<p>If ENA archive contains such information, then you can access it programatically through the <a href="https://www.ebi.ac.uk/ena/browse/programmatic-access" rel="nofollow noreferrer">EBI api</a>.</p>

<p>Also you can access the NCBI database programatically through their <a href="https://www.ncbi.nlm.nih.gov/books/NBK25500/" rel="nofollow noreferrer">eutils</a>.</p>

<p>In both cases you can access annotations, though not sure if they contain what you are looking for in all the cases.</p>

CC BY-SA 4.0
2019-03-14T19:56:40.047Z
Thanks for that! I previously tried the NCBI and it turned out to be quite messy. The ENA is a step in the right direction as I can extract the strain information quite nicely. Not quite what I was after but definitely helpful, thanks.
TW93
CC BY-SA 4.0
2019-03-14T11:57:01.997Z
2019-03-14T11:57:01.997Z
aLbAc
<p>I will preface this by saying I'm not a microbiologist, so I apologise for any haziness and I'll be happy to expand.</p>

<p>I would like to download the assemblies of different E. coli genomes and group them by their pathotypes (e.g. EPEC, ETEC, EIEC). </p>

<p>I have used enterobase previously to download salmonella genomes broadly by their subspecies, and it does have a set of E. coli genomes. However, they are mainly annotated by their serotype, and not with any broad nomination of pathogenesis. I think I would be able to use the API to grab these serotypes and map them to a type of pathogenicity but that would probably be quite messy.</p>

<p>Does such a database exist? Most I can find are broadly annotated or a are very detailed, but don't allow access to the raw annotation. </p>

<p>Thanks in advance.</p>

<genome><public-databases><assembly><microbiology>
Is there a resource where I can donwload E. coli assemblies grouped by their pathotypes?
# Is there a resource where I can donwload E. coli assemblies grouped by their pathotypes?

(Asked by: username_0 on 2019-03-07)

I will preface this by saying I'm not a microbiologist, so I apologise for any haziness and I'll be happy to expand.

I would like to download the assemblies of different E. coli genomes and group them by their pathotypes (e.g. EPEC, ETEC, EIEC).

I have used enterobase previously to download salmonella genomes broadly by their subspecies, and it does have a set of E. coli genomes. However, they are mainly annotated by their serotype, and not with any broad nomination of pathogenesis. I think I would be able to use the API to grab these serotypes and map them to a type of pathogenicity but that would probably be quite messy.

Does such a database exist? Most I can find are broadly annotated or a are very detailed, but don't allow access to the raw annotation.

Thanks in advance.

**Tags:** genome, public-databases, assembly, microbiology

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## 1 answers

### Answer by username_1 on 2019-03-14. Score: 1 | Accepted answer

If ENA archive contains such information, then you can access it programatically through the [EBI api](https://www.ebi.ac.uk/ena/browse/programmatic-access).

Also you can access the NCBI database programatically through their [eutils](https://www.ncbi.nlm.nih.gov/books/NBK25500/).

In both cases you can access annotations, though not sure if they contain what you are looking for in all the cases.

> **Comments:**
> **username_0**: Thanks for that! I previously tried the NCBI and it turned out to be quite messy. The ENA is a step in the right direction as I can extract the strain information quite nicely. Not quite what I was after but definitely helpful, thanks.  

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