specimen csv

Wiki ▸ Client CSV Import ▸ Specimens

Sepcimen CSV Import

The columns required in this CSV file are:

Column Number	Column Label	Value required/ optional	Format(s)	Description
1	Inventory ID	Required	Text - numbers, letters, or both	The inventory ID to assign this specimen. Must not exist in Biobank, must be unique in the worksheet. The maximum length is 100.
2	Parent inventory ID	Optional	Text - numbers, letters, or both	The inventory ID for its parent specimen. Must already exist in Biobank, or in worksheet. The maximum length is 100.
3	Volume	Optional	Decimal number	The volume of liquid in millilitres. Should only be used for liquid specimen types.
4	Specimen type	Required	Text	This specimen’s specimen type name (not short name). The specimen type must already exist in Biobank.
5	Created time	Required	YYYY-MM-DD HH:MM	If the specimen is a parent specimen, then this is the drawn date and time. If the specimen is a child specimen, then this is the date and time it was processed at.
6	Patient number	Optional	Text	The patient number this specimen belongs to. Must already exist in Biobank. See notes below.
7	Visit number	Optional	Positive integer number.	The visit number to assign to the collection event. See notes section following this table.
8	Waybill	Optional	Text	The waybill of the shipment this specimen was shipped in from the sending clinic. Must already exist in Biobank.
9	Source Specimen	Required	Y or N	Use the letter Y if the specimen is a parent specimen, the letter N if not. Note: it is possible to add child specimens that do not have a parent specimen.
10	Worksheet	Optional	Text	The worksheet of the processing event this specimen was a parent in. If a processing event with this worksheet number does not exist, it will be created. Required for parent specimens.
11	Origin center	Optional	Text	The short name for the center where the specimens were collected. If left blank, then origin center will be the center selected by the client when he/she logged in. The short name must already exist in Biobank.
12	Current center	Optional	Text	The short name for the center where the specimens are currently located. If left blank, then current center will be the center selected by the client when he/she logged in. The short name must already exist in Biobank.
13	Pallet product barcode	Optional	Text	The product barcode on the pallet this specimen is stored in. Must already exist in Biobank. Also, see Notes below.
14	Top parent container type	Optional (Required if column 15 is specified)	Text	The short name of container type for the top container this pallet is stored in. Must already exist in Biobank. Also, see Notes below.
15	Pallet label	Optional (Required if column 14 is specified)	Text	The label on the pallet this specimen is stored in. Must already exist in Biobank. Also, see Notes below.
16	Specimen position in pallet	Optional (Required if columns 13, 14, or 15 are specified)	Text	Must adhere to pallet’s child labeling scheme. The position string where this specimen is stored in. Should not include the pallet label. Must be a valid position on the pallet. Also, see Notes below.
17	Comment	Optional	Text	The comment to apply to this specimen. There is no size limit.

Template file

Here is a link to download a template CSV file: template

Notes

For source specimens:

• columns 6 and 7, Patient Number and Visit Number respectively, are mandatory.

For aliquoted specimens:

• If column 2, Parent Inventory ID, is not present, then columns 6 and 7, Patient Number and Visit Number respectively, are mandatory.

If a parent specimen is specified, and a collection event with the visit number does not exist, the collection event will be created along with the specimen.

If a parent specimen is specified, and a processing event with the worksheet number does not exist, the processing event will be created along with the specimen.

Assigning a position

To specify a specimen position, use one of the following options:

• only fill in columns 13 and 16,
• only fill in columns 14, 15, and 16,
• fill in columns 13, 14, 15, and 16 (not recommended since it is redundant)