peptide-repo-core/CONTEXT.md

Peptide Repo Core — Domain Glossary (CONTEXT.md)

This file defines domain terms introduced or used in the peptide-repo-core codebase. Per AGENT-OPERATING-STANDARD v1.2.0, update this file in the same PR as any change that introduces, renames, or redefines a domain term.

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Peptide

A short chain of amino acids studied for biological activity. In this codebase, a "peptide" refers to one of the 93 canonical monograph posts (post_type = 'peptide') on peptiderepo.com. Each monograph covers identity, mechanism, evidence, and regulatory status. No dosing data appears in schema output (YMYL constraint).

Monograph

A single-peptide page (/peptides/{slug}/) containing the canonical research profile for that compound. Populated from the peptide CPT plus its associated meta fields, dosing rows (pr_dosing_rows table), and legal cells (pr_legal_cells table).

Drug node

The schema.org/Drug structured-data entity emitted on each monograph page. Stable @id is {permalink}#drug — this URI is the cross-plugin linking target used by PRAutoBlogger article about references (per jsonld-contract-v1, ratified 2026-06-11).

MedicalWebPage

A schema.org/MedicalWebPage subtype of WebPage. Applied to peptide monograph pages via the wpseo_schema_webpage_type Yoast filter. Signals to search engines and LLMs that the page carries medical/scientific content reviewed by an organization.

FAQPage

A schema.org/FAQPage node emitted when _pr_faq_items post-meta is populated. Contains Question/Answer pairs curated by the CMO content sprint (v0.6.0 ships the meta key and emitter; population is a separate sprint). Emitted only when items exist — never an empty node.

_pr_molecular_formula

Post-meta key (string). Stores the molecular formula of a peptide compound (e.g., C62H98N16O22). Written by migration 0004 from PSA's psa_molecular_formula key. Sanitized: only [A-Za-z0-9().\[\]{}] characters allowed.

_pr_molecular_weight

Post-meta key (string). Stores the molecular weight of a peptide compound as a float string (e.g., "1419.5"). Unit: g/mol (equivalent to Da, but g/mol is the standard SI label used in schema.org QuantitativeValue). Written by migration 0004 from PSA's psa_molecular_weight — "Da" suffix stripped, floatval() applied.

_pr_aliases

Post-meta key (string, JSON array). Stores alternate names / synonyms for a peptide (e.g., '["Body Protection Compound-157","PL 14736","Bepecin"]'). Written by migration 0004 from PSA's comma-separated psa_aliases. Each alias sanitized via sanitize_text_field. Maps to schema.org/alternateName array on the Drug node.

_pr_faq_items

Post-meta key (string, JSON array of objects). Stores curated FAQ entries for a peptide monograph, each as {question: string, answer: string}. Registered in v0.6.0; population is a CMO content sprint. Maps to schema.org/FAQPage when non-empty. Sanitized by PR_Core_Schema_Sanitizers::sanitize_faq_items() on save. Purged on uninstall.

Schema-input meta

The collective term for the four _pr_* meta keys (_pr_molecular_formula, _pr_molecular_weight, _pr_aliases, _pr_faq_items) introduced in v0.6.0. These are the data-layer inputs to the JSON-LD emitter. The emitter reads only these keys at render time — it never reads PSA's psa_* keys directly (no cross-plugin read coupling). Sourced from PSA via migration 0004 (one-time backfill).

psa_* meta

Post-meta keys written by Peptide Search AI (PSA) plugin using its PubChem integration. Includes psa_molecular_formula, psa_molecular_weight, psa_aliases, psa_pubchem_cid, psa_cas_number, psa_drugbank_id. Migration 0004 treats all psa_* values as UNTRUSTED and sanitizes them before writing to PR Core's _pr_* keys. PR Core never reads psa_* keys at render time.

PubChem CID

A numeric compound identifier in the NCBI PubChem database (e.g., 9941957 for BPC-157). Used by migration 0004 as a fallback lookup for the 4 peptide posts that lack psa_molecular_formula. Fetched via PR_Core_Pubchem_Client.

