Item
Room temperature (1)
CL Item
Controlled Room temperature (2)
CL Item
2 - 10 °C (3)
CL Item
(-35) to (-18) °C (4)
CL Item
(-85) to (-60) °C / dry ice (5)
CL Item
Liquid nitrogen (6)
CL Item
Unknown (7)
Item Group
Transport of the specimen
C2347026 (UMLS CUI-1)
C0040756 (UMLS CUI-2)
C1511726 (UMLS CUI-3)
C2585021 (UMLS CUI-4)
C2347026 (UMLS CUI-5)
Item
For internal use only - precision if transported item is the unprocessed specimen or if specimen has already been processed (=sample)
integer
C2347026 (UMLS CUI [1,1])
C1522240 (UMLS CUI [1,2])
C0332307 (UMLS CUI [1,3])
transport_sample_type
Code List
For internal use only - precision if transported item is the unprocessed specimen or if specimen has already been processed (=sample)
CL Item
Processed (1)
CL Item
Unprocessed (2)
CL Item
Unknown  (3)
transport_person
Item
Forename and surname of person who transports specimen (or sample)
text
C2347026 (UMLS CUI [1,1])
C0040756 (UMLS CUI [1,2])
C1522390 (UMLS CUI [1,3])
C199911 (UMLS CUI [1,4])
C0027365 (UMLS CUI [1,5])
Item
Transport mode - migth be important depending on the application
integer
C1550400 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
transport_mode
Code List
Transport mode - migth be important depending on the application
CL Item
Manual (1)
CL Item
Pneumatic tube (2)
CL Item
Other (3)
CL Item
Unknown (4)
Item
Date & time when transport starts
integer
C2347026 (UMLS CUI [1,1])
C1273722 (UMLS CUI [1,2])
C0808070 (UMLS CUI [1,3])
C0040223 (UMLS CUI [1,4])
transport_mode
Code List
Date & time when transport starts
CL Item
Known  (1)
CL Item
Unknown (2)
CL Item
No answer (3)
transport_time_specify
Item
If date & time when transport starts is known, please fill in:
datetime
C2347026 (UMLS CUI [1,1])
C1273722 (UMLS CUI [1,2])
C0808070 (UMLS CUI [1,3])
C0040223 (UMLS CUI [1,4])
Item
Temperature conditions during transport
integer
C2347026 (UMLS CUI [1,1])
C1273722 (UMLS CUI [1,2])
C0039476 (UMLS CUI [1,3])
transport_temp
Code List
Temperature conditions during transport
CL Item
RT (1)
CL Item
Controlled RT (2)
CL Item
2-10 °C (3)
CL Item
(-35) to (-18) °C (4)
CL Item
(-85) to (-60) °C/ dry ice (5)
CL Item
LN (6)
CL Item
Unknown (7)
Item Group
Reception of the specimen
C2347026 (UMLS CUI-1)
C0544683 (UMLS CUI-2)
C1511726 (UMLS CUI-3)
C2585021 (UMLS CUI-4)
C2347026 (UMLS CUI-5)
reception_person
Item
Forename and surname of person who receives specimen (or sample)
text
C0544683 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C1522390 (UMLS CUI [1,3])
C199911 (UMLS CUI [1,4])
C0027365 (UMLS CUI [1,5])
Item
Date & time when specimen (or sample) arrives at reception
integer
C2347026 (UMLS CUI [1,1])
C0544683 (UMLS CUI [1,2])
C1264639 (UMLS CUI [1,3])
reception_time
Code List
Date & time when specimen (or sample) arrives at reception
CL Item
Known (1)
CL Item
Unknown (2)
CL Item
No answer (3)
reception_time_specify
Item
If date & time when specimen (or sample) arrives at reception is known, please fill in:
datetime
C2347026 (UMLS CUI [1,1])
C0544683 (UMLS CUI [1,2])
C1264639 (UMLS CUI [1,3])
Item
Is the person from which the specimen was extracted infected?
integer
C2347026 (UMLS CUI [1,1])
C0013018 (UMLS CUI [1,2])
C0517627 (UMLS CUI [1,3])
specimen_infectious
Code List
Is the person from which the specimen was extracted infected?
