TREC Biobanking Support in LabID

Here we described how we implemented support for TREC Biobanking at EMBL Heidelberg

Only users who belong to the TREC can register TREC entries

to request TREC membership, please send an email to modis@embl.de indicating your username

Information slides to stick on SHUB walls [EMBL only]

The TREC project collects thousands of samples (from soil, air, sediments, ...) at various sites in Europe.

All collected samples are shipped to EMBL for long-term storage in freezers (-80C & -20C), nitrogen tanks (-180C) and a cold room (4C). These samples will be processed (wet & dry processing) by different teams within and outside EMBL. Upon reception, the samples and their storage location should be registered in the LabID data management system using their unique barcode as the identification key (stored both in the name and code fields).
To ensure full traceability, sample shipment to external partners (and/or local use of samples) should be reflected and recorded in the system.

All metadata (e.g. from log sheets) of the collected samples will be stored in the EBI BioSamples database using the same barcodes as accession numbers. This metadata will not initially be stored in LabID and should be retrieved from BioSamples.

The collected samples are recorded as a new Specimen type named TREC that offers a few custom properties. The new TREC Specimen model is described in the TREC Specimen Model section below and the steps detailing how to register a batch of TREC Specimen upon reception are described in the TREC Specimen registration section.

TREC Specimen are stored in e.g. (cryo)boxes, bottles, bags or other "containers" that are stored in freezers, cold room, cryotanks, Euroboxes, cryoboxes... that are all located in the Bio Hub Storage (Building 9). The detailed storage organization of the TREC Biobank is described in the Biobank Storage Organisation section.

Finally, the procedure to collect TREC specimen from the Biobank, either to ship them away or process them in a local lab, is implemented as a Shipment. The steps describing how to create a Shipment of one or many TREC specimen is detailed in the Shipping & Using TREC Specimen section

The TREC Specimen Model

The TREC Specimen model catches key aspects of the material collected during expeditions

The TREC Specimen creation form

The TREC Specimen implements the following properties:

• ID: the LabID internal unique universal ID (uuid)
• Name: this should be the barcode as scanned from the received biomaterial
• Code: this must be the barcode as scanned from the received biomaterial
• MTA Required: True/False indicating if a Material Transfer Agreement is required prior to shipping this material outside EMBL
• Protocol Type: The optional protocol type used to collect this specimen. The available options are predefined; please get in touch with your admin to add missing terms.
• Collection Type: The mandatory collection type (e.g. shallow water, soil, sediment, leaf...). The available options are predefined; please get in touch with your admin to add missing terms.
• Collection Day: The day the TREC Specimen was collected, optional, will be set with data extracted from log sheets
• Collection Time (UTC): The time (of the Collection Day) the TREC Specimen was collected, optional, will be set with data extracted from log sheets
• Conditioning Container: The mandatory TREC specimen conditioning container e.g. in a bag, a tube, a bottle. The available options are predefined; please get in touch with your admin to add missing terms.
• Preservative: Free optional text describing how the TREC specimen is preserved e.g. ethanol, salt water...
• Registered Quantity: Mandatory free text describing how much material was received e.g. 2ml, 50g... This potentially matches the Conditioning Container
• Left Quantity: Mandatory free text describing how much material is left in the Biobank. It is the responsibility of the people collecting the biomaterial from the Biobank to keep this value up-to-date.
• Registration Date: Optional registration date. Note that LabID will automatically set a creation date reflecting when the entry was created in the database. You may use this registration date to set an alternative date reflecting the reception.
• Quality at Registration: Optional free text describing a quality issue at reception e.g. broken vial, damaged bag...
• Description: Optional free text description
• Organism: The mandatory organism. Set the correct organism if applicable. The available options are predefined; please get in touch with your admin to add missing terms.
  • Mixed Organisms or unknown should be used in most cases
• Origin/vendor: the optional origin of this specimen. You may use this field to track e.g. the collecting team
• Storage Locations: describes where the specimen is located in the biobank e.g. freezer > shelf > rack > rack compartment > box. The detailed storage organization of the TREC Biobank is described in the Shipping Specimen section
• Responsible person: the optional person to contact to enquire about this specimen
• Status: turn to “not available” when specimen is not in the EMBL BioBank anymore
• Maintained: True as long as the TREC specimen is available somewhere

Several properties offer a controlled list of options

please get in touch with your admin to add missing terms (protocol types, collection types, conditioning containers, organisms...).

