ID_patient
Item
Unique identifier of the patient -specific to each pathology Institute - institution
text
C1269815 (UMLS CUI [1])
ID_patient_local
Item
Unique identifier generated by the biobank and externalisable without compromising patient identity
text
C1269815 (UMLS CUI [1,1])
C0205276 (UMLS CUI [1,2])
ID_patient_global
Item
Unique identifier of patient at the Swiss level (correspond to H code of Patholink) - not yet defined
text
C1269815 (UMLS CUI [1,1])
C2348867 (UMLS CUI [1,2])
Item
Sex of the subject
text
C0079399 (UMLS CUI [1])
Code List
Sex of the subject
CL Item
Not applicable (N)
ID_pathology
Item
Unique identifier specific to each pathology Institute
text
C0030664 (UMLS CUI [1,1])
C0600091 (UMLS CUI [1,2])
ID_case
Item
Unique identifier of case (may include different sample types) specific to each institute
text
C0868928 (UMLS CUI [1,1])
C0600091 (UMLS CUI [1,2])
Item
Type of consent signed by the patient allowing sampling and use of specimen
text
C0009797 (UMLS CUI [1,1])
C0200345 (UMLS CUI [1,2])
Code List
Type of consent signed by the patient allowing sampling and use of specimen
CL Item
Specific consent (Specific consent)
CL Item
General consent (General consent)
Item
Last answer of the patient to the selected type of consent
text
C0021430 (UMLS CUI [1,1])
C1517741 (UMLS CUI [1,2])
C1519814 (UMLS CUI [1,3])
Code List
Last answer of the patient to the selected type of consent
Item
Date of the last update of the consent decision
text
C0021430 (UMLS CUI [1,1])
C1517741 (UMLS CUI [1,2])
C1519814 (UMLS CUI [1,3])
C0011008 (UMLS CUI [1,4])
Code List
Date of the last update of the consent decision
consent_date_specify
Item
If "Known" selected, please specify:
date
C0021430 (UMLS CUI [1,1])
C1517741 (UMLS CUI [1,2])
C1519814 (UMLS CUI [1,3])
C0011008 (UMLS CUI [1,4])
Item
Patient age at sampling
text
C0001779 (UMLS CUI [1,1])
C0200345 (UMLS CUI [1,2])
Code List
Patient age at sampling
patient_age_at_collection_specify
Item
If "Known" selected, please specify:
integer
C0001779 (UMLS CUI [1,1])
C0200345 (UMLS CUI [1,2])
Item
Unit for patient age at collection (8)
text
C0001779 (UMLS CUI [1,1])
C0439148 (UMLS CUI [1,2])
Code List
Unit for patient age at collection (8)
Item
Primary disease diagnosis
text
C0277554 (UMLS CUI [1,1])
C0011900 (UMLS CUI [1,2])
Code List
Primary disease diagnosis
CL Item
No disease reported (No disease reported)
patient_prim_disease_specify
Item
If "Known" selected, please specify:
text
C0277554 (UMLS CUI [1,1])
C0011900 (UMLS CUI [1,2])
Item
Other diseases, different from primary disease - can be multiple
text
C2359476 (UMLS CUI [1,1])
C0011900 (UMLS CUI [1,2])
Code List
Other diseases, different from primary disease - can be multiple
CL Item
No disease reported (No disease reported)
patient_sec_disease_specify
Item
If "Known" selected, please specify:
text
C2359476 (UMLS CUI [1,1])
C0011900 (UMLS CUI [1,2])
collection_institution
Item
Localisation of specimen source
text
C0449416 (UMLS CUI [1,1])
C0370003 (UMLS CUI [1,2])
C0450429 (UMLS CUI [1,3])
collection_department
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 person who collects specimen
text
C2347027 (UMLS CUI [1,1])
C1522390 (UMLS CUI [1,2])
C1999110 (UMLS CUI [1,3])
C0027365 (UMLS CUI [1,4])
collection_year
Item
Year of sampling: calculated from resection_time (23)
date
C2347027 (UMLS CUI [1,1])
C0439234 (UMLS CUI [1,2])
specimen_ID
Item
Unique Identifier of specimen (primary sample)
text
C0370003 (UMLS CUI [1,1])
C0600091 (UMLS CUI [1,2])
Item
Date and time when organ is deprived of its normal blood supply
text
C0040223 (UMLS CUI [1,1])
C1883710 (UMLS CUI [1,2])
Code List
Date and time when organ is deprived of its normal blood supply
clamping_time_specify
Item
If "Known" selected, please specify:
datetime
C0040223 (UMLS CUI [1,1])
C1883710 (UMLS CUI [1,2])
Item
Date and time when specimen is taken out of the body
text
C2347027 (UMLS CUI [1,1])
C0040223 (UMLS CUI [1,2])
Code List
Date and time when specimen is taken out of the body
collection_time_specify
Item
If "Known" selected, please specify:
datetime
C2347027 (UMLS CUI [1,1])
C0040223 (UMLS CUI [1,2])
Item
Acquisition method of specimen
text
C2347027 (UMLS CUI [1,1])
C2700391 (UMLS CUI [1,2])
Code List
Acquisition method of specimen
CL Item
Autopsy <6 h post-mortem (A06)
CL Item
Autopsy 6-12 h post-mortem (2A12)
CL Item
