{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.wm-liv-020","code":"wm-liv-020-microbiome-biological-community","url":"https://ver.cy/models/wm-liv-020-microbiome-biological-community/","name":"Microbiome / Biological Community","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.MIC"],"industry":["Cross-industry"],"navPath":"NAV.PHY.LIV.MIC","tags":["microbiome","biological","community","phy.liv.mic"],"facets":{}},"whatItIs":"A microbiome or biological community is the set of organisms living together in a defined habitat or host at a sampled time, described through its composition, abundance and function as inferred from samples. The subject is the community as sampled and analysed, with its own sampling lifecycle; single organisms, single taxa and the habitat itself are separate subjects.","purpose":"Community composition has its own sampling lifecycle","scope":{"in":[],"out":[],"boundaries":[]},"distinguishingFeatures":["The unit is an assemblage of many organisms, not a single organism or taxon.","Composition is always relative to a sample, a method and a reference database, so results are method-dependent.","Has its own sampling lifecycle from collection to profile, separate from the population model, its parent.","Distinct from habitat, which describes the place, and from pathogen records, which concern one harmful organism."],"structure":{"bundles":[{"id":"LIV020-B1","name":"Sample and context","description":"Where and how the community was sampled.","layers":[{"id":"LIV020-B1-L1","name":"Sampling event","description":"The sample, its host or environment, time and method.","findings":[{"id":"LIV020-F01","name":"Sample origin","description":"The host or environment, location and time of sampling.","questions":[{"text":"Which host or environment, at which site and time, was sampled?","id":"LIV020-Q01"},{"text":"Which environmental or host metadata were recorded with the sample?","id":"LIV020-Q02"}]},{"id":"LIV020-F02","name":"Collection and preservation","description":"How the sample was collected, stored and transported.","questions":[{"text":"Which collection method and preservation conditions were used?","id":"LIV020-Q03"},{"text":"Could storage or contamination have altered the community before analysis?","id":"LIV020-Q04"}]}]}]},{"id":"LIV020-B2","name":"Composition","description":"Which organisms are present and how abundant they are.","layers":[{"id":"LIV020-B2-L1","name":"Community profile","description":"Taxa and their relative or absolute abundance, from a named method.","findings":[{"id":"LIV020-F03","name":"Profiling method","description":"The sequencing or culture method, reference database and pipeline version.","questions":[{"text":"Was the profile made by amplicon sequencing, shotgun metagenomics or culture?","id":"LIV020-Q05"},{"text":"Which reference database and pipeline version assigned the taxa?","id":"LIV020-Q06"}]},{"id":"LIV020-F04","name":"Abundance and diversity","description":"Abundances and diversity measures with their normalization.","questions":[{"text":"Are abundances relative or absolute, and how were they normalized?","id":"LIV020-Q07"},{"text":"Which diversity measures were calculated, and on which rarefaction or depth?","id":"LIV020-Q08"}]}]}]},{"id":"LIV020-B3","name":"Function and change","description":"What the community does and how it changes.","layers":[{"id":"LIV020-B3-L1","name":"Functional profile and dynamics","description":"Inferred functions and differences between samples over time or conditions.","findings":[{"id":"LIV020-F05","name":"Function and comparison","description":"Gene or pathway content and comparisons across samples.","questions":[{"text":"Which functions or pathways were inferred, and from measured or predicted genes?","id":"LIV020-Q09"},{"text":"Which samples or time points is this community compared with, and is the difference significant?","id":"LIV020-Q10"}]}]}]}]},"agentConduct":{"may":["Record samples with their metadata following community minimum information standards.","Summarize composition and diversity with the method and database version stated.","Compare communities across samples and flag method differences that limit comparison.","Submit sequence data to public archives on the owner's instruction."],"mustNot":["Present microbiome results as a medical diagnosis or treatment advice.","Compare profiles made with incompatible methods as if they were equivalent.","Release human-associated samples with host data that could identify a person.","Infer causation from correlation between community and condition without saying so.","Discard negative controls or contamination evidence from the record."],"requiresHuman":["Releasing data from human hosts for open access.","Interpreting results for a patient's care.","Introducing organisms into an environment or host to change its community."]},"ethics":{"considerations":["Human microbiome data can carry host DNA and health information, so consent and privacy apply.","Overstated health claims from microbiome studies can mislead patients and consumers.","Samples from communities and countries carry benefit-sharing duties under access and benefit-sharing rules."],"affectedParties":["People whose bodies were sampled","Communities and countries providing environmental samples","Researchers and clinicians using the results"]},"owners":{"steward":"The research group or laboratory that collected the samples owns the sample and analysis records.","roles":[],"masterSystems":["International nucleotide sequence archives","Biobank and sample management systems"]},"relations":[{"target":"WM-LIV-003","type":"parent"}],"interaction":{"identity":{"applicability":"required","items":["A sample is identified by its biosample accession in the international sequence archives and the collector's sample code.","Sequence runs and analyses are identified by archive run and project accessions.","Taxa in the profile are identified by taxonomy database identifiers."]},"properties":{"applicability":"required","items":["Relative abundance of each taxon as a proportion or percentage of reads.","Absolute abundance in cells or gene copies per gram or millilitre where measured.","Sequencing depth in reads per sample.","Diversity indices such as Shannon index or observed richness, with the rarefaction depth.","Sample environmental parameters such as temperature in degrees Celsius and pH."]},"recognition":{"applicability":"required","items":["A community is recognized only through sampling and analysis, not by direct observation.","Visible forms such as biofilms, mats or colonies can mark a community but do not show its composition.","Easily confused with a single culture, a contaminated sample or a reagent background signal."]},"capabilities":{"applicability":"required","items":["A community changes in composition with host, diet, treatment, season and environment.","Communities perform functions such as nutrient cycling, digestion or degradation of pollutants."]},"hazards":{"applicability":"required","items":["Samples may contain pathogens and must be handled at the appropriate biosafety level.","Contamination and batch effects can produce false community profiles.","Re-identification of people from host reads in human samples."]},"interfaces":{"applicability":"required","items":["MIxS minimum information standards from the Genomic Standards Consortium.","International Nucleotide Sequence Database Collaboration archives for raw reads and samples.","BIOM format for community abundance tables."]},"context":{"applicability":"required","items":["Studied in human and animal health, soil, water, food production and industrial processes.","Access to environmental samples across borders falls under the Nagoya Protocol where it applies."]}},"sources":[{"title":"Minimum Information about any (x) Sequence (MIxS), Genomic Standards Consortium"},{"title":"International Nucleotide Sequence Database Collaboration (INSDC)"},{"title":"Nagoya Protocol on Access and Benefit-sharing, Convention on Biological Diversity"}],"openQuestions":["Planned model: boundary questions, research and every section remain to be written."],"resources":{"spec":"https://ver.cy/models/wm-liv-020-microbiome-biological-community/spec.yaml","agents":"https://ver.cy/models/wm-liv-020-microbiome-biological-community/AGENTS.md"},"provenance":{"origin":"planned (registry candidate)","builtFrom":["models/runtime-index.json","ver-cy/world-models/card-supplements/wm-liv-020-microbiome-biological-community.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":"filled","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.","_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}}