Return the results of a classification as JSON.
The returned JSON has the following top-level structure:
The total number of reads (or FASTA contigs/records) in sample.
An array of the taxonomy ID for all known hosts in the sample. Filtering out the
The results in a tabular format. Results will typically be sorted by
table object has the results for all taxa in the sample and the following fields:
A taxonomy ID. Currently, these are NCBI taxonomy IDs and strictly versioned as part of the job.
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
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.
The immediate parent of the taxon. Guaranteed to be consistent for all classifications using a given job.
The number of reads (or records or contigs for FASTA files) classified at the given taxon.
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,
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/
An estimated, cumulative relative microbial abundance of all of the children of a given taxon. E.g., the
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.