{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T08:30:00Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 23.3, "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: 01a094bb-d1a9-7f03-8fcd-136d52aab21a\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: cell line\nSense to describe: (none recorded)\nDomain code: SOC.ORG\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 043: 1001 regis", "usd": 0.0, "recall": true }, "codex": { "seconds": 69.5, "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: 01a094bb-d1b8-77e2-abce-9389d789134c\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: cell line\nRegistry id: vr.tr.cell-line\nPlane / domain: SOC / SOC.ORG\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nCont" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:11:05+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "standards_and_regulation", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:28+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q21014462", "registryId": "vr.tr.cell-line", "name": "cell line", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "SOC.ORG" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q21014462/", "model": { "registry_id": "vr.tr.cell-line", "name": "cell line", "purpose": "Enable an AI agent to identify a cell line, assess whether its available material is trustworthy and suitable for an intended use, and determine permitted handling and transfer.", "definition": "A cell line is a population of cells established by subculturing a primary culture and maintained through successive passages, with either a finite proliferative lifespan or the capacity for continuous propagation.", "scope_statement": "This model owns the identity, derivation, biological properties, culture history, quality evidence and use constraints of a laboratory cell line, while distinguishing the line from individual stocks, cultures and experiments; the supplied SOC / SOC.ORG classification requires review because a cell line is biological material rather than an organisation.", "in_scope": [ "Line identity, aliases, accession identifiers and relationships to parental lines and derivatives", "Organism, tissue and donor provenance, derivation method and finite or continuous growth status", "Culture requirements, passage history and stability of defining properties", "Authentication, contamination evidence and stock-specific quality", "Fitness for intended applications and applicable consent, licensing and handling constraints" ], "out_of_scope": [ "The donor organism or person as a complete biological or personal record", "Primary specimens and primary cultures before establishment of a cell line", "Individual vial inventory, freezer equipment and facility operations", "Complete experimental protocols, datasets and study conclusions", "The supplying repository or laboratory as an organisation" ], "distinguishing_features": [ "Represents a propagated population of cultured cells with a traceable derivation, rather than an organism, tissue specimen or isolated cell.", "Has a lineage identity that can span multiple cultures and frozen stocks; differences between stocks do not automatically establish a new line.", "May have finite proliferative capacity or continuous growth; immortality must not be assumed from the term cell line.", "Is not necessarily clonal or genetically uniform; clonality and population heterogeneity require separate evidence.", "A subclone, engineered derivative or selected population needs an explicit relationship to its parent and evidence supporting any separate identity." ], "characteristics": [ { "name": "Line identifiers and aliases", "kind": "relation", "unit_or_values": "Repository or registry accession, identifier namespace, preferred name and documented aliases", "why_it_matters": "Separates reliable identity links from coincidental name matches." }, { "name": "Biological origin", "kind": "relation", "unit_or_values": "Source organism, tissue or cell type, donor or specimen reference where permitted", "why_it_matters": "Constrains biological interpretation and connects the line to its derivation evidence." }, { "name": "Proliferative status", "kind": "category", "unit_or_values": "Finite, continuous or unresolved; supporting evidence and observation date", "why_it_matters": "Determines whether replicative exhaustion or a documented immortalisation history must be considered." }, { "name": "Derivation and modification history", "kind": "relation", "unit_or_values": "Parent line, derivation event, cloning method, immortalisation method and engineered changes", "why_it_matters": "Distinguishes inherited properties from changes introduced during derivation." }, { "name": "Culture phenotype", "kind": "category", "unit_or_values": "Adherent, suspension or mixed growth; documented morphology and relevant markers", "why_it_matters": "Supports recognition and detection of departures from expected culture behaviour." }, { "name": "Replicative history", "kind": "measurement", "unit_or_values": "Passage count with counting convention; cumulative population doublings when available", "why_it_matters": "Supports comparison of stocks without treating passage count as equivalent to population doublings." }, { "name": "Growth performance", "kind": "measurement", "unit_or_values": "Doubling time in hours, with medium, temperature, density and measurement method", "why_it_matters": "Makes growth observations interpretable under their actual culture conditions." }, { "name": "Authentication status", "kind": "state", "unit_or_values": "Supported, inconclusive, conflicting or untested; method, reference, tested stock and date", "why_it_matters": "Prevents an unverified label from being treated as established identity." }, { "name": "Contamination status", "kind": "state", "unit_or_values": "Not detected, detected, inconclusive or untested, separately for each target and sampled stock", "why_it_matters": "Avoids extending a