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Antibiotic Susceptibility Test (AST) data at GCP AMR Documentation TOC Main documentation page

ALPHA RELEASE -- This is under active development and while we strive to maintain correctness, it is possible results may be unstable, unavailable, or incorrect at times. Please contact us by email at pd-help@ncbi.nlm.nih.gov before relying on this data for production analyses.

What data is available on the Google Cloud? AST Browser data in BigQuery Main documentation page

For a list of all resources see Pathogen Detection Resources at Google Cloud Platform

Update Frequency AST Browser data in BigQuery Main documentation page

The AST table at Google Cloud BigQuery is updated daily. For this reason the contents may not agree exactly with those shown in the AST browser. If you see unexpected discrepancies please let us know by emailing us at pd-help@ncbi.nlm.nih.gov.

Getting started with BigQuery AST Browser data in BigQuery Main documentation page

Our Getting started with BigQuery page has instructions on how to run queries with BigQuery.

Linking to Isolates Browser data in BigQuery AST Browser data in BigQuery Main documentation page

NCBI Pathogen Detection also maintains Isolates Browser and MicroBIGG-E data in the BigQuery table ncbi-pathogen-detect.pdbrowser.isolates and ncbi-pathogen-detect.pdbrowser.microbigge tables respectively. There are several fields in common between the tables, but we generally recommend joining on the target_acc field. See Isolates Browser Data at Google Cloud Platform for examples of joining two tables.

Example searches AST Browser data in BigQuery Main documentation page

How many isolates were tested for ertapenem resistance AST Browser data in BigQuery Main documentation page

select count(distinct(target_acc))
from `ncbi-pathogen-detect.pdbrowser.ast`
where antibiotic = 'ertapenem'

What organism groups were tested for ertapenem resistance? AST Browser data in BigQuery Main documentation page

select taxgroup_name, count(distinct(target_acc)) num_isolates
from `ncbi-pathogen-detect.pdbrowser.ast`
where antibiotic = 'ertapenem'
group by taxgroup_name
order by num_isolates desc