CL Item
Yes (1)
CL Item
No (2)
CL Item
Unknown (3)
Item
If the specimen is know to be infected (specimen_infectious Y), precision of type of infection
integer
C2347026 (UMLS CUI [1,1])
C0013018 (UMLS CUI [1,2])
C0457463 (UMLS CUI [1,3])
specimen_infectious
Code List
If the specimen is know to be infected (specimen_infectious Y), precision of type of infection
CL Item
HIV (1)
CL Item
Hepatitis B (2)
CL Item
Hepatitis C (3)
CL Item
No answer  (4)
CL Item
Other (5)
specimen_infectious_details_text
Item
If "Other" selected: Precision of type of infection
text
C2347026 (UMLS CUI [1,1])
C0013018 (UMLS CUI [1,2])
C0205394 (UMLS CUI [1,3])
C0457463 (UMLS CUI [1,4])
Item Group
Sample processing
C0037793 (UMLS CUI-1)
C1511726 (UMLS CUI-2)
C2585021 (UMLS CUI-3)
C0370003 (UMLS CUI-4)
processing_person
Item
Forename and surename of person who processes specimen
text
C1709694 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C0027361 (UMLS CUI [1,3])
Item
Date & time when processing starts
integer
C1709694 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C0808070 (UMLS CUI [1,3])
C0040223 (UMLS CUI [1,4])
processing_start_time
Code List
Date & time when processing starts
CL Item
Known  (1)
CL Item
Unknown (2)
CL Item
No answer (3)
processing_start_time
Item
If "Yes" selected, please fill in the date & time when processing started
datetime
C1709694 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C0808070 (UMLS CUI [1,3])
C0040223 (UMLS CUI [1,4])
Item
Temperature conditions during processing = temperature before centrifugation (if applicable)
integer
C1709694 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C0039476 (UMLS CUI [1,3])
processing_start_time
Code List
Temperature conditions during processing = temperature before centrifugation (if applicable)
CL Item
RT (1)
CL Item
Controlled RT (2)
CL Item
2-10 °C (3)
CL Item
(-35) to (-18) °C (4)
CL Item
(-85) to (-60) °C/ dry ice (5)
CL Item
LN (6)
CL Item
Unknown (7)
Item
Special conditions during processing
integer
C1709694 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C0205555 (UMLS CUI [1,3])
C0348080 (UMLS CUI [1,4])
processing_start_time
Code List
Special conditions during processing
CL Item
None (1)
CL Item
Sterile (2)
CL Item
RNAse free (3)
CL Item
None standard additives (4)
CL Item
Other (5)
processing_special_conditions_text
Item
If "Other" selected: Description of special conditions
text
C1709694 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C0205555 (UMLS CUI [1,3])
C0348080 (UMLS CUI [1,4])
C0205394 (UMLS CUI [1,5])
Item
Force of first centrifugation
integer
C0205435 (UMLS CUI [1,1])
C0007703 (UMLS CUI [1,2])
C0441722 (UMLS CUI [1,3])
prim_centrifug_force
Code List
Force of first centrifugation
CL Item
Known (1)
CL Item
Unknown (2)
CL Item
No answer (3)
prim_centrifug_force_specify
Item
If the force of first centrifugation is known, please fill in:
integer
C0205435 (UMLS CUI [1,1])
C0007703 (UMLS CUI [1,2])
C0441722 (UMLS CUI [1,3])
Item
Temperature conditions during first centrifugation
integer
C0205435 (UMLS CUI [1,1])
C0007703 (UMLS CUI [1,2])
C0039476 (UMLS CUI [1,3])
prim_centrifug_force
Code List
Temperature conditions during first centrifugation
CL Item
RT (1)
CL Item
2-10 °C (2)
CL Item
35-38 °C (3)
CL Item
Unknown (4)
CL Item
No answer (5)
Item
Duration of first centrifugation
integer
C0205435 (UMLS CUI [1,1])
C0007703 (UMLS CUI [1,2])
C0449238 (UMLS CUI [1,3])
prim_centrifug_force
Code List
Duration of first centrifugation
CL Item
Known (1)
CL Item
Unknown (2)
CL Item
No answer (3)
prim_centrifug_duration_specify
Item
If the duration of first centrifugation is known, please fill in:
integer
C0205435 (UMLS CUI [1,1])
C0007703 (UMLS CUI [1,2])
C0449238 (UMLS CUI [1,3])
Item
Is the brake on during decelaration?
integer
C0205435 (UMLS CUI [1,1])
C0007703 (UMLS CUI [1,2])
C0011100 (UMLS CUI [1,3])
C0337108 (UMLS CUI [1,4])
undefined item
Code List
Is the brake on during decelaration?
