<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>

CC BY-SA 4.0
2022-03-15T10:13:02.070Z
It is a fair point Entrez has an explicit API as described in detail here https://www.ncbi.nlm.nih.gov/books/NBK25498/
M__
CC BY-SA 4.0
2022-03-15T08:26:06.510Z
2022-03-15T08:26:06.510Z
Vovin
<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>

<python><database><public-dataset>
Database to download with information of bacteria?
# 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

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## 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/  

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