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ClarID reference implementation

ClarID-Tools

Human-readable and compact identifiers for biomedical metadata

A command-line implementation for encoding and decoding subject and biosample identifiers using versioned YAML codebooks and schema validation.

QuickstartSpecificationPublished paper
Illustrative biosampleHuman-readable format
CNAG_Test-HomSap-00042-LIV-TUM-RNA-C15.3-TRT-P1M
CNAG_Testproject
HomSapspecies
00042subject
LIVtissue
TUMsample type
RNAassay
C15.3condition
TRTtimepoint
P1Mduration

Encoding model

From structured metadata to two identifier formats.

ClarID-Tools validates the codebook and applies its mappings to generate human-readable and compact stub identifiers from the same input record.

Structured biosample metadata and a validated codebook entering ClarID-Tools and producing human-readable and stub identifiers
The codebook keeps project vocabulary explicit; the CLI applies it consistently to individual records and bulk tables.

Current scope

Supported operations

Implemented for subject and biosample entities in the current release.

Encode

Generate identifiers

Map structured subject and biosample metadata to human or stub formats.

Decode

Recover encoded fields

Decode human-readable or stub identifiers back into structured values.

Validate

Check YAML codebooks

Validate codebook structure against the schema before processing data.

Process

Run table and QR workflows

Process individual records or CSV files and generate or decode QR codes.

Documentation

Guides, reference, and examples

Start with a working command, inspect the CLI options, or browse example output.

GuideQuickstartCopy-paste commands for encoding and decoding.ReferenceCLI ReferenceAll commands, arguments, and output modes.ExamplesUse CasesBrowsable GDC-derived subject and biosample examples.