<h1 id="2023-06-08">2023-06-08<a aria-hidden="true" class="anchor-heading icon-link" href="#2023-06-08"></a></h1>
<h1 id="this-is-maëlles-dbgi-daily-open-notebook">This is Maëlle's DBGI daily open-notebook.<a aria-hidden="true" class="anchor-heading icon-link" href="#this-is-maëlles-dbgi-daily-open-notebook"></a></h1>
<p>Today is 2023.06.08</p>
<h2 id="todo">TODO<a aria-hidden="true" class="anchor-heading icon-link" href="#todo"></a></h2>
<ul>
<li>Check discussion: <a href="https://github.com/orgs/digital-botanical-gardens-initiative/discussions">https://github.com/orgs/digital-botanical-gardens-initiative/discussions</a></li>
<li>Check Zulip</li>
</ul>
<h3 id="todo-browse-whole-dataset">TODO Browse whole dataset<a aria-hidden="true" class="anchor-heading icon-link" href="#todo-browse-whole-dataset"></a></h3>
<ul class="contains-task-list">
<li class="task-list-item"><input type="checkbox" disabled> Structure
<ul class="contains-task-list">
<li class="task-list-item"><input type="checkbox" checked disabled> Fetch InChi from JSME</li>
<li class="task-list-item"><input type="checkbox" disabled> Substructure search algo
<ul class="contains-task-list">
<li class="task-list-item"><input type="checkbox" checked disabled> Ulmann</li>
<li class="task-list-item"><input type="checkbox" disabled> DF</li>
<li>[ ]</li>
</ul>
</li>
<li class="task-list-item"><input type="checkbox" checked disabled> Tanimoto algo</li>
<li class="task-list-item"><input type="checkbox" checked disabled> Search in taxo group</li>
<li class="task-list-item"><input type="checkbox" disabled> Return options
<ul class="contains-task-list">
<li class="task-list-item"><input type="checkbox" disabled> Graph</li>
<li class="task-list-item"><input type="checkbox" disabled> Table</li>
</ul>
</li>
</ul>
</li>
<li class="task-list-item"><input type="checkbox" disabled> Text
<ul class="contains-task-list">
<li class="task-list-item"><input type="checkbox" disabled> Advanced search</li>
<li class="task-list-item"><input type="checkbox" disabled> Return options
<ul class="contains-task-list">
<li class="task-list-item"><input type="checkbox" disabled> Graph</li>
<li class="task-list-item"><input type="checkbox" disabled> Table</li>
</ul>
</li>
</ul>
</li>
</ul>
<h2 id="code">CODE<a aria-hidden="true" class="anchor-heading icon-link" href="#code"></a></h2>
<h2 id="notes">NOTES<a aria-hidden="true" class="anchor-heading icon-link" href="#notes"></a></h2>
<ul>
<li>Should work on optimization of substructure search and Tanimoto search 
<ul>
<li>=> takes 1-2 minutes to get the results</li>
</ul>
</li>
</ul>
<h2 id="todo-next">TODO NEXT<a aria-hidden="true" class="anchor-heading icon-link" href="#todo-next"></a></h2>
<ul class="contains-task-list">
<li class="task-list-item"><input type="checkbox" disabled> add plots</li>
<li class="task-list-item"><input type="checkbox" disabled> LCMS data</li>
<li class="task-list-item"><input type="checkbox" disabled> add SPARQL</li>
<li class="task-list-item"><input type="checkbox" disabled> Browse wholedataset part
<ul class="contains-task-list">
<li class="task-list-item"><input type="checkbox" disabled> add visualization options</li>
<li class="task-list-item"><input type="checkbox" checked disabled> Display JSME</li>
<li class="task-list-item"><input type="checkbox" checked disabled> Display input</li>
<li class="task-list-item"><input type="checkbox" checked disabled> Display table - JSME
<ul class="contains-task-list">
<li class="task-list-item"><input type="checkbox" checked disabled> add Links</li>
<li class="task-list-item"><input type="checkbox" disabled> Display images</li>
</ul>
</li>
<li class="task-list-item"><input type="checkbox" checked disabled> Display table - input
<ul class="contains-task-list">
<li class="task-list-item"><input type="checkbox" checked disabled> add Links</li>
<li class="task-list-item"><input type="checkbox" disabled> Display images</li>
</ul>
</li>
<li class="task-list-item"><input type="checkbox" checked disabled> similarity or exact search
<ul class="contains-task-list">
<li class="task-list-item"><input type="checkbox" checked disabled> Level of similarity?</li>
</ul>
</li>
</ul>
</li>
<li class="task-list-item"><input type="checkbox" checked disabled> search bar for browse molecule/organism</li>
<li class="task-list-item"><input type="checkbox" checked disabled> style all app in css file</li>
<li class="task-list-item"><input type="checkbox" checked disabled> create a MVC structure</li>
<li class="task-list-item"><input type="checkbox" checked disabled> add wikidata images to organism visu</li>
<li class="task-list-item"><input type="checkbox" checked disabled> Link from home to pages</li>
<li class="task-list-item"><input type="checkbox" checked disabled> README</li>
<li class="task-list-item"><input type="checkbox" checked disabled> display molecules structure</li>
</ul>
<h2 id="important-for-redaction">Important for redaction<a aria-hidden="true" class="anchor-heading icon-link" href="#important-for-redaction"></a></h2>

