{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T10:01:26Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 25.2, "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: 01a0950f-5e4f-7ee1-8538-13858691da5a\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: glycophorin\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 043: 1001 reg", "usd": 0.0, "recall": true }, "codex": { "seconds": 79.2, "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: 01a0950f-5e48-7713-adf5-b10b5f69433a\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: glycophorin\nRegistry id: vr.tr.glycophorin\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\n" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:52:10+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "standards_and_regulation", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:29+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q24724397", "registryId": "vr.tr.glycophorin", "name": "glycophorin", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q24724397/", "model": { "registry_id": "vr.tr.glycophorin", "name": "glycophorin", "purpose": "Enable an agent to identify a glycophorin, assess its molecular and experimental state, and select evidence-supported characterization or handling actions.", "definition": "Glycophorin denotes a family of sialic-acid-rich transmembrane glycoproteins of the erythrocyte membrane whose members carry blood-group antigens and contribute to cell-surface properties or membrane organization.", "scope_statement": "This model owns glycophorin as a class of erythrocyte membrane sialoglycoproteins, with member-specific sequences, glycoforms, variants, interactions and preparation states recorded beneath vr.tr.glycophorin; it does not assume that the unqualified name means glycophorin A.", "in_scope": [ "Glycophorin member identity, species, sequence and mature protein boundaries", "Glycosylation, sialylation and experimentally altered glycoforms", "Membrane topology, assembly and partner associations", "Member-specific antigen presentation and ligand recognition", "Native, extracted and recombinant preparation quality and assay suitability" ], "out_of_scope": [ "Whole erythrocyte physiology and blood component quality", "Glycophorin genes as genomic entities and their inheritance", "Blood group systems and clinical transfusion decisions", "Antibodies, pathogens and other binding partners as independently modeled things", "Manufacturing processes, assay platforms and commercial reagent formulations" ], "distinguishing_features": [ "Require sequence or member-specific identification evidence; erythrocyte origin and sialic acid content alone do not establish glycophorin identity.", "Distinguish the glycoprotein molecule from its encoding gene, a carbohydrate epitope and the erythrocyte carrying it.", "Check compatibility with a membrane-spanning protein and an extracellular glycosylated region; annotate soluble fragments separately from intact molecules.", "Resolve glycophorin A from other members before transferring properties: its extracellular region carries MN determinants, according to [UniProt GYPA](https://www.uniprot.org/uniprotkb/P02724/entry).", "Use sequence and preparation evidence to distinguish an authentic member or hybrid from cross-reactivity, proteolysis or an anomalous electrophoretic band." ], "characteristics": [ { "name": "Member and organism", "kind": "category", "unit_or_values": "Named glycophorin member or unresolved; species and taxonomy identifier", "why_it_matters": "Determines which reference sequence and functional evidence apply." }, { "name": "Sequence and processing", "kind": "relation", "unit_or_values": "Versioned protein accession, sequence variant, mature residue range and numbering convention", "why_it_matters": "Separates precursor numbering, mature chains, hybrids and experimental fragments." }, { "name": "Glycan occupancy and sialylation", "kind": "measurement", "unit_or_values": "Site occupancy percentage; glycan composition; mol sialic acid/mol protein with method", "why_it_matters": "Supports interpretation of molecular heterogeneity and glycan-dependent recognition." }, { "name": "Mass and migration", "kind": "measurement", "unit_or_values": "Da or kDa; calculated backbone mass, measured glycoprotein mass or apparent electrophoretic mass", "why_it_matters": "Prevents gel migration from being treated as a direct molecular identity measurement." }, { "name": "Presentation state", "kind": "state", "unit_or_values": "Cell-associated, membrane vesicle, detergent-solubilized, reconstituted, soluble fragment or denatured", "why_it_matters": "Determines accessibility and whether membrane-dependent