{ "model": { "rank": 14223, "code": "thing-q422476", "model_id": "vr.tr.phosphatase", "name": "phosphatase", "purpose": "Let an agent explain phosphatases and their classes, relay mechanisms, roles in signalling and metabolism and clinical uses from biochemistry sources, describe the families the registry aliases name, and distinguish phosphatases from kinases, from phosphodiesterases and from phosphorylases.", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.MAT", "industry": "", "version": "", "url": "/models/thing/q422476/", "tier": 2, "score": 36, "payload": { "layer": "wikidata", "aliases": [ "protein phosphatase", "Trehalose 6-phosphate OTSB-like", "MAPK phosphatase", "Inositol polyphosphate-related phosphatase family", "Phospholipid phosphatase", "Protein phosphatase Slingshot-like", "Phosphoserine phosphatase family", "Protein-tyrosine-phosphatase IBR5-like", "Phosphatidylglycerophosphatase and protein-tyrosine phosphatase 1-like", "Inositol polyphosphate 5-phosphatase, plant", "RNA polymerase II subunit A", "Phosphatidate phosphatase LPIN1", "Tyrosine/serine-protein phosphatase IphP-type", "Tyrosine-protein phosphatase non-receptor type 13", "Receptor tyrosine-protein phosphatase, alpha/epsilon-type", "Phosphatase IpgD/SopB", "Phosphoprotein phosphatase PPZ/Ppq1", "Serine/threonine protein phosphatase, BSU1", "HAD-superfamily phosphatase, YqeG-like", "Arsenate reductase ArsC", "Phosphate regulon sensor protein PhoR", "Purple acid phosphatase", "Acid phosphatase, AcpA", "M-phase inducer phosphatase", "Bifunctional phosphatidylinositol trisphosphate phosphatase/dual specificity phosphatase PTEN", "Protein-tyrosine phosphatase, non-receptor type-6, -11", "Protein-tyrosine phosphatase, KIM-containing", "Fructose-1,6-bisphosphatase class 1", "Protein-tyrosine phosphatase, low molecular weight", "Tyrosine-protein phosphatase 1", "Tyrosine-protein phosphatase CDC14", "Fructose-1,6-bisphosphatase class 2/Sedoheputulose-1,7-bisphosphatase", "ComB-like", "Protein-tyrosine phosphatase, non-receptor type-1/2", "Fructose-1,6-bisphosphatase class 3", "Protein-tyrosine phosphatase, non-receptor type-14, -21", "Type III secreted modular tyrosine phosphatase, SptP/YopH", "Receptor-type tyrosine-protein phosphatase C", "serine/threonine-protein phosphatase with EF-hands", "Sporulation stage II, protein E" ], "aliasCount": 231, "merged": 234, "knownIn": 36, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q422476", "url": "https://www.wikidata.org/wiki/Q422476", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-13T15:04:03Z", "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": 4, "engine": "claude" }, "metaModel": { "id": "THING-Q422476", "registryId": "vr.tr.phosphatase", "name": "phosphatase", "version": "0.2.0-wave.4", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q422476/", "model": { "registry_id": "vr.tr.phosphatase", "name": "phosphatase", "purpose": "Let an agent explain phosphatases and their classes, relay mechanisms, roles in signalling and metabolism and clinical uses from biochemistry sources, describe the families the registry aliases name, and distinguish phosphatases from kinases, from phosphodiesterases and from phosphorylases.", "definition": "An enzyme that removes a phosphate group from its substrate by hydrolysing a phosphoric ester bond, including protein phosphatases that reverse the action of kinases in cell signalling, such as MAPK phosphatases and Slingshot phosphatases, phospholipid phosphatases, inositol polyphosphate phosphatases, trehalose 6-phosphate phosphatases in microbial and plant metabolism, and alkaline and acid phosphatases used as clinical markers; phosphatases are central to regulation and metabolism.", "what_it_is_for": "Not applicable; an enzyme class.", "affordances": [ "explain the enzyme class", "relay mechanisms and roles", "describe families", "distinguish related enzymes" ], "distinguishing_features": [ "Dephosphorylation", "Counterpart of kinases", "Many families", "Clinical markers" ], "appearance": "Not a visible object; a protein.", "visual_identification": [ "Enzyme removing phosphate groups", "Protein phosphatase, MAPK phosphatase, Slingshot-like phosphatase, phospholipid phosphatase, inositol polyphosphate phosphatase, trehalose 6-phosphate phosphatase", "Kinases add phosphate; phosphodiesterases cleave diesters; phosphorylases add phosphate to substrates" ], "physical_properties": [ { "quantity": "EC class", "typical_range": "EC 3.1.3", "unit": "note", "note": "phosphoric monoester hydrolases" }, { "quantity": "human protein phosphatases", "typical_range": "about 200", "unit": "count", "note": "" }, { "quantity": "alkaline phosphatase", "typical_range": "clinical liver and bone marker", "unit": "note", "note": "" } ], "families_and_kinds": [ "serine/threonine protein phosphatases", "tyrosine phosphatases", "dual-specificity phosphatases such as MAPK phosphatases", "Slingshot phosphatases", "lipid phosphatases such as phospholipid and inositol polyphosphate phosphatases", "metabolic phosphatases such as trehalose 6-phosphate phosphatase", "alkaline and acid phosphatases" ], "related_models": [ { "relation": "is a kind of", "target": "phosphoric