Autopsy 12-24 h post-mortem (A24)
CL Item
Autopsy 24-48 h post-mortem (A48)
CL Item
Autopsy 48-72 h post-mortem (A72)
CL Item
Biopsy in culture media (BCM)
CL Item
Biopsy in normal saline or phosphate buffered saline (BSL)
CL Item
Biopsy in tissue low-temperature transport media (BTM)
CL Item
Fine needle aspirate (FNA)
CL Item
Surgical excision in culture media (SCM)
CL Item
Surgical excision (SRG)
CL Item
Surgical excision in normal saline or phosphate buffered saline (SSL)
CL Item
Surgical excision in tissue low-temperature transport media (STM)
CL Item
Surgical excision in vacuum container (VAC)
Item
Type of specimen collected
text
C2347027 (UMLS CUI [1,1])
C0332307 (UMLS CUI [1,2])
Code List
Type of specimen collected
CL Item
Cells from fine needle aspirate (FNA)
CL Item
Cells from laser capture microdissected tissue (LCM)
CL Item
Cells from non-blood specimen type (e.g. dissociated tissue), non-viable (PEN)
CL Item
Cells from non-blood specimen type (e.g. dissociated tissue), viable (CLN)
CL Item
Disrupted tissue, non-viable (TCM)
CL Item
Fresh cells from non-blood specimen type (e.g. biopsy) (CEN)
CL Item
Solid tissue (TIS)
specimen_morphological_code
Item
Description of cell type (or histology) of tumor and behaviour (malignant or benign)
integer
C0449475 (UMLS CUI [1,1])
C0027651 (UMLS CUI [1,2])
C0475436 (UMLS CUI [2])
specimen_topographical_code
Item
Description of the anatomical site of origin (or organ system) of the tumor
integer
C1515974 (UMLS CUI [1,1])
C0027651 (UMLS CUI [1,2])
Item
Additives or specific conditions applied
text
C0442796 (UMLS CUI [1,1])
C0185125 (UMLS CUI [1,2])
C0205369 (UMLS CUI [2,1])
C0348080 (UMLS CUI [2,2])
C0442796 (UMLS CUI [2,3])
Code List
Additives or specific conditions applied
CL Item
Rnase free (Rnase free)
CL Item
Sterile (Sterile)
CL Item
Non standard additives (Non standard additives)
Item
If "Other" selected: Description of special conditions (free text)
text
C0442796 (UMLS CUI [1,1])
C0185125 (UMLS CUI [1,2])
C0205369 (UMLS CUI [2,1])
C0348080 (UMLS CUI [2,2])
C0442796 (UMLS CUI [2,3])
Code List
If "Other" selected: Description of special conditions (free text)
Item
Metabolic status of patient
text
C0311400 (UMLS CUI [1,1])
C0449438 (UMLS CUI [1,2])
C0030705 (UMLS CUI [1,3])
Code List
Metabolic status of patient
Item
Temperature conditions before transport
text
C0039476 (UMLS CUI [1,1])
C0332152 (UMLS CUI [1,2])
C0040756 (UMLS CUI [1,3])
Code List
Temperature conditions before transport
CL Item
Controlled RT (Controlled RT)
CL Item
2 - 10 °C (2 - 10 °C)
CL Item
(-35) to (-18) °C ((-35) to (-18) °C)
CL Item
(-85) to (-60) °C / dry ice ((-85) to (-60) °C / dry ice)
Item
For internal use only - precision if transported item is the unprocessed specimen or if specimen has already been processed (=sample)
text
C3517336 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C1522240 (UMLS CUI [1,3])
C0332307 (UMLS CUI [1,4])
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 (Processed)
CL Item
Unprocessed (Unprocessed)
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])
C1999110 (UMLS CUI [1,4])
C0027365 (UMLS CUI [1,5])
Item
Transport mode - migth be important depending on the application
text
C1550400 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
Code List
Transport mode - migth be important depending on the application
CL Item
Pneumatic tube (Pneumatic tube)
Item
Date & time when specimen (or sample) arrives at reception
text
C2347026 (UMLS CUI [1,1])
C0544683 (UMLS CUI [1,2])
C1264639 (UMLS CUI [1,3])
Code List
Date & time when specimen (or sample) arrives at reception
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
Temperature conditions during transport
text
C2347026 (UMLS CUI [1,1])
C1273722 (UMLS CUI [1,2])
C0039476 (UMLS CUI [1,3])
Code List
Temperature conditions during transport
CL Item
Controlled RT (Controlled RT)
CL Item
2 - 10 °C (2 - 10 °C5)
CL Item
(-35) to (-18) °C ((-35) to (-18) °C)
CL Item
(-85) to (-60) °C / dry ice ((-85) to (-60) °C / dry ice)
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])
C1999110 (UMLS CUI [1,4])
C0027365 (UMLS CUI [1,5])
Item
Date & time when specimen (or sample) arrives at reception
text
C2347026 (UMLS CUI [1,1])
C0544683 (UMLS CUI [1,2])
C1264639 (UMLS CUI [1,3])
Code List
Date & time when specimen (or sample) arrives at reception
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?
