{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.germ","code":"thing-q1377980","url":"https://ver.cy/models/thing/q1377980/","name":"germ","alternateNames":[],"kind":"thing","status":"research-draft","version":"0.1.0-research.1","language":"en","classifiers":{"family":"Thing Registry","category":"Physical world and living systems","entryKind":"thing","plane":"PHY","domain":["PHY.LIV"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"In its common biological sense, a germ is a microorganism or infectious agent, especially one capable of causing disease, rather than a formally defined taxonomic group.","purpose":"Enable an AI agent to recognise what is being called a germ, assess the evidence for its presence and biological significance, and identify appropriate handling or investigation.","scope":{"in":["Disambiguation of germ and identification of the biological referent","Agent identity at the resolution supported by evidence","Presence, quantity, viability or infectivity in a specified sample or setting","Relationships to hosts, reservoirs, environmental conditions and exposure routes","Evidence supporting handling, further investigation or control decisions"],"out":["Seed embryos, cereal germ and germ cells","Mathematical germs and figurative beginnings of ideas","Diseases, symptoms and patient treatment plans","Complete taxonomic models of named microbial species","Laboratory equipment, disinfectant products and facility operating procedures"],"boundaries":[]},"distinguishingFeatures":["The referent must concern a microorganism or infectious agent; a seed component, reproductive cell or mathematical construction requires another sense of germ.","The label germ does not by itself establish a species, taxonomic group or pathogenic role.","A positive sample result must be distinguishable from an identified individual agent, isolate, strain or population.","Evidence of agent material must be distinguished from evidence of viability, infectivity or transmission.","Presence in a host or environment must be distinguished from evidence that the agent caused disease."],"structure":{"bundles":[{"id":"germ-sense-and-identity","name":"Germ sense and identity","description":"Establish what the label denotes and how precisely its biological referent is known.","layers":[{"id":"meaning-and-boundary","name":"Meaning and boundary","description":"Resolve the intended sense and the kind of entity being described.","findings":[{"id":"intended-germ-referent","name":"Intended germ referent","description":"Record whether germ denotes a biological agent and whether the subject is a kind, population, isolate or observed occurrence.","questions":[{"text":"Does germ here mean a microorganism or infectious agent, or does the source intend another sense?","id":"intended-germ-referent-q01","kind":"definition"},{"text":"Is the subject an agent kind, a strain or isolate, a population, or an occurrence in a sample?","id":"intended-germ-referent-q02","kind":"boundary"}]}]},{"id":"identification-and-authority","name":"Identification and authority","description":"Connect the referent to supported biological identification.","findings":[{"id":"supported-agent-identity","name":"Supported agent identity","description":"Record identification evidence, its resolution and any authoritative record used to interpret it.","questions":[{"text":"What evidence supports the proposed agent group, species, strain or isolate identity?","id":"supported-agent-identity-q01","kind":"provenance"},{"text":"Which authoritative identifier and classification version apply, and what identity remains unresolved?","id":"supported-agent-identity-q02","kind":"provenance"}]}]}]},{"id":"detection-and-biological-state","name":"Detection and biological state","description":"Describe what was observed and what the observation establishes about the agent.","layers":[{"id":"sample-and-detection","name":"Sample and detection","description":"Anchor evidence to the sampled material, collection context and detection method.","findings":[{"id":"interpretable-detection","name":"Interpretable detection","description":"Record the sampled setting and whether the method targets agent material, observable agents or another indicator.","questions":[{"text":"What host material or environmental medium was sampled, where, when and by which collection method?","id":"interpretable-detection-q01","kind":"provenance"},{"text":"What does the detection method measure, and what controls address contamination or misleading results?","id":"interpretable-detection-q02","kind":"measurement"}]}]},{"id":"quantity-and-activity","name":"Quantity and activity","description":"Represent burden and biological state without treating unlike measurements as interchangeable.","findings":[{"id":"burden-and-activity-evidence","name":"Burden and activity evidence","description":"Keep method-specific quantity separate from assessments of viability or infectivity.","questions":[{"text":"What quantity was measured, in which units and sample denominator, with what uncertainty and detection limit?","id":"burden-and-activity-evidence-q01","kind":"measurement"},{"text":"Was viability or infectivity assessed separately, and what does that assessment establish or leave unresolved?","id":"burden-and-activity-evidence-q02","kind":"measurement"}]}]}]},{"id":"host-and-exposure-context","name":"Host and exposure context","description":"Connect the agent to its setting, possible exposure and evidenced host effects.","layers":[{"id":"reservoir-and-transfer","name":"Reservoir