{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T22:38:08Z", "providers": [ "Claude" ], "breadth": "written by Claude from model knowledge without web access - no source was read, every claim is a lead to verify", "pass": 2, "wave": 3, "engine": "claude", "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T10:00:00Z", "ingestedAt": "2026-10-06T07:01:27+00:00", "fields": [ "agent_conduct", "ethics", "owners" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-06T19:51:57+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q2332446", "registryId": "vr.tr.staining", "name": "staining", "version": "0.2.0-wave.3", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.ACT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q2332446/", "model": { "registry_id": "vr.tr.staining", "name": "staining", "purpose": "Let an agent explain staining as a technique, identify kinds and their targets, relay protocols and standards in general terms from laboratory references, and distinguish staining from other visualisation methods.", "definition": "A laboratory technique that applies dyes, pigments, metals or labelled molecules to biological specimens so that cells, tissues, organisms or molecules become visible or distinguishable under a microscope, including histological stains such as haematoxylin and eosin, special stains such as acid-fast and Luxol fast blue, silver methods such as Ag-NOR staining, and immunostaining and fluorescence staining with antibodies and probes.", "what_it_is_for": "Making biological structures visible for microscopy and diagnosis.", "affordances": [ "explain principles and kinds", "identify stains and their targets", "relay standards and quality control", "distinguish from other methods" ], "distinguishing_features": [ "Contrast by binding", "Specific and general stains", "Diagnostic and research use", "Standardised protocols" ], "appearance": "Coloured or fluorescent specimens on slides, viewed under a microscope.", "visual_identification": [ "Dye, metal or label applied to specimens for contrast", "Histological, microbiological, immuno and fluorescence stains", "Unstained phase contrast and electron microscopy contrast differ; tissue staining in dentistry and textile dyeing are other senses" ], "physical_properties": [], "families_and_kinds": [ "general histological stains such as haematoxylin and eosin", "special stains such as acid-fast, PAS and Luxol fast blue", "silver and metal stains such as Ag-NOR", "microbiological stains such as Gram stain", "immunostaining and immunohistochemistry", "fluorescence staining and live-cell dyes" ], "related_models": [ { "relation": "is a kind of", "target": "lab technique", "why": "in registry terms" }, { "relation": "is a kind of", "target": "histological assay", "why": "in registry terms" }, { "relation": "is used in", "target": "microscopy", "why": "the observation method" }, { "relation": "includes", "target": "Gram stain", "why": "a classic example" } ], "identifiers": [], "standards_and_regulation": [ "Laboratory accreditation standards such as ISO 15189", "Quality control schemes for histology and immunohistochemistry", "Chemical safety for dyes and fixatives" ], "failure_modes_and_hazards": [ "Artefacts and false results", "Toxic reagents", "Batch variation without controls" ], "in_scope": [], "out_of_scope": [], "characteristics": [], "agent_conduct": { "may": [ "Describe staining techniques and what each reveals in a specimen.", "Record stain batches, controls and protocols in a laboratory information system it is authorized to use.", "Flag possible artefacts in a stained slide for review by a qualified person." ], "must_not": [ "Report a diagnosis from a stained slide without review by a qualified pathologist.", "Run staining without positive and negative controls when results are used clinically.", "Dispose of toxic staining reagents down the drain.", "Alter images of stained specimens without disclosure." ], "requires_human": [ "Releasing a clinical result based on staining." ] }, "ethics": { "considerations": [ "Stains guide cancer and infection diagnoses; false results harm patients.", "Some reagents are toxic to laboratory staff and the environment." ], "affected_parties": [ "Patients", "Laboratory staff", "Researchers" ] }, "owners": { "steward": "The laboratory that performs it, under its accreditation body.", "master_systems": [] } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q2332446: staining", "url": "https://www.wikidata.org/wiki/Q2332446", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Staining", "url": "https://en.wikipedia.org/wiki/Staining", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What staining is.", "rationale": "Science.", "layers": [ { "id": "principle", "name": "Principle", "description": "Principles.", "findings": [ { "id": "principle-finding", "name": "Principle", "description": "Principle.", "questions": [ { "text": "How does staining create contrast, and what determines specificity?", "kind": "definition" }, { "text": "Is the question about laboratory staining or another sense of the word?", "kind": "boundary" } ] } ] }, { "id": "kinds", "name": "Kinds", "description": "Kinds of stain.", "findings": [ { "id": "kinds-finding", "name": "Kinds", "description": "Kinds.", "questions": [ { "text": "What kinds of stain exist, and what does each target?", "kind": "definition" }, { "text": "Which entry fits the specific stain?", "kind": "action" } ] } ] } ] }, { "id": "practice", "name": "Practice", "description": "Protocols and quality.", "rationale": "Practice.", "layers": [ { "id": "protocols", "name": "Protocols", "description": "Protocols.", "findings": [ { "id": "protocols-finding", "name": "Protocols", "description": "Protocols.", "questions": [ { "text": "How are staining protocols performed and optimised, in general terms?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "quality", "name": "Quality", "description": "Quality control.", "findings": [ { "id": "quality-finding", "name": "Quality", "description": "Quality.", "questions": [ { "text": "How are controls and accreditation used to ensure reliable staining?", "kind": "provenance" }, { "text": "Which entry fits laboratory quality control?", "kind": "action" } ] } ] } ] }, { "id": "apply", "name": "Apply", "description": "Applications.", "rationale": "Application.", "layers": [ { "id": "diagnosis", "name": "Diagnosis", "description": "Diagnostic use.", "findings": [ { "id": "diagnosis-finding", "name": "Diagnosis", "description": "Diagnosis.", "questions": [ { "text": "How are stains used in pathology and microbiology diagnosis?", "kind": "provenance" }, { "text": "Is the user asking about a personal result, which needs a clinician?", "kind": "boundary" } ] } ] }, { "id": "research", "name": "Research", "description": "Research use.", "findings": [ { "id": "research-finding", "name": "Research", "description": "Research.", "questions": [ { "text": "How are immunostaining and fluorescence staining used in research?", "kind": "provenance" }, { "text": "Which entry fits immunohistochemistry?", "kind": "action" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "History and safety.", "rationale": "Context.", "layers": [ { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How did staining develop from early dyes to Gram, Golgi and modern methods?", "kind": "provenance" }, { "text": "Which entry fits the history of histology?", "kind": "action" } ] } ] }, { "id": "safety", "name": "Safety", "description": "Safety.", "findings": [ { "id": "safety-finding", "name": "Safety", "description": "Safety.", "questions": [ { "text": "What hazards do staining reagents present, and how are they managed?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Should immunostaining and each classic stain be separate entries?", "How should protocol references be linked?", "The registry entry has merged aliases naming specific stains; should they be split off?" ], "statistics": { "bundles": 4, "layers": 8, "findings": 8, "questions": 16 } }