{ "model": { "rank": 4893, "code": "thing-q179991", "model_id": "vr.tr.biopsy", "name": "biopsy", "purpose": "Let an agent explain biopsies and their kinds in general terms from clinical sources, describe what to expect, risks and how results are used, and route personal questions to clinicians.", "family": "Thing Registry", "category": "Activities and processes", "status": "research-draft", "kind": "thing", "plane": "ACT", "domain": "ACT.ACT", "industry": "", "version": "", "url": "/models/thing/q179991/", "tier": 2, "score": 71, "payload": { "layer": "wikidata", "aliases": [ "bone marrow biopsy", "bronchoscopic cryobiopsy", "gut biopsy", "transthoracic biopsy", "pleural biopsy", "muscle biopsy", "liquid biopsy", "liver biopsy", "prostate biopsy", "breast biopsy", "Endometrial biopsy", "lung biopsy", "sentinel lymph node biopsy", "lymph node biopsy", "needle-localized biopsy", "image-guided biopsy", "needle biopsy", "renal biopsy", "skin biopsy", "bone biopsy", "MRI/Ultrasound fusion biopsy", "lymph node puncture", "punch biopsy" ], "aliasCount": 23, "merged": 23, "knownIn": 71, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q179991", "url": "https://www.wikidata.org/wiki/Q179991", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-13T01:44:01Z", "providers": [ "Claude" ], "breadth": "written by Claude from model knowledge without web access - no source was read, every claim is a lead to verify", "pass": 2, "wave": 3, "engine": "claude" }, "metaModel": { "id": "THING-Q179991", "registryId": "vr.tr.biopsy", "name": "biopsy", "version": "0.2.0-wave.3", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.ACT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q179991/", "model": { "registry_id": "vr.tr.biopsy", "name": "biopsy", "purpose": "Let an agent explain biopsies and their kinds in general terms from clinical sources, describe what to expect, risks and how results are used, and route personal questions to clinicians.", "definition": "A medical procedure that removes a sample of tissue or cells from the body for examination, usually under a microscope, to diagnose disease, especially cancer, inflammation and infection, in forms such as needle, core, excisional and endoscopic biopsies, bone marrow biopsy, muscle biopsy, pleural and transthoracic lung biopsies, gut biopsies and bronchoscopic cryobiopsy; biopsies are invasive tests with small risks and are central to pathology and personalised treatment.", "what_it_is_for": "Diagnosing disease from tissue samples.", "affordances": [ "explain kinds and purposes", "relay procedure and risks in general terms", "describe how results are used", "route personal questions" ], "distinguishing_features": [ "Tissue removal", "Histopathological analysis", "Diagnostic gold standard for many conditions", "Invasive with risks" ], "appearance": "A procedure with a needle, scalpel or endoscope; a small tissue sample in a container.", "visual_identification": [ "Tissue sampling for examination", "Needle, core, excisional, endoscopic, bone marrow, muscle, lung, gut biopsies", "Blood tests sample fluid; imaging does not remove tissue; liquid biopsy analyses blood for tumour DNA" ], "physical_properties": [], "families_and_kinds": [ "fine needle aspiration and core needle biopsy", "excisional and incisional biopsy", "endoscopic biopsies such as gut biopsy", "bone marrow biopsy", "muscle and nerve biopsy", "lung biopsies including transthoracic, pleural and bronchoscopic cryobiopsy", "image-guided biopsies", "liquid biopsy as a related non-tissue test" ], "related_models": [ { "relation": "is a kind of", "target": "invasive test", "why": "in registry terms" }, { "relation": "is a kind of", "target": "sampling", "why": "in registry terms" }, { "relation": "is analysed by", "target": "histopathology", "why": "the discipline" }, { "relation": "is guided by", "target": "medical imaging", "why": "in many cases" } ], "identifiers": [ { "scheme": "MeSH", "value_or_pattern": "D001706", "note": "biopsy" } ], "standards_and_regulation": [ "Clinical guidelines for biopsy indications and techniques", "Informed consent rules", "Pathology laboratory accreditation" ], "failure_modes_and_hazards": [ "Bleeding, infection and pneumothorax in lung biopsies", "Sampling error and false negatives", "Agents giving personal medical advice", "Anxiety while awaiting results" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What a biopsy is.", "rationale": "Clinical.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition and kinds.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What is a biopsy, and what kinds exist?", "kind": "definition" }, { "text": "Is the question about a tissue biopsy, a liquid biopsy or another test?", "kind": "boundary" } ] } ] }, { "id": "purpose", "name": "Purpose", "description": "Why biopsies are done.", "findings": [ { "id": "purpose-finding", "name": "Purpose", "description": "Purpose.", "questions": [ { "text": "Why are biopsies performed, and how do results guide diagnosis and treatment?", "kind": "definition" }, { "text": "Which entry fits the specific biopsy type?", "kind": "action" } ] } ] } ] }, { "id": "procedure", "name": "Procedure", "description": "Procedure and risks.", "rationale": "Clinical.", "layers": [ { "id": "expect", "name": "Expect", "description": "What to expect.", "findings": [ { "id": "expect-finding", "name": "Expect", "description": "Expect.", "questions": [ { "text": "What happens before, during and after common biopsies, in general terms?", "kind": "provenance" }, { "text": "Is the user asking about their own procedure, which needs their clinician?", "kind": "boundary" } ] } ] }, { "id": "risks", "name": "Risks", "description": "Risks and consent.", "findings": [ { "id": "risks-finding", "name": "Risks", "description": "Risks.", "questions": [ { "text": "What risks do biopsies carry, and how is consent handled?