ester hydrolase", "why": "in registry terms" }, { "relation": "is a kind of", "target": "esterase", "why": "in registry terms" }, { "relation": "is contrasted with", "target": "kinase", "why": "which adds phosphate" }, { "relation": "is exemplified by", "target": "alkaline phosphatase", "why": "a clinical marker" } ], "identifiers": [ { "scheme": "EC", "value_or_pattern": "3.1.3", "note": "phosphoric monoester hydrolases" }, { "scheme": "MeSH", "value_or_pattern": "D010744", "note": "Phosphoric Monoester Hydrolases" } ], "standards_and_regulation": [ "IUBMB enzyme nomenclature" ], "failure_modes_and_hazards": [ "Confusing phosphatases with kinases or phosphorylases", "Registry aliases mixing families at different levels", "Overinterpreting clinical marker values" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What a phosphatase is.", "rationale": "Science.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What is a phosphatase, and how does it differ from a kinase, phosphodiesterase and phosphorylase?", "kind": "definition" }, { "text": "Is the question about the class, a family, signalling, metabolism or a clinical test?", "kind": "boundary" } ] } ] }, { "id": "families", "name": "Families", "description": "Families.", "findings": [ { "id": "families-finding", "name": "Families", "description": "Families.", "questions": [ { "text": "What are protein, MAPK, Slingshot, phospholipid, inositol polyphosphate and trehalose 6-phosphate phosphatases?", "kind": "definition" }, { "text": "Which entry fits the specific family?", "kind": "action" } ] } ] } ] }, { "id": "biochemistry", "name": "Biochemistry", "description": "Mechanism and roles.", "rationale": "Science.", "layers": [ { "id": "mechanism", "name": "Mechanism", "description": "Mechanism.", "findings": [ { "id": "mechanism-finding", "name": "Mechanism", "description": "Mechanism.", "questions": [ { "text": "How do phosphatases catalyse dephosphorylation, and how are they classified?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "signalling", "name": "Signalling", "description": "Signalling.", "findings": [ { "id": "signalling-finding", "name": "Signalling", "description": "Signalling.", "questions": [ { "text": "How do phosphatases regulate kinase cascades and cell processes?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] } ] }, { "id": "medicine", "name": "Medicine", "description": "Medicine and metabolism.", "rationale": "Application.", "layers": [ { "id": "clinical", "name": "Clinical", "description": "Clinical.", "findings": [ { "id": "clinical-finding", "name": "Clinical", "description": "Clinical.", "questions": [ { "text": "How are alkaline and acid phosphatase used as clinical markers, and what diseases involve phosphatases?", "kind": "provenance" }, { "text": "Which entry fits alkaline phosphatase?", "kind": "action" } ] } ] }, { "id": "metabolism", "name": "Metabolism", "description": "Metabolism.", "findings": [ { "id": "metabolism-finding", "name": "Metabolism", "description": "Metabolism.", "questions": [ { "text": "What roles do phosphatases play in metabolism, such as trehalose synthesis?", "kind": "provenance" }, { "text": "Which entry fits trehalose?", "kind": "action" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "Drugs and history.", "rationale": "Context.", "layers": [ { "id": "drugs", "name": "Drugs", "description": "Drug targets.", "findings": [ { "id": "drugs-finding", "name": "Drugs", "description": "Drugs.", "questions": [ { "text": "How are phosphatases targeted by drugs and toxins such as okadaic acid?", "kind": "provenance" }, { "text": "Which entry fits enzyme inhibitor?", "kind": "action" } ] } ] }, { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How were phosphatases discovered and characterised?", "kind": "provenance" }, { "text": "Which entry fits the history of biochemistry?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should protein phosphatase and alkaline phosphatase be separate primary entries?", "How should biochemistry sources be linked?", "The registry entry has merged aliases naming families at different levels; 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": "chemical substance or material", "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 phosphatase, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain phosphatases and their classes, relay mechanisms, roles in signalling and metabolism and clinical uses from biochemistry sources, describe the families the registry aliases name, and distinguish phosphatases from kinases, from phosphodiesterases and from phosphorylases.", "characteristics": { "substance": "material", "origin": "natural", "agency": "inert", "mobility": "varies" }, "whatYouCanDoWithIt": [ "observed and measured", "consumed or used up" ], "distinguishingFeatures": [ "Names folded into this entry, which a task may need to split apart again: protein phosphatase, Trehalose 6-phosphate OTSB-like, MAPK phosphatase, Inositol polyphosphate-related phosphatase family, Phospholipid phosphatase, Protein phosphatase Slingshot-like, Phosphoserine phosphatase family, Protein-tyrosine-phosphatase IBR5-like, Phosphatidylglycerophosphatase and