text
C2347026 (UMLS CUI [1,1])
C0013018 (UMLS CUI [1,2])
C0517627 (UMLS CUI [1,3])
Code List
Is the person from which the specimen was extracted infected?
Item
If the specimen is know to be infected (specimen_infectious Y), precision of type of infection
text
C2347026 (UMLS CUI [1,1])
C0013018 (UMLS CUI [1,2])
C0457463 (UMLS CUI [1,3])
Code List
If the specimen is know to be infected (specimen_infectious Y), precision of type of infection
CL Item
Hepatitis B (Hepatitis B)
CL Item
Hepatitis C (Hepatitis C)
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])
Code List
If "Other" selected: Precision of type of infection
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])
Code List
Date & time when processing starts
processing_start_time_specify
Item
If "Known" 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
Specimen type/category
text
C1709694 (UMLS CUI [1,1])
C2347029 (UMLS CUI [1,2])
Code List
Specimen type/category
CL Item
Normal adjacent (Normal adjacent)
CL Item
Normal distant (Normal distant)
CL Item
Metastasis (Metastasis)
CL Item
Diseased (Diseased)
Item
Temperature conditions during processing
text
C1709694 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C0039476 (UMLS CUI [1,3])
Code List
Temperature conditions during processing
CL Item
2 - 10 °C (2 - 10 °C)
CL Item
(-35) to (-18) °C ((-35) to (-18) °C)
sample_ID
Item
Unique Identifier of sample
text
C1299222 (UMLS CUI [1])
Item
Type of sample
text
C2347029 (UMLS CUI [1])
CL Item
Cells from fine needle aspirate (FNA)
CL Item
Cells from laser capture microdissected tissue (LCM)
CL Item
Cells from non-blood specimen type (e.g. dissociated tissue), non-viable (PEN)
CL Item
Cells from non-blood specimen type (e.g. dissociated tissue), viable (CLN)
CL Item
Disrupted tissue, non-viable (TCM)
CL Item
Fresh cells from non-blood specimen type (e.g. biopsy) (CEN)
CL Item
Solid tissue (TIS)
Item
Is the size of the tissue or volume (liquid biospy) known?
text
C0242618 (UMLS CUI [1])
Code List
Is the size of the tissue or volume (liquid biospy) known?
sample_size_specify
Item
If "Known" selected, please specify the size of the tissue or volume (liquid biospy)
float
C0242618 (UMLS CUI [1])
Item
Is the unit of sample size known?
text
C0242618 (UMLS CUI [1,1])
C0439148 (UMLS CUI [1,2])
Code List
Is the unit of sample size known?
Item
If the unit of sample size is known, please specify:
text
C0242618 (UMLS CUI [1,1])
C0439148 (UMLS CUI [1,2])
Code List
If the unit of sample size is known, please specify:
Item
Storage container type for long term storage
text
C1698986 (UMLS CUI [1,1])
C0180098 (UMLS CUI [1,2])
C0332307 (UMLS CUI [1,3])
Code List
Storage container type for long term storage
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)
Item
Fixation or stabilization type
text
C1522662 (UMLS CUI [1,1])
C0332307 (UMLS CUI [1,2])
Code List
Fixation or stabilization type
CL Item
Alcohol based (ETH)
CL Item
Aldehyde-based (ALD)
CL Item
Heat stabilization (HST)
CL Item
Neutral buffered formalin (NBF)
CL Item
Nonaldehyde based without acetic acid (NAA)
CL Item
Non-aldehyde with acetic acid (ACA)
CL Item
Nonbuffered formalin (FOR)
CL Item
Optimum cutting temperature medium (OCT)
CL Item
PAXgene tissue (PXT)
CL Item
Snap freezing (SNP)
CL Item
Vacuum technology stabilization (VAC)
CL Item
Allprotect ® tissue reagent (ALL)
Item
Are start date & time of fixation/stabilization known?
