{ "model": { "rank": 6147, "code": "thing-q48360", "model_id": "vr.tr.hippocampus", "name": "hippocampus", "purpose": "Enable an agent to recognise a hippocampal anatomical instance, assess its observed structural and functional state, and determine which observations or interventions are justified.", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.LIV", "industry": "", "version": "", "url": "/models/thing/q48360/", "tier": 2, "score": 62, "payload": { "layer": "wikidata", "aliases": [ "mouse hippocampus", "developing hippocampus", "rat hippocampus" ], "aliasCount": 3, "merged": 3, "knownIn": 62, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": "vr.tr.hippocampus", "source": { "dataset": "wikidata", "item": "Q48360", "url": "https://www.wikidata.org/wiki/Q48360", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-07T11:49:13Z", "providers": [ "Codex", "Grok" ], "missingProviders": [], "pass": 2, "cost": { "grok": { "usd": 0.0088077, "turns": 1, "seconds": 146, "error": null }, "codex": { "seconds": 89.5, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.3\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: 01a07baf-5f03-75b1-a773-08b47be80242\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: hippocampus\nRegistry id: vr.tr.hippocampus\nPlane / domain: PHY / PHY.LIV\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\nA" } } }, "metaModel": { "id": "THING-Q48360", "registryId": "vr.tr.hippocampus", "name": "hippocampus", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.LIV" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q48360/", "model": { "registry_id": "vr.tr.hippocampus", "name": "hippocampus", "purpose": "Enable an agent to recognise a hippocampal anatomical instance, assess its observed structural and functional state, and determine which observations or interventions are justified.", "definition": "A paired three-layered allocortical formation of the medial temporal lobe, comprising the dentate gyrus and hippocampus proper (cornu ammonis fields CA1-CA3, often with the hilar CA4), that is necessary for encoding episodic memory and for spatial mapping and that interfaces with neocortex chiefly through the entorhinal cortex and the fimbria-fornix.", "scope_statement": "This draft interprets vr.tr.hippocampus as the brain structure, provisionally in mammals; it owns instance identity, anatomical extent, local organisation, condition and action constraints, with explicit conventions for whether dentate gyrus and subiculum are included.", "in_scope": [ "Host organism, hemisphere and anatomical or specimen identity", "Hippocampal boundaries, longitudinal regions and subfield assignments", "Local tissue organisation and connections to neighbouring structures", "Structural condition and locally measured physiological activity", "Evidence supporting comparisons, interpretations and permitted actions" ], "out_of_scope": [ "The seahorse genus Hippocampus and its member organisms", "Whole-brain anatomy and global neurological state", "Independent models of the amygdala, entorhinal cortex and connecting white-matter tracts", "Whole-person memory ability, behaviour and psychiatric assessment", "Disease definitions, diagnostic criteria and treatment protocols" ], "distinguishing_features": [ "Establish that the referent is a brain structure within an identified organism, rather than a seahorse or a computational component named after the hippocampus.", "For a human instance, verify its medial temporal location and relationship to the temporal horn using anatomical landmarks; proximity to the amygdala alone is insufficient. Anatomical reference: [The Anatomy of the Hippocampus](https://www.ncbi.nlm.nih.gov/books/NBK575732/).", "Use an explicitly named anatomical convention to distinguish hippocampus proper from the broader hippocampal formation; separately state inclusion of dentate gyrus and subiculum. Terminology reference: [Neuroanatomy, Hippocampus](https://www.ncbi.nlm.nih.gov/books/NBK482171/).", "Where tissue resolution permits, test the proposed identity against field organisation and neuronal layering rather than accepting any curved temporal-lobe region as hippocampus. Anatomical reference: [The Anatomy of the Hippocampus](https://www.ncbi.nlm.nih.gov/books/NBK575732/)." ], "characteristics": [ { "name": "Host and biological context", "kind": "relation", "unit_or_values": "Organism identifier, species, developmental stage and age with unit", "why_it_matters": "Determines which anatomical references and comparison populations are applicable." }, { "name": "Hemisphere and instance extent", "kind": "category", "unit_or_values": "Left, right or unresolved; whole structure, partial structure or tissue sample", "why_it_matters": "Prevents bilateral measurements and partial specimens from being mistaken for one complete hippocampus." }, { "name": "Boundary convention", "kind": "category", "unit_or_values": "Named atlas or protocol with explicit included and excluded regions", "why_it_matters": "Makes