{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.wm-liv-011","code":"wm-liv-011-genome-genomic-assembly","url":"https://ver.cy/models/wm-liv-011-genome-genomic-assembly/","name":"Genome / Genomic Assembly","alternateNames":[],"kind":"world-model","status":"todo","version":"unversioned","language":"en","classifiers":{"family":"World Models","category":"Physical world and living systems","entryKind":"standalone-mm","plane":"","domain":["PHY.LIV.MOL"],"industry":["Cross-industry"],"navPath":"NAV.PHY.LIV.MOL","tags":["genome","genomic","assembly","phy.liv.mol"],"facets":{}},"whatItIs":"A genome assembly is a versioned reconstruction of the genome sequence of an organism or individual from sequencing reads, organized into contigs, scaffolds and chromosomes and used as a reference for coordinates and annotation. The class covers the assembly as a reference with its quality and version history; the physical DNA, single sequencing runs and gene annotations built on the assembly are separate subjects.","purpose":"Versioned genome-level biological reference","scope":{"in":[],"out":[],"boundaries":[]},"distinguishingFeatures":["It is a versioned reference sequence, not the physical DNA or a single sequencing run.","Coordinates are meaningful only with the assembly version, so annotations and variants must cite it.","It differs from a genome annotation, which describes features placed on the assembly.","Assemblies of human individuals carry personal data duties that species reference assemblies usually do not."],"structure":{"bundles":[{"id":"LIV011-B1","name":"Assembly identity","description":"Which assembly, of which organism and in which version.","layers":[{"id":"LIV011-B1-L1","name":"Source and version","description":"The organism, sample and assembly version.","findings":[{"id":"LIV011-F01","name":"Source organism","description":"The taxon and sample from which the assembly was built.","questions":[{"text":"Which taxon and which specimen or sample was sequenced?","id":"LIV011-Q01"},{"text":"Is the source sample deposited in a collection or biobank with an identifier?","id":"LIV011-Q02"}]},{"id":"LIV011-F02","name":"Version lineage","description":"The assembly version and what changed from the previous one.","questions":[{"text":"Which assembly version is this, and which version did it replace?","id":"LIV011-Q03"},{"text":"Are patches or coordinate changes documented between versions?","id":"LIV011-Q04"}]}]}]},{"id":"LIV011-B2","name":"Assembly quality","description":"How complete and correct the assembly is.","layers":[{"id":"LIV011-B2-L1","name":"Contiguity and completeness","description":"Measures of contiguity, completeness and error.","findings":[{"id":"LIV011-F03","name":"Quality metrics","description":"Contiguity, completeness and base accuracy measures.","questions":[{"text":"What contig and scaffold N50, gap count and total length are reported?","id":"LIV011-Q05"},{"text":"How complete is the assembly against a conserved gene set, and how was this measured?","id":"LIV011-Q06"}]},{"id":"LIV011-F04","name":"Method","description":"Sequencing technologies and assembly method.","questions":[{"text":"Which sequencing technologies and coverage depth were used?","id":"LIV011-Q07"},{"text":"Which assembly method and version produced the assembly?","id":"LIV011-Q08"}]}]}]},{"id":"LIV011-B3","name":"Use and access","description":"How the assembly is deposited, cited and used.","layers":[{"id":"LIV011-B3-L1","name":"Deposition and terms","description":"Archive deposition and the terms of use.","findings":[{"id":"LIV011-F05","name":"Public record","description":"The archive accession and any use restrictions.","questions":[{"text":"Under which archive accession is the assembly deposited?","id":"LIV011-Q09"},{"text":"Does the assembly come from a human individual, and what consent and access terms apply?","id":"LIV011-Q10"}]}]}]}]},"agentConduct":{"may":["Retrieve public assemblies by accession and report their version and quality metrics.","Convert coordinates between assembly versions using published mappings.","Compare assemblies and report differences in contiguity and completeness.","Flag annotations or variants that do not state their assembly version."],"mustNot":["Mix coordinates from different assembly versions without conversion.","Share an assembly of an identifiable human individual outside its consent and access terms.","Attempt to re-identify individuals from genomic data.","Overwrite a published assembly version instead of issuing a new one."],"requiresHuman":["Releasing a human individual assembly or granting controlled access to it.","Adopting a new reference assembly version for clinical or production use.","Resolving disputes about sample origin and benefit sharing for genetic resources."]