{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T11:50:54Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 18.5, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a09573-e0e4-7951-a7a3-a8f6e19113c3\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: P2RY12\nSense to describe: (none recorded)\nDomain code: PHY.OBJ\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 044: 1001 register", "usd": 0.0, "recall": true }, "codex": { "seconds": 60.3, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a09573-e0d4-7180-a8c5-ad97b9052eae\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: P2RY12\nRegistry id: vr.tr.p2ry12\nPlane / domain: PHY / PHY.OBJ\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nContext fo" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:57:57+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "standards_and_regulation", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:26+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q14916330", "registryId": "vr.tr.p2ry12", "name": "P2RY12", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.OBJ" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q14916330/", "model": { "registry_id": "vr.tr.p2ry12", "name": "P2RY12", "purpose": "Enable an agent to identify P2RY12, distinguish its gene and receptor product, and assess what expression, signaling and perturbation evidence supports in a specified biological context.", "definition": "P2RY12 is the human gene encoding the P2Y12 receptor, an ADP-activated, Gi-coupled purinergic receptor involved in platelet activation and expressed by microglia and other cell populations.", "scope_statement": "This model owns the molecular identity and evidence needed to interpret registry entry vr.tr.p2ry12 in PHY / PHY.OBJ, provisionally treating P2RY12 as the gene encoding the P2Y12 purinergic receptor while keeping gene, transcript and protein observations distinct; the registry's intended species and molecular referent remain unresolved.", "in_scope": [ "Species-qualified P2RY12 gene identity and links to its transcripts and receptor product", "Reference sequences, variants and experimental receptor constructs", "P2RY12 expression and P2Y12 receptor abundance and localization", "ADP-responsive receptor signaling in a defined cellular and assay context", "Evidence attributing perturbation responses to P2RY12" ], "out_of_scope": [ "Other purinergic receptors, including their independent molecular models", "ADP and antagonist molecules as independently characterized chemical substances", "Whole platelet, microglial or organism models", "Clinical diagnosis, prescribing and patient-specific treatment decisions", "General GPCR biology and complete coagulation pathways" ], "distinguishing_features": [ "Resolve the symbol against a species-qualified accession: human P2RY12 is NCBI Gene 64805, whereas similarly written symbols in other organisms require their own records. [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/64805)", "Distinguish the coding locus from its product: human P2Y12 receptor is represented by reviewed UniProt accession Q9H244; a gene measurement and a receptor measurement are different observations. [UniProt](https://www.uniprot.org/uniprotkb/Q9H244/entry)", "Check sequence identity and receptor-family assignment rather than identifying P2Y12 from ADP responsiveness alone.", "Use receptor-specific controls alongside the expected inhibition of adenylyl cyclase signaling; that signaling response alone does not establish molecular identity. [UniProt](https://www.uniprot.org/uniprotkb/Q9H244/entry)" ], "characteristics": [ { "name": "Molecular referent", "kind": "category", "unit_or_values": "gene | transcript | receptor protein | engineered construct", "why_it_matters": "Prevents DNA variation, RNA expression and receptor activity from being treated as interchangeable." }, { "name": "Species and reference accession", "kind": "relation", "unit_or_values": "Taxonomy identifier plus versioned gene, transcript or protein accession", "why_it_matters": "Anchors identification and limits transfer of observations between orthologs." }, { "name": "Sequence or construct deviation", "kind": "relation", "unit_or_values": "Reference-relative variant, isoform, tag, truncation or substitution", "why_it_matters": "Links functional conclusions to the molecular form actually tested." }, { "name": "Transcript abundance", "kind": "measurement", "unit_or_values": "TPM, normalized counts or assay-specific relative expression with normalization stated", "why_it_matters": "Records P2RY12 transcription without implying surface receptor abundance." }, { "name": "Surface receptor abundance", "kind": "measurement", "unit_or_values": "Receptors per cell or calibrated assay signal with detection limits", "why_it_matters": "Separates receptor availability from total