hippocampal identity and measurements interpretable across differing definitions." }, { "name": "Longitudinal position", "kind": "category", "unit_or_values": "Species-appropriate regional label and coordinate system", "why_it_matters": "Local observations must retain their position rather than being generalised to the entire structure." }, { "name": "Subfield assignment", "kind": "category", "unit_or_values": "Protocol-defined field label, combined region or unresolved", "why_it_matters": "Records regional specificity without claiming distinctions beyond the evidence resolution." }, { "name": "Volume", "kind": "measurement", "unit_or_values": "mm³ with acquisition date, segmentation method and uncertainty", "why_it_matters": "Supports structural comparison when anatomical extent and measurement methods agree." }, { "name": "Tissue condition", "kind": "state", "unit_or_values": "Observed morphology and signal or histological abnormalities, with location and confidence", "why_it_matters": "Separates direct observations from proposed causes or diagnoses." }, { "name": "Local physiological activity", "kind": "measurement", "unit_or_values": "Modality-specific values such as Hz, µV or percentage signal change, with task and recording context", "why_it_matters": "Allows activity to be interpreted in relation to sampling location and measurement method." }, { "name": "Connection evidence", "kind": "relation", "unit_or_values": "Connected region, pathway, supported direction and evidence method", "why_it_matters": "Distinguishes observed connectivity from atlas expectations or functional correlations." }, { "name": "Preparation and viability", "kind": "state", "unit_or_values": "In vivo, freshly excised, viable preparation, fixed tissue or unresolved", "why_it_matters": "Determines which measurements and manipulations remain meaningful." } ], "affordances": [ "Locate and delineate a hippocampal instance using a species-appropriate anatomical reference.", "Measure whole-region or supported subfield morphology and compare compatible observations.", "Associate local recordings with anatomical position, behavioural context and acquisition conditions.", "Track regional tissue changes while preserving uncertainty about their causes.", "Evaluate a proposed recording, stimulation, sampling or resection against target evidence and explicit authorization." ] }, "sources": [ { "id": "hippocampus-book-2007", "title": "The Hippocampus Book", "url": "", "what_it_supports": "Specialist definition of the hippocampal formation, CA fields and dentate gyrus, connectivity (entorhinal and fornix), and the memory and spatial-mapping functions used in the definition and neighbour tests." }, { "id": "duvernoy-human-hippocampus", "title": "The Human Hippocampus: Functional Anatomy, Vascularization and Serial Sections with MRI", "url": "", "what_it_supports": "Gross and MRI anatomy of the human hippocampus (head, body, tail; relation to the temporal horn, amygdala, and parahippocampal gyrus) used for measurements, neighbours, and real-world imaging use." }, { "id": "ilae-hs-2013", "title": "International consensus classification of hippocampal sclerosis in temporal lobe epilepsy: a Task Force report from the ILAE Commission on Diagnostic Methods", "url": "https://pubmed.ncbi.nlm.nih.gov/23674853/", "what_it_supports": "ILAE hippocampal-sclerosis types as a kind people actually distinguish, and the neuropathological failure mode in mesial temporal lobe epilepsy.", "url_status": "live" }, { "id": "ta-fipat", "title": "Terminologia Anatomica (TA98 and successive FIPAT releases)", "url": "", "what_it_supports": "Official anatomical name Hippocampus, Latin/English term status, and the TA identifier scheme." }, { "id": "wikidata-q19118", "title": "Wikidata item Q19118 (hippocampus, anatomical structure)", "url": "https://www.wikidata.org/wiki/Q19118", "what_it_supports": "Stable public identifier and crosswalks toward FMA, MeSH, UBERON and related anatomy ontologies.", "url_status": "live" }, { "id": "harp-eadc-adni", "title": "EADC-ADNI Harmonized Protocol for manual hippocampal segmentation on MRI (HarP)", "url": "", "what_it_supports": "How hippocampal volume is operationally measured in memory-clinic and Alzheimer research MRI, including landmark rules that separate hippocampus from amygdala and parahippocampal cortex." } ], "structure": { "bundles": [ { "id": "hippocampal-identity-and-extent", "name": "Hippocampal identity and extent", "description": "Establish which anatomical instance the name denotes and where its boundaries lie.", "rationale": "A hippocampal claim is uninterpretable without species, hemisphere and an explicit inclusion convention.", "layers": [ { "id": "host-and-instance", "name": "Host and instance", "description": "Anchor the structure to an organism and distinguish whole structures from samples.", "findings": [ { "id": "anatomical-instance", "name": "Anatomical instance", "description": "Require evidence linking the referent