{ "card": { "schema": "https://ver.cy/schemas/card/1.0.0", "id": "vr.tr.biological-database", "code": "thing-q4117139", "url": "https://ver.cy/models/thing/q4117139/", "name": "biological database", "alternateNames": [ "The NAR online Molecular Biology Database Collection Categories", "stem cell registry", "trait database", "biodiversity database", "DNA database", "sequence database", "enzyme database", "global species database", "protein structure database", "RNA modification database", "taxonomic database", "national DNA database", "protein database", "gene database" ], "kind": "thing", "status": "draft-generated", "version": "vr.draft.v3", "language": "en", "classifiers": { "family": "Thing Registry", "category": "Information and virtual systems", "entryKind": "work, medium or creative form", "plane": "INF", "domain": [ "INF.MED" ], "industry": [], "navPath": "", "tags": [], "facets": [] }, "whatItIs": "An informational thing registered under INF.MED. The registry names it; this draft has not been given a definition yet.", "purpose": "Give an agent a durable, checkable way to recognise a biological database, record what state it is in, and decide what may be done with it.", "scope": { "in": [], "out": [], "boundaries": [] }, "distinguishingFeatures": [ "Names folded into this entry, which a task may need to split apart again: The NAR online Molecular Biology Database Collection Categories, stem cell registry, trait database, biodiversity database, DNA database, sequence database, enzyme database, global species database, protein structure database, RNA modification database, taxonomic database, national DNA database.", "14 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 12 Wikipedia languages, which is a measure of how widely the thing is known, not of how important it is." ], "structure": { "bundles": [ { "id": "identity-and-classification", "name": "Identity, naming and classification", "description": "How an agent tells one biological database from another, and a biological database from things that resemble it.", "rationale": "Recognition comes before every other claim. Without stable identity nothing else in the model can be trusted to be about the same thing twice.", "layers": [ { "id": "naming-and-identifiers", "name": "Names and identifiers", "description": "The names this thing goes by and the identifiers that survive translation and time.", "findings": [ { "id": "preferred-name-and-aliases", "name": "Preferred name, aliases and local names", "description": "Which name to use, which names mean the same thing, and which merely sound similar.", "questions": [ { "id": "preferred-name-and-aliases-q01", "text": "What identifies and describes the name of a biological database, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "preferred-name-and-aliases-q02", "text": "Who or what asserted this about the name of a biological database, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "preferred-name-and-aliases-q03", "text": "What may an agent decide or do once the name of a biological database is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "stable-identifiers", "name": "Stable identifiers and external keys", "description": "Identifiers that keep pointing at this kind of thing across systems and languages.", "questions": [ { "id": "stable-identifiers-q01", "text": "What identifies and describes an identifier for a biological database, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stable-identifiers-q02", "text": "Who or what asserted this about an identifier for a biological database, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stable-identifiers-q03", "text": "What may an agent decide or do once an identifier for a biological database is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "classification-and-granularity", "name": "Classification and granularity", "description": "Where a biological database sits among kinds, and how finely a task needs to cut it.", "findings": [ { "id": "kind-and-parents", "name": "Kind, parents and neighbouring kinds", "description": "The classes this thing belongs to and the ones it is next to.", "questions": [ { "id": "kind-and-parents-q01", "text": "What identifies and describes the kind of a biological database, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "kind-and-parents-q02", "text": "Who or what asserted this about the kind of a biological database, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "kind-and-parents-q03", "text": "What may an agent decide or do once the kind of a biological database is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "distinguishing-features", "name": "Distinguishing features", "description": "What separates a biological database from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a biological database, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "distinguishing-features-q02", "text": "Who or what asserted this about what distinguishes a biological database, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "distinguishing-features-q03", "text": "What may an agent decide or do once what distinguishes a biological database is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "state-and-lifecycle", "name": "State and lifecycle", "description": "The states a biological database passes through and the events that move it between them.", "rationale": "Most decisions about a thing depend on what state it is in now, which is a claim with a time on it, not a property.", "layers": [ { "id": "lifecycle-stages", "name": "Lifecycle stages", "description": "From coming into existence to ceasing to be one of these.", "findings": [ { "id": "stages-and-transitions", "name": "Stages and transitions", "description": "The stages worth naming and