August 24, 2023
Hello, CDD Vault users, welcome to the Q3 2023 Vault Snack. Last quarter’s Vault Snack highlighted a few of the new tools available in CDD Vault Visualization. This quarter, I thought we’d review some of the enhancements for managing your biological assay (Protocol) data.
As a quick recap, biological/assay data is managed in Vault using Protocol “containers” that usually have many Runs of data (think experiments) associated with them. Protocols also contain Readout Definitions which store all of the data points you need to capture for an assay; these can be raw values, custom calculations, and dose-response plots. This Vault snack will focus on the Protocol and Run definitions.
Protocol Fields
Your Vault Administrator is responsible for creating any number of top-level Protocol fields that can be used to fully describe an assay. These fields are Vault specific and may be optional, required, or conditionally required. These values are fixed for all runs of an assay. Any metadata that doesn’t change over time can be captured in the Protocol definition in a structured manner. By default, all Protocol fields will be immediately available for every Protocol definition as soon as they are defined.
Helpful Hint: Don’t rely on a verbose “Name” to convey all information. Use Protocol Fields to capture the necessary details and use a shorter, more concise Name for your Protocols.
Run Fields
Complementing Protocol Fields and Readout definitions, Run Fields are used to annotate each experiment. These values can change over time but will be consistent for all data imported to a single Run. Similar business rules can be applied and you can also designate which fields show up in drop-down lists along with the run date. These fields will be shown anytime a run is created or edited.
Protocol Forms
Often Protocol and Run Fields will only apply to a subset of your Protocols. To streamline the creation process, use Protocol Forms to define a concise set of relevant fields for that category of assay (animal, biochemical, biophysical, cell, enzyme, etc.). Forms can be selected when creating new Protocols or editing existing ones, and you can update forms over time without losing data since the fields are stored for every Protocol; the Form simply dictates which fields are displayed.
A single Protocol Form will control which fields are shown on the Protocol and Run definitions since these are correlated. By adding dedicated fields, you ensure more data is captured in a structured manner. So do away with the empty text box and take advantage of Protocol Forms.
Helpful Hints:
- Optional fields can be made required for specific forms
- Provide default values to speed up data capture
- Lock values for specific fields thus providing more detail about that type of assay without creating more work for the person defining the Protocol
Ontology Templates
Taking Protocol Forms one step further, you can even include ontology terms in your Protocol and Run definitions. The Common Assay Template is a set of ontology terms provided, by default, for all Vaults. This includes common assay descriptors which can be used to better annotate your assays (FAIR). Forms allow you to pick and choose which fields from the ontology are relevant for each category of assay.
The implementation of Protocol and Run Forms within your assay informatics strategy can:
- Bring assay awareness to each scientist so key details are captured
- Ensure assays are fully and consistently annotated so data isn’t lost over time
- Shorten Protocol creation time by providing specific fields instead of generic text boxes
- Elucidate which assays have been performed and how they relate to each other, key for QSAR/AI models
- Share assay details with collaborators, CROs, publications, etc. using a common universal vocabulary
- Make assay data precisely searchable: find protocols with specific characteristics, either using specific terms or branch categories within the ontology
CDD Support is always happy to schedule a working session to review these, or any other, features in CDD Vault. ust email CDD Support to schedule your feature review!
If this Vault Snack leaves you hungry for more, all previous Vault Snacks can be found here and as always, feel free to contact CDD Support — we are available to help you succeed in using CDD Vault