to a particular host, side and extent.", "questions": [ { "text": "Which organism, species and hemisphere does this hippocampal instance belong to?", "kind": "definition", "id": "anatomical-instance-q01" }, { "text": "What imaging, dissection or specimen record establishes that identity and whether the instance is complete?", "kind": "provenance", "id": "anatomical-instance-q02" } ] } ] }, { "id": "inclusion-convention", "name": "Inclusion convention", "description": "Make the meaning of hippocampus explicit at its interfaces with neighbouring regions.", "findings": [ { "id": "hippocampal-boundary", "name": "Hippocampal boundary", "description": "Record the adopted definition and the evidence used to apply it.", "questions": [ { "text": "Does this instance include hippocampus proper alone, or also dentate gyrus and subiculum?", "kind": "boundary", "id": "hippocampal-boundary-q01" }, { "text": "Which atlas, landmarks and protocol version delimit it from amygdala, entorhinal cortex and adjacent tissue?", "kind": "provenance", "id": "hippocampal-boundary-q02" } ] } ] } ] }, { "id": "regional-and-cellular-organisation", "name": "Regional and cellular organisation", "description": "Represent the internal anatomical distinctions supported by the observation.", "rationale": "Whole-hippocampus labels can conceal regional differences and falsely imply subfield precision.", "layers": [ { "id": "longitudinal-and-subfield-location", "name": "Longitudinal and subfield location", "description": "Place observations along the structure and within the chosen parcellation.", "findings": [ { "id": "regional-assignment", "name": "Regional assignment", "description": "Require region labels to retain their coordinate system and assignment uncertainty.", "questions": [ { "text": "Where along the hippocampal longitudinal axis was this observation obtained?", "kind": "measurement", "id": "regional-assignment-q01" }, { "text": "Which subfield distinctions can the acquisition resolve, and which must remain combined or unresolved?", "kind": "boundary", "id": "regional-assignment-q02" } ] } ] }, { "id": "tissue-architecture", "name": "Tissue architecture", "description": "Capture cellular and laminar evidence when the specimen and modality support it.", "findings": [ { "id": "laminar-and-cellular-observation", "name": "Laminar and cellular observation", "description": "Separate directly observed tissue organisation from labels inferred through an atlas.", "questions": [ { "text": "Which neuronal layers, cell populations or architectural features are directly identifiable in this hippocampal sample?", "kind": "measurement", "id": "laminar-and-cellular-observation-q01" }, { "text": "Which stain, marker, imaging method and sampling location support each identification?", "kind": "provenance", "id": "laminar-and-cellular-observation-q02" } ] } ] } ] }, { "id": "hippocampal-circuit-and-activity", "name": "Hippocampal circuit and activity", "description": "Relate local observations to internal circuitry, external connections and recording context.", "rationale": "Activity or connectivity evidence must establish what was measured before supporting a functional interpretation.", "layers": [ { "id": "circuit-relationships", "name": "Circuit relationships", "description": "Describe evidenced relationships among hippocampal regions and their neighbours.", "findings": [ { "id": "connection-assignment", "name": "Connection assignment", "description": "Record pathway endpoints and distinguish measured connections from reference expectations.", "questions": [ { "text": "Which hippocampal subregion and external or internal endpoint does the proposed connection join?", "kind": "definition", "id": "connection-assignment-q01" }, { "text": "Does its evidence demonstrate anatomical continuity, synaptic direction, functional correlation or only an atlas expectation?", "kind": "provenance", "id": "connection-assignment-q02" } ] } ] }, { "id": "activity-and-functional-attribution", "name": "Activity and functional attribution", "description": "Bind recordings to local sampling and the conditions under which they were obtained.", "findings": [ { "id": "local-activity-interpretation", "name": "Local activity interpretation", "description": "Require spatial and experimental support before attributing activity or a task contribution to this instance.", "questions": [ { "text": "What hippocampal location, signal type, sampling interval and awake, sleep, anaesthetic or task condition describe this recording?", "kind": "measurement", "id": "local-activity-interpretation-q01" }, { "text": "What evidence distinguishes locally generated activity from nearby signals or measurement artefacts?", "kind": "provenance", "id": "local-activity-interpretation-q02" }, { "text": "What supports linking this observation to memory or navigation, and how far does that evidence permit the attribution to extend?", "kind": "boundary", "id": "local-activity-interpretation-q03" } ] } ] } ] }, { "id": "hippocampal-condition-and-change", "name": "Hippocampal