and transfer","description":"Identify supported locations and pathways connecting an agent occurrence to a potential host.","findings":[{"id":"supported-exposure-pathway","name":"Supported exposure pathway","description":"Distinguish an observed agent location from an evidenced reservoir or transfer route.","questions":[{"text":"What evidence identifies the observed location as a reservoir, temporary carrier or incidental detection site?","id":"supported-exposure-pathway-q01","kind":"provenance"},{"text":"Which exposure route to which host is supported, and which links in that route are only suspected?","id":"supported-exposure-pathway-q02","kind":"boundary"}]}]},{"id":"host-role-and-causation","name":"Host role and causation","description":"Describe the agent's relationship to a host without equating detection with disease.","findings":[{"id":"evidenced-host-role","name":"Evidenced host role","description":"Record evidence distinguishing presence, carriage, colonisation, infection and causal involvement.","questions":[{"text":"What evidence supports the assigned relationship between this agent and this host?","id":"evidenced-host-role-q01","kind":"provenance"},{"text":"What additional evidence is needed before attributing a disease or harmful effect to this agent?","id":"evidenced-host-role-q02","kind":"boundary"}]}]}]},{"id":"handling-and-control-evidence","name":"Handling and control evidence","description":"Support context-specific handling and evaluate attempts to reduce the relevant agent state or exposure.","layers":[{"id":"action-selection","name":"Action selection","description":"Determine which guidance applies to the agent, material and setting.","findings":[{"id":"applicable-handling-basis","name":"Applicable handling basis","description":"Record the authoritative basis and unresolved prerequisites for handling, further assessment or control.","questions":[{"text":"Which current handling or control guidance applies to this agent identity, sample material and setting?","id":"applicable-handling-basis-q01","kind":"provenance"},{"text":"What identification or state uncertainty requires further assessment before the proposed action can be selected?","id":"applicable-handling-basis-q02","kind":"action"}]}]},{"id":"outcome-verification","name":"Outcome verification","description":"Evaluate whether the selected action achieved its stated biological or exposure objective.","findings":[{"id":"verified-control-outcome","name":"Verified control outcome","description":"Link the action to a defined endpoint, suitable observations and the limits of the resulting conclusion.","questions":[{"text":"Does the action aim to remove agent material, reduce viable or infectious agents, or interrupt an exposure route?","id":"verified-control-outcome-q01","kind":"action"},{"text":"Which observations support achievement of that endpoint, and what residual uncertainty or recontamination possibility remains?","id":"verified-control-outcome-q02","kind":"measurement"}]}]}]},{"id":"evidence-and-external-alignment","name":"Evidence and external alignment","description":"What the world already says about this thing, gathered so the model can be checked against it.","layers":[{"id":"reported-evidence","name":"Reported evidence","description":"Findings from the breadth pass, kept separate from the structural claims.","findings":[{"id":"evidence-confidence-notes","name":"Check these first","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these check these first hold for the sense of germ this model covers, and on what evidence?","id":"evidence-confidence-notes-q01","kind":"provenance"}]},{"id":"evidence-kinds","name":"Kinds and varieties","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these kinds and varieties hold for the sense of germ this model covers, and on what evidence?","id":"evidence-kinds-q01","kind":"provenance"}]},{"id":"evidence-identifiers","name":"Identifiers and schemes","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these identifiers and schemes hold for the sense of germ this model covers, and on what evidence?","id":"evidence-identifiers-q01","kind":"provenance"}]},{"id":"evidence-real-world-use","name":"Real-world use","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these real-world use hold for the sense of germ this model covers, and on what evidence?","id":"evidence-real-world-use-q01","kind":"provenance"}]},{"id":"evidence-failure-modes-and-hazards","name":"Failure modes and hazards","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these failure modes and hazards hold for the sense of germ this model covers, and on what evidence?","id":"evidence-failure-modes-and-hazards-q01","kind":"provenance"}]},{"id":"evidence-neighbours","name":"Neighbouring kinds and how to tell them apart","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these neighbouring kinds and how to tell them apart hold for the sense of germ this model covers, and on what evidence?","id":"evidence-neighbours-q01","kind":"provenance"}]}]}]}]},"agentConduct":{"may":["Disambiguate the label and link the referent to an existing agent or taxon model.","Record and compare sample observations with their methods and uncertainty.","Assess whether evidence supports presence, viability, infectivity or a host-associated role.","Map supported reservoir, exposure and host relationships.","Identify applicable handling guidance and missing evidence before selecting an action.","Track control actions and evaluate their measured outcomes."],"mustNot":[],"requiresHuman":["Assuming that an embryo or its surrounding seed is edible can expose people or animals to species-specific toxins or seed treatments."]