<h1 id="ressources"><a aria-hidden="true" class="anchor-heading icon-link" href="#ressources"></a>Ressources</h1>
<h1 id="pheknowlator"><a aria-hidden="true" class="anchor-heading icon-link" href="#pheknowlator"></a>PheKnowLator</h1>
<p>What is PheKnowLator?
PheKnowLator (Phenotype Knowledge Translator) or pkt_kg is the first fully customizable knowledge graph (KG) construction framework enabling users to build complex KGs that are Semantic Web compliant and amenable to automatic Web Ontology Language (OWL) reasoning, generate contemporary property graphs, and are importable by today’s popular graph toolkits. Please see the project Wiki for additional information.</p>
<p><a href="https://github.com/callahantiff/PheKnowLator/wiki">https://github.com/callahantiff/PheKnowLator/wiki</a></p>
<h1 id="kg-hub"><a aria-hidden="true" class="anchor-heading icon-link" href="#kg-hub"></a>KG-Hub</h1>
<p>Welcome
KG-Hub: A collection of biological and biomedical Knowledge Graphs, including their component data sources.</p>
<p><a href="https://knowledge-graph-hub.github.io/">https://knowledge-graph-hub.github.io/</a></p>
<h1 id="napdi-kg"><a aria-hidden="true" class="anchor-heading icon-link" href="#napdi-kg"></a>NaPDI-KG</h1>
<p>NaPDI-KG is a knowledge graph framework to identify and generate mechanistic hypotheses for pharmacokinetic natural product-drug interactions (NPDIs). This repository has been forked from the Knowledge-Graph-Hub. NaPDI-KG uses the PheKnowLator ecosystem to create the ontology-grounded KG and the KG-Hub ecosystem to integrate the nodes and edges extracted from natural product-related biomedical literature. NaPDI-KG includes the following components -</p>
<p><a href="https://github.com/sanyabt/np-kg-hub">https://github.com/sanyabt/np-kg-hub</a></p>
<p>actually at </p>
<p><a href="https://github.com/sanyabt/np-kg">https://github.com/sanyabt/np-kg</a></p>
<p><img src="/commons-dws-public/assets/images/2022-09-17-12-52-16.png"></p>
<p>By <a title="Private" href="https://wiki.dendron.so/notes/hfyvYGJZQiUwQaaxQO27q.html" target="_blank" class="private">people.sanya-bathla-taneja (Private)</a></p>

Ressources

Concrete steps to access and contribute to the DBGI Dendron


![](/assets/images/allard-lab.jpg)

Welcome the the COMMONS Lab Open Dendron !

In the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.

For this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.

## What is this note

This note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.

## Tutorial

### Dendron. 

#### What is Dendron ?

> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.
> 
> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.

#### Where to get more info on Dendron ?

- You can get more information in the Dendron system at the official website www.dendron.so
- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.

#### Concrete steps to access and contribute to the DBGI Dendron

1. Install [VSCode](https://code.visualstudio.com/download)
2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace 
3. Clone the COMMONS Dendron repo

    In your terminal
    ```
    git clone https://github.com/commons-research/commons-dws-public.git
    ```
4. In VSCode open (File/Open) the cloned repository.
5. Voila ! You should now be in the COMMONS Lab Open Dendron.

Feel free to explore and contribute.
A first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]


## Questions, comments, suggestions ?

Feel free to contribute here https://github.com/orgs/commons-research/discussions

