{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.glycophorin","code":"thing-q24724397","url":"https://ver.cy/models/thing/q24724397/","name":"glycophorin","alternateNames":[],"kind":"thing","status":"published","version":"0.1.0-research.1","language":"en","classifiers":{"family":"Thing Registry","category":"Physical world and living systems","entryKind":"thing","plane":"PHY","domain":["PHY.MAT"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"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.","purpose":"Enable an agent to identify a glycophorin, assess its molecular and experimental state, and select evidence-supported characterization or handling actions.","scope":{"in":["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":["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"],"boundaries":[]},"distinguishingFeatures":["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."],"structure":{"bundles":[{"id":"member-and-molecular-identity","name":"Member and molecular identity","description":"Resolve what the name glycophorin denotes in each observation.","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?","id":"supported-member-assignment-q01","kind":"definition"},{"text":"Which species, versioned protein accession and identification method support the assignment?","id":"supported-member-assignment-q02","kind":"provenance"}]}]},{"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?","id":"actual-chain-identity-q01","kind":"definition"},{"text":"Is the observed difference an inherited variant, hybrid sequence, processing event or preparation-induced cleavage?","id":"actual-chain-identity-q02","kind":"boundary"}]}]}]},{"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.","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?","id":"measured-glycoform-q01","kind":"measurement"},{"text":"What sialic acid content and linkage information were measured, using which method and normalization?","id":"measured-glycoform-q02","kind":"measurement"}]}]},{"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?","id":"interpretable-molecular-profile-q01","kind":"boundary"},{"text":"What evidence explains changes following desialylation, deglycosylation or proteolysis?","id":"interpretable-molecular-profile-q02","kind":"measurement"}]}]}]},{"id":"membrane-presentation-and-assembly","name":"Membrane presentation and assembly","description":"Describe how the molecule is oriented, exposed and associated in its membrane environment.","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?","id":"verified-presentation-q01","kind":"definition"},{"text":"What evidence establishes orientation and accessible fraction in this cell or membrane preparation?","id":"verified-presentation-q02","kind":"measurement"}]}]},{"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?","id":"contextual-association-q01","kind":"provenance"},{"text":"Were these associations observed in intact cells, detergent, a membrane mimic or an isolated domain?","id":"contextual-association-q02","kind":"boundary"}]}]}]},{"id":"antigens-and-ligand-recognition","name":"Antigens and ligand recognition","description":"Describe recognition of a particular glycophorin sequence and glycoform by specified binding partners.","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?","id":"member-specific-antigen-evidence-q01","kind":"definition"},{"text":"Could reduced probe binding reflect epitope alteration or masking rather than loss of glycophorin?","id":"member-specific-antigen-evidence-q02","kind":"boundary"}]}]},{"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?","id":"controlled-recognition-q01","kind":"measurement"},{"text":"How do sequence variation, glycan treatment and presentation affect the measured interaction?","id":"controlled-recognition-q02","kind":"measurement"},{"text":"What additional evidence is needed before using binding to predict a cellular or pathogen-related outcome?","id":"controlled-recognition-q03","kind":"boundary"}]}]}]},{"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.","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?","id":"traceable-preparation-q01","kind":"provenance"},{"text":"Which co-purified membrane proteins, residual lipids, tags or host-dependent glycans could affect its intended use?","id":"traceable-preparation-q02","kind":"boundary"}]}]},{"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?","id":"qualified-use-state-q01","kind":"measurement"},{"text":"Which buffer, detergent or lipid environment, temperature and freeze-thaw history preserve those properties?","id":"qualified-use-state-q02","kind":"measurement"},{"text":"Should this preparation be used, recharacterized or rejected for the proposed assay based on its acceptance criteria?","id":"qualified-use-state-q03","kind":"action"}]}]}]},{"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.","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.","questions":[{"text":"Which of these check these first hold for the sense of glycophorin this model covers, and on what evidence?","id":"evidence-confidence-notes-q01","kind":"provenance"}]},{"id":"evidence-kinds","name":"Kinds and varieties","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these kinds and varieties hold for the sense of glycophorin this model covers, and on what