<h1 id="cucumis-sativus-in-domain-bacteria">Cucumis Sativus (In Domain Bacteria)<a aria-hidden="true" class="anchor-heading icon-link" href="#cucumis-sativus-in-domain-bacteria"></a></h1>
<p>This is the page dedicated to <strong>Cucumis<em>sativus</em>(in_domain_Bacteria)</strong></p>
<h2 id="otol-taxonomy">OTOL Taxonomy<a aria-hidden="true" class="anchor-heading icon-link" href="#otol-taxonomy"></a></h2>
<p>Direct link to OTOL entry: <a href="https://tree.opentreeoflife.org/opentree/argus/opentree13.4@ott5893675">https://tree.opentreeoflife.org/opentree/argus/opentree13.4@ott5893675</a></p>

    
    <iframe src="https://tree.opentreeoflife.org/opentree/argus/opentree13.4@ott5893675" width="800" height="400" frameborder="0" allowfullscreen> </iframe>
    

    
<h2 id="wikipedia-entry-of-the-taxa">Wikipedia entry of the taxa<a aria-hidden="true" class="anchor-heading icon-link" href="#wikipedia-entry-of-the-taxa"></a></h2>
<p>Direct link to Wikipedia entry: <a href="https://en.wikipedia.org/wiki/Cucumis_sativus_(in_domain_Bacteria)">https://en.wikipedia.org/wiki/Cucumis_sativus_(in_domain_Bacteria)</a></p>

    
    <iframe src="https://en.wikipedia.org/wiki/Cucumis_sativus_(in_domain_Bacteria)" width="800" height="400" frameborder="0" allowfullscreen> </iframe>
    

    
<h2 id="metabolites-found-in-the-taxa">Metabolites found in the taxa<a aria-hidden="true" class="anchor-heading icon-link" href="#metabolites-found-in-the-taxa"></a></h2>

 
  <iframe src="https://query.wikidata.org/embed.html#SELECT%20%3Fmesh_id%20%3Fmesh_idLabel%20%3Fchemical_compound%20%3Fchemical_compoundLabel%20%3Fqueried_taxa%20%20%3Fqueried_taxaLabel%20%3Fqueried_taxall%20%3Fqueried_taxallLabel%20%3Freference%20%3FreferenceLabel%20WHERE%20%7B%0A%20%20VALUES%20%3Fchemical_classes%20%7B%0A%20%20%20%20wd%3AQ11173%20%23%20chemical%20compound%0A%20%20%20%20wd%3AQ59199015%20%23%20group%20of%20stereoisomers%0A%20%20%7D%0A%20%20%3Fchemical_compound%20wdt%3AP31%20%3Fchemical_classes.%20%23%20We%20select%20instance%20of%20the%20chemical%20classes%20%28chemical%20compound%20or%20group%20of%20stereoisomers%29%0A%20%20VALUES%20%3Fqueried_taxa%20%7B%0A%20%20%20%20wd%3Anan%0A%20%20%20%20%23Enter%20the%20Wikidata%20identifier%20of%20your%20taxa%20of%20interest%20%28here%20Streptomyces%20coelicolor%29.%0A%20%20%20%20%23%20You%20can%20remove%20the%20Qxxxxxxx%20id%20and%20hit%20Ctrl%2Bspace%2C%20thype%20in%20the%20first%20letters%20and%20it%20should%20autocomplete%0A%20%20%7D%0A%20%20%7B%0A%20%20%20%20%3Fchemical_compound%20p%3AP703%20%3Fstmt.%23%20We%20selecte%20chemical%20classes%20having%20the%20found%20in%20taxon%20statement%0A%20%20%20%20%3Fqueried_taxall%20wdt%3AP171%2a%20%3Fqueried_taxa.%0A%20%20%20%20%3Fstmt%20ps%3AP703%20%3Fqueried_taxall.%20%23%20and%20the%20restrict%20the%20found%20in%20taxon%20statement%20to%20match%20our%20queried%20taxa%0A%20%20%20%20%23%3Fchemical_compound%20p%3AP2868%20%3Fmesh.%0A%20%20%20%20%23%3Fmesh%20ps%3AP2868%20%3Fmesh_id.%0A%20%20%7D%0A%20%20%20%20%20%20OPTIONAL%20%7B%0A%20%20%20%20%20%20%3Fstmt%20prov%3AwasDerivedFrom%20%3Fref.%0A%20%20%20%20%20%20%3Fref%20pr%3AP248%20%3Freference.%20%23%20We%20optionally%20return%20the%20reference%20if%20present%20stated%20in%0A%20%20%20%20%7D%0A%20%20%0A%20%0A%20%20SERVICE%20wikibase%3Alabel%20%7B%20bd%3AserviceParam%20wikibase%3Alanguage%20%22%5BAUTO_LANGUAGE%5D%2Cen%22.%20%7D%0A%7D" width="800" height="400" frameborder="0" allowfullscreen></iframe>
 