condition and change", "description": "Assess morphology, tissue findings and change using compatible evidence.", "rationale": "A small, asymmetric or unusual-looking hippocampus needs contextual interpretation rather than an automatic disease label.", "layers": [ { "id": "morphology-and-comparison", "name": "Morphology and comparison", "description": "Make regional size and shape observations comparable.", "findings": [ { "id": "morphometric-assessment", "name": "Morphometric assessment", "description": "Retain anatomical coverage, measurement uncertainty and the basis of comparison.", "questions": [ { "text": "What volume or shape measure was obtained for each hemisphere and supported hippocampal region?", "kind": "measurement", "id": "morphometric-assessment-q01" }, { "text": "Which species, age, head-size adjustment and acquisition characteristics make the chosen reference appropriate?", "kind": "provenance", "id": "morphometric-assessment-q02" }, { "text": "Could segmentation differences or incomplete coverage explain the apparent asymmetry or longitudinal change?", "kind": "measurement", "id": "morphometric-assessment-q03" } ] } ] }, { "id": "regional-tissue-abnormalities", "name": "Regional tissue abnormalities", "description": "Localise abnormal observations and separate them from causal interpretations.", "findings": [ { "id": "tissue-state-evidence", "name": "Tissue state evidence", "description": "Record the extent, timing and evidential basis of suspected hippocampal injury or alteration.", "questions": [ { "text": "Which regions show altered signal, diffusion, cellular loss, gliosis or other directly documented abnormalities?", "kind": "measurement", "id": "tissue-state-evidence-q01" }, { "text": "Which observations support the proposed interpretation, and which alternative explanations remain unresolved?", "kind": "provenance", "id": "tissue-state-evidence-q02" }, { "text": "What repeat observation or additional assessment would clarify progression, reversibility or a possible preparation artefact?", "kind": "action", "id": "tissue-state-evidence-q03" } ] } ] } ] }, { "id": "hippocampal-access-and-intervention", "name": "Hippocampal access and intervention", "description": "Determine which observations and manipulations are feasible and authorized for the instance.", "rationale": "Recording, stimulation and tissue removal require precise hippocampal targeting and explicit limits on what their results establish.", "layers": [ { "id": "preparation-and-observability", "name": "Preparation and observability", "description": "Relate available methods to tissue preparation and anatomical coverage.", "findings": [ { "id": "measurement-feasibility", "name": "Measurement feasibility", "description": "Establish which anatomical or physiological questions the present instance can support.", "questions": [ { "text": "Is this hippocampus in vivo, excised, maintained as a viable preparation or fixed, and what evidence establishes its current condition?", "kind": "provenance", "id": "measurement-feasibility-q01" }, { "text": "Which imaging, recording or histological observation can resolve the target hippocampal region in this preparation?", "kind": "action", "id": "measurement-feasibility-q02" }, { "text": "Which hippocampal regions or connections are missing, severed or inaccessible in the available sample?", "kind": "boundary", "id": "measurement-feasibility-q03" } ] } ] }, { "id": "targeting-and-action-limits", "name": "Targeting and action limits", "description": "Bind a proposed manipulation to a verified target and an approved procedure.", "findings": [ { "id": "intervention-readiness", "name": "Intervention readiness", "description": "Require target evidence, authorization and outcome criteria before recommending execution.", "questions": [ { "text": "Which hemisphere, longitudinal region and subfield are intended for recording, stimulation, sampling or resection, and how will targeting be verified?", "kind": "action", "id": "intervention-readiness-q01" }, { "text": "Which clinical or experimental authorization specifies the permitted procedure, operator and stopping conditions?", "kind": "action", "id": "intervention-readiness-q02" }, { "text": "How will the procedure assess effects on the intended hippocampal region and detect involvement of neighbouring tissue?", "kind": "measurement", "id": "intervention-readiness-q03" } ] } ] } ] }, { "id": "evidence-and-external-alignment", "name": "Evidence and external alignment", "description": "What the world already says about this thing, gathered so the model can be checked against it.", "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.", "layers": [ { "id": "reported-evidence", "name": "Reported evidence", "description": "Findings from the breadth pass, kept separate from the structural claims.", "findings": [ { "id": "evidence-kinds", "name": "Kinds and varieties", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ "Hippocampus proper / cornu ammonis (CA1, CA2, CA3, and often hilar CA4)", "Dentate gyrus (including granule-cell layer, molecular layer, and hilus)", "Anterior (human) / ventral (rodent) hippocampus", "Posterior (human) / dorsal (rodent) hippocampus", "Hippocampal formation (hippocampus plus subiculum, sometimes with presubiculum and parasubiculum)", "Left versus right hippocampus (material-specific memory laterality in humans)", "Hippocampal sclerosis as a clinical-pathological type (ILAE HS types 1-3 and no-HS)", "Incomplete hippocampal inversion / hippocampal malrotation as a developmental variant" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of hippocampus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-identifiers", "name": "Identifiers and schemes", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ { "scheme": "Wikidata", "value_or_pattern": "Q19118", "note": "Anatomical structure 'hippocampus'; not the seahorse genus." }, { "scheme": "Terminologia Anatomica (TA98)", "value_or_pattern": "A14.1.09.321", "note": "Latin term Hippocampus; subsequent TA2 codes should be preferred when a local atlas has migrated." }, { "scheme": "Foundational Model of Anatomy", "value_or_pattern": "FMA:275020", "note": "FMA class for hippocampus." }, { "scheme": "UBERON", "value_or_pattern": "UBERON:0002421", "note": "Multi-species anatomy ontology class 'hippocampus'." }, { "scheme": "MeSH", "value_or_pattern": "D006624", "note": "MeSH Heading Hippocampus (A08 anatomical term)." }, { "scheme": "NCI Thesaurus", "value_or_pattern": "C12444", "note": "NCI concept Hippocampus." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of hippocampus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-standards-and-regulation", "name": "Standards and regulation", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ "Terminologia Anatomica - FIPAT of the International Federation of Associations of Anatomists (IFAA): official anatomical nomenclature.", "ILAE consensus classification of hippocampal sclerosis (2013) - International League Against Epilepsy Commission on Diagnostic Methods: histopathological typing used in epilepsy surgery.", "EADC-ADNI Harmonized Hippocampal Protocol (HarP) - European Alzheimer's Disease Consortium and Alzheimer's Disease Neuroimaging Initiative: standard landmarks for manual MRI volumetry.", "NINDS Common Data Elements for epilepsy neuroimaging - National Institute of Neurological Disorders and Stroke: recommended imaging and volumetric data elements that include hippocampus." ], "questions": [ { "id": "evidence-standards-and-regulation-q01", "text": "Which of these standards and regulation hold for the sense of hippocampus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-real-world-use", "name": "Real-world use", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ "Memory-clinic 3T MRI: visual medial-temporal rating and automated or HarP-style volumetry in mild cognitive impairment and Alzheimer disease.", "Epilepsy surgery: MRI, PET and histopathology of the resected hippocampus in mesial temporal lobe epilepsy; anterior temporal lobectomy or selective amygdalohippocampectomy.", "Acute neurology: DWI/T2 of CA1 in transient global amnesia; medial-temporal necrosis in HSV-1 encephalitis; anoxic CA1 injury after cardiac arrest.", "Experimental and human systems neuroscience: place cells, grid-cell input, and fMRI encoding/retrieval designs that treat hippocampus as the dependent region of interest.", "Neuropathology: Braak and related staging schemes score transentorhinal and hippocampal involvement in Alzheimer-type tau pathology." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of hippocampus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-measurements", "name": "Typical measurements", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ { "quantity": "MRI hippocampal volume (one side, intracranial-volume adjusted context)", "typical_range": "about 2.5-4.5 in healthy adults; lower with age and in Alzheimer disease or hippocampal sclerosis", "unit": "mL (cm³)" }, { "quantity": "Rostrocaudal length of the hippocampal body (head-tail)", "typical_range": "about 40-50 in the adult human", "unit": "mm" }, { "quantity": "CA1 pyramidal-neuron density (surgical or autopsy histology)", "typical_range": "markedly reduced versus reference cortex in ILAE HS type 1; nearer normal in no-HS specimens", "unit": "neurons/mm² (protocol-dependent)" }, { "quantity": "T2 or FLAIR signal of hippocampus relative to contralateral side", "typical_range": "qualitatively increased in established unilateral sclerosis; quantitative T2 often tens of milliseconds above the contralateral hippocampus", "unit": "ms (T2) or dimensionless contrast rating" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of hippocampus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-failure-modes-and-hazards", "name": "Failure modes and hazards", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ "Hippocampal sclerosis: