# 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)
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{% 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: 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:

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

The question should be specific, self-contained, and written in natural language.
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.