Return the results of a classification as JSON.

The returned JSON has the following top-level structure:

Property

Description

n_reads
integer

The total number of reads (or FASTA contigs/records) in sample.

host_tax_ids
array of strings

An array of the taxonomy ID for all known hosts in the sample. Filtering out the host_tax_ids and any non-unique mappings (e.g., those to "root" and "cellular organisms") can be used to produce a table of exclusively microbial taxa.

table
object

The results in a tabular format. Results will typically be sorted by readcount_w_children (descending). See below for more details.

The table object has the results for all taxa in the sample and the following fields:

Property

Description

tax_id
string

A taxonomy ID. Currently, these are NCBI taxonomy IDs and strictly versioned as part of the job. tax_id should be handled as a string in part to support future compatibility with non-NCBI taxonomies.

name
string

The name of the taxon. This is provided strictly for convenience and names for a given taxa are not guaranteed to remain identical over time. Use tax_id when comparing equality across different taxa.

rank
string

The taxonomic rank. This is also provided for convenience and guaranteed to be consistent for a given job but may change over time as, e.g., previously poorly characterized organisms are better characterized and taxonomically re-labeled.

parent_tax_id
string

The immediate parent of the taxon. Guaranteed to be consistent for all classifications using a given job.

readcount
integer

The number of reads (or records or contigs for FASTA files) classified at the given taxon.

readcount_w_children
integer

The number of reads classified at the given taxon and all of its children. E.g., if 50 reads map to Enterobacteriaceae in a sample and 50 reads map to E. coli, readcount would be 50 for Enterobacteriaceae and readcount_w_children would be 100.

abundance
number

An estimated relative microbial abundance for the organism. Currently, this will only be provided for classifications using the One Codex database and will only include estimates at the species level (example). Where available, this field should provide substantially improved relative abundance estimates over read-based summaries. See our announcement on this functionality for more detail: http://blog.onecodex.com/2016/04/25/2-0/

Note on future changes (): We do likely plan to add additional top-level fields to the returned JSON, e.g., whether the analysis contains abundance estimates or other similar metrics and descriptive features. We do not anticipate removing any top-level fields or fields in the table of results provided.

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