protein and downstream response." }, { "name": "Receptor functional state", "kind": "state", "unit_or_values": "basal | agonist-responsive | inhibited | desensitized | unresolved", "why_it_matters": "Qualifies state by ligand exposure, timing and measured response." }, { "name": "ADP response", "kind": "measurement", "unit_or_values": "Concentration in mol/L, exposure time in seconds or minutes, and endpoint-specific response", "why_it_matters": "Makes sensitivity and efficacy interpretable within the tested preparation." }, { "name": "Perturbation attribution", "kind": "category", "unit_or_values": "association only | pharmacological support | genetic support | convergent support | unresolved", "why_it_matters": "Distinguishes a changed endpoint from evidence that P2RY12 caused the change." } ], "affordances": [ "Resolve an accession or alias to a species-qualified P2RY12 referent.", "Attach expression and functional observations to the correct molecular form and cell context.", "Compare ADP-response measurements when preparations, endpoints and normalization are compatible.", "Evaluate whether genetic and pharmacological controls support P2RY12-specific attribution.", "Identify missing controls before accepting a receptor-state or phenotype claim." ], "agent_conduct": { "may": [ "Describe P2RY12 and the platelet receptor it encodes, citing sources.", "Explain in general terms that common antiplatelet medicines act on this receptor." ], "must_not": [ "Recommend starting, stopping or changing an antiplatelet medicine for a person.", "Interpret a person's variant or platelet test as a treatment decision.", "Share genetic or test data without consent.", "Downplay bleeding risk when such medicines are discussed." ], "requires_human": [ "Any decision about antiplatelet treatment.", "Returning genetic results that affect medicine choice." ] }, "ethics": { "considerations": [ "Stopping antiplatelet medicine without advice can cause heart attacks or strokes.", "Bleeding risks must be stated honestly." ], "affected_parties": [ "Patients on antiplatelet medicines", "Clinicians", "People with bleeding disorders" ] }, "owners": { "steward": "The person whose genome carries it; laboratories hold records.", "master_systems": [ "Gene and variant databases" ] }, "visual_identification": [ "Not visible; known from sequence data and platelet function tests.", "Identified by its approved gene symbol; the receptor name differs slightly." ], "failure_modes_and_hazards": [ "Bleeding or clotting events from medicine changes.", "Confusion between gene symbol and receptor name." ], "standards_and_regulation": [ "Human gene nomenclature, HUGO Gene Nomenclature Committee (HGNC), which approves the gene symbol." ], "what_it_is_for": [ "P2RY12 is encountered in human genetics, platelet biology and studies of microglial identity and function.", "Researchers examine its sequence, expression and perturbation to investigate ADP-dependent signaling in specified cell populations.", "Expression measurements help characterize cells but do not independently establish receptor activity or a causal biological role." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q14916330: P2RY12", "url": "https://www.wikidata.org/wiki/Q14916330", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: P2Y12", "url": "https://en.wikipedia.org/wiki/P2Y12", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "p2ry12-molecular-identity", "name": "P2RY12 molecular identity", "description": "Resolve what biological entity the registry name and each observation denote.", "rationale": "P2RY12 names a gene, while many associated observations concern its receptor product.", "layers": [ { "id": "gene-product-boundary", "name": "Gene and product boundary", "description": "Keep the registered referent and its encoding relationships explicit.", "findings": [ { "id": "human-gene-anchor", "name": "Human gene anchor", "description": "NCBI identifies human P2RY12 as a protein-coding gene; this provides a candidate identity anchor, not evidence that the registry intended the human gene. [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/64805)", "questions": [ { "text": "Does vr.tr.p2ry12 denote a gene, its receptor product or a species-independent concept?", "kind": "boundary", "id": "human-gene-anchor-q01" }, { "text": "Which registry source identifier establishes the intended species and molecular referent?", "kind": "provenance", "id": "human-gene-anchor-q02" } ] } ] }, { "id": "reference-and-variant-resolution", "name": "Reference and variant resolution", "description": "Specify the sequence underlying each molecular observation.", "findings": [ { "id": "sequence-qualified-observations", "name": "Sequence-qualified observations", "description": "Resolve transcript, protein and engineered construct identifiers separately before combining