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] } ] }, { "id": "results", "name": "Results", "description": "Analysis and results.", "rationale": "Clinical.", "layers": [ { "id": "pathology", "name": "Pathology", "description": "Pathology analysis.", "findings": [ { "id": "pathology-finding", "name": "Pathology", "description": "Pathology.", "questions": [ { "text": "How are samples processed and examined, including molecular testing?", "kind": "provenance" }, { "text": "Which entry fits histopathology?", "kind": "action" } ] } ] }, { "id": "limits", "name": "Limits", "description": "Limits and errors.", "findings": [ { "id": "limits-finding", "name": "Limits", "description": "Limits.", "questions": [ { "text": "What are sampling error and false negatives, and how are they managed?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "History and future.", "rationale": "Context.", "layers": [ { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How did biopsy develop as a diagnostic method?", "kind": "provenance" }, { "text": "Which entry fits the history of pathology?", "kind": "action" } ] } ] }, { "id": "future", "name": "Future", "description": "Liquid biopsy and imaging.", "findings": [ { "id": "future-finding", "name": "Future", "description": "Future.", "questions": [ { "text": "How are liquid biopsies and imaging changing the need for tissue biopsies, as research reports?", "kind": "provenance" }, { "text": "Which entry fits liquid biopsy?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should bone marrow biopsy and liquid biopsy be separate entries?", "How should clinical guidelines be linked?", "The registry entry has merged aliases naming specific procedures; should they be split off?" ], "statistics": { "bundles": 4, "layers": 8, "findings": 8, "questions": 16 } }, "draft": { "generator": "vr.draft.v3", "status": "draft-generated", "researched": false, "archetype": "abstract concept", "method": "Written from the archetype playbook - what this kind of thing needs beyond identity and provenance - and from the structure that recurred across 6,333 models already researched by two engines. Applied to this entry by rule. No source was read for this thing and no claim here is researched. This entry carries no facets of its own, so they were inferred from its domain - a guess about a whole domain applied to one thing.", "facetsInferred": true, "nextPass": "A researcher replaces this draft with a sourced specification. Treat every sentence below as a proposal to argue with.", "purpose": "Give an agent a durable, checkable way to recognise a biopsy, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain biopsies and their kinds in general terms from clinical sources, describe what to expect, risks and how results are used, and route personal questions to clinicians.", "characteristics": { "substance": "activity", "origin": "conceptual", "agency": "inert" }, "whatYouCanDoWithIt": [ "observed and measured" ], "distinguishingFeatures": [ "Names folded into this entry, which a task may need to split apart again: bone marrow biopsy, bronchoscopic cryobiopsy, gut biopsy, transthoracic biopsy, pleural biopsy, muscle biopsy, liquid biopsy, liver biopsy, prostate biopsy, breast biopsy, Endometrial biopsy, lung biopsy.", "23 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 71 Wikipedia languages, which is a measure of how widely the thing is known, not of how important it is." ], "openQuestionsForResearch": [ "Which of the bundles below does a real task actually need, and which are ceremony?", "What does this thing have that the facets do not capture at all?", "Which neighbouring kind is most often confused with a biopsy, and on what evidence are they told apart?" ], "whatItIsMadeOf": "something that happens over time", "physicalCharacter": [ "Does nothing on its own; everything it does, something else did to it.", "These come from the domain this entry sits in rather than from the entry itself, so treat them as a first guess about the whole domain applied to one thing." ], "whatCanBeDoneWithIt": [ "observe it, measure it, record its state" ], "howItIsRecognised": [ "Nothing to see. What is recognised is an instance of it, and which instances count is exactly what is argued about." ], "relatedModels": [ { "relation": "covers", "note": "Finer kinds folded into this entry because telling them apart needs a task that asks for it. Each is a model waiting to be split out when one does.", "targets": [ "bone marrow biopsy", "bronchoscopic cryobiopsy", "gut biopsy", "transthoracic biopsy", "pleural biopsy", "muscle biopsy", "liquid biopsy", "liver biopsy", "prostate biopsy", "breast biopsy", "Endometrial biopsy", "lung biopsy" ] } ], "standing": "Described in 71 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 23 finer distinctions are held inside this entry as names rather than as separate models.", "structure": { "bundles": [ { "id": "identity-and-classification", "name": "Identity, naming and classification", "description": "How an agent tells one biopsy from another, and a biopsy from things that resemble it.", "rationale": "Recognition comes before every other claim. Without stable identity nothing else in the model