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<h1 id="antibiotic-susceptibility-test-a">Antibiotic Susceptibility Test (AST) data at GCP <a href="/pathogens/pathogens_help/#amr"><img alt="AMR 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="#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="#linking-to-isolates-browser-data">Linking to Isolates Browser data in BigQuery</a></li>
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<li><a href="#example-searches">Example searches</a><ul>
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<li><a href="#how-many-isolates-were-tested-fo">How many isolates were tested for ertapenem resistance</a></li>
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<li><a href="#what-organism-groups-were-tested">What organism groups were tested for ertapenem resistance?</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="AST Browser data in BigQuery" 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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<h3 id="update-frequency">Update Frequency <a href="#TOC"><img alt="AST Browser data in BigQuery" 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 AST table at Google Cloud BigQuery is updated daily. For this reason the contents may
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not agree exactly with those shown in the <a href="/pathogens/ast/">AST
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browser</a>. If you see unexpected discrepancies please let us know by emailing us at pd-help@ncbi.nlm.nih.gov.</p>
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<h2 id="getting-started-with-bigquery"><a href="/pathogens/docs/getting_started_bigquery">Getting started with BigQuery</a> <a href="#TOC"><img alt="AST Browser data in BigQuery" 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>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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<h2 id="linking-to-isolates-browser-data">Linking to Isolates Browser data in BigQuery <a href="#TOC"><img alt="AST Browser data in BigQuery" 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>NCBI Pathogen Detection also maintains <a href="/pathogens/pathogens_help/#isolates-browser">Isolates Browser</a> and
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<a href="/pathogens/pathogens_help/#microbigge">MicroBIGG-E</a> data in the BigQuery table
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<code>ncbi-pathogen-detect.pdbrowser.isolates</code> and
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<code>ncbi-pathogen-detect.pdbrowser.microbigge</code> tables respectively. There are
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||
several fields in common between the tables, but we generally recommend
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joining on the <code>target_acc</code> field. See <a href="/pathogens/docs/isolates_gcp">Isolates Browser Data at Google Cloud
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||
Platform</a> for examples of joining two tables.</p>
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|
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<h2 id="example-searches">Example searches <a href="#TOC"><img alt="AST Browser data in BigQuery" 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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<h3 id="how-many-isolates-were-tested-fo">How many isolates were tested for ertapenem resistance <a href="#TOC"><img alt="AST Browser data in BigQuery" 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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<pre><code>select count(distinct(target_acc))
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from `ncbi-pathogen-detect.pdbrowser.ast`
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where antibiotic = 'ertapenem'
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</code></pre>
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|
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<h3 id="what-organism-groups-were-tested">What organism groups were tested for ertapenem resistance? <a href="#TOC"><img alt="AST Browser data in BigQuery" 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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<pre><code>select taxgroup_name, count(distinct(target_acc)) num_isolates
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from `ncbi-pathogen-detect.pdbrowser.ast`
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where antibiotic = 'ertapenem'
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group by taxgroup_name
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order by num_isolates desc
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</code></pre>
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