Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
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Answers.UserDisplayName: Bastian Schiffthaler
Answers.Body: <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>
  
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Body: <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>
  
Tags: <phylogenetics><phylogeny><taxonomy>
Title: Download complete Phylogenetic Tree as JSON
ThreadText: # 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:
  
  ```json
  [{
    "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
  
  
  ---
  
  ## 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>
  
  
  ---
  
  ### 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..
  
  
  ---
  
  