measurements are interpretable." }, { "name": "Assembly and membrane partners", "kind": "relation", "unit_or_values": "Identified partners, oligomer stoichiometry, experimental context and evidence", "why_it_matters": "Separates isolated molecule behavior from behavior in membrane complexes." }, { "name": "Surface abundance", "kind": "measurement", "unit_or_values": "Molecules/cell or calibrated relative signal with cell population and uncertainty", "why_it_matters": "Distinguishes altered expression from altered accessibility or binding." }, { "name": "Epitope or ligand accessibility", "kind": "state", "unit_or_values": "Detected, reduced, absent or unresolved for a named probe under stated conditions", "why_it_matters": "Avoids interpreting a negative binding result as proof that the protein is absent." }, { "name": "Preparation quality", "kind": "measurement", "unit_or_values": "Protein concentration in mg/mL; purity, intact fraction and aggregate fraction in percent with methods", "why_it_matters": "Establishes whether a preparation supports the intended experiment." } ], "affordances": [ "Assign a member and sequence reference using orthogonal molecular and binding evidence.", "Characterize glycosylation and compare native, recombinant and enzymatically modified preparations.", "Measure surface presentation or probe binding with controls for epitope accessibility.", "Extract or reconstitute glycophorin under conditions qualified for the intended membrane-dependent assay.", "Compare variants or hybrids while tracking sequence, glycoform and expression differences.", "Accept, qualify or reject a preparation for a specified assay using integrity and stability evidence." ], "agent_conduct": { "may": [ "Describe glycophorins and their role in red cell membranes and blood groups from scientific sources.", "Report blood group antigens on glycophorins using standard terminology." ], "must_not": [ "Infer or publish a person's blood group or genotype without consent.", "Interpret blood group results for transfusion outside an accredited laboratory.", "Link blood group antigens to personality, ethnicity or worth." ], "requires_human": [ "Any transfusion or compatibility decision involving its antigens." ] }, "ethics": { "considerations": [ "Wrong blood group results can kill a transfusion recipient.", "Genetic data about blood groups is personal and can reveal ancestry." ], "affected_parties": [ "Transfusion patients", "Blood donors", "Pregnant women and their babies" ] }, "owners": { "steward": "Nobody owns the molecule; blood services and laboratories answer for testing.", "master_systems": [] }, "visual_identification": [ "Not visible; identified by serological tests or molecular analysis of red cells." ], "failure_modes_and_hazards": [ "Antibodies to its antigens can cause transfusion reactions and disease of the newborn." ], "standards_and_regulation": [ "Red Cell Immunogenetics and Blood Group Terminology, International Society of Blood Transfusion." ], "what_it_is_for": [ "Glycophorins are encountered in studies of erythrocyte membranes, cell-surface properties and blood-group antigens.", "They are characterized in transfusion research and laboratory investigations that distinguish family members, variants and antigen expression." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q24724397: glycophorin", "url": "https://www.wikidata.org/wiki/Q24724397", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Glycophorin", "url": "https://en.wikipedia.org/wiki/Glycophorin", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "member-and-molecular-identity", "name": "Member and molecular identity", "description": "Resolve what the name glycophorin denotes in each observation.", "rationale": "An unqualified class name cannot safely inherit the properties of its best-studied member.", "layers": [ { "id": "member-resolution", "name": "Member resolution", "description": "Connect the observed molecule to a species and named glycophorin member.", "findings": [ { "id": "supported-member-assignment", "name": "Supported member assignment", "description": "Record evidence sufficient to distinguish a particular member from an unresolved glycophorin preparation.", "questions": [ { "text": "Does glycophorin identify the class, a specific member or a mixture in this record?", "kind": "definition", "id": "supported-member-assignment-q01" }, { "text": "Which species, versioned protein accession and identification method support the assignment?", "kind": "provenance", "id": "supported-member-assignment-q02" } ] } ] }, { "id": "chain-and-variant-boundaries", "name": "Chain and variant boundaries", "description": "Resolve processing, sequence variation and