},"ethics":{"considerations":["Human genome data is identifying and reveals information about relatives as well as the donor.","Genetic resources from a country or community can carry access and benefit-sharing obligations.","Reference assemblies that represent few populations can bias research and clinical results."],"affectedParties":["Donors of human samples and their relatives","Countries and communities providing genetic resources","Researchers and clinicians using the reference"]},"owners":{"steward":"The sequencing consortium or research group that produced the assembly, with archive curators maintaining the deposited record.","roles":[],"masterSystems":["International nucleotide sequence archives","Genome assembly databases","Controlled-access archives for human genomic data"]},"relations":[{"target":"WM-LIV-002","type":"parent"}],"interaction":{"identity":{"applicability":"required","items":["An assembly is identified by its archive accession with version, such as an INSDC assembly accession.","Well-known references also carry assembly names; the source organism is identified by a taxonomy identifier."]},"properties":{"applicability":"not-applicable","items":[]},"recognition":{"applicability":"optional","items":["An assembly is recognized by its sequence files, an accession with version and an assembly report.","Often confused with raw sequencing reads, with a gene annotation or with the physical specimen."]},"capabilities":{"applicability":"required","items":["Serves as a coordinate system for genes, variants and other annotations.","Can be compared with other assemblies to find structural differences.","Can be updated by patches or new versions with documented coordinate changes."]},"hazards":{"applicability":"required","items":["Wrong variant calls or annotations when coordinates from different versions are mixed.","Re-identification of donors from human genomic data.","Misleading results from contaminated or misassembled regions."]},"interfaces":{"applicability":"required","items":["FASTA for sequences and AGP for the placement of contigs into scaffolds.","INSDC archive submission and retrieval services.","GA4GH standards such as refget for sequence retrieval and data access."]},"context":{"applicability":"required","items":["Used in genomics research, breeding, biodiversity science and clinical genetics.","Human genomic data is subject to data protection law, and genetic resources may fall under the Nagoya Protocol."]}},"sources":[{"title":"International Nucleotide Sequence Database Collaboration (INSDC)"},{"title":"Genome Reference Consortium"},{"title":"Global Alliance for Genomics and Health (GA4GH) standards"}],"openQuestions":["Planned model: boundary questions, research and every section remain to be written."],"resources":{"spec":"https://ver.cy/models/wm-liv-011-genome-genomic-assembly/spec.yaml","agents":"https://ver.cy/models/wm-liv-011-genome-genomic-assembly/AGENTS.md"},"provenance":{"origin":"planned (registry candidate)","builtFrom":["models/runtime-index.json","ver-cy/world-models/card-supplements/wm-liv-011-genome-genomic-assembly.json"],"providers":[],"researchStatus":"todo","generatedAt":"","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":"not-applicable","interaction.recognition":"filled","interaction.capabilities":"filled","interaction.hazards":"filled","interaction.interfaces":"filled","interaction.context":"filled","sources":"filled"},"notes":{"_":"Planned entry, hidden from the catalogue until researched.","interaction.properties":"A genome assembly is a digital sequence reference; physical measurements belong to the DNA sample, and assembly quality metrics are recorded in the structure.","_supplement":"Sections authored in card supplement 1.0.0 by Claude (Opus 5.5) (2026-10-06, unreviewed). Written from the card's existing content and established practice in the field; no new sources were read. Unreviewed."},"score":1.0}}