text
C1522662 (UMLS CUI [1,1])
C3897500 (UMLS CUI [1,2])
Code List
Are start date & time of fixation/stabilization known?
fixation_start_time_ specify
Item
If start date & time of fixation/stabilization is known, please specify:
datetime
C1522662 (UMLS CUI [1,1])
C3897500 (UMLS CUI [1,2])
Item
Are stop date & time of fixation/stabilization known?
text
C1522662 (UMLS CUI [1,1])
C1522314 (UMLS CUI [1,2])
C0806020 (UMLS CUI [1,3])
Code List
Are stop date & time of fixation/stabilization known?
Item
Are stop date & time of fixation/stabilization known?
integer
C1522662 (UMLS CUI [1,1])
C1522314 (UMLS CUI [1,2])
C0806020 (UMLS CUI [1,3])
Code List
Are stop date & time of fixation/stabilization known?
Item
Method applied to assess the sample quality
text
C2347026 (UMLS CUI [1,1])
C0332306 (UMLS CUI [1,2])
C2911685 (UMLS CUI [1,3])
Code List
Method applied to assess the sample quality
CL Item
DNA lengths (DNA lengths)
CL Item
Composition (Composition)
CL Item
HE staining (HE staining)
CL Item
Nucleic acid integrity (Nucleic acid integrity)
Item
Are tissue content or results after quality control known?
text
C2347026 (UMLS CUI [1,1])
C0034378 (UMLS CUI [1,2])
C1274040 (UMLS CUI [1,3])
Code List
Are tissue content or results after quality control known?
CL Item
Not done (Not done)
sample_quality_control_specify
Item
If "Known" selected, please specify:
text
C2347026 (UMLS CUI [1,1])
C0034378 (UMLS CUI [1,2])
C1274040 (UMLS CUI [1,3])
aliquot_number
Item
Number of aliquots: number of identical samples derived from one specimen_ID
integer
C1510844 (UMLS CUI [1,1])
C0237753 (UMLS CUI [1,2])
Item
Date & time when sample is physically stored in the freezer
text
C1264639 (UMLS CUI [1,1])
C0200367 (UMLS CUI [1,2])
Code List
Date & time when sample is physically stored in the freezer
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
text
C1698986 (UMLS CUI [1,1])
C0039476 (UMLS CUI [1,2])
C0370003 (UMLS CUI [1,3])
Code List
Storage temperature
CL Item
2 - 10 °C (2 - 10 °C)
CL Item
(-35) to (-18) °C ((-35) to (-18) °C)
CL Item
(-85) to (-60) °C ((-85) to (-60) °C)
CL Item
<(-135) °C (Mechanical freezer) (<(-135) °C (Mechanical freezer))
CL Item
LN after temporary (-85) to (-60) °C (LN after temporary (-85) to (-60) °C)
CL Item
Programmable freezing to <(-135) °C (Programmable freezing to <(-135) °C)
storage_place
Item
Storage location of sample
text
C0337174 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
Item
Actual sample status
text
C0449438 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
Code List
Actual sample status
CL Item
Destroyed (Destroyed)
CL Item
Not processed (Not processed)
CL Item
Quaranteen (Quaranteen)
CL Item
Reserved (Reserved)
CL Item
Shipped (Shipped)
Item
Is the actual sample status known?
text
C0449438 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C0205309 (UMLS CUI [1,3])
Code List
Is the actual sample status known?
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
Date when sample is physically retrieved from storage
text
C1514918 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C0011008 (UMLS CUI [1,3])
Code List
Date when sample is physically retrieved from storage
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
text
C3146298 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C1524063 (UMLS CUI [1,3])
Code List
Reason why sample is used
CL Item
Diagnosis (Diagnosis)
CL Item
Internal control (Internal control)
CL Item
Research (Research)
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
text
C1547902 (UMLS CUI [1,1])
C1709701 (UMLS CUI [1,2])
C2347026 (UMLS CUI [1,3])
Code List
For tracability, precision of project for which sample is retrieved
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
text
C0039476 (UMLS CUI [1,1])
C0348080 (UMLS CUI [1,2])
C0183391 (UMLS CUI [1,3])
Code List
Temperature conditions in shipment container
CL Item
Controlled RT (Controlled RT)
CL Item
2 - 10 °C (2 - 10 °C)
CL Item
(-35) to (-18) °C ((-35) to (-18) °C)
CL Item
(-85) to (-60) °C / dry ice ((-85) to (-60) °C / dry ice)