{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.molecule","code":"thing-q11369","url":"https://ver.cy/models/thing/q11369/","name":"molecule","alternateNames":["monomer molecule","dinuclear copper","helium dimer","nitrogen monofluoride","mercury polycation","mTOR inhibitors","(¹⁶O₂)dioxygen","(¹⁷O₂)dioxygen","(¹⁴N₂)dinitrogen","ditritium","(¹⁵N₂)dinitrogen","motor protein"],"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.MAT"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"An electrically neutral group of two or more atoms held together by chemical bonds, such as H2O, O2 or large biomolecules; the smallest unit of a substance that keeps its chemical properties.","purpose":"Let an agent handle molecules by composition, structure, properties, identifiers and representation.","scope":{"in":[],"out":[],"boundaries":[]},"distinguishingFeatures":["Bonded group of atoms","Neutral overall","Defined composition","Property of a substance"],"structure":{"bundles":[{"id":"identity","name":"Identity","description":"Which molecule.","layers":[{"id":"name","name":"Name","description":"Formula and name.","findings":[{"id":"name-finding","name":"Name","description":"Name and formula.","questions":[{"text":"What are its formula and IUPAC name?","kind":"definition"},{"text":"What are its InChI and CAS number?","kind":"provenance"}]}]},{"id":"isomers","name":"Isomers","description":"Structure.","findings":[{"id":"isomers-finding","name":"Isomers","description":"Isomers.","questions":[{"text":"Which isomer or stereoisomer is meant?","kind":"boundary"},{"text":"How does it differ from others?","kind":"definition"}]}]}]},{"id":"structure","name":"Structure","description":"Bonding.","layers":[{"id":"bonds","name":"Bonds","description":"Bonding.","findings":[{"id":"bonds-finding","name":"Bonds","description":"Bonding.","questions":[{"text":"What bonds and shape does the molecule have?","kind":"definition"},{"text":"Is it polar?","kind":"definition"}]}]},{"id":"models","name":"Models","description":"Representation.","findings":[{"id":"models-finding","name":"Models","description":"Representation.","questions":[{"text":"How should it be represented in software?","kind":"action"},{"text":"Which file format is used?","kind":"definition"}]}]}]},{"id":"properties","name":"Properties","description":"Data.","layers":[{"id":"physical","name":"Physical","description":"Mass and phase.","findings":[{"id":"physical-finding","name":"Physical","description":"Physical properties.","questions":[{"text":"What are its molar mass, melting and boiling points?","kind":"measurement"},{"text":"From which database?","kind":"provenance"}]}]},{"id":"hazards","name":"Hazards","description":"Safety.","findings":[{"id":"hazards-finding","name":"Hazards","description":"Hazards.","questions":[{"text":"What hazards does the substance have, according to its safety data sheet?","kind":"provenance"},{"text":"How should it be handled?","kind":"action"}]}]}]},{"id":"learning","name":"Learning","description":"Teaching.","layers":[{"id":"explain","name":"Explain","description":"Simple terms.","findings":[{"id":"explain-finding","name":"Explain","description":"Explanation.","questions":[{"text":"How can molecules be explained with models?","kind":"action"},{"text":"Which examples help?","kind":"action"}]}]},{"id":"scale","name":"Scale","description":"Size.","findings":[{"id":"scale-finding","name":"Scale","description":"Scale.","questions":[{"text":"How large is the molecule?","kind":"measurement"},{"text":"How can its scale be visualised?","kind":"action"}]}]}]}]},"agentConduct":{"may":["Describe molecules, their structures and properties from chemistry databases, citing them.","Model molecular structures for teaching and legitimate research."],"mustNot":["Help design, make or use molecules intended to harm people, such as chemical weapons or poisons.","Present unverified predicted properties as measured facts.","Give health claims for molecules that the evidence does not support."],"requiresHuman":["Ordering or synthesising new compounds.","Sharing research on compounds of concern."]},"ethics":{"considerations":["Molecular knowledge underpins medicine and industry and can also be misused.","Toxicity data protects workers and consumers when reported honestly."],"affectedParties":["Researchers and students","Workers handling chemicals","The public"]},"owners":{"steward":"Nobody: a concept of chemistry held in common; chemical databases record known molecules.","roles":[],"masterSystems":["Chemical substance registries"]},"relations":[{"target":"Q2393187","type":"parent","note":"registry parent class"},{"target":"molecular entity","type":"related","note":"category"},{"target":"atom","type":"related","note":"components"},{"target":"chemical bond","type":"related","note":"bonding"},{"target":"InChI and CAS number","type":"related","note":"identifiers"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.molecule","Wikidata: Q11369 (https://www.wikidata.org/wiki/Q11369)","InChI: IUPAC identifier structure","CAS Registry Number: numeric substance"]},"properties":{"applicability":"required","items":["Molecular mass:  Da - Molecular mass is determined from isotopic composition or measured using mass spectrometry with appropriate interpretation of detected ions.","Molecular dimensions:  nm - Dimensions are estimated from structural measurements or molecular models using a stated geometric definition and conformation.","Electric dipole moment:  D - The molecular dipole moment is determined by spectroscopy or calculation for a specified molecular state and conformation."]},"recognition":{"applicability":"required","items":["Molecular formulas and structures","Identifiers such as InChI and SMILES","Ions and ionic lattices are related but different","Invisible to the eye; shown as formulas, models and computer structures."]},"capabilities":{"applicability":"required","items":["identify molecules by formula and name","describe structure and bonding","look up properties in databases","represent molecules in software"]},"hazards":{"applicability":"required","items":["Confusing molecules and ions","Ambiguous names"]},"interfaces":{"applicability":"required","items":["IUPAC nomenclature","REACH substance registration"]},"context":{"applicability":"required","items":["Understanding chemistry, materials and biology.","diatomic molecules","small organic molecules","macromolecules and polymers","biomolecules","molecular ions (related)"]}},"sources":[{"title":"Wikidata item Q11369: molecule","url":"https://www.wikidata.org/wiki/Q11369","note":"identity and sense of the item"},{"title":"Wikipedia: Molecule","url":"https://en.wikipedia.org/wiki/Molecule","note":"general description of the item"}],"openQuestions":["Should molecule classes be separate entries?","How should chemical databases be linked?","How should stereoisomers be handled?"],"resources":{"spec":"/models/things/publications/thing-q11369/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q11369/spec.json"],"providers":["Claude"],"researchStatus":"unreviewed","generatedAt":"2026-09-11T10:25:10Z","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 2026-10-07T10:10:25+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass"},"score":1.0}}