evidence?","id":"evidence-kinds-q01","kind":"provenance"}]},{"id":"evidence-identifiers","name":"Identifiers and schemes","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these identifiers and schemes hold for the sense of glycophorin this model covers, and on what evidence?","id":"evidence-identifiers-q01","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.","questions":[{"text":"Which of these standards and regulation hold for the sense of glycophorin this model covers, and on what evidence?","id":"evidence-standards-and-regulation-q01","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.","questions":[{"text":"Which of these real-world use hold for the sense of glycophorin this model covers, and on what evidence?","id":"evidence-real-world-use-q01","kind":"provenance"}]},{"id":"evidence-measurements","name":"Typical measurements","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these typical measurements hold for the sense of glycophorin this model covers, and on what evidence?","id":"evidence-measurements-q01","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.","questions":[{"text":"Which of these failure modes and hazards hold for the sense of glycophorin this model covers, and on what evidence?","id":"evidence-failure-modes-and-hazards-q01","kind":"provenance"}]},{"id":"evidence-regional-variation","name":"Regional variation","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these regional variation hold for the sense of glycophorin this model covers, and on what evidence?","id":"evidence-regional-variation-q01","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.","questions":[{"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?","id":"evidence-neighbours-q01","kind":"provenance"}]}]}]}]},"agentConduct":{"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."],"mustNot":["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."],"requiresHuman":["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."],"affectedParties":["Transfusion patients","Blood donors","Pregnant women and their babies"]},"owners":{"steward":"Nobody owns the molecule; blood services and laboratories answer for testing.","roles":[],"masterSystems":[]},"relations":[{"target":"Q8054","type":"parent","note":"registry parent class"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.glycophorin","Wikidata: Q24724397 (https://www.wikidata.org/wiki/Q24724397)"]},"properties":{"applicability":"required","items":["Member and organism: Named glycophorin member or unresolved; species and taxonomy identifier","Sequence and processing: Versioned protein accession, sequence variant, mature residue range and numbering convention","Glycan occupancy and sialylation: Site occupancy percentage; glycan composition; mol sialic acid/mol protein with method","Mass and migration: Da or kDa; calculated backbone mass, measured glycoprotein mass or apparent electrophoretic mass","Presentation state: Cell-associated, membrane vesicle, detergent-solubilized, reconstituted, soluble fragment or denatured","Assembly and membrane partners: Identified partners, oligomer stoichiometry, experimental context and evidence","Surface abundance: Molecules/cell or calibrated relative signal with cell population and uncertainty","Epitope or ligand accessibility: Detected, reduced, absent or unresolved for a named probe under stated conditions","Preparation quality: Protein concentration in mg/mL; purity, intact fraction and aggregate fraction in percent with methods"]},"recognition":{"applicability":"required","items":["Not visible; identified by serological tests or molecular analysis of red cells."]},"capabilities":{"applicability":"required","items":["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."]},"hazards":{"applicability":"required","items":["Antibodies to its antigens can cause transfusion reactions and disease of the newborn."]},"interfaces":{"applicability":"required","items":["Red Cell Immunogenetics and Blood Group Terminology, International Society of Blood Transfusion."]},"context":{"applicability":"required","items":["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":[{"title":"Wikidata item Q24724397: glycophorin","url":"https://www.wikidata.org/wiki/Q24724397","note":"identity and sense of the item"},{"title":"Wikipedia: Glycophorin","url":"https://en.wikipedia.org/wiki/Glycophorin","note":"general description of the item"}],"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?"],"resources":{"spec":"/models/things/publications/thing-q24724397/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q24724397/spec.json"],"providers":["Codex"],"researchStatus":"unreviewed","generatedAt":"2026-09-12T10:01:26Z","builder":"tools/build_cards.py@1.0.0"},"completeness":{"sections":{"classifiers":"filled","whatItIs":"filled","purpose":"filled","distinguishingFeatures":"filled","structure":"filled","agentConduct":"filled","ethics":"filled","owners":"filled","relations":"filled","interaction.identity":"filled","interaction.properties":"filled","interaction.recognition":"filled","interaction.capabilities":"filled","interaction.hazards":"filled","interaction.interfaces":"filled","interaction.context":"filled","sources":"filled"},"notes":{"_gate":"Published through the thing publication gate 1.0 on 2026-10-07T10:10:29+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass"},"score":1.0}}