Answers.Body: <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>
  
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Answers.Text: 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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Body: <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>
  
Tags: <genome><public-databases><assembly><microbiology>
Title: Is there a resource where I can donwload E. coli assemblies grouped by their pathotypes?
ThreadText: # 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
  
  
  ---
  
  ## 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.  
  
  ---
  
  