limited test result to every contaminant or every stock." }, { "name": "Use and transfer constraints", "kind": "relation", "unit_or_values": "Applicable consent terms, material transfer agreement, licence and handling assessment", "why_it_matters": "Determines whether a proposed activity is permitted for the particular material." } ], "affordances": [ "Resolve a supplied name to a documented line identity and flag ambiguous or conflicting matches.", "Trace a stock through its parental line, derivation events and repository records.", "Compare observed culture behaviour with condition-specific reference properties.", "Assess whether authentication, contamination and stability evidence support a proposed use.", "Recommend release, quarantine, reauthentication or replacement of a stock based on recorded evidence.", "Check whether acquisition, modification, sharing or intended use fits the material's documented constraints." ], "agent_conduct": { "may": [ "Record a cell line's origin, passage number and authentication results in the lab's records.", "Report identity and contamination test results for lines it is authorized to manage." ], "must_not": [ "Use a cell line without checking that its use is covered by the donor's consent and the provider's terms.", "Publish results from a line that has not been authenticated or is known to be misidentified.", "Share donor-identifying information or genetic data linked to a line.", "Handle lines carrying pathogens outside the required containment level." ], "requires_human": [ "Deriving a new line from human tissue.", "Releasing a line or its data to other institutions." ] }, "ethics": { "considerations": [ "Human cell lines come from people whose consent and privacy deserve respect, as famous cases have shown.", "Misidentified lines have wasted years of research and misled medicine." ], "affected_parties": [ "Donors and their families", "Researchers", "Patients relying on research" ] }, "owners": { "steward": "The institution or biobank that holds it under its material transfer terms.", "master_systems": [ "Cell line repositories and biobank catalogues", "Registers of misidentified cell lines" ] }, "visual_identification": [ "Cells growing in labelled flasks or plates in an incubator.", "Frozen vials with a line name, passage number and date in a cryogenic store." ], "failure_modes_and_hazards": [ "Cross-contamination and misidentification invalidate research findings.", "Some lines carry viruses or other agents that pose biosafety risks." ], "standards_and_regulation": [ "ANSI/ATCC ASN-0002, Authentication of Human Cell Lines: Standardization of STR Profiling, American National Standards Institute." ], "what_it_is_for": [ "Cell lines are maintained in laboratories as repeatable sources of living cells for studying biological processes.", "They are used in disease research, toxicity testing, drug development and production of biological materials.", "Suitability for a particular use depends on documented identity, culture history and relevant biological characteristics." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q21014462: cell line", "url": "https://www.wikidata.org/wiki/Q21014462", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Cell line", "url": "https://en.wikipedia.org/wiki/Cell_line", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "identity-and-lineage", "name": "Identity and lineage", "description": "Establishes which cell line is represented and how it relates to specimens, parents and derivatives.", "rationale": "Names alone cannot distinguish aliases, misidentified material and biologically distinct derivatives.", "layers": [ { "id": "line-identity", "name": "Line identity", "description": "Connects names and accessions to an explicit biological identity.", "findings": [ { "id": "identifier-resolution", "name": "Identifier resolution", "description": "Record accession-backed identity and unresolved naming conflicts without merging records solely by name.", "questions": [ { "text": "Which repository or registry accessions identify this line, and which names are documented aliases?", "kind": "definition", "id": "identifier-resolution-q01" }, { "text": "Does a conflicting name denote the same line, a derivative or misidentified material?", "kind": "boundary", "id": "identifier-resolution-q02" } ] } ] }, { "id": "biological-derivation", "name": "Biological derivation", "description": "Traces source material and events that established the line.", "findings": [ { "id": "origin-and-parentage", "name": "Origin and parentage", "description": "Separate reported donor and tissue origin from documented parental, cloning and modification relationships.", "questions": [ { "text": "What source organism, specimen, tissue and derivation records support the claimed origin?", "kind": "provenance", "id": "origin-and-parentage-q01" }, { "text": "Which cloning, immortalisation, reprogramming or engineering events connect this line to its parent?", "kind": "provenance", "id": "origin-and-parentage-q02" }, { "text": "What evidence justifies treating this population as a distinct line rather than a stock of its parent?", "kind": "boundary", "id": "origin-and-parentage-q03" } ] } ] } ] }, { "id": "culture-and-propagation", "name": "Culture and propagation", "description": "Captures the conditions and replicative history needed to maintain interpretable cell populations.", "rationale": "Culture conditions and propagation history can change growth, phenotype and suitability.", "layers": [ { "id": "culture-dependencies", "name": "Culture dependencies", "description": "Records the environment and supporting materials associated with successful maintenance.", "findings": [ { "id": "documented-culture-conditions", "name": "Documented culture conditions", "description": "Associate medium, supplements, substrate, feeder dependence and environmental requirements with their evidence.", "questions": [ { "text": "Which medium, supplements, substrate