{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.protein","code":"thing-q8054","url":"https://ver.cy/models/thing/q8054/","name":"protein","alternateNames":[],"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":"A biomolecule or biomolecule complex largely consisting of one or more chains of amino acid residues, with folded regions, intrinsically disordered regions or both, carrying out functions such as catalysis, structure, transport and signalling.","purpose":"Let an agent handle proteins by identity, sequence, structure, function and organism, using standard identifiers, and nutrition as a separate sense.","scope":{"in":[],"out":[],"boundaries":[]},"distinguishingFeatures":["Proteins consist largely of amino acid chains that may be folded, intrinsically disordered or both.","Function depends on sequence, structure and molecular dynamics.","Proteins are encoded by genes.","Dietary protein is a nutrition concept."],"structure":{"bundles":[{"id":"identity","name":"Identity","description":"Which protein.","layers":[{"id":"accession","name":"Accession","description":"UniProt and gene.","findings":[{"id":"accession-finding","name":"Accession","description":"Identifiers.","questions":[{"text":"What is its UniProt accession and gene name?","kind":"provenance"},{"text":"Which organism?","kind":"definition"}]}]},{"id":"sequence","name":"Sequence","description":"Amino acid sequence.","findings":[{"id":"sequence-finding","name":"Sequence","description":"The sequence.","questions":[{"text":"What is its sequence and length?","kind":"measurement"},{"text":"Which isoform?","kind":"boundary"}]}]}]},{"id":"structure","name":"Structure","description":"Shape.","layers":[{"id":"experimental","name":"Experimental","description":"PDB.","findings":[{"id":"experimental-finding","name":"Structure","description":"Experimental structures.","questions":[{"text":"Is there an experimental structure, at what resolution?","kind":"provenance"},{"text":"Which method?","kind":"provenance"}]}]},{"id":"predicted","name":"Predicted","description":"Models.","findings":[{"id":"predicted-finding","name":"Prediction","description":"Predicted models.","questions":[{"text":"Is a predicted model available, and how confident is it?","kind":"measurement"},{"text":"Where might it be wrong?","kind":"boundary"}]}]}]},{"id":"function","name":"Function","description":"What it does.","layers":[{"id":"role","name":"Role","description":"Molecular function.","findings":[{"id":"role-finding","name":"Function","description":"Molecular and biological role.","questions":[{"text":"What does the protein do?","kind":"definition"},{"text":"How is that known?","kind":"provenance"}]}]},{"id":"disease","name":"Disease","description":"Links to disease.","findings":[{"id":"disease-finding","name":"Disease links","description":"Disease associations.","questions":[{"text":"Is it linked to disease?","kind":"provenance"},{"text":"Is it a drug target?","kind":"provenance"}]}]}]},{"id":"use","name":"Use","description":"Production and diet.","layers":[{"id":"production","name":"Production","description":"Recombinant.","findings":[{"id":"production-finding","name":"Production","description":"How it is produced.","questions":[{"text":"How is it produced for use?","kind":"definition"},{"text":"Which rules apply?","kind":"provenance"}]}]},{"id":"diet","name":"Diet","description":"Nutrition and allergy.","findings":[{"id":"diet-finding","name":"Nutrition","description":"Dietary aspects.","questions":[{"text":"Is it a food allergen?","kind":"boundary"},{"text":"How much dietary protein is recommended, by whom?","kind":"provenance"}]}]}]}]},"agentConduct":{"may":["Describe proteins' structure and function from cited databases and literature.","Report dietary protein content from food composition data."],"mustNot":["Assist in designing or producing proteins intended to harm people, such as toxins.","Present predicted structures as experimentally confirmed.","Give personal dietary or supplement advice to a person with a medical condition.","Misattribute data from shared databases."],"requiresHuman":["Releasing designs or data for proteins with possible dual use."]},"ethics":{"considerations":["Protein science serves medicine but some proteins are toxins with misuse potential.","Shared databases rely on honest attribution and accuracy."],"affectedParties":["Patients","Researchers","The public"]},"owners":{"steward":"Nobody owns proteins in nature; protein data banks curate shared records.","roles":[],"masterSystems":["Protein sequence and structure databases"]},"relations":[{"target":"Q3084232","type":"parent","note":"registry parent class"},{"target":"Q422649","type":"parent","note":"registry parent class"},{"target":"Q424689","type":"parent","note":"registry parent class"},{"target":"Q66560214","type":"parent","note":"registry parent class"},{"target":"amino acids","type":"related","note":"monomers"},{"target":"gene","type":"related","note":"DNA"},{"target":"cell","type":"related","note":"context"},{"target":"food","type":"related","note":"dietary protein"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.protein","Wikidata: Q8054 (https://www.wikidata.org/wiki/Q8054)","UniProt accession: for example P69905 protein sequence and function","PDB id: four characters structures"]},"properties":{"applicability":"required","items":["length: 50-35000 amino acids - titin is the largest","mass: 5-3800 kDa"]},"recognition":{"applicability":"required","items":["UniProt accession and gene name","PDB structures","Dietary protein on labels is a nutrient, not a specific protein","Invisible to the eye; shown as structure models, sequences or bands on gels."]},"capabilities":{"applicability":"required","items":["identify it, by sequence and accession","determine its structure","study its function","produce it, recombinantly, under biosafety rules"]},"hazards":{"applicability":"required","items":["Allergenic proteins in food","Misfolding diseases","Confusing orthologs across species"]},"interfaces":{"applicability":"required","items":["Biosafety rules for recombinant proteins","Medicines regulation for protein therapeutics","Food labelling rules on protein content"]},"context":{"applicability":"required","items":["Proteins do most of the work in cells; in diets, protein supplies amino acids.","enzymes","structural proteins","transport proteins","signalling proteins and receptors","antibodies"]}},"sources":[{"title":"Wikidata item Q8054: protein","url":"https://www.wikidata.org/wiki/Q8054","note":"identity and sense of the item"},{"title":"Wikipedia: Protein","url":"https://en.wikipedia.org/wiki/Protein","note":"general description of the item"}],"openQuestions":["Should proteins be instances with UniProt accessions?","How should dietary and biochemical senses be separated?","How should predicted structures be marked?"],"resources":{"spec":"/models/things/publications/thing-q8054/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q8054/spec.json"],"providers":["Claude"],"researchStatus":"unreviewed","generatedAt":"2026-09-11T05:28:49Z","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 2026-10-07T10:10:32+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass"},"score":1.0}}