Cloud-based Taxonomy Analysis Table

Overview

The Taxonomy Analysis Table (tax_analysis) contains the taxonomy information of the run as determined by the SRA Taxonomy Analysis Tool offsite image. New records are added hourly. This is useful when you want to filter hundreds of thousands of Runs by specific taxonomic content. It is also possible to build local taxonomy trees using the ilevel, ileft, and iright values.

Linking to other tables:

  • to Metadata Table (sra.metadata) by acc column
  • to Taxonomy Analysis Information (tax_analysis_info) table by acc column
  • to Taxonomy (tax) table by tax_id column
  • to kmer (kmer) table by tax_id column

Column name Type Desription
acc STRING SRA Run accession in the form of SRR######## (ERR or DRR for INSDC partners)
tax_id INTEGER Integer ID of the taxonomy record
rank STRING The taxonomic rank
name STRING Scientific name of the rank/organism
total_count INTEGER The total count is the number of kmer hits for the records and all it’s children
self_count INTEGER The count of kmer hits for the record itself
ilevel INTEGER Level of the tree
ileft INTEGER Left mapping value
iright INTEGER Right mapping value

Example queries for Big Query UI

Searches for the SRA accessions for all records that were identified to have a kmer hit to Coronaviridae:

SELECT m.acc, m.sample_acc, m.biosample, m.sra_study, m.bioproject
FROM `nih-sra-datastore.sra.metadata` as m, `nih-sra-datastore.sra_tax_analysis_tool.tax_analysis` as tax
WHERE m.acc=tax.acc and tax_id=11118
ORDER BY m.bioproject, m.sra_study, m.biosample, m.sample_acc

Build a local taxonomic tree by ordering the data based on ileft and ilevel for a metagenomic data set:

SELECT * FROM `nih-sra-datastore.sra_tax_analysis_tool.tax_analysis` WHERE acc = 'SRR11094509' order by ileft, ilevel

Search for SRA Runs by taxonomic name:

SELECT * FROM `nih-sra-datastore.sra_tax_analysis_tool.tax_analysis` WHERE name = 'Sarbecovirus' and total_count > 1

Contact SRA

Contact SRA staff for assistance at sra@ncbi.nlm.nih.gov

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Last updated: 2021-08-04T19:22:50Z