{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.genome","code":"thing-q7020","url":"https://ver.cy/models/thing/q7020/","name":"genome","alternateNames":["viral RNA","kinetoplast","mitochondrial DNA","Leishmania panamensis mitochondrial genome","Leishmania donovani mitochondrial genome","Leishmania tarentolae mitochondrial genome","Leishmania aethiopica mitochondrial genome","Leishmania tropica mitochondrial genome","Leishmania amazonensis mitochondrial genome","Selfish mitochondrial DNA","Leishmania peruviana mitochondrial genome","Leishmania lainsoni mitochondrial genome"],"kind":"thing","status":"published","version":"0.2.0-wave.3","language":"en","classifiers":{"family":"Thing Registry","category":"Physical world and living systems","entryKind":"thing","plane":"PHY","domain":["PHY.OBJ"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"The complete set of genetic material of an organism or virus, comprising all its DNA or, in some viruses, RNA, including chromosomes in the nucleus and separate genomes of organelles such as mitochondrial DNA and the kinetoplast DNA of trypanosomatids like Leishmania, encoding genes and regulatory and non-coding sequences; genomes range from a few thousand bases in small viruses to billions in plants and animals, and are sequenced, annotated and compared in genomics.","purpose":"Let an agent explain genomes and their organisation, relay sizes, sequencing and organelle genomes from genomics references, describe applications in medicine and evolution, and distinguish genomes from genes, transcriptomes and proteomes.","scope":{"in":[],"out":[],"boundaries":[]},"distinguishingFeatures":["Complete genetic content","Nuclear and organelle parts","Huge size range","Sequenced and annotated"],"structure":{"bundles":[{"id":"understand","name":"Understand","description":"What a genome is.","layers":[{"id":"definition","name":"Definition","description":"Definition and organisation.","findings":[{"id":"definition-finding","name":"Definition","description":"Definition.","questions":[{"text":"What is a genome, and how are genes, regulatory and non-coding sequences organised in chromosomes?","kind":"definition"},{"text":"Is the question about a genome, a gene, the transcriptome or the proteome?","kind":"boundary"}]}]},{"id":"kinds","name":"Kinds","description":"Kinds.","findings":[{"id":"kinds-finding","name":"Kinds","description":"Kinds.","questions":[{"text":"How do nuclear, bacterial, viral, mitochondrial, kinetoplast and chloroplast genomes differ?","kind":"definition"},{"text":"Which entry fits the specific genome?","kind":"action"}]}]}]},{"id":"study","name":"Study","description":"Sequencing and analysis.","layers":[{"id":"sequencing","name":"Sequencing","description":"Sequencing.","findings":[{"id":"sequencing-finding","name":"Sequencing","description":"Sequencing.","questions":[{"text":"How are genomes sequenced, assembled and annotated?","kind":"provenance"},{"text":"Which references are standard?","kind":"provenance"}]}]},{"id":"comparison","name":"Comparison","description":"Comparative genomics.","findings":[{"id":"comparison-finding","name":"Comparison","description":"Comparison.","questions":[{"text":"What do genome comparisons reveal about evolution and gene function?","kind":"provenance"},{"text":"Which entry fits comparative genomics?","kind":"action"}]}]}]},{"id":"apply","name":"Apply","description":"Applications.","layers":[{"id":"medicine","name":"Medicine","description":"Medicine.","findings":[{"id":"medicine-finding","name":"Medicine","description":"Medicine.","questions":[{"text":"How are genomes used in diagnosis, pharmacogenomics and personalised medicine, in general terms?","kind":"provenance"},{"text":"Is the user asking about their own genetic results, which need a clinician or genetic counsellor?","kind":"boundary"}]}]},{"id":"parasites","name":"Parasites","description":"Parasite genomes.","findings":[{"id":"parasites-finding","name":"Parasites","description":"Parasites.","questions":[{"text":"What is known about Leishmania mitochondrial and kinetoplast genomes, and why do they matter?","kind":"provenance"},{"text":"Which sources are cited?","kind":"provenance"}]}]}]},{"id":"context","name":"Context","description":"Ethics and history.","layers":[{"id":"ethics","name":"Ethics","description":"Privacy and ethics.","findings":[{"id":"ethics-finding","name":"Ethics","description":"Ethics.","questions":[{"text":"What privacy and ethical issues surround genomic data, with positions attributed?","kind":"provenance"},{"text":"Which entry fits genetic