CL Item
With braking (1)
CL Item
No braking (2)
CL Item
Unknown (3)
CL Item
No answer (4)
Item
Force of second centrifugation
integer
C0205436 (UMLS CUI [1,1])
C0007703 (UMLS CUI [1,2])
C0441722 (UMLS CUI [1,3])
sec_centrifug_force
Code List
Force of second centrifugation
CL Item
Known (1)
CL Item
Unknown (2)
CL Item
No answer (3)
sec_centrifug_force_specify
Item
If the force of second centrifugation is known, please fill in:
text
C0205436 (UMLS CUI [1,1])
C0007703 (UMLS CUI [1,2])
C0441722 (UMLS CUI [1,3])
Item
Temperature conditions during second centrifugation
integer
C0205436 (UMLS CUI [1,1])
C0007703 (UMLS CUI [1,2])
C0039476 (UMLS CUI [1,3])
sec_centrifug_force
Code List
Temperature conditions during second centrifugation
CL Item
RT (1)
CL Item
2-10 °C (2)
CL Item
35-38 °C (3)
CL Item
Unknown (4)
CL Item
No answer (5)
Item
Duration of second centrifugation
integer
C0205436 (UMLS CUI [1,1])
C0007703 (UMLS CUI [1,2])
C2926735 (UMLS CUI [1,3])
sec_centrifug_force
Code List
Duration of second centrifugation
CL Item
Known (1)
CL Item
Unknown (2)
CL Item
No answer (3)
Item
Is the brake on during decelaration?
integer
C0205436 (UMLS CUI [1,1])
C0007703 (UMLS CUI [1,2])
C0011100 (UMLS CUI [1,3])
C0337108 (UMLS CUI [1,4])
sec_centrifug_force
Code List
Is the brake on during decelaration?
CL Item
With braking (1)
CL Item
No braking  (2)
CL Item
Unknown (3)
CL Item
No answer (4)
Item
Temperature conditions during processing after centrifugation
integer
C0687676 (UMLS CUI [1,1])
C0007703 (UMLS CUI [1,2])
C0039476 (UMLS CUI [1,3])
sec_centrifug_force
Code List
Temperature conditions during processing after centrifugation
CL Item
RT (1)
CL Item
2-10 °C (2)
CL Item
35-38 °C (3)
CL Item
Unknown (4)
CL Item
No answer (5)
Item
Date & time when processing stops. Can be similar as free freezing_time
integer
C1709694 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C0806020 (UMLS CUI [1,3])
C1522314 (UMLS CUI [1,4])
processing_stop_time
Code List
Date & time when processing stops. Can be similar as free freezing_time
CL Item
Known (1)
CL Item
Unknown (2)
CL Item
No answer (3)
processing_stop_time_specify
Item
If date & time when processing stops is known, please fill in:
datetime
C1709694 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C0806020 (UMLS CUI [1,3])
C1522314 (UMLS CUI [1,4])
sample_ID
Item
Unique Identifier of sample
text
C1299222 (UMLS CUI [1])
Item
Type of samples
integer
C2347029 (UMLS CUI [1])
sample_type
Code List
Type of samples
CL Item
Ascites fluid (1)
CL Item
Amniotic fluid (2)
CL Item
Bronchoalveolar lavage (3)
CL Item
Blood (whole) (4)
CL Item
Bone marrow aspirate (5)
CL Item
Breast milk (6)
CL Item
Buccal cells (7)
CL Item
Non-density-gradient-centrifugation-separated buffy coat, viable (8)
CL Item
Non-density-gradient-centrifugation-separated buffy coat, non-viable (9)
CL Item
Density-gradient-centrifugation-separated mononuclear cells, viable (10)
CL Item
Fresh cells from nonblood specimen type (11)
CL Item
Cells from non blood specimen type(e.g. ascites, amniotic), viable (12)
CL Item
Cord blood (13)
CL Item
Cerebrospinal fluid (14)
CL Item
Enriched (physicochemically) circulating tumor cells (15)
CL Item
Dried whole blood (e.g. Guthrie cards) (16)
CL Item
Nasal washing; (17)
CL Item
Density-gradient-centrifugation-separated mononuclear cells, non viable (18)
CL Item
Cells from non blood specimen type (e.g. ascites, amniotic), non-viable (19)
CL Item
Pleural fluid (20)
CL Item
Dental pulp (21)
CL Item
Plasma, single spun (22)
CL Item
Plasma, double spun (23)
CL Item
Red blood cells (24)
CL Item
Saliva (25)
CL Item
Semen (26)
CL Item
Serum (27)
CL Item
Sputum (28)
CL Item
Stool (29)
CL Item
Synovial fluid (30)
CL Item
Tears (31)
CL Item
24 h urine (32)
CL Item
Urine, random (“spot”) (33)
CL Item
Urine, first morning (34)
CL Item
Urine, timed (35)
CL Item
DNA (36)
CL Item
RNA (37)
CL Item
Other (38)
Item
Type of sample additives
integer
C2347029 (UMLS CUI [1,1])
C0442796 (UMLS CUI [1,2])
sample_additive
Code List
Type of sample additives
CL Item
DMSO 10% (1)
CL Item
TE buffer (2)
CL Item
H2O (3)
CL Item
None (4)
CL Item
Other (5)
sample_additive_text
Item
If "Other" selected: Precision of additive
text
C0205394 (UMLS CUI [1,1])
C2347029 (UMLS CUI [1,2])
C0442796 (UMLS CUI [1,3])
Item
Volume of sample known?