protein-tyrosine phosphatase 1-like, Inositol polyphosphate 5-phosphatase, plant, RNA polymerase II subunit A, Phosphatidate phosphatase LPIN1.", "234 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 36 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 phosphatase, and on what evidence are they told apart?" ], "whatItIsMadeOf": "matter you can touch", "physicalCharacter": [ "Mobility varies between examples.", "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", "use it up, and then need more of it" ], "howItIsRecognised": [ "Not recognisable by sight in any reliable way. Appearance varies with grade, form and additives; identification is by label, by documentation, or by assay." ], "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": [ "protein phosphatase", "Trehalose 6-phosphate OTSB-like", "MAPK phosphatase", "Inositol polyphosphate-related phosphatase family", "Phospholipid phosphatase", "Protein phosphatase Slingshot-like", "Phosphoserine phosphatase family", "Protein-tyrosine-phosphatase IBR5-like", "Phosphatidylglycerophosphatase and protein-tyrosine phosphatase 1-like", "Inositol polyphosphate 5-phosphatase, plant", "RNA polymerase II subunit A", "Phosphatidate phosphatase LPIN1" ] } ], "standing": "Described in 36 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 234 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 phosphatase from another, and a phosphatase 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 phosphatase, 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 phosphatase, 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 phosphatase 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 phosphatase, 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 phosphatase, 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 phosphatase 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 phosphatase 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 phosphatase, 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 phosphatase, 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 phosphatase 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 phosphatase from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a phosphatase, 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 phosphatase, 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 phosphatase is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "form-and-composition", "name": "Form, composition and condition", "description": "What a phosphatase is made of, what shape and size it takes, and what state it is in.", "rationale": "A physical thing can be measured, and a model that cannot record its measurements cannot support any decision that depends on them.", "layers": [ { "id": "form-and-dimensions", "name": "Form and dimensions", "description": "Shape, size, mass and the ranges these take across examples.", "findings": [ { "id": "measurable-dimensions", "name": "Measurable dimensions and their units", "description": "The quantities worth recording and the units they are recorded in.", "questions": [ { "id": "measurable-dimensions-q01", "text": "What identifies and describes the dimensions of a phosphatase, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "measurable-dimensions-q02", "text": "Who or what asserted this about the dimensions of a phosphatase, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "measurable-dimensions-q03", "text": "What may an agent decide or do once the dimensions of a phosphatase is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "material-and-composition", "name": "Material and composition", "description": "Materials, parts and how they are put together.", "findings": [ { "id": "parts-and-materials", "name": "Parts and materials", "description": "What a phosphatase is built from and which parts are replaceable.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a phosphatase, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "parts-and-materials-q02", "text": "Who or what asserted this about the composition of a phosphatase, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "parts-and-materials-q03", "text": "What may an agent decide or do once the composition of a phosphatase is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "condition-and-integrity", "name": "Condition and integrity", "description": "Wear, damage, health and the difference between working and broken.", "findings": [ { "id": "condition-assessment", "name": "Condition, damage and health", "description": "How the condition of a phosphatase is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a phosphatase, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "condition-assessment-q02", "text": "Who or what asserted this about the condition of a phosphatase, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "condition-assessment-q03", "text": "What may an agent decide or do once the condition of a phosphatase is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "place-and-movement", "name": "Place and movement", "description": "Where a phosphatase is, how it got there and where it may go (varies).", "rationale": "A thing that can move needs its position recorded with a