neuronal loss and gliosis, typically CA1 and often CA4, causing drug-resistant mesial temporal lobe epilepsy.", "Selective CA1 necrosis after hypoxia-ischemia (cardiac arrest, severe hypotension).", "Progressive atrophy, especially CA1 and subiculum, in Alzheimer disease, tracking episodic-memory decline.", "Necrotizing medial-temporal destruction in herpes simplex encephalitis, with lasting amnesia.", "Transient global amnesia: reversible CA1 diffusion lesion and hours-long anterograde amnesia.", "Material-specific memory loss after dominant (verbal) or nondominant (visuospatial) temporal resection that includes hippocampus.", "Incomplete inversion or malrotation: anatomical variant that complicates MRI reading and is over-represented in some epilepsy cohorts; not by itself a diagnosis of sclerosis." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of hippocampus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-regional-variation", "name": "Regional variation", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ "Human clinical and MRI literature names the long axis anterior-posterior; rodent experimental literature names the homologous axis ventral-dorsal.", "Schools and atlases disagree on whether 'hippocampus' stops at CA plus dentate gyrus or includes the subiculum (and, loosely, entorhinal cortex) under 'hippocampal formation'.", "German-language anatomy still uses Ammonshorn as the ordinary term for hippocampus proper; English clinical usage says hippocampus.", "The same word Hippocampus is the ICZN genus of seahorses; that is a separate nomenclatural system and the main cross-domain name collision, not a regional anatomical variant." ], "questions": [ { "id": "evidence-regional-variation-q01", "text": "Which of these regional variation hold for the sense of hippocampus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-neighbours", "name": "Neighbouring kinds and how to tell them apart", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ { "name": "Amygdala", "difference": "Nuclear mass immediately anterior and superior to the hippocampal head, not a three-layered allocortical roll; on MRI the uncal recess of the temporal horn and HarP landmarks separate the two." }, { "name": "Parahippocampal gyrus", "difference": "The gyral envelope of periallocortex/neocortex; the hippocampus is the infolded allocortex in the floor of the temporal horn, not the visible gyrus on the ventral brain surface." }, { "name": "Subiculum", "difference": "Cortex distal to the CA1-subiculum border (often via prosubiculum); transitional lamination, not a CA field; included in hippocampal formation but not in hippocampus proper." }, { "name": "Entorhinal cortex (Brodmann area 28)", "difference": "Lies on the parahippocampal gyrus and issues the perforant path; it is the main interface, not the hippocampal roll itself." }, { "name": "Fornix (fimbria-fornix)", "difference": "Myelinated output tract, not grey-matter hippocampus; follows from the fimbria along the ventricle toward the mammillary bodies." }, { "name": "Genus Hippocampus (seahorses)", "difference": "A teleost fish genus under ICZN, named for the same classical seahorse shape; separated by domain and by taxonomic versus TA/FMA/UBERON identifiers (Wikidata Q19118 versus the genus item)." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of hippocampus this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the registry intend the brain structure, and should coverage be restricted to mammals or include explicitly defined homologues in other vertebrates?", "Which hippocampus-versus-hippocampal-formation convention should be the default, especially for dentate gyrus, subiculum and disputed subfield boundaries?", "Which species-specific atlases and acquisition protocols support reproducible regional assignments at the intended observation resolutions?", "What reference populations and measurement uncertainty are sufficient to judge unusual morphology or meaningful change without implying a diagnosis?", "What evidence threshold should support attributing a memory or navigation contribution to one hippocampal instance rather than to a wider neural system?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 18, "questions": 33 } }, "draft": { "generator": "vr.draft.v3", "status": "draft-generated", "researched": false, "archetype": "organism", "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 hippocampus, record what state it is in, and decide what may be done with it.", "whatItIs": "Enable an agent to recognise a hippocampal anatomical instance, assess its observed structural and functional state, and determine which observations or interventions are justified.", "characteristics": { "substance": "living", "origin": "natural", "agency": "autonomous", "mobility": "self-moving" }, "whatYouCanDoWithIt": [ "observed and measured" ], "distinguishingFeatures": [ "Names folded into this entry, which a task may need to split apart again: mouse hippocampus, developing