Other generally available properties are also present:

• Owner: will be automatically set to the person registering the specimen. Only users who belong to the TREC group can create TREC specimen
• Owned by Group: will be automatically set to TREC.
• Created, Modified: properties to track when the entrie was created and last modified
• Deleted, Deleted By & Deleted Date: properties to track deletion details upon item deletion (note that item are soft deleted i.e. they may be resurrected)

Sharing options are available under the Permissions section and sharing details are described under Features | Sharing items menu

Biobank Storage Organisation

The biobank room is named 9 E-1 Bio Hub Storage and is the place where all TREC specimen are physically located. It contains storage equipment to store specimen at -80C, -20C, 4C and room temperature:

• Freezers (-20C & -80C) which have shelves. Specimen are usually stored in cryoboxes that may be further stored in Rack Compartment or direclty on a freezer's shelf.
• Euroboxes (RT & 4C).

Sketching out storage organisation and storage naming scheme

The TREC storage naming scheme for -80C Freezers

Organization of the -80C Freezers

-80C freezers have shelves on which racks are stored. Each rack is made of 12 compartments (3x4) in which cryoboxes are stored. Finally, tubes are stored in cryoboxes which have different layouts (4x4, 6x6, 9x9...). Hence, the location of a specimen is positioned by selecting (1) the cryobox and (2) optionally indicating its position in the cryobox

Final naming scheme:

• Freezers:
  • There are 13 -80C freezers named TREC -80C Freezer N with N=1..13.
  • Unique code convention: trec-80-freezer-<n> with =1..13.
  • Found in menu Storage Equipment | Freezers
• Shelves:
  • Each freezer has 3 shelves (A,B & C) named TREC -80C Freezer Shelf [1..13][A..C]e.g.TREC -80C Freezer Shelf 10A.
  • Unique code convention: trec-80-freezer-<n>-shelf-<x> with <n>=1..13; <x>=[a..c]
  • In our model, a freezer shelf cannot be moved i.e. it belongs to a particular freezer.
  • Found in menu Storage Equipment | Shelf
• Racks:
  • Racks are named like TREC Rack [1..N].
  • Unique code convention: trec-80-rack-<n> with <n>=1..n;
  • Racks have no pre-assigned shelf, it is therefore the responsibility of the user to set the rack's location when the rack is used the first time or moved.
  • Found in menu Storage Equipment | Rack
• (Rack) Compartment:
  • (rack) compartments are named like TREC Rack Compartment [1..60] [A..L].
  • Unique code convention: trec-80-rack-<n>-compartment-<x> with <n>=1..n; <x>=[A..L]
  • In our model, a compartment belongs to a particular rack. The compartments' location has been therefore predefined to its compartment.
  • Found in menu Storage Equipment | Compartment
• (cryo)Box:
  • (Cryo)boxes must be created as needed (we could not pre-created them as the layouts is not known a priori)
  • Cryoboxes should have a unique number and be named like TREC -80 cryobox [1...N]
  • Unique code convention: trec-80-cryobox-n with <n>=1..n
  • Found in menu Storage Equipment | Box

Most storage equipments have been already be created in LabID

• The 13 -80C freezers (TREC -80C Freezer [1..13]) have already been created and their location have been set to 9 E-1 Bio Hub Storage
• All freezer shelves (TREC -80C Freezer Shelf [1..13][A..C]) have already been created and their location have been set to the relevant freezer.
• 60 racks (TREC Rack [1..60]) have been pre-created. They do not have a preset location
• 720 (60*12) rack compartments have been precreated. They are already assigned to their rack.
• cryoboxes must be created upon need. The use of racks being optinal, the box's location shoudl be set to either a rack compartment or a shelf.

