{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.organelle","code":"thing-q45948","url":"https://ver.cy/models/thing/q45948/","name":"organelle","alternateNames":["nitroplast","extrusome","polar tubule","semiautonomous organelle","trichocyst","intracellular organelle","Vesiculo-vacuolar organelle","micronucleus","Proplastid","cortical alveolum","membrane-bounded organelle","extracellular organelle"],"kind":"thing","status":"published","version":"0.2.0-wave.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":"A specialised structure within a cell that performs a particular function, such as the nucleus, mitochondria, chloroplasts, endoplasmic reticulum, Golgi apparatus, lysosomes and vacuoles; mitochondria and plastids are semiautonomous with their own DNA, and new organelles such as the nitrogen-fixing nitroplast continue to be described.","purpose":"Let an agent explain organelles by structure, function, origin and research, for learners and researchers.","scope":{"in":[],"out":[],"boundaries":[]},"distinguishingFeatures":["Compartmentalised function","Often membrane-bound","Some have own DNA","Vary among organisms"],"structure":{"bundles":[{"id":"function","name":"Function","description":"What organelles do.","layers":[{"id":"roles","name":"Roles","description":"Functions.","findings":[{"id":"roles-finding","name":"Roles","description":"Functions.","questions":[{"text":"What does this organelle do in the cell?","kind":"definition"},{"text":"How does it interact with others?","kind":"definition"}]}]},{"id":"compare","name":"Compare","description":"Across organisms.","findings":[{"id":"compare-finding","name":"Compare","description":"Comparison.","questions":[{"text":"Which organelles are found in plant cells but not animal cells?","kind":"definition"},{"text":"Which unusual organelles do protists have?","kind":"provenance"}]}]}]},{"id":"origin","name":"Origin","description":"Evolution.","layers":[{"id":"endosymbiosis","name":"Endosymbiosis","description":"Origins.","findings":[{"id":"endosymbiosis-finding","name":"Endosymbiosis","description":"Endosymbiosis.","questions":[{"text":"What evidence supports the endosymbiotic origin of mitochondria and plastids?","kind":"provenance"},{"text":"Who proposed the theory?","kind":"provenance"}]}]},{"id":"new","name":"New","description":"Newly described organelles.","findings":[{"id":"new-finding","name":"New","description":"New organelles.","questions":[{"text":"What is the nitroplast, and how was it described, according to recent studies?","kind":"provenance"},{"text":"Is its status as an organelle accepted?","kind":"boundary"}]}]}]},{"id":"methods","name":"Methods","description":"Studying organelles.","layers":[{"id":"imaging","name":"Imaging","description":"Microscopy.","findings":[{"id":"imaging-finding","name":"Imaging","description":"Microscopy.","questions":[{"text":"Which microscopy methods show this organelle?","kind":"definition"},{"text":"Which stains or markers are used?","kind":"provenance"}]}]},{"id":"ontology","name":"Ontology","description":"Terminology.","findings":[{"id":"ontology-finding","name":"Ontology","description":"Ontology.","questions":[{"text":"Which Gene Ontology term describes this organelle?","kind":"provenance"},{"text":"Which databases list proteins localised there?","kind":"provenance"}]}]}]},{"id":"health","name":"Health","description":"Disease links.","layers":[{"id":"disorders","name":"Disorders","description":"Organelle disorders.","findings":[{"id":"disorders-finding","name":"Disorders","description":"Organelle disorders.","questions":[{"text":"Which disorders involve mitochondria or lysosomes, according to medical sources?","kind":"provenance"},{"text":"How strong is the evidence?","kind":"boundary"}]}]},{"id":"personal","name":"Personal","description":"Personal questions.","findings":[{"id":"personal-finding","name":"Personal","description":"Personal advice limits.","questions":[{"text":"Is the user asking about their own diagnosis?","kind":"boundary"},{"text":"How should the agent refer them to a clinician?","kind":"action"}]}]}]}]},"agentConduct":{"may":["Explain organelles and their functions, citing scientific sources.","Help researchers find literature and imaging data."],"mustNot":["Present early findings on new organelles as established.","Present mitochondrial health supplements as proven therapies."],"requiresHuman":["Interpreting organelle-related findings for a patient's diagnosis or treatment."]},"ethics":{"considerations":["Research claims must not overstate findings, especially when health products are sold on them.","Cell lines and tissues used to study organelles come from donors whose consent should be respected."],"affectedParties":["Students and the public","Patients","Tissue donors"]},"owners":{"steward":"Nobody: a biological structure; researchers answer for their claims.","roles":[],"masterSystems":[]},"relations":[{"target":"Q70551253","type":"parent","note":"registry parent class"},{"target":"cellular anatomical entity","type":"related","note":"category"},{"target":"cell","type":"related","note":"unit"},{"target":"mitochondrion","type":"related","note":"example"},{"target":"cellular respiration","type":"related","note":"process"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.organelle","Wikidata: Q45948 (https://www.wikidata.org/wiki/Q45948)"]},"properties":{"applicability":"required","items":["Characteristic length:  micrometre - Measure the longest dimension using calibrated microscopy because size depends on organelle type and cellular state.","Volume:  cubic micrometre - Estimate volume from segmented three-dimensional microscopy images with the organelle boundary explicitly defined.","Surface area:  square micrometre - Measure the defined outer boundary from reconstructed microscopy images while distinguishing it from internal membrane surfaces."]},"recognition":{"applicability":"required","items":["Membrane-bound compartments","Mitochondria and chloroplasts","Ribosomes are complexes often not counted as membrane organelles","Microscopic compartments seen in light and electron micrographs."]},"capabilities":{"applicability":"required","items":["describe organelle functions","explain endosymbiotic origins","compare plant, animal and protist organelles","find imaging and ontology resources"]},"hazards":{"applicability":"required","items":["Oversimplified textbook diagrams","Confusing organelles across kingdoms"]},"interfaces":{"applicability":"required","items":["Gene Ontology cellular component terms"]},"context":{"applicability":"required","items":["Cell biology education and research.","nucleus","mitochondria and plastids","endomembrane system","lysosomes, peroxisomes and vacuoles","protist organelles such as trichocysts and extrusomes"]}},"sources":[{"title":"Wikidata item Q45948: organelle","url":"https://www.wikidata.org/wiki/Q45948","note":"identity and sense of the item"},{"title":"Wikipedia: Organelle","url":"https://en.wikipedia.org/wiki/Organelle","note":"general description of the item"}],"openQuestions":["Should each organelle be a separate entry?","How should Gene Ontology be linked?","How should newly described organelles be tracked?"],"resources":{"spec":"/models/things/publications/thing-q45948/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q45948/spec.json"],"providers":["Claude"],"researchStatus":"unreviewed","generatedAt":"2026-09-11T14:24:29Z","builder":"tools/build_cards.py@1.0.0"},"completeness":{"sections":{"classifiers":"filled","whatItIs":"filled","purpose":"filled","distinguishingFeatures":"filled","structure":"filled","agentConduct":"filled","ethics":"filled","owners":"filled","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":{"_gate":"Published through the thing publication gate 1.0 on 2026-10-07T10:10:31+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass"},"score":1.0}}