# openmedlab/awesome-medical-dataset architecture

> Architecture diagram of the GitHub repository openmedlab/awesome-medical-dataset, generated by GitDiagram from its file tree, README and a sample of source files (last updated 2026-08-13). It is an AI-made overview: check details against the source.

- Interactive diagram: https://gitdiagram.com/openmedlab/awesome-medical-dataset
- Repository: https://github.com/openmedlab/awesome-medical-dataset

## Overview

#### Purpose and Entry Point
This is a static “awesome list” repository cataloging public medical datasets, benchmarks, related methods, and external tooling. The primary reader entry point is `README.md`, which provides the navigable taxonomy, dataset summaries, and links to detailed records.

#### Catalog Index
`README.md` is the curated index and presentation layer. It groups datasets by imaging anatomy/modality, image-text, and text datasets, then links each dataset name to a dedicated Markdown record. It also contains outbound links to benchmarks, SOTA methods, dataset platforms, and related repositories.

#### Dataset Record Store
Each dataset is represented by an independently maintained Markdown document under `resources/`. These files are the repository’s durable content units and are referenced from the root catalog:
- `resources/CT-ORG.md`
- `resources/TotalSegmentator.md`
- `resources/MedQA.md`

The boundary is intentionally documentation-only: records describe and link to datasets rather than containing the datasets themselves.

#### Domain Taxonomy
The root index organizes imaging datasets into clinical/anatomical collections such as whole body, head and neck, chest, abdomen, heart, bones, endoscopy, retina, skin, and microscopic imaging. It separately models multimodal and text-only resources. Representative records spanning those divisions include:
- `resources/BraTS2021.md`
- `resources/Cholec80.md`
- `resources/PMC-VQA.md`

This taxonomy is implemented through Markdown headings, tables, anchors, and relative links rather than code or a data schema.

#### Supplemental Assets and Exceptions
`resources/appendix/` contains supplementary materials, primarily image/media assets associated with selected dataset entries, plus an additional Markdown record:
- `resources/appendix/3D-IRCADB_0.avif`
- `resources/appendix/SegPC21_0.avis`
- `resources/appendix/BONBID-HIE.md`

These assets support documentation presentation; the main catalog does not contain application logic for processing them.

#### External-Service Boundary
The repository delegates dataset hosting, downloads, challenges, and documentation to external providers. Linked services include Grand Challenge, Kaggle, TCIA, Synapse, CodaLab/Codabench, GitHub, Hugging Face, Zenodo, and Tianchi. Individual resource files and `README.md` contain those outbound URLs; no credentials, APIs, deployment infrastructure, or executable runtime are present.

#### Maintenance Model
Content changes are editorial: add or update a `resources/*.md` dataset record, then add or revise its categorized row/link in `README.md`; optional associated media belongs under `resources/appendix/`. There are no visible source modules, build pipeline, tests, package manifests, or server/client entry points in the repository tree.

Main entry points: [`README.md`](https://github.com/openmedlab/awesome-medical-dataset/blob/main/README.md) (Imaging taxonomy), [`resources/CT-ORG.md`](https://github.com/openmedlab/awesome-medical-dataset/blob/main/resources/CT-ORG.md) (CT-ORG), [`resources/TotalSegmentator.md`](https://github.com/openmedlab/awesome-medical-dataset/blob/main/resources/TotalSegmentator.md) (TotalSegmentator), [`resources/MedQA.md`](https://github.com/openmedlab/awesome-medical-dataset/blob/main/resources/MedQA.md) (MedQA)