Organization of the -20C Freezers

-20C freezers have shelves in which cryoboxes are directly stored. When relevant, tubes are stored in cryoboxes which have different layouts (4x4, 6x6, 9x9...). Hence, the location of a specimen is positioned by selecting (1) the cryobox and (2) optionally indicating its position in the cryobox.

Final naming scheme:

• Freezers:
  • There are 8 -20C freezers named TREC -20C Freezer N with N=1..8.
  • Unique code convention: trec-20-freezer-<n> with =1..8.
  • Found in menu Storage Equipment | Freezers
• Shelves:
  • Each freezer has 6 shelves (A..F) named TREC -20C Freezer Shelf [1..8][A..F]e.g.TREC -20C Freezer Shelf 1F.
  • Unique code convention: trec-20-freezer-<n>-shelf-<x> with <n>=1..8; <x>=[a..f]
  • In our model, a freezer shelf cannot be moved i.e. it belongs to a particular freezer.
  • Found in menu Storage Equipment | Shelf
• (cryo/black)Box:
  • (Cryo-/Black-)boxes must be created as needed (we could not pre-created them as the layouts is not known a priori)
  • Cryoboxes/Blackboxes should have a unique number and be named like TREC -20 cryobox [1...N]
  • Unique code convention: trec-20-cryobox-n with <n>=1..n
  • Found in menu Storage Equipment | Box

Storage equipments have been already be created in LabID

• The 8 -20C freezers (TREC -20C Freezer [1..8]) have already been created and their location have been set to 9-103 Storage
• All freezer shelves (TREC -20C Freezer Shelf [1..8][A..F]) have already been created and their location have been set to the relevant freezer.
• cryoboxes must be created upon need.

Organization of the rooms

There are 2 rooms:

• the cold room (9-102 Cold Room)
• the corridor (9-101 Corridor)

At the moment, no cabinet has been created, only Eurobox (found under menu Storage Equipment | Box):

• Euroboxes located in the cold room are named like TREC 4C Eurobox [1..N] with code like trec-4C-eurobox-<n>
• Euroboxes located in the cabinets at room temperature are named like TREC RT Eurobox [1..N] with code like trec-RT-eurobox-<n>

When specimen are stored in cryobox (which are placed in Eurobox), please follow the naming convention:

• Cryobox Name: TREC 4C cryobox [1...N] (4C storage) and TREC RT cryobox [1...N]
• Cryobox Code: trec-4C-cryobox-n and trec-rt-cryobox-n with <n>= 1..n

Euroboxes have been already be created in LabID

• 40 Euroboxes located in the cold room have been pre-created named TREC 4C Eurobox [1..40]
• 120 Euroboxes located at room temperature have been pre-created named TREC RT Eurobox [1..120]

Registering TREC specimen

Specimen are shipped in batch to EMBL. Each batch contains dozens or hundreds of specimen that share several aspects e.g. protocol and collection types, MTA requirement, conditioning container, preservative...
Each specimen of a batch will mainly differ for their barcode and their location in the biobank. The most indicated option to register these specimen is to use the Excel-based batch item creation which is demonstrated with antibodies in the training section.

Step 1: Pre-create all the boxes needed to store your samples

You should first prepare all the boxes needed to store the specimen that need to be registered. You need to create them for real and register them in LabID immediately to avoid other users to name their boxes the same:

• Download a fresh Excel template from the Box list page using the Download template for batch create option above the table

Excel creation template to register many (cryo)boxes at once

Column with bold headers are mandatory (e.g. A, C, J, N). Although not enforced by LabID, you should provide the Location Name of each box e.g. the rack compartment. Note that you can delete all columns with light-grey headers (H, I, K...) as well as the Responsible Person, Produced, Public & Note columns (irrelevant in this context).

