1
$\begingroup$

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.

Improve this question
$\endgroup$

1 Answer 1

Reset to default
1
$\begingroup$

You can try Entrez in Biopython. Although, there is hassle with additional information.

from Bio import Entrez

Entrez.email = "[email protected]"
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))
Improve this answer
$\endgroup$
1

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.