## Diagram (Mermaid)

```mermaid
flowchart TD

subgraph group_catalog["Catalog and taxonomy"]
  node_readme["Root catalog<br/>Markdown index<br/>[README.md]"]
  node_imaging_taxonomy["Imaging taxonomy<br/>Markdown sections<br/>[README.md]"]
  node_multimodal_text_taxonomy["Multimodal and text taxonomy<br/>Markdown sections<br/>[README.md]"]
end

subgraph group_records["Dataset records"]
  node_ct_org["CT-ORG<br/>Dataset record<br/>[CT-ORG.md]"]
  node_totalsegmentator["TotalSegmentator<br/>Dataset record"]
  node_medqa["MedQA<br/>Dataset record<br/>[MedQA.md]"]
  node_brats2021["BraTS2021<br/>Dataset record<br/>[BraTS2021.md]"]
  node_cholec80["Cholec80<br/>Dataset record<br/>[Cholec80.md]"]
  node_pmc_vqa["PMC-VQA<br/>Dataset record<br/>[PMC-VQA.md]"]
  node_record_collection["Other resource records<br/>Markdown collection"]
end

subgraph group_appendix["Supplemental assets"]
  node_appendix_media["Appendix media<br/>Image/media assets<br/>[3D-IRCADB_0.avif]"]
  node_segpc_media["SegPC21 media<br/>Image/media asset<br/>[SegPC21_0.avis]"]
  node_bonbid_hie["BONBID-HIE<br/>Appendix record<br/>[BONBID-HIE.md]"]
end

subgraph group_external["External providers"]
  node_external_providers{{"Dataset and benchmark providers<br/>External services"}}
  node_external_methods{{"Methods and related catalogs<br/>External references"}}
end

node_readme -->|"organizes"| node_imaging_taxonomy
node_readme -->|"organizes"| node_multimodal_text_taxonomy
node_imaging_taxonomy -->|"links to"| node_ct_org
node_imaging_taxonomy -->|"links to"| node_totalsegmentator
node_imaging_taxonomy -->|"links to"| node_brats2021
node_imaging_taxonomy -->|"links to"| node_cholec80
node_imaging_taxonomy -->|"links to"| node_record_collection
node_multimodal_text_taxonomy -->|"links to"| node_medqa
node_multimodal_text_taxonomy -->|"links to"| node_pmc_vqa
node_readme -->|"references"| node_external_methods
node_readme -->|"links out"| node_external_providers
node_ct_org -.->|"describes or links to"| node_external_providers
node_totalsegmentator -.->|"describes or links to"| node_external_providers
node_medqa -.->|"describes or links to"| node_external_providers
node_brats2021 -.->|"describes or links to"| node_external_providers
node_cholec80 -.->|"describes or links to"| node_external_providers
node_pmc_vqa -.->|"describes or links to"| node_external_providers
node_appendix_media -.->|"supports presentation"| node_ct_org
node_segpc_media -.->|"supports presentation"| node_record_collection
node_bonbid_hie -.->|"supplements"| node_record_collection

click node_readme "https://github.com/openmedlab/awesome-medical-dataset/blob/main/README.md"
click node_imaging_taxonomy "https://github.com/openmedlab/awesome-medical-dataset/blob/main/README.md"
click node_multimodal_text_taxonomy "https://github.com/openmedlab/awesome-medical-dataset/blob/main/README.md"
click node_ct_org "https://github.com/openmedlab/awesome-medical-dataset/blob/main/resources/CT-ORG.md"
click node_totalsegmentator "https://github.com/openmedlab/awesome-medical-dataset/blob/main/resources/TotalSegmentator.md"
click node_medqa "https://github.com/openmedlab/awesome-medical-dataset/blob/main/resources/MedQA.md"
click node_brats2021 "https://github.com/openmedlab/awesome-medical-dataset/blob/main/resources/BraTS2021.md"
click node_cholec80 "https://github.com/openmedlab/awesome-medical-dataset/blob/main/resources/Cholec80.md"
click node_pmc_vqa "https://github.com/openmedlab/awesome-medical-dataset/blob/main/resources/PMC-VQA.md"
click node_appendix_media "https://github.com/openmedlab/awesome-medical-dataset/blob/main/resources/appendix/3D-IRCADB_0.avif"
click node_segpc_media "https://github.com/openmedlab/awesome-medical-dataset/blob/main/resources/appendix/SegPC21_0.avis"
click node_bonbid_hie "https://github.com/openmedlab/awesome-medical-dataset/blob/main/resources/appendix/BONBID-HIE.md"

classDef toneNeutral fill:#f8fafc,stroke:#334155,stroke-width:1.5px,color:#0f172a
classDef toneBlue fill:#dbeafe,stroke:#2563eb,stroke-width:1.5px,color:#172554
classDef toneAmber fill:#fef3c7,stroke:#d97706,stroke-width:1.5px,color:#78350f
classDef toneMint fill:#dcfce7,stroke:#16a34a,stroke-width:1.5px,color:#14532d
classDef toneRose fill:#ffe4e6,stroke:#e11d48,stroke-width:1.5px,color:#881337
classDef toneIndigo fill:#e0e7ff,stroke:#4f46e5,stroke-width:1.5px,color:#312e81
classDef toneTeal fill:#ccfbf1,stroke:#0f766e,stroke-width:1.5px,color:#134e4a
class node_readme,node_imaging_taxonomy,node_multimodal_text_taxonomy toneBlue
class node_ct_org,node_totalsegmentator,node_medqa,node_brats2021,node_cholec80,node_pmc_vqa,node_record_collection toneAmber
class node_appendix_media,node_segpc_media,node_bonbid_hie toneMint
class node_external_providers,node_external_methods toneRose
```

## Components

### Catalog and taxonomy

Markdown-based reader navigation.

