<p>NCBI maintains an SQL dump of their <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2018/02/22/new-taxonomy-files-available-with-lineage-type-and-host-information/" rel="nofollow noreferrer">taxonomic database</a></p>
<p>You can see what that contains <a href="https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/taxdump_readme.txt" rel="nofollow noreferrer">here</a></p>
<p>For smaller requests (depending on what you need), you might also consider the ENSEMBL REST API - although I don't know of a way to retrieve the complete tree (shoot them an email): <a href="https://rest.ensembl.org/taxonomy/classification/53399?content-type=application/json" rel="nofollow noreferrer">https://rest.ensembl.org/taxonomy/classification/53399?content-type=application/json</a></p>

CC BY-SA 4.0
2020-10-21T09:28:13.947Z
2020-10-21T09:28:13.947Z
Bastian Schiffthaler
<p>It would be worth looking at the <a href="http://tolweb.org/tree/" rel="nofollow noreferrer">Tree of Life</a> web project, it isn't downloadable but its a reference source that can be improved on and updated in your website.</p>
<p>ToL contains trees linking everything from bacteria, archaea through to the complete diversity of eukaryotes, but its a bit old with 2008 from my taxonomic knowledge being the last update for some of the entries, e.g. Plasmodium spp..</p>

CC BY-SA 4.0
2020-10-21T11:59:01.017Z
2020-10-21T11:59:01.017Z
M__
<p>I would like to integrate the phylogenetic tree into a website. Does anyone know where I can download the complete tree? Best would be a JSON, which looks something like this:</p>
<pre class="lang-json prettyprint-override"><code>[{
  &quot;level&quot;: &quot;domain&quot;,
  &quot;name&quot;: &quot;eukaryota&quot;,
  &quot;commonNames&quot;: {
    &quot;en&quot;: [&quot;eukaryotes&quot;],
    &quot;de&quot;: [&quot;Eukaryoten&quot;, &quot;Eukaryonten&quot;]
  },
  &quot;children&quot;: [
    {
      &quot;level&quot;: &quot;kingdom&quot;,
      &quot;name&quot;: &quot;plantae&quot;,
      &quot;commonNames&quot;: {
        &quot;en&quot;: [&quot;plants&quot;],
        &quot;de&quot;: [&quot;Pflanzen&quot;]
      },
      &quot;children&quot;: [...]
    },
    {
      &quot;level&quot;: &quot;kingdom&quot;,
      &quot;name&quot;: &quot;animalia&quot;,
      &quot;commonNames&quot;: {
        &quot;en&quot;: [&quot;animals&quot;],
        &quot;de&quot;: [&quot;Tiere&quot;]
      },
      &quot;children&quot;: [...]
    },
    ...
  ]
},
{
  &quot;level&quot;: &quot;domain&quot;,
  &quot;name&quot;: &quot;bacteria&quot;,
  &quot;commonNames&quot;: {
    &quot;en&quot;: [&quot;bacteria&quot;],
    &quot;de&quot;: [&quot;Bakterien&quot;]
  },
  &quot;children&quot;: [...]
}]
</code></pre>
<p>Other formats and structures are ok, too. The important thing is that the level of the nodes can be retrieved. In the end I only want to have the main levels Domain, Kingdom, Phylum, Class, Order, Family, Genus and Species in the tree. (<a href="https://en.wikipedia.org/wiki/Taxonomy_(biology)#/media/File:Biological_classification_L_Pengo_vflip.svg" rel="nofollow noreferrer">https://en.wikipedia.org/wiki/Taxonomy_(biology)#/media/File:Biological_classification_L_Pengo_vflip.svg</a>) So if there are more nodes from other levels like Clade, Tribe or Subfamily, it must be possible to identify and remove them.
Thanks a lot!</p>

<phylogenetics><phylogeny><taxonomy>
Download complete Phylogenetic Tree as JSON
# Download complete Phylogenetic Tree as JSON

(Asked by: username_0 on 2020-10-21)

I would like to integrate the phylogenetic tree into a website. Does anyone know where I can download the complete tree? Best would be a JSON, which looks something like this:
[{
  "level": "domain",
  "name": "eukaryota",
  "commonNames": {
    "en": ["eukaryotes"],
    "de": ["Eukaryoten", "Eukaryonten"]
  },
  "children": [
    {
      "level": "kingdom",
      "name": "plantae",
      "commonNames": {
        "en": ["plants"],
        "de": ["Pflanzen"]
      },
      "children": [...]
    },
    {
      "level": "kingdom",
      "name": "animalia",
      "commonNames": {
        "en": ["animals"],
        "de": ["Tiere"]
      },
      "children": [...]
    },
    ...
  ]
},
{
  "level": "domain",
  "name": "bacteria",
  "commonNames": {
    "en": ["bacteria"],
    "de": ["Bakterien"]
  },
  "children": [...]
}]

Other formats and structures are ok, too. The important thing is that the level of the nodes can be retrieved. In the end I only want to have the main levels Domain, Kingdom, Phylum, Class, Order, Family, Genus and Species in the tree. (https://en.wikipedia.org/wiki/Taxonomy_(biology)#/media/File:Biological_classification_L_Pengo_vflip.svg) So if there are more nodes from other levels like Clade, Tribe or Subfamily, it must be possible to identify and remove them.
Thanks a lot!

**Tags:** phylogenetics, phylogeny, taxonomy

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## 2 answers

### Answer by username_1 on 2020-10-21. Score: 4

NCBI maintains an SQL dump of their [taxonomic database](https://ncbiinsights.ncbi.nlm.nih.gov/2018/02/22/new-taxonomy-files-available-with-lineage-type-and-host-information/)

You can see what that contains [here](https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/taxdump_readme.txt)

For smaller requests (depending on what you need), you might also consider the ENSEMBL REST API - although I don't know of a way to retrieve the complete tree (shoot them an email): <https://rest.ensembl.org/taxonomy/classification/53399?content-type=application/json>


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### Answer by username_2 on 2020-10-21. Score: 1

It would be worth looking at the [Tree of Life](http://tolweb.org/tree/) web project, it isn't downloadable but its a reference source that can be improved on and updated in your website.

ToL contains trees linking everything from bacteria, archaea through to the complete diversity of eukaryotes, but its a bit old with 2008 from my taxonomic knowledge being the last update for some of the entries, e.g. Plasmodium spp..


---