experimental construct boundaries.", "findings": [ { "id": "actual-chain-identity", "name": "Actual chain identity", "description": "Define the chain present without confusing mature protein, precursor, hybrid or fragment.", "questions": [ { "text": "What sequence and residue numbering describe the mature chain or experimental construct?", "kind": "definition", "id": "actual-chain-identity-q01" }, { "text": "Is the observed difference an inherited variant, hybrid sequence, processing event or preparation-induced cleavage?", "kind": "boundary", "id": "actual-chain-identity-q02" } ] } ] } ] }, { "id": "glycans-and-molecular-heterogeneity", "name": "Glycans and molecular heterogeneity", "description": "Describe glycophorin as a population of glycosylated molecules rather than one invariant chemical formula.", "rationale": "Backbone identity alone does not establish the composition or recognition properties of a glycophorin preparation.", "layers": [ { "id": "glycan-decoration", "name": "Glycan decoration", "description": "Characterize occupied glycosylation sites and terminal sialylation.", "findings": [ { "id": "measured-glycoform", "name": "Measured glycoform", "description": "Separate directly measured glycan features from sequence predictions or assumptions about the expression host.", "questions": [ { "text": "Which N-linked and O-linked sites, occupancies and glycan compositions are experimentally supported?", "kind": "measurement", "id": "measured-glycoform-q01" }, { "text": "What sialic acid content and linkage information were measured, using which method and normalization?", "kind": "measurement", "id": "measured-glycoform-q02" } ] } ] }, { "id": "mass-and-modification", "name": "Mass and modification", "description": "Interpret heterogeneous masses and migration after preparation or treatment.", "findings": [ { "id": "interpretable-molecular-profile", "name": "Interpretable molecular profile", "description": "Keep backbone mass, glycosylated mass, apparent gel mass and assembly effects distinguishable.", "questions": [ { "text": "Does each reported mass represent a calculated chain, intact glycoprotein, apparent gel band or molecular assembly?", "kind": "boundary", "id": "interpretable-molecular-profile-q01" }, { "text": "What evidence explains changes following desialylation, deglycosylation or proteolysis?", "kind": "measurement", "id": "interpretable-molecular-profile-q02" } ] } ] } ] }, { "id": "membrane-presentation-and-assembly", "name": "Membrane presentation and assembly", "description": "Describe how the molecule is oriented, exposed and associated in its membrane environment.", "rationale": "Extraction and reconstitution can alter the context needed to interpret glycophorin behavior.", "layers": [ { "id": "topology-and-accessibility", "name": "Topology and accessibility", "description": "Locate extracellular, membrane-spanning and cytoplasmic regions in the actual preparation.", "findings": [ { "id": "verified-presentation", "name": "Verified presentation", "description": "Record whether relevant domains are intact and accessible in cells, vesicles or reconstituted membranes.", "questions": [ { "text": "Which residues occupy extracellular, transmembrane and cytoplasmic regions for this member?", "kind": "definition", "id": "verified-presentation-q01" }, { "text": "What evidence establishes orientation and accessible fraction in this cell or membrane preparation?", "kind": "measurement", "id": "verified-presentation-q02" } ] } ] }, { "id": "assembly-and-partners", "name": "Assembly and partners", "description": "Resolve member-specific self-association and membrane-complex relationships.", "findings": [ { "id": "contextual-association", "name": "Contextual association", "description": "Separate measured association from assumed family-wide behavior; glycophorin A has documented ankyrin-complex and SLC4A1 relationships in [UniProt GYPA](https://www.uniprot.org/uniprotkb/P02724/entry).", "questions": [ { "text": "Which oligomeric state and membrane or cytoskeletal partners are supported for this member?", "kind": "provenance", "id": "contextual-association-q01" }, { "text": "Were these associations observed in intact cells, detergent, a membrane mimic or an isolated domain?", "kind": "boundary", "id": "contextual-association-q02" } ] } ] } ] }, { "id": "antigens-and-ligand-recognition", "name": "Antigens and ligand recognition", "description": "Describe recognition of a particular glycophorin sequence and glycoform by specified binding partners.", "rationale": "Probe recognition depends on member identity and presentation and cannot substitute automatically for either.", "layers": [ { "id": "antigenic-presentation", "name": "Antigenic