evidence.", "questions": [ { "text": "Which accession and version define the P2RY12 sequence used in this observation?", "kind": "provenance", "id": "sequence-qualified-observations-q01" }, { "text": "Which variants, tags or other construct changes distinguish the tested receptor from that reference?", "kind": "definition", "id": "sequence-qualified-observations-q02" } ] } ] } ] }, { "id": "p2ry12-expression-and-localization", "name": "P2RY12 expression and localization", "description": "Describe where expression was detected and whether receptor protein is available at the cell surface.", "rationale": "Transcript detection cannot establish receptor localization or signaling competence.", "layers": [ { "id": "cell-context", "name": "Cell context", "description": "Attach expression claims to an identified biological preparation.", "findings": [ { "id": "expression-context-resolution", "name": "Expression context resolution", "description": "Record species, cell identity, preparation and biological state alongside P2RY12 detection.", "questions": [ { "text": "Which cell population and preparation yielded the P2RY12 signal?", "kind": "provenance", "id": "expression-context-resolution-q01" }, { "text": "Does the assay resolve individual cells or could a mixed population explain the signal?", "kind": "boundary", "id": "expression-context-resolution-q02" } ] } ] }, { "id": "receptor-availability", "name": "Receptor availability", "description": "Separate RNA, total receptor protein and surface receptor measurements.", "findings": [ { "id": "surface-versus-total-detection", "name": "Surface versus total detection", "description": "Receptor availability requires an appropriate protein-localization measurement rather than inference from transcription.", "questions": [ { "text": "Does the measurement quantify P2RY12 RNA, total P2Y12 protein or surface-accessible receptor?", "kind": "measurement", "id": "surface-versus-total-detection-q01" }, { "text": "Which controls establish detection-reagent specificity for P2Y12?", "kind": "provenance", "id": "surface-versus-total-detection-q02" } ] } ] } ] }, { "id": "p2y12-ligand-and-signaling", "name": "P2Y12 ligand and signaling", "description": "Represent ligand exposure, receptor-proximal signaling and response state.", "rationale": "Functional identification requires both a defined stimulus and evidence linking the response to P2Y12.", "layers": [ { "id": "adp-exposure", "name": "ADP exposure", "description": "Specify the stimulus used to probe receptor function.", "findings": [ { "id": "adp-response-conditions", "name": "ADP response conditions", "description": "ADP is a ligand of P2Y12; record its concentration and exposure conditions with each response. [UniProt](https://www.uniprot.org/uniprotkb/Q9H244/entry)", "questions": [ { "text": "What ADP concentration, exposure duration and preparation conditions produced the response?", "kind": "measurement", "id": "adp-response-conditions-q01" }, { "text": "How were contributions from other nucleotide-responsive receptors assessed?", "kind": "boundary", "id": "adp-response-conditions-q02" } ] } ] }, { "id": "signaling-readout", "name": "Signaling readout", "description": "Distinguish receptor-proximal measurements from downstream phenotypes.", "findings": [ { "id": "adenylyl-cyclase-inhibition", "name": "Adenylyl cyclase inhibition", "description": "P2Y12 couples to inhibitory G-protein signaling affecting adenylyl cyclase; assay interpretation requires the baseline and stimulation conditions. [UniProt](https://www.uniprot.org/uniprotkb/Q9H244/entry)", "questions": [ { "text": "Which endpoint measures the response, and against what baseline or stimulated control?", "kind": "measurement", "id": "adenylyl-cyclase-inhibition-q01" }, { "text": "What evidence distinguishes receptor inhibition from reduced receptor abundance or impaired downstream signaling?", "kind": "boundary", "id": "adenylyl-cyclase-inhibition-q02" } ] } ] } ] }, { "id": "p2ry12-perturbation-and-phenotype", "name": "P2RY12 perturbation and phenotype", "description": "Assess evidence connecting receptor perturbations to biological outcomes.", "rationale": "An observed phenotype does not by itself identify the receptor responsible or justify a clinical conclusion.", "layers": [ { "id": "target-attribution", "name": "Target attribution", "description": "Evaluate genetic and pharmacological evidence for P2RY12 involvement.", "findings": [ { "id": "perturbation-specificity", "name": "Perturbation specificity", "description": "Record the exact intervention and controls before assigning an effect to P2RY12.", "questions": [ { "text": "What genetic alteration or pharmacological exposure was applied, and was its effect on P2RY12 verified?", "kind": "provenance", "id": "perturbation-specificity-q01" }, { "text": "Which rescue, independent