or feeder cells and environmental conditions are documented for this line?", "kind": "definition", "id": "documented-culture-conditions-q01" }, { "text": "Under what conditions were the reference growth rate and morphology measured?", "kind": "measurement", "id": "documented-culture-conditions-q02" } ] } ] }, { "id": "replicative-history", "name": "Replicative history", "description": "Tracks expansion and recovery without assuming all cultures remain equivalent.", "findings": [ { "id": "propagation-window", "name": "Propagation window", "description": "Record passage conventions, population doublings, freeze-thaw history and evidence of finite or continuous growth.", "questions": [ { "text": "What passage count, counting convention and population-doubling history are known for the available stock?", "kind": "measurement", "id": "propagation-window-q01" }, { "text": "What evidence establishes finite or continuous growth and any validated range of propagation?", "kind": "provenance", "id": "propagation-window-q02" }, { "text": "When should observed senescence, altered growth or poor recovery trigger replacement or investigation?", "kind": "action", "id": "propagation-window-q03" } ] } ] } ] }, { "id": "authentication-and-contamination", "name": "Authentication and contamination", "description": "Evaluates whether sampled material has the expected identity and assessed contamination status.", "rationale": "Misidentification and contamination can invalidate use even when culture appearance seems normal.", "layers": [ { "id": "identity-testing", "name": "Identity testing", "description": "Links authentication conclusions to suitable methods, reference profiles and sampled stocks.", "findings": [ { "id": "authentication-evidence", "name": "Authentication evidence", "description": "Record species-appropriate identity testing, reference provenance and conflicts between claimed and measured identity.", "questions": [ { "text": "Which authentication method is appropriate for this species and line, and what reference supports comparison?", "kind": "definition", "id": "authentication-evidence-q01" }, { "text": "Which stock was tested, when was it tested and what match or discrepancy was observed?", "kind": "measurement", "id": "authentication-evidence-q02" } ] } ] }, { "id": "contamination-evidence", "name": "Contamination evidence", "description": "Keeps test coverage and contamination decisions specific to sampled material.", "findings": [ { "id": "contaminant-assessment", "name": "Contaminant assessment", "description": "Distinguish mycoplasma, other microbial contamination and cross-contamination with other cells.", "questions": [ { "text": "Which contaminants were assessed, using what methods and sampling dates, and with what results?", "kind": "measurement", "id": "contaminant-assessment-q01" }, { "text": "What evidence supports releasing, quarantining, discarding or retesting this stock?", "kind": "action", "id": "contaminant-assessment-q02" } ] } ] } ] }, { "id": "biological-properties-and-use", "name": "Biological properties and use", "description": "Connects observed properties and their stability to the intended experimental application.", "rationale": "An authenticated cell line can still lack the phenotype or performance required for a particular task.", "layers": [ { "id": "defining-properties", "name": "Defining properties", "description": "Records measured characteristics without assuming every stock retains historical attributes.", "findings": [ { "id": "phenotype-and-genotype", "name": "Phenotype and genotype", "description": "Track relevant markers, variants, ploidy, differentiation capacity and population heterogeneity with measurement context.", "questions": [ { "text": "Which genetic and phenotypic properties define the line or derivative for the intended application?", "kind": "definition", "id": "phenotype-and-genotype-q01" }, { "text": "Which properties were measured in the current material, and how do they vary across passages or conditions?", "kind": "measurement", "id": "phenotype-and-genotype-q02" } ] } ] }, { "id": "application-fitness", "name": "Application fitness", "description": "Separates historical use from demonstrated suitability for a specific assay or biological inference.", "findings": [ { "id": "use-specific-validation", "name": "Use-specific validation", "description": "Record application-specific performance evidence, acceptance criteria and limits of biological representation.", "questions": [ { "text": "What functional evidence and acceptance criteria establish fitness for the proposed assay?", "kind": "measurement", "id": "use-specific-validation-q01" }, { "text": "Which properties of the source tissue, disease or organism are unsupported by this cell-line model?", "kind": "boundary", "id": "use-specific-validation-q02" }, { "text": "What additional validation is required before this stock can support the proposed inference?", "kind": "action", "id": "use-specific-validation-q03" } ] } ] } ] }, { "id": "access-and-responsible-use", "name": "Access and responsible use", "description": "Connects available material to acquisition records, permissions and handling requirements.", "rationale": "Biological identity alone does not establish that a stock may be obtained, manipulated or shared.", "layers": [ { "id": "material-provenance", "name": "Material provenance", "description": "Connects received stocks to suppliers and documented transfer histories.", "findings": [ { "id": "stock-to-line-traceability", "name": "Stock-to-line traceability", "description": "Link supplier lots and local stocks to line records while exposing gaps in custody or documentation.", "questions": [ { "text": "Which supplier, accession, lot and acquisition records connect the available stock to this line?", "kind": "provenance", "id": "stock-to-line-traceability-q01" }, { "text": "Which gaps in transfer or stock history require verification before use or