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<h1 id="ncbi-minute-20230329-introductio"><a href="https://ncbiinsights.ncbi.nlm.nih.gov/event/ncbi-pathogen-detection-in-cloud-03-2023/">NCBI Minute 2023-03-29: Introduction to NCBI Pathogen Detection and antimicrobial resistance data in Google BigQuery</a></h1>
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<!-- <iframe width="560" height="315" src="https://www.youtube.com/embed/j4dzFOo2FmI" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe> -->
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<li><a href="https://www.ncbi.nlm.nih.gov/pathogens/docs/HowTo/">https://www.ncbi.nlm.nih.gov/pathogens/docs/HowTo/</a></li>
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<h1 id="example-queries-used-in-talk">Example queries used in talk</h1>
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<h3 id="count-the-isolates-from-enoki-mu">Count the isolates from enoki mushrooms</h3>
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||
<pre><code class="language-sql">-- How many isolates were isolated from "enoki"?
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SELECT COUNT(*)
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FROM `ncbi-pathogen-detect.pdbrowser.isolates`
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WHERE isolation_source LIKE '%enoki%'
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||
</code></pre>
|
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<h3 id="get-info-about-a-given-isolate">Get info about a given isolate</h3>
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||
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<pre><code class="language-sql">-- Get info about a given isolate
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SELECT taxgroup_name, isolate_identifiers, erd_group, isolation_source
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FROM `ncbi-pathogen-detect.pdbrowser.isolates`
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WHERE biosample_acc = 'SAMN21357979'
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</code></pre>
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|
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<h3 id="find-the-really-bad-contigs-with">Find the really bad contigs with the most AMR genes</h3>
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<pre><code class="language-sql">-- Find the contigs with the most AMR genes
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SELECT contig_acc, COUNT(*) num_genes, COUNT(DISTINCT(element_symbol)) num_unique_genes
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FROM `ncbi-pathogen-detect.pdbrowser.microbigge`
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WHERE subtype = 'AMR'
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GROUP BY contig_acc
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ORDER BY num_genes DESC
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LIMIT 10
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</code></pre>
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|
||
<h3 id="what-are-the-genes-on-those-cont">What are the genes on those contigs?</h3>
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<p>Looks like there were maybe some errors </p>
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<pre><code class="language-sql">-- What are the genes on the contigs with the most AMR genes
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SELECT mb.contig_acc, mb.start_on_contig, mb.element_symbol, mb.element_name, mb.subclass, top10.num_unique_genes, top10.num_genes
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FROM `ncbi-pathogen-detect.pdbrowser.microbigge` mb
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JOIN (
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SELECT contig_acc, COUNT(*) num_genes, COUNT(DISTINCT(element_symbol)) num_unique_genes
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FROM `ncbi-pathogen-detect.pdbrowser.microbigge`
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WHERE subtype = 'AMR'
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GROUP BY contig_acc
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ORDER BY num_genes DESC
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LIMIT 10
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) top10
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ON top10.contig_acc = mb.contig_acc
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ORDER BY num_genes DESC, start_on_contig
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||
</code></pre>
|
||
|
||
<h3 id="isolates-tested-resistant-to-car">Isolates tested resistant to carbapenems</h3>
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||
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||
<p>Here we filter based on one of the complex fields (<code>AST_phenotypes</code>)</p>
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||
|
||
<pre><code class="language-sql">--- Find all the isolates tested resistant to carbapenems
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||
SELECT target_acc, AST_phenotypes
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||
FROM `ncbi-pathogen-detect.pdbrowser.isolates` isolates
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||
WHERE
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||
(SELECT COUNT(*)
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||
FROM UNNEST(isolates.AST_phenotypes)
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||
WHERE antibiotic LIKE '%penem' AND phenotype = 'resistant'
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||
) >= 1
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||
</code></pre>
|
||
|
||
<h3 id="bonus-wont-explain-in-detail-fin">Bonus, won't explain in detail, find all the isolates tested resistant to carbapenems without a known carbapenem resistance gene or point mutation</h3>
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||
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||
<pre><code class="language-sql">--- find all the isolates tested resistant to carbapenems without a known
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--- carbapenem resistance gene or point mutation
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||
SELECT isolates.target_acc,
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||
ARRAY(select AS STRUCT antibiotic, phenotype from UNNEST(AST_phenotypes) WHERE antibiotic LIKE "%penem") AST,
|
||
isolates.refgene_db_version, isolates.taxgroup_name, isolates.scientific_name
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||
FROM `ncbi-pathogen-detect.pdbrowser.isolates` isolates
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||
LEFT JOIN `ncbi-pathogen-detect.pdbrowser.microbigge` microbigge
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||
ON isolates.target_acc = microbigge.target_acc
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||
AND microbigge.subclass = 'CARBAPENEM' -- Only carbapenem genes / point mutations
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WHERE
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(SELECT count(1) FROM unnest(AST_phenotypes) AS ast
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||
WHERE antibiotic like "%penem" AND phenotype = 'resistant') >= 1
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||
AND isolates.amrfinderplus_version IS NOT NULL -- AMRFinderPlus was run on this target
|
||
AND isolates.asm_acc IS NOT NULL -- AMRFinderPlus results should be in MicroBIGG-E because assembly is public
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||
AND microbigge.subclass IS NULL -- There are no rows in MicroBIGG-E with subclass = CARBAPENEM
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||
ORDER BY isolates.target_acc
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||
</code></pre>
|
||
|
||
<h2 id="get-contig-sequence-for-an-eleme">Get contig sequence for an element</h2>
|
||
|
||
<h3 id="find-the-amrfinderplus-results-f">Find the AMRFinderPlus results for an isolate</h3>
|
||
|
||
<pre><code class="language-sql">SELECT element_symbol, element_name, subclass, contig_acc, isolation_source, contig_url
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FROM `ncbi-pathogen-detect.pdbrowser.microbigge`
|
||
WHERE biosample_acc = 'SAMN21357979'
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||
ORDER BY contig_acc, start_on_contig
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</code></pre>
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