intervention or receptor-negative control supports target attribution?", "kind": "action", "id": "perturbation-specificity-q02" } ] } ] }, { "id": "platelet-outcome-interpretation", "name": "Platelet outcome interpretation", "description": "Connect receptor evidence to platelet measurements while retaining the limits of inference.", "findings": [ { "id": "platelet-function-link", "name": "Platelet function link", "description": "P2RY12 is implicated in platelet aggregation, and variants are associated with platelet-type bleeding disorder 8; an individual finding still needs variant-specific and functional evidence. [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/64805)", "questions": [ { "text": "Which platelet endpoint was measured, with what stimulus, units and comparator?", "kind": "measurement", "id": "platelet-function-link-q01" }, { "text": "Does the evidence establish a P2RY12-dependent functional effect, a clinical association or both?", "kind": "boundary", "id": "platelet-function-link-q02" } ] } ] } ] }, { "id": "evidence-and-external-alignment", "name": "Evidence and external alignment", "description": "What the world already says about this thing, gathered so the model can be checked against it.", "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.", "layers": [ { "id": "reported-evidence", "name": "Reported evidence", "description": "Findings from the breadth pass, kept separate from the structural claims.", "findings": [ { "id": "evidence-confidence-notes", "name": "Check these first", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "The registry provides no sense or species; confirm whether it intends the human gene, its protein product or an ortholog.", "The batch's device-oriented guidance does not fit this biological entity.", "Microglial P2RY12 expression varies with biological state and should not be treated as a universal or exclusive microglial marker." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of P2RY12 this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-identifiers", "name": "Identifiers and schemes", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "scheme": "HGNC gene symbol", "value_or_pattern": "P2RY12", "note": "Identifies the human gene; P2Y12 is the usual designation for its receptor protein." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of P2RY12 this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-real-world-use", "name": "Real-world use", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Investigation of inherited platelet function disorders involving impaired ADP responses.", "Its encoded receptor is the target of antiplatelet drugs including clopidogrel, prasugrel and ticagrelor.", "P2RY12 expression and receptor immunostaining are used in microglial research, with interpretation dependent on cell state and tissue context." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of P2RY12 this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-failure-modes-and-hazards", "name": "Failure modes and hazards", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Loss-of-function variants can impair platelet aggregation and cause a bleeding disorder.", "Inhibition of the encoded receptor reduces platelet-mediated thrombosis but can increase bleeding." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of P2RY12 this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-neighbours", "name": "Neighbouring kinds and how to tell them apart", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "name": "P2Y12 receptor", "difference": "The receptor is the protein product; P2RY12 formally identifies the gene encoding it." }, { "name": "P2RY1", "difference": "Encodes a different ADP-responsive receptor, P2Y1, which primarily couples to Gq rather than Gi." }, { "name": "P2RY13", "difference": "Encodes another ADP-responsive, Gi-coupled receptor with distinct molecular identity and biological roles." }, { "name": "P2RX7", "difference": "Encodes an ATP-gated ion channel rather than an ADP-responsive G protein-coupled receptor." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of P2RY12 this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the registry source identify P2RY12 as the human gene, the P2Y12 receptor protein or a broader ortholog concept?", "Does an existing Vercy world model already own this concept and require this entry to link to it?", "Which transcript and protein references should anchor the model once species and molecular scope are confirmed?", "Which non-platelet contexts, including microglial observations, require dedicated layers supported by primary research?", "Which validated assays and perturbation controls are sufficient for the intended use to distinguish P2Y12 function from other purinergic signaling?" ], "statistics": { "bundles": 5, "layers": 9, "findings": 13, "questions": 21 } }