integer
C2347026 (UMLS CUI [1,1])
C0449468 (UMLS CUI [1,2])
sample_additive
Code List
Volume of sample known?
CL Item
Known (1)
CL Item
Unknown (2)
sample_volume_specify
Item
If the volume of sample is known, please fill in:
integer
C2347026 (UMLS CUI [1,1])
C0449468 (UMLS CUI [1,2])
Item
Storage container type for long term storage
text
C1698986 (UMLS CUI [1,1])
C0180098 (UMLS CUI [1,2])
C0332307 (UMLS CUI [1,3])
sample_additive
Code List
Storage container type for long term storage
CL Item
Bag (Q)
CL Item
Cryotube 1 to 2 mL (C)
CL Item
Dry technology medium (R)
CL Item
Microplate well (L)
CL Item
Original primary container (Y)
CL Item
Paraffin block (P)
CL Item
Plastic cryo straw (O)
CL Item
PP tube > = 5 mL (J)
CL Item
PP tube 0.5 to 2 mL (A)
CL Item
PP tube 40 to 500 uL (S)
CL Item
Straw (G)
CL Item
Unknown (X)
CL Item
Other (Z)
storage_container_specify
Item
If "Other" selected, please specify the storage container type for long term storage
text
C0205394 (UMLS CUI [1,1])
C1698986 (UMLS CUI [1,2])
C0180098 (UMLS CUI [1,3])
C0332307 (UMLS CUI [1,4])
Item
Freezing mode of the sample
integer
C0016701 (UMLS CUI [1,1])
C2348146 (UMLS CUI [1,2])
freezing_mode
Code List
Freezing mode of the sample
CL Item
Controlled freezing (1)
CL Item
Freezing (-20) °C (2)
CL Item
Freezing (-80) °C (3)
CL Item
Snap freezed (4)
CL Item
No answer (5)
Item
Date & time of freezing known?
integer
C1264639 (UMLS CUI [1,1])
C0200367 (UMLS CUI [1,2])
freezing_time
Code List
Date & time of freezing known?
CL Item
Known (1)
CL Item
Unknown (2)
CL Item
No answer (3)
freezing_time
Item
If the date & time of freezing is known, please fill in:
datetime
C1264639 (UMLS CUI [1,1])
C0200367 (UMLS CUI [1,2])
Item
Is the delay between collection_time and Freezing_time known?
integer
C0522486 (UMLS CUI [1,1])
C0552379 (UMLS CUI [1,2])
C0016701 (UMLS CUI [1,3])
C0040223 (UMLS CUI [1,4])
freezing_delay
Code List
Is the delay between collection_time and Freezing_time known?