can be trusted to be about the same thing twice.", "layers": [ { "id": "naming-and-identifiers", "name": "Names and identifiers", "description": "The names this thing goes by and the identifiers that survive translation and time.", "findings": [ { "id": "preferred-name-and-aliases", "name": "Preferred name, aliases and local names", "description": "Which name to use, which names mean the same thing, and which merely sound similar.", "questions": [ { "id": "preferred-name-and-aliases-q01", "text": "What identifies and describes the name of a biopsy, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "preferred-name-and-aliases-q02", "text": "Who or what asserted this about the name of a biopsy, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "preferred-name-and-aliases-q03", "text": "What may an agent decide or do once the name of a biopsy is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "stable-identifiers", "name": "Stable identifiers and external keys", "description": "Identifiers that keep pointing at this kind of thing across systems and languages.", "questions": [ { "id": "stable-identifiers-q01", "text": "What identifies and describes an identifier for a biopsy, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stable-identifiers-q02", "text": "Who or what asserted this about an identifier for a biopsy, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stable-identifiers-q03", "text": "What may an agent decide or do once an identifier for a biopsy is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "classification-and-granularity", "name": "Classification and granularity", "description": "Where a biopsy sits among kinds, and how finely a task needs to cut it.", "findings": [ { "id": "kind-and-parents", "name": "Kind, parents and neighbouring kinds", "description": "The classes this thing belongs to and the ones it is next to.", "questions": [ { "id": "kind-and-parents-q01", "text": "What identifies and describes the kind of a biopsy, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "kind-and-parents-q02", "text": "Who or what asserted this about the kind of a biopsy, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "kind-and-parents-q03", "text": "What may an agent decide or do once the kind of a biopsy is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "distinguishing-features", "name": "Distinguishing features", "description": "What separates a biopsy from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a biopsy, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "distinguishing-features-q02", "text": "Who or what asserted this about what distinguishes a biopsy, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "distinguishing-features-q03", "text": "What may an agent decide or do once what distinguishes a biopsy is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "state-and-lifecycle", "name": "State and lifecycle", "description": "The states a biopsy passes through and the events that move it between them.", "rationale": "Most decisions about a thing depend on what state it is in now, which is a claim with a time on it, not a property.", "layers": [ { "id": "lifecycle-stages", "name": "Lifecycle stages", "description": "From coming into existence to ceasing to be one of these.", "findings": [ { "id": "stages-and-transitions", "name": "Stages and transitions", "description": "The stages worth naming and what moves a biopsy between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a biopsy, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stages-and-transitions-q02", "text": "Who or what asserted this about the lifecycle of a biopsy, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stages-and-transitions-q03", "text": "What may an agent decide or do once the lifecycle of a biopsy is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "observations-and-status", "name": "Observations and current status", "description": "What is observed about a biopsy, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a biopsy is recorded so that it can be superseded rather than overwritten.", "questions": [ { "id": "observation-record-q01", "text": "What identifies and describes an observation of a biopsy, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "observation-record-q02", "text": "Who or what asserted this about an observation of a biopsy, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "observation-record-q03", "text": "What may an agent decide or do once an observation of a biopsy is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "process-and-outcome", "name": "Process, inputs and outcome", "description": "How a biopsy proceeds, what it needs and what it leaves behind.", "rationale": "An activity is known by its steps and its results, and both have to be recordable while it is still running.", "layers": [ { "id": "steps-and-sequence", "name": "Steps and sequence", "description": "The steps of a biopsy, their order and what may run in parallel.", "findings": [ { "id": "steps-and-preconditions", "name": "Steps, preconditions and completion", "description": "What has to be true before each step of a biopsy and what marks it done.", "questions": [ { "id": "steps-and-preconditions-q01", "text": "What identifies and describes a step of a biopsy, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "steps-and-preconditions-q02", "text": "Who or what asserted this about a step of a biopsy, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "steps-and-preconditions-q03", "text": "What may an agent decide or do