Module: biospecimens

Module Contents

  1. block-spec
    1.CENTER_NO (*PK)
    2.PERSON_ID
    3.TUMOR_NO
    4.BLOCK_SPEC_CID (*PK)
    5.FRESH_SPEC_CID
    6.BLOCK_CUSTODY
    7.BLOCK_SOURCE
    8.COLLECTION_CID
    9.DATE_RECEIVED
    10.DATE_TAKEN
    11.IS_DEPLETED
    12.TISSUE_TYPE
    13.POLYP_NO
    14.PATH_REPORT_RECEIVED

1 CENTER_NO (*PK) number (2,0) Required:true
Center Identification Number. *CENTER_NO + BLOCK_SPEC_CID are the primary key for the table.
Allowable Values
11 Sinai Health Systems (formerly Cancer Care Ontario)
12 Cedars-Sinai & Cleveland Clinic (formerly USC Consortium)
13 University of Melbourne
14 University of Hawaii Cancer Center
15 Mayo Clinic
16 Fred Hutch, Seattle
17 UCSF: University of California at San Franscisco (formerly CPIC, originally Northern California (NCCC))


2 PERSON_ID string (12) Required:true
Number that uniquely identifies an individual.

3 TUMOR_NO number (2,0) Required:false
Sequential number, starting with "1", assigned to each tumor for a given individual when entered into the local system.
Allowable Values
1 to 99 or -9, -15 Range
1, 2, 3, ... Number of tumor on cancer table.
-9 NA/Out of scope: Tissue is not cancer or contiguous adenoma
-15 Information Unknown

Error Description
If TISSUE_TYPE is 1 or 4 TUMOR_NO must not be null


4 BLOCK_SPEC_CID (*PK) string (15) Required:true
Unique local identifier used at a center to uniquely identify a block tissue specimen. *CENTER_NO + BLOCK_SPEC_CID are the primary key for the table.

5 FRESH_SPEC_CID string (9) Required:false
Unique local identifier used at a center to uniquely identify a fresh tissue specimen.

6 BLOCK_CUSTODY number (2,0) Required:true
Indicates whether or not the center is currently in custody of tissue specimen.
Allowable Values
1 Yes
2 No
9 Not Known


7 BLOCK_SOURCE string (16) Required:true
The tissue source or origin in as much detail as is known. For tumor tissue, ICD-O-3 site code should be used.

8 COLLECTION_CID string (30) Required:true
Identifier used internally by centers to denote a unique surgical event

9 DATE_RECEIVED string (8) Required:true
Date specimen was received into the laboratory of a CRC-CFR center.
Date Value Check
The date must follow to the following format:

Format YYYYMMDD. Must consist of valid date.
Components of date should be right justified and zero filled.
MM = 01 - 12, 88, 99
DD = 01 - 31, 88, 99
YYYY = Minimum year - system date year, 8888, 9999
Use 88, 8888 for not currently known, in progress to obtain information.
Use 99, 9999 for not known.
If century is known, but year is unknown then give an estimate of year or code YYYY = 9999.
If MM = 99 then DD must = 99.
If century is known, but year is unknown then give an estimate of year or code YYYY = 9999.
If YYYY = 9999 then MM and DD must = 99.

The following special parameters are used:
1980 Minimum year

Error Description
must be a valid date of format with minimum year of 1980
DATE_RECEIVED must be greater or equal to DATE_TAKEN

10 DATE_TAKEN string (8) Required:true
Date specimen was taken from patient.
Date Value Check
The date must follow to the following format:

Format YYYYMMDD. Must consist of valid date.
Components of date should be right justified and zero filled.
MM = 01 - 12, 88, 99
DD = 01 - 31, 88, 99
YYYY = Minimum year - system date year, 8888, 9999
Use 88, 8888 for not currently known, in progress to obtain information.
Use 99, 9999 for not known.
If century is known, but year is unknown then give an estimate of year or code YYYY = 9999.
If MM = 99 then DD must = 99.
If century is known, but year is unknown then give an estimate of year or code YYYY = 9999.
If YYYY = 9999 then MM and DD must = 99.

The following special parameters are used:
1970 Minimum year

Error Description
must be a valid date of format with minimum year of 1970
DATE_TAKEN must be less than or equal to DATE_RECEIVED

11 IS_DEPLETED number (1,0) Required:true
Indicates whether the material has been depleted through testing, processing, and dispatching.
Allowable Values
1 Yes
2 No


12 TISSUE_TYPE number (1,0) Required:true
Type of tissue specimen received.
Allowable Values
1 Tumor
2 Prophylactic material
3 Normal tissue
4 Tumor + normal tissue
5 Polyp + normal tissue
6 Polyp
9 Not Known


13 POLYP_NO number (2,0) Required:false
Sequential number over range of 1 to 3 to distinguish a polyp removed on a particular date. The tuple PERSON_ID, DATE_COLLECTED, and POLYP_NO uniquely identify a physical polyp globally within the CFR database.
Allowable Values
   
-9 NA/Out of scope. Tissue is not a polyp
-1 Polyp has IHC/MSI result but center is currently unable to locate polyp pathology information. Center review to obtain this information is currently underway

Error Description
If TISSUE_TYPE is 5 or 6 POLYP_NO must not be null


14 PATH_REPORT_RECEIVED number (1,0) Required:false
Indicates whether a pathology report has been received for subject/specimen.
Allowable Values
1 Yes
2 No
9 Not Known