# ICA Terminology

| Terms            | Meaning                                                                                                                                                                                                                                                                                                                                                                                   |
| ---------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Assay            | Procedure to detect and measure the amount of a compound or property in a **sample**.                                                                                                                                                                                                                                                                                                     |
| Assets           | Data or processing components such as files, tables, tools, pipelines, code, meta data, etc                                                                                                                                                                                                                                                                                               |
| Bundle           | Package of **assets**                                                                                                                                                                                                                                                                                                                                                                     |
| Case             | Group of **subjects** linked to **samples** and files.                                                                                                                                                                                                                                                                                                                                    |
| Cohort           | Group of **subjects** combined, because they share one or more common criteria.                                                                                                                                                                                                                                                                                                           |
| Data Catalogue   | Data Catalogues provide **views** on data coming from Illumina hardware and processes (**Instruments**, Cloud software, Informatics software and **Assays**) so that the data can be distributed to applications. This data consists of read-only tables to prevent updates by the applications which access the data and is included with professional and enterprise **subscriptions**. |
| Entitlement      | Commercial conditions for using the system, costing x **iCredits** per data volume or calculation.                                                                                                                                                                                                                                                                                        |
| Fastq            | A text-based file format to store genetic data and quality score.                                                                                                                                                                                                                                                                                                                         |
| iCredits         | iCredits are the currency used to purchase Illumina genomic data storage and analysis options.                                                                                                                                                                                                                                                                                            |
| Instrument       | Hardware such as genetic sequencers.                                                                                                                                                                                                                                                                                                                                                      |
| On Premises      | Locally installed software and hardware. The opposite of cloud software and services.                                                                                                                                                                                                                                                                                                     |
| Pipeline         | Set of tools chained together to perform a task in the background.                                                                                                                                                                                                                                                                                                                        |
| Project          | (Region-specific) **assets** (files, tables, tools, pipelines, code, meta data, etc) that belong together and can be shared across multiple users and workgroups, across tenants.                                                                                                                                                                                                         |
| Project Owner    | Owner of the **project**. The project owner has the same profile and rights as a project administrator, but can not be removed from a project without assigning another project owner first. If there are no project administrators available to change the project owner, the tenant administrator can set a new project owner.                                                          |
| Reference Genome | The genome to which your sample is compared to look for deviations.                                                                                                                                                                                                                                                                                                                       |
| Sample           | Groups a set of **fastq** files from a **sequencing run** or set of files from an upload                                                                                                                                                                                                                                                                                                  |
| Sequencing Run   | The actual process of producing genomics information in an **instrument**.                                                                                                                                                                                                                                                                                                                |
| Subject          | A biological entity (person, mouse, dinosaur, plant,...)                                                                                                                                                                                                                                                                                                                                  |
| Subscription     | Determine if a **tenant** has access to a specific products and modules.                                                                                                                                                                                                                                                                                                                  |
| Tenant           | Legal entity in the system which can be invoiced for costs. **Users** must be linked to their tenant, usually the company for which they work. If the same user performs tasks for multiple tenants, ICA will consider them as separate individuals to ensure the correct tenant is charged. Individuals connected to the system on their own are considered a tenant with 1 user.        |
| Tool             | Executable code, packed as docker image which is a building block for **pipelines**.                                                                                                                                                                                                                                                                                                      |
| User             | An individual, known in the system and linked to one or more **tenants**, who is able to perform actions in ICA.                                                                                                                                                                                                                                                                          |
| Variant          | The difference between genome sequence and the **reference genome**.                                                                                                                                                                                                                                                                                                                      |
| View             | Read-only access to data. You can view the data, but not modify it.                                                                                                                                                                                                                                                                                                                       |
| Workflow         | Steps for a process going from initial lab work all the way to report delivery.                                                                                                                                                                                                                                                                                                           |
| Workgroup        | Combines a group of **users** for practical purposes such as assigning security permission in the various systems. A user can belong to multiple workgroups.                                                                                                                                                                                                                              |