Draft status: This content reflects the current working spec and may be revised.

Overview

Phenotype List String (PL-String) is a compact, machine-readable grammar for representing antigen- and protein-level information used in antibody assays and clinical interpretation (e.g., unacceptable/acceptable antigens). It complements GL-String—used for genotyping—by focusing on phenotypes observed or asserted in assays and interpretations.

PL-String Code (PLSC) binds a PL-String to a namespace (e.g., IPD-IMGT/HLA, OPTN, Eurotransplant, NMDP) and a version (or date) so that each expression is fully traceable and interoperable across labs, registries, and allocation systems.

Together, PL-String and PLSC enable:

  • Structured representation of reagent composition (e.g., SAB bead contents, class II heterodimers).
  • Structured representation of test results (positive/negative/equivocal or specificity lists).
  • Structured representation of clinical interpretation (e.g., antibody specificities; acceptable/unacceptable antigens).

This project defines the grammar and its operators; it does not alter or renormalize the vocabularies in any namespace (e.g., WHO/IMGT names, OPTN/ET antigen codes, NMDP MACs). Provenance and naming policies remain governed by the respective authorities.

When to use PL-String

Use PL-String when you need a lossless, computable representation of:

PLSC 1.0 Syntax

  1. Reagents: The phenotypic composition of materials used in an assay
    (e.g., “proteins present on a bead” or “heterodimer pairs used in class II reagents”).
  2. Results: The phenotypic reactivities detected in a sample with a given reagent set (including ambiguity).
  3. Interpretations: Curated lists of antibody specificities that drive downstream decisions (e.g., screening donors by unacceptable antigens).

Scenario (end-to-end): A patient is typed by NGS and reported as a GL-String. SAB reagents are described with PL-Strings. The patient’s antibody specificities (interpretation) are encoded as PL-Strings. Donor candidates carrying any unacceptable antigens are auto-filtered in match reports.

Core ideas

  • Namespaces: Every atom (protein/antigen/epitope) comes from one declared, versioned namespace (e.g., IPD-IMGT/HLA release; OPTN/ET mapping). You may not mix namespaces inside a single PL-String.
  • Delimiters with precedence: Operators encode composition, ambiguity, and heterodimeric pairing (see Syntax page for full details).
  • Phenotype-first: PL-Strings describe what is present/observed/claimed at the protein/antigen level; they do not assert genotype, chromosomal phase, or locus order.

Namespaces (examples)

  • IPD-IMGT/HLA — protein-level (2-field) HLA designations and associated antigens (per WHO).
  • OPTN — allocation codes/mappings used in U.S. solid organ transplant.
  • Eurotransplant (ET) — ET codes and match determinants.
  • NMDP — registry codes, including MACs for protein ambiguity.

A namespace must have clear governance, public documentation, versioning, and stable identifiers.

PL-String Code (PLSC)

A PLSC binds a PL-String to its vocabulary context:

<namespace>#<version or date>#<pl-string>
  • <namespace>: e.g., who, optn, et, nmdp
  • <version or date>: a release like 3.61.0, or an ISO date 2025-11-02 (when a release tag is not applicable)
  • <pl-string>: the actual PL-String expression

Example:
hla#3.61.0#HLA-DQA1*05:01~HLA-DQB1*02:01+HLA-DPB1*04:01

See the Syntax page for complete operator rules, constraints, and examples.

Interoperability notes

  • Within a single PL-String, do not mix identifiers from different namespaces. If multiple namespaces are needed in one report, use separate PLSCs, each with its own namespace+version (or date).
  • If a release version is unavailable, use the date the reagent/result/ interpretation was created—not the collection/export date.
  • PLSC is designed to embed cleanly in exchange formats (e.g., HAML / HL7 FHIR) as a code with system + version + value.
  • Syntax (PLSC 1.0): PLSC Syntax & Operators
  • GL-String background: Milius et al., 2013; Mack et al., 2023
  • IMGT/HLA database: Barker et al., 2023

This page updates and consolidates earlier drafts to reflect the PL-String + PLSC scope (reagents, results, interpretations) and namespace/version requirements, replacing prior placeholder text in earlier pages.