- [Root catalog](https://github.com/openmedlab/awesome-medical-dataset/blob/main/README.md): Markdown index · Curated taxonomy, summaries, and outbound links. · `README.md`
- [Imaging taxonomy](https://github.com/openmedlab/awesome-medical-dataset/blob/main/README.md): Markdown sections · Anatomy and modality categories expressed with headings and tables. · `README.md`
- [Multimodal and text taxonomy](https://github.com/openmedlab/awesome-medical-dataset/blob/main/README.md): Markdown sections · Separate image-text and text-only catalog divisions. · `README.md`

### Dataset records

Independently maintained dataset descriptions.

- [CT-ORG](https://github.com/openmedlab/awesome-medical-dataset/blob/main/resources/CT-ORG.md): Dataset record · `resources/CT-ORG.md`
- [TotalSegmentator](https://github.com/openmedlab/awesome-medical-dataset/blob/main/resources/TotalSegmentator.md): Dataset record · `resources/TotalSegmentator.md`
- [MedQA](https://github.com/openmedlab/awesome-medical-dataset/blob/main/resources/MedQA.md): Dataset record · `resources/MedQA.md`
- [BraTS2021](https://github.com/openmedlab/awesome-medical-dataset/blob/main/resources/BraTS2021.md): Dataset record · `resources/BraTS2021.md`
- [Cholec80](https://github.com/openmedlab/awesome-medical-dataset/blob/main/resources/Cholec80.md): Dataset record · `resources/Cholec80.md`
- [PMC-VQA](https://github.com/openmedlab/awesome-medical-dataset/blob/main/resources/PMC-VQA.md): Dataset record · `resources/PMC-VQA.md`
- **Other resource records**: Markdown collection · Additional dataset records under the resource directory.

### Supplemental assets

Optional record media and appendix content.

- [Appendix media](https://github.com/openmedlab/awesome-medical-dataset/blob/main/resources/appendix/3D-IRCADB_0.avif): Image/media assets · Presentation assets associated with selected entries. · `resources/appendix/3D-IRCADB_0.avif`
- [SegPC21 media](https://github.com/openmedlab/awesome-medical-dataset/blob/main/resources/appendix/SegPC21_0.avis): Image/media asset · `resources/appendix/SegPC21_0.avis`
- [BONBID-HIE](https://github.com/openmedlab/awesome-medical-dataset/blob/main/resources/appendix/BONBID-HIE.md): Appendix record · `resources/appendix/BONBID-HIE.md`

### External providers

Hosting, challenge, and documentation services.

- **Dataset and benchmark providers**: External services · Grand Challenge, Kaggle, TCIA, Synapse, CodaLab, GitHub, Hugging Face, Zenodo, and Tianchi.
- **Methods and related catalogs**: External references · Benchmarks, SOTA methods, platforms, and related repositories.

## Connections

- Root catalog → Imaging taxonomy: organizes
- Root catalog → Multimodal and text taxonomy: organizes
- Imaging taxonomy → CT-ORG: links to
- Imaging taxonomy → TotalSegmentator: links to
- Imaging taxonomy → BraTS2021: links to
- Imaging taxonomy → Cholec80: links to
- Imaging taxonomy → Other resource records: links to
- Multimodal and text taxonomy → MedQA: links to
- Multimodal and text taxonomy → PMC-VQA: links to
- Root catalog → Methods and related catalogs: references
- Root catalog → Dataset and benchmark providers: links out
- CT-ORG → Dataset and benchmark providers: describes or links to
- TotalSegmentator → Dataset and benchmark providers: describes or links to
- MedQA → Dataset and benchmark providers: describes or links to
- BraTS2021 → Dataset and benchmark providers: describes or links to
- Cholec80 → Dataset and benchmark providers: describes or links to
- PMC-VQA → Dataset and benchmark providers: describes or links to
- Appendix media → CT-ORG: supports presentation
- SegPC21 media → Other resource records: supports presentation
- BONBID-HIE → Other resource records: supplements