once a step of a biopsy is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "inputs-and-results", "name": "Inputs, resources and results", "description": "What a biopsy consumes and what it produces.", "findings": [ { "id": "inputs-and-outputs", "name": "Inputs, outputs and side effects", "description": "The resources a biopsy takes and the results it leaves, wanted or not.", "questions": [ { "id": "inputs-and-outputs-q01", "text": "What identifies and describes the inputs and results of a biopsy, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "inputs-and-outputs-q02", "text": "Who or what asserted this about the inputs and results of a biopsy, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "inputs-and-outputs-q03", "text": "What may an agent decide or do once the inputs and results of a biopsy is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "definitions-in-contest", "name": "Definitions and who holds them", "description": "What biopsy is taken to mean, and by whom.", "rationale": "When a field disagrees about a concept, the disagreement is the content. A model that picks one definition silently destroys the information.", "layers": [ { "id": "competing-definitions", "name": "Competing definitions", "description": "The main readings and the traditions behind them.", "findings": [ { "id": "definition-map", "name": "Definitions and their holders", "description": "Each definition with the school or body that holds it.", "questions": [ { "id": "definition-map-q01", "text": "Which definitions of biopsy are in use, and which tradition or body holds each?", "kind": "definition" }, { "id": "definition-map-q02", "text": "What turns on the difference between them in practice?", "kind": "boundary" } ] } ] }, { "id": "operationalisation", "name": "Operationalisation", "description": "How it is measured or applied when it has to be.", "findings": [ { "id": "operational-record", "name": "Measures and proxies", "description": "Instruments and indicators used to stand in for it.", "questions": [ { "id": "operational-record-q01", "text": "How is biopsy operationalised or measured in practice, and by what instrument?", "kind": "measurement" }, { "id": "operational-record-q02", "text": "What does that operationalisation leave out, and when does that matter?", "kind": "boundary" } ] } ] } ] }, { "id": "instances-and-use", "name": "Instances, use and consequence", "description": "What counts as an instance of biopsy and what follows from calling something that.", "rationale": "Applying a concept is an act with consequences, so a model must say what the label licenses and what it does not.", "layers": [ { "id": "instances", "name": "What counts as an instance", "description": "Clear cases, borderline cases and non-cases.", "findings": [ { "id": "instance-tests", "name": "Tests for an instance", "description": "What would settle whether something falls under it.", "questions": [ { "id": "instance-tests-q01", "text": "What would settle whether something is an instance of biopsy?", "kind": "boundary" }, { "id": "instance-tests-q02", "text": "Which borderline cases are argued about, and on what grounds?", "kind": "definition" } ] } ] }, { "id": "consequence", "name": "Consequence of application", "description": "Rights, duties or decisions that follow from the label.", "findings": [ { "id": "consequence-record", "name": "What the label licenses", "description": "What an agent may do once something is classified this way.", "questions": [ { "id": "consequence-record-q01", "text": "What follows practically once something is treated as biopsy?", "kind": "action" }, { "id": "consequence-record-q02", "text": "What must an agent not infer from the label alone?", "kind": "action" } ] } ] } ] }, { "id": "provenance-and-evidence", "name": "Provenance, evidence and time", "description": "Where every claim about a biopsy came from and when it held.", "rationale": "A claim without a source and a time cannot be superseded, only overwritten, and an agent that overwrites loses the ability to explain itself.", "layers": [ { "id": "source-and-authority", "name": "Source and authority", "description": "Who said it, on what evidence, and how strongly.", "findings": [ { "id": "claim-provenance", "name": "Claim provenance and confidence", "description": "The authority behind each claim about a biopsy and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a biopsy, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "claim-provenance-q02", "text": "Who or what asserted this about a claim about a biopsy, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "claim-provenance-q03", "text": "What may an agent decide or do once a claim about a biopsy is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "time-and-versions", "name": "Time, versions and supersession", "description": "When a claim was true, when it was learnt, and what replaced it.", "findings": [ { "id": "validity-and-supersession", "name": "Validity period and supersession", "description": "How an old claim about a biopsy is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a biopsy, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "validity-and-supersession-q02", "text": "Who or what asserted this about the validity of a claim about a biopsy, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "validity-and-supersession-q03", "text": "What may an agent decide or do once the validity of a claim about a biopsy is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 6, "layers": 12, "findings": 14, "questions": 38 } } } }