presentation", "description": "Connect epitopes to molecular identity and measured accessibility.", "findings": [ { "id": "member-specific-antigen-evidence", "name": "Member-specific antigen evidence", "description": "Distinguish an antigen-bearing protein from a complete blood group phenotype; human glycophorins A and B bear MN and Ss determinants respectively in the [NCBI GYPA record](https://www.ncbi.nlm.nih.gov/gene/2993).", "questions": [ { "text": "Which antigen or epitope is supported for this sequence, glycoform and species?", "kind": "definition", "id": "member-specific-antigen-evidence-q01" }, { "text": "Could reduced probe binding reflect epitope alteration or masking rather than loss of glycophorin?", "kind": "boundary", "id": "member-specific-antigen-evidence-q02" } ] } ] }, { "id": "specific-binding", "name": "Specific binding", "description": "Qualify antibody and other ligand interactions under defined conditions.", "findings": [ { "id": "controlled-recognition", "name": "Controlled recognition", "description": "Require specificity controls and distinguish molecular binding from downstream biological outcomes.", "questions": [ { "text": "Which named ligand binds this member, and what controls exclude cross-reactivity or nonspecific membrane binding?", "kind": "measurement", "id": "controlled-recognition-q01" }, { "text": "How do sequence variation, glycan treatment and presentation affect the measured interaction?", "kind": "measurement", "id": "controlled-recognition-q02" }, { "text": "What additional evidence is needed before using binding to predict a cellular or pathogen-related outcome?", "kind": "boundary", "id": "controlled-recognition-q03" } ] } ] } ] }, { "id": "preparation-integrity-and-use", "name": "Preparation integrity and use", "description": "Determine whether a glycophorin-containing sample retains the properties required for its intended assay.", "rationale": "Native membrane protein, recombinant material and isolated fragments are not automatically interchangeable.", "layers": [ { "id": "origin-and-comparability", "name": "Origin and comparability", "description": "Track source, expression system and purification effects relevant to glycophorin.", "findings": [ { "id": "traceable-preparation", "name": "Traceable preparation", "description": "Connect each preparation to its biological source or construct and document features limiting comparison.", "questions": [ { "text": "Was the material obtained from erythrocytes, another biological source or a specified recombinant expression system?", "kind": "provenance", "id": "traceable-preparation-q01" }, { "text": "Which co-purified membrane proteins, residual lipids, tags or host-dependent glycans could affect its intended use?", "kind": "boundary", "id": "traceable-preparation-q02" } ] } ] }, { "id": "stability-and-assay-readiness", "name": "Stability and assay readiness", "description": "Assess integrity and retained recognition after storage, extraction or reconstitution.", "findings": [ { "id": "qualified-use-state", "name": "Qualified use state", "description": "Define preparation-specific acceptance criteria using observed stability rather than generic small-molecule constants.", "questions": [ { "text": "What measurements establish intact protein, aggregation, concentration and retained epitope or ligand accessibility?", "kind": "measurement", "id": "qualified-use-state-q01" }, { "text": "Which buffer, detergent or lipid environment, temperature and freeze-thaw history preserve those properties?", "kind": "measurement", "id": "qualified-use-state-q02" }, { "text": "Should this preparation be used, recharacterized or rejected for the proposed assay based on its acceptance criteria?", "kind": "action", "id": "qualified-use-state-q03" } ] } ] } ] }, { "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": [ "This is recalled knowledge, not source-verified research; the description is primarily about human erythrocyte glycophorins.", "Confirm whether the registry intends the protein family or specifically glycophorin A, which is sometimes shortened to glycophorin.", "Molecular mass, abundance, antigen profile, and receptor function depend on the family member, variant, and glycosylation state; no single substance formula or physical-constant set represents the family." