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Glossary of common terms

The glossary of terms goes over the basic objects and concepts of CDD Vault. Short descriptions provide hyperlinks to detailed articles on each subject.

Vault

Project

 

Molecule

Batch

Collection

 

Protocol

Readout Definition

Run

Readout

 

Vault

The private and secure database within the CDD Vault server, containing all projects and data. Data may not be shared between vaults, but public data may be viewed together with private vault data. Vault membership is determined by the Vault Administrator with CDD support.

User role

Vault members have roles that are determined by the vault administrator. Vault member may range from read-only to full access and vault administrator. Read this article for a complete list of roles.

Project

A partition of the vault that includes a subset of molecules/batches and protocol data, and includes a subset of vault members. Data may be shared between two or more projects, so that the same set of molecules may be shared across several projects. Project membership for users is determined by the vault administrator. A member of a vault may be part of one or more projects, and will have visibility of all the data in his/her projects.

Venn diagram represents two projects A and B that are sharing data and/or members.

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Project role

In addition to the vault level role, project members have a project role determined by the project administrator. Read this article for complete list of roles.

Molecule

A unique record is created within the database for each testable structure or substance. The record is uniquely identified by an automatically generated 7 digit ID with a predefined prefix (e.g. ABC-00002341). The details of ID generation and chemical registration are usually determined when the vault is established by the vault administrator. While "molecule" is This record type default name, it may have alternate nomenclature within your specific vault. For example it may be called "compound", "substance", or "gene". Molecule records may be shared between multiple projects within the vault with all of the associated user-defined fields. All molecule related data is searchable.

User-defined fields

UDF's for short are customer defined fields that are associated with a molecule record. These fields are text only, and data in these fields is not required to be unique. New fields may be defined on the fly during a data import, and all available fields are shown in a drop-down during a data import. UDF's are shared between projects when a molecule record is shared.

Chemical Properties

CDD Vault automatically calculates physicochemical properties of molecules, such as molecular weight, lipophilicity, heavy atom count, etc. Detailed information may be found in this linked article. These properties are displayed for every imported structure, and may be searched within the CDD Vault, and used in CDD Vision calculations.

Batch

When the same molecules is synthesised or purchased multiple times, a new batch is registered in the vault for each preparation or shipment. A batch will have a set of associated meta-data, in addition to the batch ID, such as the chemist name, and vendor/source. Assay data will be associated with both Molecule ID and a specific Batch ID. Batch registration rules will vary between vaults, so if you are not certain what information is required to register new batches, please consult your vault admin, or CDD support. While "batch" is the default name of this record type, it may have alternate nomenclature within your specific vault. For example it may be called "lot", "sample", or "siRNA".

Salt and hydrate data

Salts present in the chemical structure are automatically stripped and stored as a batch field. CDD Vault also supports solvent of crystallization stripping. A CDD Vault salt table determines recognized salts, and new salts may be added upon request.

Formula Weight

Batch formula weight is calculated based on the molecular weight of the core structure plus salt and hydrate data.

Batch Fields

Batch fields are customer defined fields that are associated with batches of molecules. These fields are created and managed by the vault administrator, and are displayed for all batches across the vault (not project-specific). Batch fields may be defined as text, numeric, date, or file data types. Batch fields may be defined as required, optional, conditionally required, or unique values.  All batch related data is searchable. Please see this article for specific guidance on batch fields.

Collection

A collection of molecules is a static list of molecule IDs. Collections are not automatically updated based on any search criteria, but molecules may be added or removed from existing collections by users. Collections are saved for future use in data searches, or as a quick mechanism to identify a library of molecules, or to create hit-lists for follow-up analysis. How to create a molecule collection. How to search by collection.

Protocol

Protocols are designed to capture experimental results and associated meta-data. Each distinct laboratory assay will be represented as a new protocol record in the vault. Protocols can be defined prior to importing experimental results by your vault admin or by you, if you have sufficient permissions, based on the assay SOPs. While "protocol" is the default name of this record type, it may have alternate nomenclature within your specific vault. For example it may be called "assay", "screen", or "procedure". Get started creating protocols.

Readout Definition

Readout definitions are added to the protocol when it's defined, and represent all of the result types that are captured in the database for any specific assay. The result types may include all of the following: conditions, experimental data, calculated results, and meta-data such as experiment # and assay order. While "readout definition" is the default name of this record type, it may have alternate nomenclature within your specific vault. For example it may be called "assay parameter" or "result type". All readout data is searchable within CDD Vault.

Readout Definition

The standard readout definition is added to capture a final value. A readout definition may have a text, number,  file, or "PubMed Reference" data-type. When defined as a number, this type of readout may also be "normalized" to controls by creating a % Inhibition/Activation, % Control, z-score calculation.

Calculated Readout Definition

A calculated readout definition is added to average a standard (numeric) readout definition. With CDD Vision subscription, the calculated readout can be used to calculate sums, averages, and medians of standard readout definitions, as well as other types of supported calculations. Please read this article for specific guidance on creating calculations.

Dose-Response Calculation

A dose-response calculation is added to perform a non-linear regression fit, using the Hill equation for a concentration-response series of data. Please look at the Dose-Response Toolkit for more information on this type of data analysis.

Condition
Condition is a "flag" on a standard readout definition. Marking a readout definition as a condition sets the readout as a category, or a grouping variable, for other readout definitions. For example, a condition readout definition "Species" will allow calculation of IC50's based on species when data from multiple species is imported into a protocol.

Run

A run represents a set of assay results from a single experiment. For each laboratory experiment, a new run is created in the corresponding protocol when results are imported. Runs are entered into the protocol by date, and include responsible person, Lab, and conditions sections. While "run" is the default name of this record type, it may have alternate nomenclature within your specific vault. For example it may be called "experiment" or "screen".

 

Readout

Readouts are simply the values entered into runs for each of the defined readout definitions. While "readout" is the default name of this record type, it may have alternate nomenclature within your specific vault. For example it may be called "result" or "data".

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