redistribution?", "kind": "action", "id": "stock-to-line-traceability-q02" } ] } ] }, { "id": "use-permissions-and-handling", "name": "Use permissions and handling", "description": "Records constraints applicable to the actual stock, modification and proposed activity.", "findings": [ { "id": "permitted-activities", "name": "Permitted activities", "description": "Associate documented consent, transfer terms and risk assessments with decisions about use and sharing.", "questions": [ { "text": "Which consent, licence or transfer terms constrain research, commercial use, genetic modification or onward sharing?", "kind": "provenance", "id": "permitted-activities-q01" }, { "text": "What handling and containment assessment applies to this material and the proposed activity?", "kind": "action", "id": "permitted-activities-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 ordinary biological meaning is used here; domain code SOC.ORG appears inconsistent with that meaning and should be checked against the original registry record.", "Cell line does not necessarily mean immortalized; terminology concerning lines and strains varies across disciplines.", "Growth rate, passage limits, culture conditions and authentication methods depend on the particular line and species, so no universal measurement ranges are supplied." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of cell line 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": [ "Finite cell lines", "Continuous or immortalized cell lines", "Clonal cell lines", "Tumour-derived cell lines", "Adherent cell lines", "Suspension cell lines" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of cell line 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": "Cellosaurus accession", "value_or_pattern": "CVCL_ followed by a four-character alphanumeric identifier", "note": "Identifies a cell-line record; names and aliases alone may be ambiguous." }, { "scheme": "Research Resource Identifier (RRID)", "value_or_pattern": "RRID:CVCL_XXXX", "note": "Uses the Cellosaurus accession to identify a cell line in research reporting." }, { "scheme": "Cell-bank catalogue number", "value_or_pattern": "Repository-specific catalogue identifier", "note": "Repositories such as ATCC and ECACC assign identifiers to their holdings; these are distinct from lot numbers." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of cell line 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": [ "ATCC consensus standard for authentication of human cell lines using short tandem repeat profiling.", "OECD Guidance Document on Good In Vitro Method Practices (GIVIMP), covering cell and tissue culture practices used in in vitro testing." ], "questions": [ { "id": "evidence-standards-and-regulation-q01", "text": "Which of these standards and regulation hold for the sense of cell line 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": [ "Studying cellular processes, gene function and disease mechanisms.", "Screening compounds and assessing cellular responses or toxicity.", "Producing recombinant proteins and other biological products.", "Propagating viruses for research or vaccine production.", "Developing and validating laboratory assays." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of cell line 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": [ "Misidentification or cross-contamination with another cell line.", "Mycoplasma or other microbial contamination that alters results or destroys cultures.", "Genetic and phenotypic drift during prolonged cultivation.", "Senescence, loss of viability or selection of unintended subpopulations.", "Exposure to infectious agents potentially present in source material or introduced during use." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of cell line 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": [ "Requirements for donor consent, provenance, import and use of human-derived material vary by jurisdiction.", "Biosafety and genetically modified organism requirements depend on jurisdiction and the properties of the cells and introduced material." ], "questions": [ { "id": "evidence-regional-variation-q01", "text": "Which of these regional variation hold for the sense of cell line 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": "Primary cell culture", "difference": "A primary culture is established directly from source tissue; a cell line arises through subsequent subculture." }, { "name": "Cell strain", "difference": "A cell strain is a selected or cloned population with specified properties derived from a primary culture or cell line; terminology can overlap." }, { "name": "Cell type", "difference": "A cell type classifies cells by biological identity or function; a cell line is a particular propagated population." }, { "name": "Cell clone", "difference": "A clone descends from a single cell; a cell line need not be clonal." }, { "name": "Cell bank", "difference": "A cell bank is a stored collection of cell preparations, or an organisation maintaining such collections; a cell line is the biological population being preserved." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of cell line this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Why is vr.tr.cell-line assigned to SOC / SOC.ORG, and which registry classification should represent the biological concept?", "Which authoritative definition should govern the boundary between primary culture, cell line, cell strain and established continuous line?", "Does an existing Vercy world model already cover cell lines, requiring this registry entry to link to it?", "Which authentication references and decision criteria are appropriate across human, nonhuman animal, plant and other cell lines?", "What evidence should establish separate identity for subclones and engineered derivatives, and which quality decisions must remain specific to individual stocks?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 18, "questions": 31 } }