Answers.Body: <p>You can try Entrez in Biopython. Although, there is hassle with additional information.</p>
  <pre><code>from Bio import Entrez
  
  Entrez.email = &quot;your.letterbox@any.com&quot;
  Entrez.api_key = &quot;your_key&quot;
  
  TaxID = Entrez.read(Entrez.esearch(db=&quot;taxonomy&quot;, term=&quot;Hepatovirus A&quot;))[&quot;IdList&quot;][0]
  Entrez.read(Entrez.efetch(db=&quot;taxonomy&quot;, id=TaxID))
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-03-15T10:13:02.070Z
Answers.Text: It is a fair point Entrez has an explicit API as described in detail here https://www.ncbi.nlm.nih.gov/books/NBK25498/
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-03-15T08:26:06.510Z
Answers.LastActivityDate: 2022-03-15T08:26:06.510Z
Answers.UserDisplayName: Vovin
Body: <p>I am looking for tidy tabular dataset that contains known bacteria and fungi down to the species level. Basically a table that includes genus and species names and other higher-level information. For example, whether it is gram-positive or negative, or anaerobic etc. A database with API would work too.</p>
  <p>I found <a href="https://bacteria.ensembl.org/" rel="nofollow noreferrer">https://bacteria.ensembl.org/</a>, but this is not so easy to use/automate.</p>
  
Tags: <python><database><public-dataset>
Title: Database to download with information of bacteria?
ThreadText: # Database to download with information of bacteria?
  
  (Asked by: username_0 on 2022-03-15)
  
  I am looking for tidy tabular dataset that contains known bacteria and fungi down to the species level. Basically a table that includes genus and species names and other higher-level information. For example, whether it is gram-positive or negative, or anaerobic etc. A database with API would work too.
  
  I found <https://bacteria.ensembl.org/>, but this is not so easy to use/automate.
  
  **Tags:** python, database, public-dataset
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-03-15. Score: 1
  
  You can try Entrez in Biopython. Although, there is hassle with additional information.
  
  ```
  from Bio import Entrez
  
  Entrez.email = "your.letterbox@any.com"
  Entrez.api_key = "your_key"
  
  TaxID = Entrez.read(Entrez.esearch(db="taxonomy", term="Hepatovirus A"))["IdList"][0]
  Entrez.read(Entrez.efetch(db="taxonomy", id=TaxID))
  
  ```
  
  > **Comments:**
  > **username_2**: It is a fair point Entrez has an explicit API as described in detail here https://www.ncbi.nlm.nih.gov/books/NBK25498/  
  
  ---
  
  