CL Item
known (1)
CL Item
No answer (2)
freezing_delay_specify
Item
If the delay between collection_time and Freezing_time is known, please fill in:
integer
C0522486 (UMLS CUI [1,1])
C0552379 (UMLS CUI [1,2])
C0016701 (UMLS CUI [1,3])
C0040223 (UMLS CUI [1,4])
aliquot_number
Item
Number of aliquots: number of identical samples derived from one specimen_ID
integer
C2347026 (UMLS CUI [1,1])
C0237753 (UMLS CUI [1,2])
C1510844 (UMLS CUI [1,3])
Item Group
Storage of the sample
C2347026 (UMLS CUI-1)
C1698986 (UMLS CUI-2)
C1511726 (UMLS CUI-3)
C0370003 (UMLS CUI-4)
Item
Date & time when sample is physically stored in the freezer
integer
C1264639 (UMLS CUI [1,1])
C0200367 (UMLS CUI [1,2])
storage_time
Code List
Date & time when sample is physically stored in the freezer
CL Item
known (1)
CL Item
unknown  (2)
CL Item
No answer (3)
storage_time_specify
Item
If date & time when sample is physically stored in the freezer is known, please fill in:
datetime
C1264639 (UMLS CUI [1,1])
C0200367 (UMLS CUI [1,2])
Item
Storage temperature
integer
C1698986 (UMLS CUI [1,1])
C0039476 (UMLS CUI [1,2])
C0370003 (UMLS CUI [1,3])
storage_temp
Code List
Storage temperature
CL Item
RT (1)
CL Item
2 - 10 °C (2)
CL Item
(-35) to (-18) °C (3)
CL Item
(-85) to (-60) °C (4)
CL Item
<(-135) °C (Mechanical freezer) (5)
CL Item
LN (6)
CL Item
LN after temporary (-85) to (-60) °C (7)
CL Item
Programmable freezing to <(-135) °C" (8)
storage_place
Item
Storage location of sample
text
C0337174 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
Item
Actual sample status
integer
C0449438 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
sample_status
Code List
Actual sample status
CL Item
Destroyed (1)
CL Item
Not processed (2)
CL Item
Quaranteen (3)
CL Item
Reserved (4)
CL Item
Stored (5)
CL Item
Shipped (6)
Item
Is the actual sample status known?
integer
C0449438 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C0205309 (UMLS CUI [1,3])
freeze_thaw_cycle
Code List
Is the actual sample status known?
CL Item
Known (1)
CL Item
Unknown (2)
CL Item
No answer  (3)
freeze_thaw_cycle_ specify
Item
If the actual sample status is known, please fill in:
integer
C0449438 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C0205309 (UMLS CUI [1,3])
Item Group
Distribution of the sample
C1704711 (UMLS CUI-1)
C2347026 (UMLS CUI-2)
C1511726 (UMLS CUI-3)
C2585021 (UMLS CUI-4)
C0370003 (UMLS CUI-5)
Item
Date when sample is physically retrieved from storage
integer
C1514918 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C0011008 (UMLS CUI [1,3])
retrieval_date
Code List
Date when sample is physically retrieved from storage
CL Item
Known (1)
CL Item
Unknown (2)
retrieval_date_specify
Item
If the date when sample is physically retrieved from storage is known, please fill in:
date
C1514918 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C0011008 (UMLS CUI [1,3])
Item
Reason why sample is used
integer
C3146298 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C1524063 (UMLS CUI [1,3])
retrieval_reason
Code List
Reason why sample is used
CL Item
Diagnosis (1)
CL Item
Internal control (2)
CL Item
Research (3)
CL Item
Other (4)
retrieval_reason_text
Item
If "Other" selected: Precision of retrieval reason
text
C1547902 (UMLS CUI [1,1])
C1514918 (UMLS CUI [1,2])
C0392360 (UMLS CUI [1,3])
Item
For tracability, precision of project for which sample is retrieved
integer
C1547902 (UMLS CUI [1,1])
C1709701 (UMLS CUI [1,2])
C2347026 (UMLS CUI [1,3])
retrieval_reason
Code List
For tracability, precision of project for which sample is retrieved
CL Item
known (1)
CL Item
No answer (2)
CL Item
Unknown (3)
project_destination_specify
Item
If "known" selected: Precision of project for which sample is retrieved
text
C1547902 (UMLS CUI [1,1])
C1709701 (UMLS CUI [1,2])
C2347026 (UMLS CUI [1,3])
Item
Temperature conditions in shipment container
integer
C0039476 (UMLS CUI [1,1])
C0348080 (UMLS CUI [1,2])
C0183391 (UMLS CUI [1,3])
delivery_temp
Code List
Temperature conditions in shipment container
CL Item
RT (1)
CL Item
Controlled RT  (2)
CL Item
2 - 10 °C (3)
CL Item
(-35) to (-18) °C (4)
CL Item
(-85) to (-60) °C / dry ice (5)
CL Item
LN (6)
CL Item
Unknown (7)
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