    

Cucumis Sativus (In Domain Bacteria)

dendron-jbuf

Species list of the Botanical Garden of the University of Fribourg (BGUniFr)

# Species list of the Botanical Garden of the University of Fribourg (BGUniFr)


## What is this website ?

This website is a Dendron based website. If you don't know what this is about have a look at [The Dendron Home Page](https://wiki.dendron.so/).

This project is part of the [Digital Botanical Garden Initiative](https://www.dbgi.org/dendron-dbgi/).
In the frame of the DBGI, we have curated the species list of the Botanical Garden of the University of Fribourg ([BGUniFr](https://www.unifr.ch/jardin-botanique/fr/) and https://www.wikidata.org/wiki/Q27480249), which is displayed in the current website.



## How to use this website ?

You can use the [Dendron lookup functionality](https://wiki.dendron.so/notes/a7c3a810-28c8-4b47-96a6-8156b1524af3/) (the search bar at the top of this page) to look for a specific plant. You can also look for upper taxa such as the botanical family. Here is for example a list of all [[taxo-jbuf.archaeplastida.streptophyta.magnoliopsida.gentianales.apocynaceae]] of the garden.

You should also be able to navigate through the taxonomy using the menu on the left.

At the lower level (species), for each entry you should have a view of the compounds reported in LOTUS for the given entry. 
You do not know what is LOTUS. Have a look at the paper : https://lotusnprod.github.io/lotus-manuscript/
You should be able to download the compounds table as a csv file directly from this page.

You will also find the [Open Tree of Life](https://opentreeoflife.github.io/) and the [Wikipedia](https://www.wikipedia.org/) entry.


Example : This is the page you should land on if you look for _Coffea arabica_.


![[taxo-jbuf.archaeplastida.streptophyta.magnoliopsida.gentianales.rubiaceae.coffea.coffea-arabica]]



## How was this website made ?

Starting point is the [raw species list](https://github.com/digital-botanical-gardens-initiative/taxonomical-preparator/blob/43bc1f9a5b444c391db243f2c0393e512c4f1b8b/data/in/species_list.csv).

See over there for the taxonomical curation scripts https://github.com/digital-botanical-gardens-initiative/taxonomical-preparator

This is the [cleaned output list](https://github.com/digital-botanical-gardens-initiative/taxonomical-preparator/blob/43bc1f9a5b444c391db243f2c0393e512c4f1b8b/data/out/species_list_croisee_final.csv) 

The Dendron structure seemed particularly adapted for the navigation within a taxonomy. We thus wrote a [script](https://github.com/digital-botanical-gardens-initiative/taxonomical-preparator/blob/43bc1f9a5b444c391db243f2c0393e512c4f1b8b/src/03_dendronificator.py) to create a Dendron note for each of the species of the garden.


## I have a question or a comment !

Use the link at the bottom of any of the pages to create an issue on Github. Yes, down there ! 👇 

