Answers.Body: <p>The nomenclature is no longer being followed as NCBI is moving all the files to S3/Google cloud. <a href="https://github.com/saketkc/pysradb" rel="nofollow noreferrer">pysradb</a> allows you to fetch the metadata and get the URLs for each individual SRR. See examples in <a href="https://colab.research.google.com/drive/1tOVBg7vPnhTYNjyFQTvN0K9jGT3MyrVb" rel="nofollow noreferrer">this notebook</a>.</p>
  
  <p>You can also download an entire project by doing:</p>
  
  <pre><code>pysradb download -p &lt;SRP&gt;
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-22T22:58:48.517Z
Answers.LastActivityDate: 2020-01-22T22:58:48.517Z
Answers.UserDisplayName: Saket Choudhary
Body: <p>I would like to assign a URL/URI to accession runs (i.e. SRR IDs) from the NCBI short read archive.</p>
  
  <p>In program listings, I used to list them as <code>ftp://</code> URLs, because they were available on their servers as such, e.g. <code>SRR3418242</code>:</p>
  
  <pre><code>ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR341/SRR3418242/SRR3418242.sra
  </code></pre>
  
  <p>But this approach is deprecated, plus, not all runs are available this way anymore. The now recommended approach is to use <a href="https://www.ncbi.nlm.nih.gov/sra/docs/sradownload/" rel="nofollow noreferrer">sra-tools to download the data</a>. This tool takes the SRR Ids directly, i.e. <code>prefetch "SRR3418242"</code>, and resolves them to one of many possible locations (home directory, http, etc).</p>
  
  <p>Is there an official URI scheme that can be used to reference accession runs from the short-read-archive ? I would like to disambiguate them from other types of files and URLs (S3 keys, http, file). For file manifests, spreadsheets, and publications, is there something similar to <code>srr://SRR3418242</code>?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-03-21T22:21:20.623Z
Comments.Text: No, there isn't something like srr:// and there won't be. ENA via aspera is almost always the preferred way to download data as long as ENA has it.
Comments.UserDisplayName: user172818
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-03-22T19:40:40.013Z
Comments.Text: Thanks. My concern is the namespace. I'd like to know a nomenclature which doesn't prescribe a particular software or particular read archive. As long as run numbers and sequence data agree on both archives...
Comments.UserDisplayName: init_js
Tags: <phylogenetics><sratoolkit>
Title: What is the recognized way to reference accession data (.sra files) from NCBI as a URI?
ThreadText: # What is the recognized way to reference accession data (.sra files) from NCBI as a URI?
  
  (Asked by: username_0 on 2019-03-21)
  
  I would like to assign a URL/URI to accession runs (i.e. SRR IDs) from the NCBI short read archive.
  
  In program listings, I used to list them as `ftp://` URLs, because they were available on their servers as such, e.g. `SRR3418242`:
  
  ```
  ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR341/SRR3418242/SRR3418242.sra
  
  ```
  
  But this approach is deprecated, plus, not all runs are available this way anymore. The now recommended approach is to use [sra-tools to download the data](https://www.ncbi.nlm.nih.gov/sra/docs/sradownload/). This tool takes the SRR Ids directly, i.e. `prefetch "SRR3418242"`, and resolves them to one of many possible locations (home directory, http, etc).
  
  Is there an official URI scheme that can be used to reference accession runs from the short-read-archive ? I would like to disambiguate them from other types of files and URLs (S3 keys, http, file). For file manifests, spreadsheets, and publications, is there something similar to `srr://SRR3418242`?
  
  **Tags:** phylogenetics, sratoolkit
  
  > **Comments:**
  > **username_1**: No, there isn't something like srr:// and there won't be. ENA via aspera is almost always the preferred way to download data as long as ENA has it.  
  > **username_0**: Thanks. My concern is the namespace. I'd like to know a nomenclature which doesn't prescribe a particular software or particular read archive. As long as run numbers and sequence data agree on both archives...  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2020-01-22. Score: 1
  
  The nomenclature is no longer being followed as NCBI is moving all the files to S3/Google cloud. [pysradb](https://github.com/saketkc/pysradb) allows you to fetch the metadata and get the URLs for each individual SRR. See examples in [this notebook](https://colab.research.google.com/drive/1tOVBg7vPnhTYNjyFQTvN0K9jGT3MyrVb).
  
  You can also download an entire project by doing:
  
  ```
  pysradb download -p <SRP>
  
  ```
  
  
  ---
  
  