• Fill in the name and the code columns following the naming scheme ; please make sure to strictly follow the naming convention!
• The Breadcrumb Label is an optional short name to be used when building the whole location breadcrumb. Assuming the box is named TREC 4C Cryobox 2 you may use e.g.4C cryobox 2 or cbox 2. This can always be changed later.
• Fill other relevant columns like the Grid layout and the Location name
• Make sure to fill in the mandatory columns (default value most likely)

Finding the next number to use

• The easiest is to order the storage using the creation date with additional filtering on name. For example, to find the last created eurobox at 4C, you may filter by 4C Euro on name and order by created field
• When sorting on the name or code, boxes wont order by their number due to alphanumerical sorting (i.e. these fields are not numbers)

Example of a simplified spreadsheet to batch-create many cryoboxes at once

Irrelevant (non-mandatory) columns have been removed to simplify the template.

• Batch create the boxes as demonstrated with antibodies in the training section.

Result of batch-creating many cryoboxes at once

We can now move on and register the TREC specimen

Step 2: Scan all the specimen barcode in a TREC Specimen template spreadsheet

The procedure is very similar to that of batch creating boxes.

• Download a fresh Excel template from the TREC Specimen list page using the Download template for batch create option above the table

Excel creation template to register many specimen at once

Column with bold headers are mandatory (e.g. A, C, E, F...). Although not enforced by LabID, you must provide values for the code and location details. Note that you can delete columns with light-grey headers (O, W, X).

• Prefill all the common values (protocol and collection types, MTA requirement, conditioning container, preservative...). Make sure to position the correct organism value
• Prefill all the Location Name with the relevant box name. The exact position in the box can be indicated in the Container Position column. When providing a Container Position, you must set the Container Type i.e.Box in this example
• Position your cursor in the name top cell
• Scan one-by-one your specimen and place them in the assigned box (and position)
• if your barcode scanner is set up correctly, the cursor should automatically move to the next cell below
• Once all specimen have been scanned, copy the content of the name column to the code column
• Extend all common values

Example of a simplified spreadsheet to batch-create TREC Specimen

Irrelevant (non-mandatory) columns have been removed to simplify the template.

Tricks to fill in the Excel template

• First scan barcodes and their location in an empty excel, then prepare the TREC Specimen Excel Spreadsheet to upload
• Simplify the TREC Specimen Excel template:
  • Remove columns with light grey headers
  • Remove columns with grey headers you won’t use (e.g. Note)
  • Keep the 5 location headers i.e. Location Name, Container Type, Container Name, Container Position & Location Details
• Simplify the options in the _VOCABULARIES Excel tab to keep only relevant ones
  • You can add missing values (e.g. new cryobox names in Location Names) provided that they exist in LabID at upload time and spelled correctly

• Batch create the specimen as demonstrated with antibodies in the training section.

Result of batch-creating TREC Specimen

Congrats you have sucessfully registered TREC Specimen in the TREC BioBank!

Shipping & Using TREC specimen

Here we assumed that you want to ship (or collect) a list of TREC Specimen. We assume that you have the list of barcodes corresponding to these specimen.

Whether you want to ship specimen to external TREC partners or simply collect specimen to run experiments here are EMBL, the procedure is identical.

Shipments are available through the top ellipsis menu

• Create a Shipment

Fill in the shipment form

• Click the Shipment template button

Shipped items will be described using a shipment template

• Paste in the list of TREC barcode you need to collect and click Donwload

Ship items must be identified by their barcode stored in the TREC Specimen code field

Paste the TREC specimen barcode to collect, one per line. Then click Download.

Open the downloaded template in Excel or similar. To help you physically collect the samples from the freezers, the specimen conditioning and location information is displayed.

