> ## Documentation Index
> Fetch the complete documentation index at: https://docs.atomscale.ai/llms.txt
> Use this file to discover all available pages before exploring further.

# Overview

> Understanding Atomscale's data model and core concepts

Atomscale organizes data around three core entities: **Projects**, **Physical Samples**, and **Data Items**. These form a containment hierarchy that mirrors how experimental work is structured.

## Hierarchy

```
Organization
└── Projects
    └── Physical Samples
        └── Data Items
```

| Level           | Description                                                        | Example                    |
| --------------- | ------------------------------------------------------------------ | -------------------------- |
| Organization    | Your company or institution. All users and data belong to one.     | "Acme Semiconductors"      |
| Project         | Groups physical samples for comparison and analysis.               | "GaN LED optimization"     |
| Physical Sample | Represents a growth run, grouping related data from that run.      | "GaN-2024-01-15"           |
| Data Item       | An individual uploaded file: a RHEED video, XPS scan, recipe, etc. | "rheed\_rotating\_001.mp4" |

Physical samples can belong to multiple projects, and data items can exist without being assigned to a physical sample.

## Core Entities

<CardGroup cols={2}>
  <Card title="Projects" icon="folder" href="/platform/reference/models/projects">
    Group physical samples related to a specific initiative, allowing you to view and analyze all
    their data in one place.
  </Card>

  <Card title="Physical Samples" icon="vial" href="/platform/reference/models/samples">
    Represent growth runs and group instrument and characterization data from the same run for
    comparison and analysis.
  </Card>

  <Card title="Data Items" icon="file" href="/platform/reference/models/data-items">
    Individual metrology, instrument, and characterization files uploaded to Atomscale.
  </Card>
</CardGroup>

## Metadata

You can associate metadata with physical samples and data items to add context and enable filtering:

| Metadata Type     | Description                                                          | Example                              |
| ----------------- | -------------------------------------------------------------------- | ------------------------------------ |
| Growth Instrument | The synthesis instrument used (MBE, PVD, sputter, CVD, ALD, PLD).    | "MBE-1", "Sputter System A"          |
| Target Material   | The material being grown, including substrate and layer information. | "GaN on Sapphire"                    |
| Tags              | Flexible labels organized by category for filtering and grouping.    | "experiment:doe-q1", "priority:high" |

Each of these metadata types can be managed from the **Metadata** section in the sidebar. Notes can also be attached to projects, physical samples, and data items for free-form context.