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BioProject Hierarchy at Google Cloud Platform -
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<li><a href="/pathogens/docs/gcp/">GCP</a></li>
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<li>BioProject Hierarchy at Google Cloud Platform </li>
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<h1 id="bioproject-hierarchy-at-google-c">BioProject Hierarchy at Google Cloud Platform <a href="/pathogens/docs/gcp/"><img alt="GCP Documentation TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h1>
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<p><strong>ALPHA RELEASE</strong> <em>This is under active development and while we strive to
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maintain correctness, it is possible results may be unstable, unavailable, or
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incorrect at times. Please contact us by email at pd-help@ncbi.nlm.nih.gov
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before relying on this data for production analyses.</em></p>
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<div class="toc">
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<ul>
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<li><a href="#what-data-is-available-on-the-go">What data is available on the Google Cloud?</a><ul>
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<li><a href="#pathogen-detection-resources-ava">Pathogen Detection Resources available on the Google Cloud</a></li>
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<li><a href="#update-frequency">Update Frequency</a></li>
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</ul>
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</li>
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<li><a href="#getting-started-with-bigquery">Getting started with BigQuery</a></li>
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||
<li><a href="#what-is-ncbipathogendetectpdbrow">What is ncbi-pathogen-detect.pdbrowser.bioproject_hierarchy</a></li>
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<li><a href="#fields">Fields</a></li>
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<li><a href="#examples">Examples</a><ul>
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<li><a href="#search-for-all-the-isolates-belo">Search for all the isolates belonging to a given umbrella bioproject</a></li>
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</ul>
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</li>
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</ul>
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</div>
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<h2 id="what-data-is-available-on-the-go">What data is available on the Google Cloud? <a href="#TOC"><img alt="Google Cloud Resources documentation" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h2>
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<p>For a list of all resources see <a href="/pathogens/docs/gcp/">Pathogen Detection Resources at Google Cloud Platform</a></p>
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<p>A dump of the BioProject hierarchy is available at Google Cloud Platform (GCP) in the <strong><code>ncbi-pathogen-detect.pdbrowser.bioproject_hierarchy</code></strong> table at Google BigQuery. This data includes all data BioProjects for isolates in the Pathogen Detection browsers as well as any parent umbrella BioProjects they are linked to. This data allows you to identify all the isolates for a given parent bioproject. This data is also available on our <a href="https://ftp.ncbi.nlm.nih.gov/pathogen/Results/BioProject_Hierarchy/">FTP site</a> (see the <a href="https://ftp.ncbi.nlm.nih.gov/pathogen/ReadMe.txt">ReadMe.txt</a> for details).</p>
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<h3 id="pathogen-detection-resources-ava">Pathogen Detection Resources available on the Google Cloud</h3>
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<ul>
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<li><a href="/pathogens/docs/gcp/">Pathogen Detection Resources at Google Cloud Platform</a></li>
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||
<li><a href="/pathogens/docs/microbigge_gcp/#getting-started-with-bigquery">Getting started with BigQuery</a></li>
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||
<li><a href="/pathogens/docs/microbigge_gcp/">MicroBIGG-E table in BigQuery</a></li>
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||
<li><a href="/pathogens/docs/microbigge_gcp/#contig-sequences">MicroBIGG-E contig sequences in Google Storage buckets</a></li>
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<li><a href="/pathogens/docs/microbigge_gcp/#protein-sequences">MicroBIGG-E protein sequences in Google Storage buckets</a></li>
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<li><a href="/pathogens/docs/ast_gcp/">AST Browser in BigQuery</a></li>
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<li><a href="/pathogens/docs/isolates_gcp/">Isolates Browser table in BigQuery</a></li>
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<li><a href="/pathogens/docs/isolates_gcp/#isolate_exceptions">Isolate Exceptions table in BigQuery</a></li>
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<li><a href="/pathogens/docs/bioproject_hierarchy_gcp/">BioProject Hierarchy in BigQuery</a>
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<!-- asdf_ -->
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</li>
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</ul>
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<h3 id="update-frequency">Update Frequency <a href="#TOC"><img alt="BioProject hierarchy at GCP TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h3>
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<p>The <code>bioproject_hierarchy</code> table at Google Cloud BigQuery is updated daily. The information is also updated daily on our ftp site in https://ftp.ncbi.nlm.nih.gov/pathogen/Results/BioProject_Hierarchy/ with <a href="https://ftp.ncbi.nlm.nih.gov/pathogen/Results/BioProject_Hierarchy/latest.bioproject_hierarchy.txt">latest.bioproject_hierarchy.txt</a> including the most recent dump.</p>
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<h2 id="getting-started-with-bigquery"><a href="/pathogens/docs/getting_started_bigquery">Getting started with BigQuery</a></h2>
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||
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<p>Our <a href="/pathogens/docs/getting_started_bigquery">Getting started with BigQuery</a> page has instructions on how to run queries with BigQuery.</p>
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||
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<!--
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## Fields in the table `ncbi-pathogen-detect.pdbrowser.bioproject_hierarchy`
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<table width="100%">
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<tr>
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<td width="50%" valign="top">
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<a href="#bioproject_id"><em>bioproject_id</em></a> <br />
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<a href="#bioproject_acc"><em>bioproject_acc</em></a> <br />
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||
<a href="#bioproject_name"><em>bioproject_name</em></a> <br />
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||
<a href="#bioproject_title"><em>bioproject_title</em></a> <br />
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||
<a href="#top_organization"><em>top_organization</em></a> <br />
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||
</td>
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||
<td width="50%" valign="top">
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||
<a href="#parent_bioproject_id"><em>parent_bioproject_id</em></a> <br />
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||
<a href="#parent_bioproject_acc"><em>parent_bioproject_acc</em></a> <br />
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||
<a href="#parent_bioproject_name"><em>parent_bioproject_name</em></a> <br />
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||
<a href="#parent_bioproject_title"><em>parent_bioproject_title</em></a> <br />
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||
<a href="#parent_top_organization"><em>parent_top_organization</em></a> <br />
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||
</td>
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||
</tr>
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</table>
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||
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#### _bioproject_id_ [](#TOC) [](/pathogens/pathogens_help/)
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||
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||
Bioproject ID (formerly Genome Project ID) See [BioProject help](https://www.ncbi.nlm.nih.gov/books/NBK54016/) for details.