As you collect Specimen, fill in the is_entire_quantity_shipped (True/False), shipped_quatity, left_quatity and container_type columns in the spreadsheet:

• When is_entire_quantity_shipped is set to True, shipped_quatity and left_quatity are optional and the following behavior occurs:
  • shipped_quatity is set to All unless you provide a value
  • left_quatity is always set to None even if you provide another value
• When is_entire_quantity_shipped is set to False, a value for both shipped_quatity and left_quatity is expected
• The left_quatity value is used to update the TREC Specimen's Left Quantity property
• The container_type is optional and can be used to indicate the type of container in which the specimen is shipped e.g. cryobox, tube, bag...

Overview of the Excel template to ship item

When a TREC specimen is entirely shipped, make sure to set is_entire_quantity_shipped to True.

• In the shipment page, click the Register Shipment Items button

Upload the shipment template to registered shipped TREC Specimen in the Shipment

• Drag'n'drop the Excel sheet and double-check the actions to be performed on entirely shipped items. Importantly, the actions are applied immediately upon upload of the spreadsheet. In case of error e.g. in the list of TREC specimen to be shipped, the modified values in the TREC Specimen properties Maintained, Status and Location can only be reset manually. We therefore strongly recommend to register items once the TREC Specimen list has been double-checked.

Double-check the actions to be performed when TREC Specimen are 'entirely shipped'

When a TREC specimen is entirely shipped (is_entire_quantity_shipped set to True in the spreadsheet), default actions can be performed for you and are enbaled by default: the TREC specimen Maintained and Status properties will be set to False and NOT_AVAILABLE, respectively ; and the specimen location is wiped.

• The shipment page now lists the TREC specimen in the Shipment Items table

The Shipment Items table is available at the bottom of the page

The procedure can be repeated to register more TREC Specimen in the shipment

repeat these steps to register more TREC Specimen in the shipment.

• In the table, click on one TREC specimen name to jump to its detail page.

The TREC specimen detail page now lists the shipments details

As a result of shipping Specimen away, you may have to perform additional operations to make sure LabID reflects the new situation

Indicating that TREC Specimen have been entirely shipped away

This procedure can now be automated when uploading the shipped items template file

to automate these operations, simply set the shipment template's is_entire_quantity_shipped column to True for all items that are entirely shipped away; and make sure that default actions are checked when uploading the shipped item template.

When a TREC specimen is entirely shipped, it is no longer available in the BioBank.

To avoid users thinking the specimen is still available at EMBL, we need to perform additional edits on the TREC Specimen

• Set its Maintained property to False
• Set its Status property to NOT_AVAILABLE
• Save and add a note like the entire specimen has been shipped away

You may want to use Excel-based batch edition for this:

• Download the Excel template for edition with a random TREC specimen (from the TREC Specimen list page)
• Replace the ID and Name with the values available in the shipment template
• Remove all the columns but the ID, Name, Status, Maintained & Note ones
• Set Maintained and Status to False and NOT_AVAILABLE in all cells
• We also recommend to add a note like the entire specimen has been shipped away (your name and the date will be added automatically)

Never Delete a Specimen

We do not want to delete the specimen but only reflect the fact it is not present in the BioBank anymore.

Reflecting that a TREC Box is empty or entirely shipped away

Empty (cryo)boxes or (cryo)boxes that were entirely shipped away should not be deleted from the system, rather their location should be unset.

• Unset the box's Location
• Set its Maintained property to False
• Set its Status property to NOT_AVAILABLE
• Save and add a note like Removing the box from XXX * where XXX is the current location e.g. TREC Rack Compartment 1 A*

If you have many boxes to edit, you may want to use Excel-based batch edition for this:

• Download the Excel template for the Box to edit (from the Storage Equipment Box list page)
• Remove all the columns but the ID, Name, Location Name, Location Details, Status, Maintained & Note ones
• Empty all the values in the Location Name & Location Details columns
• Set Maintained and Status to False and NOT_AVAILABLE in all cells
• We also recommend to add a note like Removing the box from XXX * where XXX is the current location e.g.TREC Rack Compartment 1 A*

Never recycle box unique number

It was decided that a box should never be recycled i.e. always create a new (cryo)box with the next available unique number