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The Metadata Resource

Metadata resources provide a means for adding structured metadata to your samples. The Metadata resource include a number of default fields, and can also be extended with arbitrary custom metadata. Permissions on metadata follow the Samples they describe – i.e., the Metadata resource for a public sample will be publicly accessible. Here is an example metadata entry:

914914

The metadata editing modal on the One Codex web application. Note that the Project is actually a property on the Sample resource.

Metadata include the following properties:

Property

Description

$uri
string

The metadata ID encoded as an addressable URI. Note that this is distinct from the sample ID (see sample below).

name
string

An optional name for the sample name that will be used for display across One Codex (up to 255 characters). When missing, the sample's filename will be used.

description
string

Free-form text description of the sample.

location_lat
number

The latitude (-90 – 90.0) of the sample location. By convention, we recommend using this for the location in which the physical specimen was collected.

location_lon
number

The longitude (-180.0 – 180.0) of the sample location.

location_string
string

A string describing the location. Currently, we do not attempt to automatically parse the lat/lon from these ( ). The One Codex web application does however set all 3 via a map.

platform
string

An enum with the name of the sequencing platform. Currently, the following values are valid: ["Illumina Genome Analyzer II", "Illumina HiSeq", "Illumina HiSeq 2000", "Illumina HiSeq 2500", "Illumina HiSeq 3000", "Illumina HiSeq 4000", "Illumina HiSeq X", "Illumina iSeq 100", "Illumina MiniSeq", "Illumina MiSeq", "Illumina NextSeq 500", "Illumina NextSeq 550", "Illumina NovaSeq 6000", "PacBio", "PacBio Sequel", "PacBio RS II", "Oxford Nanopore MinION", "Oxford Nanopore GridION X5", "Oxford Nanopore PromethION", "Ion GeneStudio S5", "Ion PGM", "Ion Proton", "Ion Torrent", "SOLiD", "454 sequencing", "Sanger", "Other"].

library_type
string

An enum with the sample type. This is currently limited to the following values: ["WGS", "Targeted/16S", "Other", null].

sample_type
string

An enum with the sample type. This is currently limited to the following values: ["Isolate", "Metagenomic", "Other", null].

date_collected
date-time

Timestamp for when the sample was collected.

date_sequenced
date-time

Timestamp for when the sample was sequenced.

external_sample_id
string

An arbitrary external sample ID, e.g., an ID in a LIMS. Up to 60 characters.

starred
boolean

Whether the sample has been starred by the user within the One Codex web application.

custom
object

Arbitrary metadata is supported as part of a custom object. custom has two constraints: (1) it must have a depth of one (i.e., no nested records); and (2) only strings, numbers, boolean, and null values are supported as values. Example:

{
  "lab_tech": "Linus Pauling",
  "amplicon_scheme": "V3/V4"
}