Overview
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- Getting Started
- Authentication
- API Documentation
- CLI & Client Library (Python)
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Samples
Metadata & Tags
- The Metadata Resource
- The Tag Resource
- Retrieve All Metadataget
- Retrieve A Metadata Recordget
- Retrieve All Tagsget
- Retrieve A Tagget
- Updating Metadatapatch
Analyses
- The Analysis Resource
- Retrieve All Analysesget
- Retrieve An Analysisget
- Retrieve Analysis Resultsget
- Retrieve Analysis Filesget
- Retrieve Analysis Output File Detailsget
- The Classification Resource
- Retrieve All Classificationsget
- Retrieve A Classificationget
- Classification Resultsget
- Read-Level Resultsget
- The Panel Resource
- Retrieve A Panelget
- Retrieve All Panelsget
- Panel Resultsget
- The Alignment Resource
- Retrieve All Alignmentsget
- Retrieve An Alignmentget
Jobs
Documents
Webhooks & Events
Sequencing
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:
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 |
|---|---|
| $uristring | The metadata ID encoded as an addressable URI. Note that this is distinct from the sample ID (see sample below). |
| namestring | 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. |
| descriptionstring | Free-form text description of the sample. |
| location_latnumber | 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_lonnumber | The longitude (-180.0 – 180.0) of the sample location. |
| location_stringstring | 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. |
| platformstring | 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_typestring | An enum with the sample type. This is currently limited to the following values: ["WGS", "Targeted/16S", "Other", null]. |
| sample_typestring | An enum with the sample type. This is currently limited to the following values: ["Isolate", "Metagenomic", "Other", null]. |
| date_collecteddate-time | Timestamp for when the sample was collected. |
| date_sequenceddate-time | Timestamp for when the sample was sequenced. |
| external_sample_idstring | An arbitrary external sample ID, e.g., an ID in a LIMS. Up to 60 characters. |
| starredboolean | Whether the sample has been starred by the user within the One Codex web application. |
| customobject | 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" } |