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||
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#### _bioproject_acc_ [](#TOC) [](/pathogens/pathogens_help/)
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||
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BioProject Accession
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#### _bioproject_name_ [](#TOC) [](/pathogens/pathogens_help/)
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||
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The Name field from the BioProject record
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||
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||
#### _bioproject_title_ [](#TOC) [](/pathogens/pathogens_help/)
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||
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||
The Title field from teh BioProject record
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||
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||
#### _top_organization_ [](#TOC) [](/pathogens/pathogens_help/)
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||
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||
The primary organization associated with the BioProject record
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||
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||
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||
#### __ [](#TOC) [](/pathogens/pathogens_help/)
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||
-->
|
||
|
||
<h2 id="what-is-ncbipathogendetectpdbrow">What is <code>ncbi-pathogen-detect.pdbrowser.bioproject_hierarchy</code></h2>
|
||
|
||
<p>The <code>bioproject_hierarchy</code> table contains information about bioprojects and
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||
their parents. A given bioproject may have multiple parents and each parent may
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||
have multiple children, so it is not a strictly tree-like structure. The
|
||
organization of the bioprojects and their membership is determined by
|
||
submitters and is not generated by NCBI or Pathogen Detection; data and
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bioproject labelling may be inconsistent. </p>
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<h2 id="fields">Fields</h2>
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<table>
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||
<thead>
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<tr>
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<th>Column</th>
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<th>Description</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td><em>bioproject_id</em></td>
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<td>BioProject ID</td>
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</tr>
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<tr>
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<td><em>bioproject_acc</em></td>
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<td>BioProject accession</td>
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</tr>
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<tr>
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<td><em>bioproject_name</em></td>
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<td>BioProject name</td>
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</tr>
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<tr>
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<td><em>bioproject_title</em></td>
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<td>BioProject title</td>
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</tr>
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<tr>
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<td><em>top_organization</em></td>
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<td>"Top organization" or primary organization associated with this submission</td>
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</tr>
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<tr>
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<td><em>parent_bioproject_id</em></td>
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<td>BioProject ID of the parent bioproject (if any) otherwise NULL</td>
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</tr>
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<tr>
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<td><em>parent_bioproject_acc</em></td>
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<td>BioProject accession of the parent bioproject (if any) otherwise NULL</td>
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</tr>
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<tr>
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<td><em>parent_bioproject_name</em></td>
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<td>BioProject name of the parent bioproject (if any) otherwise NULL</td>
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||
</tr>
|
||
<tr>
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||
<td><em>parent_bioproject_title</em></td>
|
||
<td>BioProject title of the parent bioproject (if any) otherwise NULL</td>
|
||
</tr>
|
||
<tr>
|
||
<td><em>parent_top_organization</em></td>
|
||
<td>Top organization of the parent bioproject (if any) otherwise NULL</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
<h2 id="examples">Examples</h2>
|
||
|
||
<h3 id="search-for-all-the-isolates-belo">Search for all the isolates belonging to a given umbrella bioproject</h3>
|
||
|
||
<p>The following Google BigQuery Standard SQL will identify all the isolates for umbrella BioProject PRJNA514048</p>
|
||
|
||
<pre><code>WITH RECURSIVE child_bioprojects as (
|
||
SELECT parent_bioproject_acc, bioproject_acc FROM `ncbi-pathogen-detect.pdbrowser.bioproject_hierarchy`
|
||
UNION ALL
|
||
SELECT b.parent_bioproject_acc, a.bioproject_acc
|
||
FROM `ncbi-pathogen-detect.pdbrowser.bioproject_hierarchy` a JOIN child_bioprojects b
|
||
ON b.bioproject_acc = a.parent_bioproject_acc
|
||
)
|
||
SELECT cb.parent_bioproject_acc, parent_bp.top_organization parent_organization,
|
||
cb.bioproject_acc, child_bp.bioproject_name, child_bp.top_organization,
|
||
isolates.target_acc, isolates.taxgroup_name, isolates.biosample_acc
|
||
FROM child_bioprojects cb
|
||
JOIN `ncbi-pathogen-detect.pdbrowser.isolates` isolates ON isolates.bioproject_acc = cb.bioproject_acc
|
||
JOIN `ncbi-pathogen-detect.pdbrowser.bioproject_hierarchy` parent_bp ON parent_bp.bioproject_acc = cb.parent_bioproject_acc
|
||
JOIN `ncbi-pathogen-detect.pdbrowser.bioproject_hierarchy` child_bp ON child_bp.bioproject_acc = cb.bioproject_acc
|
||
WHERE cb.parent_bioproject_acc = 'PRJNA514048'
|
||
</code></pre>
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