privacy?","kind":"action"}]}]},{"id":"history","name":"History","description":"History.","findings":[{"id":"history-finding","name":"History","description":"History.","questions":[{"text":"How did genome sequencing develop from the first viral genome to the Human Genome Project and beyond?","kind":"provenance"},{"text":"Which entry fits the history of genomics?","kind":"action"}]}]}]}]},"agentConduct":{"may":["Explain genome organization and distinguish nuclear, organellar and viral genomes.","Summarize authorized genome records while preserving uncertainty about sequence completeness and gene function."],"mustNot":["Disclose or attempt to reidentify a person's genome without authorization.","Treat a genome sequence as a complete prediction of health, behavior or personal worth.","Represent a reference genome as the exact genome of every individual in a species.","Assist in using genomic information to discriminate against people or harm organisms."],"requiresHuman":["An authorized human must decide whether identifiable genomic information may be shared or reused.","A qualified clinician must decide how genomic findings affect individual care."]},"ethics":{"considerations":["Genomic disclosure can expose sensitive information about relatives who did not consent.","Genomic research can distribute benefits unfairly when contributing communities lack a meaningful voice."],"affectedParties":["People whose genomes are recorded and their biological relatives.","Communities contributing genomic information or biological resources."]},"owners":{"steward":"The authorized custodian of the genomic record, accountable to the people or communities with relevant rights.","roles":[],"masterSystems":["Public nucleotide sequence archives and curated genome assembly repositories."]},"relations":[{"target":"Q193395","type":"parent","note":"registry parent class"},{"target":"recording medium","type":"related","note":"in registry terms, though biologists treat it as genetic material"},{"target":"DNA","type":"related","note":"or RNA in some viruses"},{"target":"genomics","type":"related","note":"through sequencing"},{"target":"mitochondrial DNA","type":"related","note":"as an organelle genome"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.genome","Wikidata: Q7020 (https://www.wikidata.org/wiki/Q7020)","MeSH: D016678 genome","GO: GO:0000229 and related genome components"]},"properties":{"applicability":"required","items":["human genome: about 3.1 billion base pairs","human mitochondrial genome: 16569 base pairs","first complete human genome: 2022 year - telomere to telomere"]},"recognition":{"applicability":"required","items":["Complete genetic material of an organism","Nuclear genomes, mitochondrial DNA, kinetoplast DNA, viral RNA genomes","A gene is one unit; the transcriptome is expressed RNA; the proteome is the proteins","Not a visible object; DNA or RNA sequences."]},"capabilities":{"applicability":"required","items":["explain organisation","relay sizes and sequencing","describe organelle genomes","distinguish from related concepts"]},"hazards":{"applicability":"required","items":["Confusing genome with gene or DNA generally","Privacy risks of genomic data","Registry parent treating the genome as a recording medium"]},"interfaces":{"applicability":"required","items":["Genome data sharing standards such as INSDC and GA4GH","Genetic privacy and data protection laws","Biobank and research ethics rules"]},"context":{"applicability":"required","items":["Not applicable; the genetic content of an organism.","nuclear genomes of eukaryotes","bacterial and archaeal genomes","viral DNA and RNA genomes","mitochondrial genomes including those of Leishmania species","kinetoplast DNA networks of trypanosomatids","chloroplast genomes","metagenomes of communities"]}},"sources":[{"title":"Wikidata item Q7020: genome","url":"https://www.wikidata.org/wiki/Q7020","note":"identity and sense of the item"},{"title":"Wikipedia: Genome","url":"https://en.wikipedia.org/wiki/Genome","note":"general description of the item"}],"openQuestions":["Should mitochondrial DNA and human genome be separate primary entries?","How should genomics references be linked?","The registry entry has merged aliases naming specific Leishmania genomes; should they be split off?"],"resources":{"spec":"/models/things/publications/thing-q7020/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q7020/spec.json"],"providers":["Claude"],"researchStatus":"unreviewed","generatedAt":"2026-09-13T04:40:26Z","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 2026-10-08T18:56:50+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass"},"score":1.0}}