time, or every later claim about it is about a place it has left.", "layers": [ { "id": "location-and-placement", "name": "Location and placement", "description": "Position, containment and the reference frame the position is given in.", "findings": [ { "id": "position-and-frame", "name": "Position, container and reference frame", "description": "Where a phosphatase is, and what that position is measured against.", "questions": [ { "id": "position-and-frame-q01", "text": "What identifies and describes the location of a phosphatase, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "position-and-frame-q02", "text": "Who or what asserted this about the location of a phosphatase, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "position-and-frame-q03", "text": "What may an agent decide or do once the location of a phosphatase is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "movement-and-transfer", "name": "Movement and transfer", "description": "How a phosphatase is carried, installed or relocated.", "findings": [ { "id": "movement-events", "name": "Movement events and constraints", "description": "What counts as a movement, what records it and what limits it.", "questions": [ { "id": "movement-events-q01", "text": "What identifies and describes the movement of a phosphatase, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "movement-events-q02", "text": "Who or what asserted this about the movement of a phosphatase, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "movement-events-q03", "text": "What may an agent decide or do once the movement of a phosphatase 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 phosphatase 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 phosphatase between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a phosphatase, 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 phosphatase, 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 phosphatase 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 phosphatase, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a phosphatase 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 phosphatase, 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 phosphatase, 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 phosphatase is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "use-and-operation", "name": "Use and operation", "description": "What can be done with a phosphatase and what it takes to do it.", "rationale": "An agent that can recognise a thing but not act on it has only half a model.", "layers": [ { "id": "intended-use", "name": "Intended use and function", "description": "What a phosphatase is for, and what it is used for anyway.", "findings": [ { "id": "function-and-purpose", "name": "Function, purpose and misuse", "description": "The function a phosphatase performs and the uses that fall outside it.", "questions": [ { "id": "function-and-purpose-q01", "text": "What identifies and describes the use of a phosphatase, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "function-and-purpose-q02", "text": "Who or what asserted this about the use of a phosphatase, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "function-and-purpose-q03", "text": "What may an agent decide or do once the use of a phosphatase is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "handling-and-procedure", "name": "Handling and procedure", "description": "The steps, skills and tools involved in using a phosphatase.", "findings": [ { "id": "procedures-and-skills", "name": "Procedures, skills and required tools", "description": "What an agent needs before it can act on a phosphatase at all.", "questions": [ { "id": "procedures-and-skills-q01", "text": "What identifies and describes handling a phosphatase, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "procedures-and-skills-q02", "text": "Who or what asserted this about handling a phosphatase, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "procedures-and-skills-q03", "text": "What may an agent decide or do once handling a phosphatase is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "supply-and-consumption", "name": "Supply and consumption", "description": "Quantities, rates and what running out means.", "findings": [ { "id": "consumption-and-stock", "name": "Consumption, stock and replenishment", "description": "How much of a phosphatase there is and how fast it goes.", "questions": [ { "id": "consumption-and-stock-q01", "text": "What identifies and describes the supply of a phosphatase, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "consumption-and-stock-q02", "text": "Who or what asserted this about the supply of a phosphatase, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "consumption-and-stock-q03", "text": "What may an agent decide or do once the supply of a phosphatase is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "composition-and-identity", "name": "Composition, grade and chemical identity", "description": "What phosphatase is made of and how pure the thing in hand is.", "rationale": "Grade decides what a substance may be used for, so a model that records only the name cannot support any decision about