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of glycophorin this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-kinds", "name": "Kinds and varieties", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Glycophorin A", "Glycophorin B", "Glycophorin C", "Glycophorin D" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of glycophorin 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 symbols", "value_or_pattern": "GYPA, GYPB, GYPC", "note": "Human genes encoding glycophorins A, B, and C/D respectively; glycophorin D is an alternative translation product of GYPC." }, { "scheme": "CD nomenclature", "value_or_pattern": "CD235a", "note": "Designation for glycophorin A, not for the entire family." }, { "scheme": "ISBT blood group system numbering", "value_or_pattern": "002 (MNS); 020 (Gerbich)", "note": "These identify associated blood group systems: MNS antigens occur on glycophorins A/B, and Gerbich antigens on glycophorins C/D." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of glycophorin this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-standards-and-regulation", "name": "Standards and regulation", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "International Society of Blood Transfusion (ISBT) blood group terminology provides standardized names and numbers for antigens associated with glycophorins." ], "questions": [ { "id": "evidence-standards-and-regulation-q01", "text": "Which of these standards and regulation hold for the sense of glycophorin 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": [ "Glycophorin A detection identifies erythroid cells in flow cytometry and tissue staining.", "Glycophorin-associated antigens are used in blood group typing and investigation of transfusion incompatibility.", "Glycophorins are studied as erythrocyte receptors involved in malaria parasite invasion.", "The glycophorin A transmembrane segment is used as a model for membrane-protein helix association." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of glycophorin this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-measurements", "name": "Typical measurements", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "quantity": "Mature human glycophorin A polypeptide length", "typical_range": "131", "unit": "amino acid residues" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of glycophorin 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": [ "Antibodies against certain glycophorin-associated blood group antigens can cause hemolytic transfusion reactions or hemolytic disease of the fetus and newborn.", "GYPC defects causing glycophorin C/D deficiency can impair membrane-skeleton attachment and are associated with hereditary elliptocytosis.", "Sequence variants and hybrid glycophorins can alter antigen expression and complicate blood group typing.", "Glycosylation differences, proteolysis, or epitope masking can affect antibody-based detection." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of glycophorin this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-regional-variation", "name": "Regional variation", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Frequencies of glycophorin alleles, hybrid genes, and associated blood group phenotypes vary among human populations." ], "questions": [ { "id": "evidence-regional-variation-q01", "text": "Which of these regional variation hold for the sense of glycophorin 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": "Glycoprotein", "difference": "The broader class includes any protein bearing covalently attached carbohydrate; glycophorins are a particular erythrocyte membrane family." }, { "name": "Glycophorin A", "difference": "A specific family member encoded by GYPA; the unqualified term glycophorin does not uniquely identify it." }, { "name": "Band 3 / anion exchanger 1", "difference": "An erythrocyte membrane protein encoded by SLC4A1 that transports anions, rather than a member of the glycophorin family." }, { "name": "MNS blood group system", "difference": "A classification of inherited antigens carried principally by glycophorins A/B, rather than the proteins themselves." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of glycophorin this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the registry intend glycophorin as the full class or as a historical shorthand for glycophorin A, and does an existing world model already own that scope?", "Which species and named members belong within the intended class, and how should historical glycophorin naming systems be reconciled?", "Which member-specific sequence, topology, glycosylation and antigen references are sufficiently authoritative to establish default expectations?", "Which membrane associations and ligand interactions remain reproducible across native cells, purified protein and reconstituted systems?", "What preparation-specific stability limits and assay acceptance criteria have been validated for the uses this registry should support?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 19, "questions": 31 } }