TREC Biobanking Support in LabID

Here we describe how we implemented support for TREC Biobanking at EMBL Heidelberg.

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 (-80 °C and -20 °C), nitrogen tanks (-180 °C), and a cold room (4 °C). These samples will be processed (wet and 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 specimens upon reception are described in the TREC Specimen registration section.

TREC specimens are stored in (cryo)boxes, bottles, bags, or other containers, which are stored in freezers, the cold room, cryotanks, Euroboxes, cryoboxes, and other equipment located in Bio Hub Storage (Building 9). The detailed storage organisation of the TREC Biobank is described in the Biobank Storage Organisation section.

The TREC Specimen Model

The TREC Specimen implements the following properties:

• ID: the LabID internal universally unique 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.
• 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. 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
• Responsible person: the optional person to contact to enquire about this specimen
• Status: set to “not available” when a specimen is not in the EMBL Biobank anymore
• Maintained: True as long as the TREC specimen is available somewhere

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 entry was created and last modified
• Deleted, Deleted By & Deleted Date: properties to track deletion details upon item deletion (note that items are soft deleted i.e. they may be resurrected)

Biobank Storage Organisation

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

• Freezers (-20 °C and -80 °C), which have shelves. Specimens are usually stored in cryoboxes that may be further stored in rack compartments or directly on a freezer shelf.
• Euroboxes (RT and 4 °C).

Organisation of the -80 °C Freezers

-80 °C 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 with 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 -80 °C freezers named TREC -80C Freezer N with N=1..13. Unique code convention: trec-80-freezer-<n> with n=1..13. Found in menu Storage Equipment | Freezers
• Shelves: Each freezer has 3 shelves (A, B, and 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.
• Racks: Racks are named like TREC Rack [1..N]. Unique code convention: trec-80-rack-<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.
• (Rack) Compartment: Compartments are named like TREC Rack Compartment [1..60] [A..L]. Unique code convention: trec-80-rack-<n>-compartment-<x>. In our model, a compartment belongs to a particular rack.
• (cryo)Box: Cryoboxes must be created as needed. They should have a unique number and be named like TREC -80 cryobox [1...N]. Unique code convention: trec-80-cryobox-n.

Organisation of the -20 °C Freezers

-20 °C freezers have shelves in which cryoboxes are directly stored. When relevant, tubes are stored in cryoboxes with 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 -20 °C freezers named TREC -20C Freezer N with N=1..8. Unique code convention: trec-20-freezer-<n> with n=1..8.
• 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>.
• (cryo/black)Box: Cryoboxes/Blackboxes must be created as needed. They should have a unique number and be named like TREC -20 cryobox [1...N]. Unique code convention: trec-20-cryobox-n.

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

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

Registering TREC specimen

Specimens are shipped in batches to EMBL. Each batch contains dozens or hundreds of specimens that share several aspects, for example protocol and collection types, MTA requirement, conditioning container, and preservative. Each specimen in a batch will mainly differ by its barcode and location in the biobank. The recommended option for registering these specimens is Excel-based batch item creation.

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

• 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
• Fill other relevant columns like the Grid layout and the Location name
• Make sure to fill in the mandatory columns (default value most likely)

• Batch create the boxes using the Excel-based batch import

→ We can now move on and register the TREC specimen

Step 2: Scan all specimen barcodes 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

• 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 your specimens one by one 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

• Batch create the specimen using the Excel-based batch import

→ You have successfully registered TREC specimens in the TREC Biobank!