use.", "layers": [ { "id": "chemical-identity", "name": "Chemical identity", "description": "Formula, structure and the registry numbers that name it unambiguously.", "findings": [ { "id": "identity-record", "name": "Identity and registry numbers", "description": "What identifies this substance across suppliers and regulators.", "questions": [ { "id": "identity-record-q01", "text": "What formula, structure and registry identifiers name phosphatase unambiguously?", "kind": "definition" }, { "id": "identity-record-q02", "text": "Which related substances share a name in common use but not an identifier?", "kind": "boundary" } ] } ] }, { "id": "grade-and-impurities", "name": "Grade, purity and impurities", "description": "The specification a batch meets and what else is in it.", "findings": [ { "id": "specification", "name": "Specification and assay", "description": "How purity is stated and measured, and which impurities matter.", "questions": [ { "id": "specification-q01", "text": "What grades of phosphatase exist, how is purity assayed, and which impurities are limited?", "kind": "measurement" }, { "id": "specification-q02", "text": "Which use requires which grade, and what happens when a lower grade is substituted?", "kind": "action" } ] } ] } ] }, { "id": "properties-and-behaviour", "name": "Properties and behaviour", "description": "How phosphatase behaves under conditions an agent can measure or change.", "rationale": "Physical constants are the part of a substance model that transfers between contexts, and each needs its unit and its conditions.", "layers": [ { "id": "physical-constants", "name": "Physical constants", "description": "Values that hold for the pure substance, with their conditions.", "findings": [ { "id": "constants-record", "name": "Constants and conditions", "description": "The quantities worth recording and the state they apply in.", "questions": [ { "id": "constants-record-q01", "text": "What are the defining physical constants of phosphatase, in what units and under what conditions?", "kind": "measurement" }, { "id": "constants-record-q02", "text": "Which of these values change with grade or form rather than being fixed?", "kind": "boundary" } ] } ] }, { "id": "stability-and-reactivity", "name": "Stability and reactivity", "description": "What it reacts with, degrades into, and how it is stored.", "findings": [ { "id": "incompatibilities", "name": "Incompatibilities and degradation", "description": "What must not meet it, and what it becomes over time.", "questions": [ { "id": "incompatibilities-q01", "text": "What is phosphatase incompatible with, and what does it degrade into under storage?", "kind": "definition" }, { "id": "incompatibilities-q02", "text": "What storage and handling does that require, and who is competent to do it?", "kind": "action" } ] } ] } ] }, { "id": "hazard-and-regulation", "name": "Hazard classification and regulation", "description": "How phosphatase can harm, and what the law says about holding and moving it.", "rationale": "A substance model without its hazard class and its regulatory identity is unusable in exactly the situations that matter.", "layers": [ { "id": "hazard-class", "name": "Hazard classification", "description": "Classified hazards, exposure limits and protective measures.", "findings": [ { "id": "classified-hazards", "name": "Classified hazards and limits", "description": "The classification, the scheme it belongs to, and the limits set.", "questions": [ { "id": "classified-hazards-q01", "text": "How is phosphatase classified for hazard, under which scheme, and what exposure limits apply?", "kind": "definition" }, { "id": "classified-hazards-q02", "text": "What protection does handling require, and what must an agent refuse to do without it?", "kind": "action" } ] } ] }, { "id": "regulatory-identity", "name": "Regulatory identity and control", "description": "Registration, restriction and transport rules by jurisdiction.", "findings": [ { "id": "controls", "name": "Controls and jurisdiction", "description": "Where it is restricted and what the restriction attaches to.", "questions": [ { "id": "controls-q01", "text": "Which registrations, restrictions or transport rules cover phosphatase, and where?", "kind": "provenance" }, { "id": "controls-q02", "text": "Does the control attach to the substance, its concentration, or its intended use?", "kind": "boundary" } ] } ] } ] }, { "id": "provenance-and-evidence", "name": "Provenance, evidence and time", "description": "Where every claim about a phosphatase 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 phosphatase and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a phosphatase, 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 phosphatase, 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 phosphatase 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 phosphatase is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a phosphatase, 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 phosphatase, 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 phosphatase is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 9, "layers": 20, "findings": 22, "questions": 60 } } } }