Yoast integration contract

The agreed schema architecture ratified 2026-06-11 (convo/prcore/decisions/2026-06-11-jsonld-contract-v1.md): PR Core integrates into Yoast's schema graph via wpseo_schema_* filters; never emits duplicate WebPage or BreadcrumbList nodes; maintains a standalone @graph fallback for when Yoast is inactive. The Drug @id convention ({permalink}#drug) is part of this contract.

Evidence strength

Ordered enum: preclinical, case-series, observational, rct-small, rct-large, meta-analysis. Stored in the evidence_strength post-meta key. Does not appear in schema.org output (dosing/evidence YMYL constraint).

Verdict

One of five editorial states assigned to a monograph: effective, promising, mixed, insufficient_evidence, avoid. Stored in post content via a verdict card Gutenberg block. Not surfaced in JSON-LD (dosing YMYL constraint).

Migration runner

PR_Core_Migration_Runner — runs numbered migrations (0001–N) sequentially on every plugins_loaded. Compares pr_core_schema_version wp_option against PR_CORE_TARGET_SCHEMA_VERSION constant. All migrations are idempotent and re-runnable.

prab* meta namespace

Post-meta keys written exclusively by PRAutoBlogger (PRAB) and read by prcore's PR_Core_Prab_Meta_Reader at render time. The namespace is _prab_ (PRAutoBlogger private). Ownership split: PRAB writes, prcore reads. No other plugin reads or writes _prab_* meta. Contract v1 keys (frozen; additive evolution only, gated by _prab_schema_version):

Key	Type	Purpose
_prab_schema_version	int (1)	Opt-in trigger; presence + value = 1 enables JSON-LD emission
_prab_citations	JSON array	[{url, doi?, title, quality_score?}] — validated sources
_prab_about_peptides	JSON array	Peptide post IDs → Drug @id references in about[]
_prab_review_mode	string	human | editorial-system
_prab_reviewed_at	string	ISO 8601 datetime → lastReviewed
_prab_reviewed_by	int	WP user ID of Review Queue approver (required when mode=human)

All _prab_* values are treated as untrusted at read time: sanitized and validated by PR_Core_Prab_Meta_Reader before any schema.org output is produced. Malformed values degrade gracefully (skipped/null); no fatal path exists. Canonical contract: convo/prcore/decisions/2026-06-11-jsonld-contract-v1.md.

Meta-reader pattern

PR_Core_Prab_Meta_Reader is the dedicated sanitizer class that isolates all _prab_* meta reading and validation from the emitter (PR_Core_Jsonld_Article). The pattern: one sanitizer class per untrusted meta namespace. The reader owns all get_post_meta calls for the namespace, validates every field, and returns typed clean values. The emitter (consumer) never calls get_post_meta directly.

This keeps the emitter testable without the meta contract details and ensures that adding a new _prab_* field never touches the emission logic. Future _prab_v2_* fields would use a v2 reader that the emitter selects by version.

ScholarlyArticle

A schema.org/ScholarlyArticle node emitted inside a citation array (citation[]) on the Article graph piece when a validated DOI is present in the PRAB citation record. Emitted with url (the citation URL), name (the citation title), and sameAs (the canonical https://doi.org/ URI). When no DOI is available, CreativeWork is emitted instead. Per contract v1, quality_score is never emitted (no schema.org mapping).

Honest reviewedBy (integrity constraint)

The reviewedBy field on the MedicalWebPage node emits a schema.org/Person node only when all three conditions hold simultaneously:

1. _prab_review_mode = human
2. _prab_reviewed_by resolves to a WP user ID > 0
3. get_userdata() returns a valid WP_User instance with a non-empty display_name

Any other combination (missing mode, zero user ID, unresolvable user, or editorial-system mode) produces a schema.org/Organization node (Peptide Repo editorial). This is an integrity constraint, not a UI choice: emitting a fabricated Person would constitute misleading structured data. The constraint is enforced in PR_Core_Prab_Meta_Reader::get_reviewed_by() and covered by dedicated unit tests.