This is Maëlle's DBGI daily open-notebook.

2023-06-08


# Overview

The Digital Botanical Gardens Initiative (DBGI, www.dbgi.org) ambitions to explore innovative solutions for the collection, management and sharing of digital information acquired on living botanical collections. A particular focus will be placed on the large scale characterization of the chemodiversity of living plants collections through mass spectrometric approaches. The acquired data will be structured, organized and connected with relevant metadata through [semantic web](https://en.wikipedia.org/wiki/Semantic_Web) technology. The gathered knowledge will then inform ecosystem functioning research and orient [biodiversity conservation](https://en.wikipedia.org/wiki/Conservation_biology) projects. The DBGI initially aims to take advantage of the readily available living collections of Swiss botanical gardens to establish robust and scalable biodiversity digitisation workflows. The ultimate goal is to apply these approaches in the field and at the global scale in wildlife ecosystems. 

# Main goals

The DBGI main goals are briefly summarized below :

![](/assets/images/2022-06-18-17-13-23.png){max-width: 400px, display: block, margin: 0 auto}

# An Open Science project


## Working with the workshop doors open

![](/assets/images/2022-06-18-17-47-56.png){max-width: 400px}

A way of working briefly described by Andy Matuschak here https://notes.andymatuschak.org/z21cgR9K3UcQ5a7yPsj2RUim3oM2TzdBByZu. 


## Open Notebook Science

If we apply this "working with the workshop doors open" idea to a scientific research endeavor we understand it as respecting the core concepts of Open Science. These is more precisely the principle of Open Notebook Science https://en.wikipedia.org/wiki/Open-notebook_science

For the projects of the DBGI we will follow such an Open Notebook Science approach in order to share early ideas and results but also the less shiny parts of the research projects. 

You can follow the DBGI related Open Notebooks here [[open-notebook]].

Expect to find strange ideas, badly formulated text and poorly written code. However if you have time and interest you should be able to participate at each step of the process. Hopefully this will lead to enhanced collaboration and participation. Maybe yes, maybe not. Let's make it a methodological experiment !

Each pages of this website are written in markdown and hosted on Github. You can edit them by clicking on the "Click here to edit this page on Github !" link at the bottom of the page. See down there 👇

If you are willing to participate the the DBGI Dendron notes have a look at the [[welcome]] section to get you started !


## What's new ?!

This web site might not necessarily seem to be change since the last time you came to visit.

If something moved recently you should be able to track this over there https://github.com/digital-botanical-gardens-initiative/dendron-dbgi/commits/main