},"ethics":{"considerations":["Prevents the word germ from being used as sufficient evidence of harm."],"affectedParties":[]},"owners":{"steward":"","roles":[],"masterSystems":[]},"relations":[{"target":"Q33196","type":"parent","note":"registry parent class"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.germ","Wikidata: Q1377980 (https://www.wikidata.org/wiki/Q1377980)"]},"properties":{"applicability":"required","items":["Intended sense: microorganism or infectious agent; other biological sense; nonbiological sense; unresolved","Identification resolution: uncharacterised agent; agent group; species; strain; isolate; unresolved","Biological identity: linked taxon or agent record, identifier authority, classification version and confidence","Observation context: sample, host or environmental location, collection time and collection method","Measured amount: method-specific count or concentration with denominator, uncertainty and detection limit; unknown","Viability or infectivity assessment: property assessed, method, result, assessment time and limitations; not assessed","Host-associated role: host and context linked to evidence of carriage, colonisation, infection or causal involvement; unresolved","Control assessment: not assessed; action proposed; action applied; outcome measured; effectiveness unresolved"]},"recognition":{"applicability":"required","items":["The embryo is an organized structure within the seed rather than the surrounding seed coat or bulk storage tissue.","Depending on the species and developmental stage, it contains recognizable embryonic root and shoot regions with one or more cotyledons.","In cereal grains, the embryo lies toward one end beside the much larger endosperm and may require magnification to inspect."]},"capabilities":{"applicability":"required","items":["Disambiguate the label and link the referent to an existing agent or taxon model.","Record and compare sample observations with their methods and uncertainty.","Assess whether evidence supports presence, viability, infectivity or a host-associated role.","Map supported reservoir, exposure and host relationships.","Identify applicable handling guidance and missing evidence before selecting an action.","Track control actions and evaluate their measured outcomes."]},"hazards":{"applicability":"required","items":["Mechanical damage to the embryo can prevent germination even when the rest of the seed appears intact.","Unsuitable storage conditions can reduce embryo viability and cause propagation failure.","Confusing this botanical sense with an infectious agent can lead to inappropriate handling or disposal.","Assuming that an embryo or its surrounding seed is edible can expose people or animals to species-specific toxins or seed treatments."]},"interfaces":{"applicability":"required","items":["The International Rules for Seed Testing, issued by the International Seed Testing Association, provide methods for seed testing that include assessment of embryo viability through tetrazolium testing."]},"context":{"applicability":"required","items":["A germ in this botanical sense is the plant embryo within a seed, encountered in seed anatomy, germination studies and crop propagation.","Its condition helps determine whether a seed can develop into a seedling.","In cereal processing, the germ is a distinct seed component that may be retained or separated during milling."]}},"sources":[{"title":"Wikidata item Q1377980: germ","url":"https://www.wikidata.org/wiki/Q1377980","note":"identity and sense of the item"}],"openQuestions":["Does the originating registry source intend the everyday microbial sense of germ, a seed or developmental sense, or another meaning?","Does the intended microbial sense include all microorganisms, only agents associated with disease, or a broader set of infectious agents?","Does an existing Vercy world model already own this concept, so that vr.tr.germ should link to it?","Should this entry primarily describe an agent kind or an occurrence in a sample, with the other represented through a neighbouring model?","Which authoritative terminology and evidence standards should govern distinctions between detection, viability, infectivity and causal involvement?","What identification or state uncertainty requires further assessment before the proposed action can be selected?","Does the action aim to remove agent material, reduce viable or infectious agents, or interrupt an exposure route?"],"resources":{"spec":"/models/things/publications/thing-q1377980/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q1377980/spec.json"],"providers":["Codex"],"researchStatus":"unreviewed","generatedAt":"2026-09-12T09:58:36Z","builder":"tools/build_cards.py@1.0.0"},"completeness":{"sections":{"classifiers":"filled","whatItIs":"filled","purpose":"filled","distinguishingFeatures":"filled","structure":"filled","agentConduct":"derived","ethics":"derived","owners":"missing","relations":"filled","interaction.identity":"filled","interaction.properties":"filled","interaction.recognition":"filled","interaction.capabilities":"filled","interaction.hazards":"filled","interaction.interfaces":"filled","interaction.context":"filled","sources":"filled"},"notes":{"agentConduct":"Affordances listed as what may be done; prohibitions collected from the text."},"score":0.882}}