hippocampus, rat hippocampus.", "3 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 62 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 hippocampus, and on what evidence are they told apart?" ], "whatItIsMadeOf": "a living thing", "physicalCharacter": [ "Moves under its own power or of its own accord.", "Acts on its own behalf.", "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": [ "Recognised by diagnostic characters, and those differ by life stage - the young of many kinds are mistaken for other kinds entirely. A sighting is settled by characters, a photograph and a place, not by a name alone." ], "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": [ "mouse hippocampus", "developing hippocampus", "rat hippocampus" ] } ], "standing": "Described in 62 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 3 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 hippocampus from another, and a hippocampus 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 hippocampus, 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 hippocampus, 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 hippocampus 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 hippocampus, 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 hippocampus, 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 hippocampus 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 hippocampus 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 hippocampus, 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 hippocampus, 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 hippocampus 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 hippocampus from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a hippocampus, 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 hippocampus, 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 hippocampus 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 hippocampus 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 hippocampus, 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 hippocampus, 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 hippocampus 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": "Anatomy, parts and life stage.", "findings": [ { "id": "parts-and-materials", "name": "Parts and life stages", "description": "The parts of a hippocampus and the stages it passes through.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a hippocampus, 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 hippocampus, 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 hippocampus 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 hippocampus is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a hippocampus, 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 hippocampus, 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 hippocampus 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 hippocampus is, how it got there and where it may go (self-moving).", "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 hippocampus is, and what that position is measured against.", "questions": [ { "id": "position-and-frame-q01", "text": "What identifies and describes the location of a hippocampus, 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 hippocampus, 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 hippocampus 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 hippocampus moves on its own.", "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 hippocampus, 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 hippocampus, 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 hippocampus 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 hippocampus 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 hippocampus between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a hippocampus, 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 hippocampus, 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 hippocampus 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 hippocampus, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a hippocampus 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 hippocampus, 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 hippocampus, 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 hippocampus is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "taxonomic-placement", "name": "Taxonomic placement and identification", "description": "What hippocampus is called scientifically, by whose authority, and how a specimen is recognised.", "rationale": "Names change with revisions while the organism does not, so a name without its authority and date cannot be reconciled later.", "layers": [ { "id": "accepted-name", "name": "Accepted name and synonymy", "description": "The current binomial, its author and date, and the names it replaced.", "findings": [ { "id": "name-and-authority", "name": "Accepted name, authority and synonyms", "description": "What to record so a later revision can be applied