> For the complete documentation index, see [llms.txt](https://medomicslab.gitbook.io/medomics-docs/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://medomicslab.gitbook.io/medomics-docs/tutorials/design/extraction-modules.md).

# Extraction Module

{% hint style="warning" %}
All extraction module components are currently disabled because they did not pass all the stability checks.
{% endhint %}

The *Extraction Module* is divided into four components. The first three are pages dedicated to simple extraction processes on various data types (images, text notes, and time series) using pre-trained models and/or *Python* libraries. The fourth component is [*MEDimage*](https://medimage.readthedocs.io/en/latest/index.html), which is the implementation of a *Python* open-source package designed for medical image processing and radiomics features extraction.

{% hint style="info" %}
In the video below, the "HAIM study" refers to [the study of Soenksen et al.](https://www.nature.com/articles/s41746-022-00689-4)
{% endhint %}

{% embed url="<https://youtu.be/eNKN7H9nwjc?si=zzTJjwQgApcLwKxu>" %}
Extraction Module Video Tutorial
{% endembed %}

**Content**

* [00:00](https://www.youtube.com/watch?v=eNKN7H9nwjc\&t=0s) Overview&#x20;
* [00:50](https://www.youtube.com/watch?v=eNKN7H9nwjc\&t=50s) Extraction Images&#x20;
* [04:24](https://www.youtube.com/watch?v=eNKN7H9nwjc\&t=264s) Extraction Time Series
* [08:29](https://www.youtube.com/watch?v=eNKN7H9nwjc\&t=509s) Extraction Text&#x20;
* [10:48](https://www.youtube.com/watch?v=eNKN7H9nwjc\&t=648s) Last Word

**Data**

* Physionet : <https://physionet.org/>&#x20;
* MIMIC-IV Demo database : <https://physionet.org/content/mimic-iv-demo/2.2/>&#x20;
* MIMIC-IV-Note : <https://physionet.org/content/mimic-iv-note/2.2/>&#x20;
* MIMIC-IV-CXR : <https://physionet.org/content/mimic-cxr-jpg/2.0.0/>&#x20;
* Study of Soenksen et al. : <https://www.nature.com/articles/s41746-022-00689-4>&#x20;

**Extraction tools**

* TorchXRayVision : <https://github.com/mlmed/torchxrayvision>
* TSfresh : <https://tsfresh.readthedocs.io>&#x20;
* BioBERT : <https://arxiv.org/abs/1901.08746>
* BioBERT weights : <https://github.com/EmilyAlsentzer/clinicalBERT>&#x20;

***

{% content-ref url="/pages/ET6whC1FKbO8FDUwNVzx" %}
[Image Extraction Page](/medomics-docs/tutorials/design/extraction-modules/image-extraction-page.md)
{% endcontent-ref %}

{% content-ref url="/pages/nJZL7Gs1vdC1UvT7IzVn" %}
[Text Extraction Page](/medomics-docs/tutorials/design/extraction-modules/text-extraction-page.md)
{% endcontent-ref %}

{% content-ref url="/pages/lnN8fvM1JaCZAiAnE7B5" %}
[Time Series Extraction Page](/medomics-docs/tutorials/design/extraction-modules/time-series-extraction-page.md)
{% endcontent-ref %}

{% content-ref url="/pages/CvmHuVPB6SIxtYIfCYig" %}
[MEDimage](/medomics-docs/tutorials/design/extraction-modules/medimage.md)
{% endcontent-ref %}


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter:

```
GET https://medomicslab.gitbook.io/medomics-docs/tutorials/design/extraction-modules.md?ask=<question>&goal=<endgoal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.