without losing the old data.", "questions": [ { "id": "name-and-authority-q01", "text": "What is the accepted scientific name of hippocampus, with its author and year, and which synonyms does it absorb?", "kind": "definition" }, { "id": "name-and-authority-q02", "text": "Which taxonomic authority is being followed, and what would a competing authority say?", "kind": "provenance" } ] } ] }, { "id": "field-identification", "name": "Field identification", "description": "The characters that separate hippocampus from what it is confused with.", "findings": [ { "id": "diagnostic-characters", "name": "Diagnostic characters and confusable kinds", "description": "Features that settle an identification, and those that only suggest it.", "questions": [ { "id": "diagnostic-characters-q01", "text": "Which observable characters distinguish hippocampus from its closest look-alikes, and at which life stage are they visible?", "kind": "boundary" }, { "id": "diagnostic-characters-q02", "text": "What evidence is enough to record an identification as confirmed rather than provisional?", "kind": "provenance" } ] } ] } ] }, { "id": "life-cycle-and-condition", "name": "Life stages, condition and behaviour", "description": "What hippocampus does over its life and how its state is judged.", "rationale": "Stage and condition change what may be done - handled, treated, harvested, left alone - and both are observations with a time.", "layers": [ { "id": "stages-and-reproduction", "name": "Stages and reproduction", "description": "Development from origin to death, including forms that look like different animals.", "findings": [ { "id": "life-stages", "name": "Life stages and their marks", "description": "The stages worth recording and what tells them apart.", "questions": [ { "id": "life-stages-q01", "text": "What stages does hippocampus pass through, and what observable change marks each transition?", "kind": "definition" }, { "id": "life-stages-q02", "text": "Which stages are so unlike the adult that they are mistaken for another kind?", "kind": "boundary" } ] } ] }, { "id": "health-and-condition", "name": "Health and condition", "description": "How condition is assessed and by whom.", "findings": [ { "id": "condition-assessment", "name": "Condition assessment", "description": "Signs of health, injury and stress, and who is competent to judge them.", "questions": [ { "id": "condition-assessment-q01", "text": "How is the condition of hippocampus judged, on what scale, and by whom?", "kind": "measurement" }, { "id": "condition-assessment-q02", "text": "What condition obliges an agent to act, and what act is permitted to whom?", "kind": "action" } ] } ] } ] }, { "id": "range-and-status", "name": "Habitat, range and conservation status", "description": "Where hippocampus lives and how threatened it is.", "rationale": "Range and status govern what is lawful, and both are assessments with an assessor and a year rather than facts of nature.", "layers": [ { "id": "habitat-and-range", "name": "Habitat and range", "description": "Native range, introductions and the habitat it needs.", "findings": [ { "id": "range-record", "name": "Range, introductions and habitat", "description": "What to record about where it is found and how it got there.", "questions": [ { "id": "range-record-q01", "text": "What is the native range of hippocampus, where has it been introduced, and what habitat does it require?", "kind": "definition" }, { "id": "range-record-q02", "text": "What distinguishes a native record from an introduced or vagrant one?", "kind": "boundary" } ] } ] }, { "id": "protection-status", "name": "Protection and legal status", "description": "Conservation assessments and the rules that follow from them.", "findings": [ { "id": "status-and-rules", "name": "Conservation status and legal consequence", "description": "The assessment, its date, and what it forbids or requires where.", "questions": [ { "id": "status-and-rules-q01", "text": "What conservation status does hippocampus hold, under which assessment and year?", "kind": "provenance" }, { "id": "status-and-rules-q02", "text": "What does that status forbid or require of an agent, and in which jurisdiction?", "kind": "action" } ] } ] } ] }, { "id": "provenance-and-evidence", "name": "Provenance, evidence and time", "description": "Where every claim about a hippocampus 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 hippocampus and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a hippocampus, 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 hippocampus, 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 hippocampus 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 hippocampus is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a hippocampus, 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 hippocampus, 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 hippocampus is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 8, "layers": 17, "findings": 19, "questions": 51 } } } }