what moves a biological database between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a biological database, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stages-and-transitions-q02", "text": "Who or what asserted this about the lifecycle of a biological database, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stages-and-transitions-q03", "text": "What may an agent decide or do once the lifecycle of a biological database is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "observations-and-status", "name": "Observations and current status", "description": "What is observed about a biological database, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a biological database is recorded so that it can be superseded rather than overwritten.", "questions": [ { "id": "observation-record-q01", "text": "What identifies and describes an observation of a biological database, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "observation-record-q02", "text": "Who or what asserted this about an observation of a biological database, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "observation-record-q03", "text": "What may an agent decide or do once an observation of a biological database is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "content-and-access", "name": "Content, encoding and access", "description": "What a biological database says, how it is encoded and who may read it.", "rationale": "An informational thing carries content that can be copied, versioned and withheld, none of which its physical carrier explains.", "layers": [ { "id": "content-and-encoding", "name": "Content and encoding", "description": "The content itself, its format and its language.", "findings": [ { "id": "content-and-format", "name": "Content, format and language", "description": "What a biological database contains and in what form it is held.", "questions": [ { "id": "content-and-format-q01", "text": "What identifies and describes the content of a biological database, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "content-and-format-q02", "text": "Who or what asserted this about the content of a biological database, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "content-and-format-q03", "text": "What may an agent decide or do once the content of a biological database is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "access-and-rights", "name": "Access, rights and retention", "description": "Who may read, copy or change it, and for how long it is kept.", "findings": [ { "id": "access-rules", "name": "Access rules and retention", "description": "The permissions attached to a biological database and the period it survives.", "questions": [ { "id": "access-rules-q01", "text": "What identifies and describes access to a biological database, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "access-rules-q02", "text": "Who or what asserted this about access to a biological database, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "access-rules-q03", "text": "What may an agent decide or do once access to a biological database is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "work-and-manifestation", "name": "Work, version and copy", "description": "Which level of biological database a statement is about.", "rationale": "The work, the edition, the file and the copy in hand are four things; rights and content attach to different ones.", "layers": [ { "id": "levels", "name": "Levels of the thing", "description": "Work, expression, manifestation and item, in plain terms.", "findings": [ { "id": "level-rules", "name": "What belongs at each level", "description": "Which facts hold for the work and which only for one copy.", "questions": [ { "id": "level-rules-q01", "text": "For biological database, which facts belong to the work itself, which to a version, and which to a single copy?", "kind": "boundary" }, { "id": "level-rules-q02", "text": "What identifier exists at each level, and which one is being cited?", "kind": "definition" } ] } ] }, { "id": "versions", "name": "Versions, editions and variants", "description": "How versions differ and which is canonical to whom.", "findings": [ { "id": "version-record", "name": "Versions and canonicity", "description": "Differences that matter and who calls one authoritative.", "questions": [ { "id": "version-record-q01", "text": "Which versions or editions of biological database exist, and how do they differ substantively?", "kind": "definition" }, { "id": "version-record-q02", "text": "Who treats which version as authoritative, and for what purpose?", "kind": "provenance" } ] } ] } ] }, { "id": "authorship-and-rights", "name": "Authorship, rights and permitted use", "description": "Who made biological database and what may be done with it.", "rationale": "Rights are jurisdictional, time-limited and attached to a level, and an agent that ignores that will copy what it may not.", "layers": [ { "id": "authorship", "name": "Authorship and contribution", "description": "Who contributed what, and in what capacity.", "findings": [ { "id": "contribution-record", "name": "Contributors and roles", "description": "The people and bodies behind it, with their roles.", "questions": [ { "id": "contribution-record-q01", "text": "Who authored or contributed to biological database, in what roles, and how is that attested?", "kind": "provenance" }, { "id": "contribution-record-q02", "text": "Where authorship is disputed or anonymous, what is recorded instead?", "kind": "boundary" } ] } ] }, { "id": "rights", "name": "Rights and permissions", "description": "Which rights subsist, where, until when, and what they permit.", "findings": [ { "id": "rights-record", "name": "Rights, term and permitted acts", "description": "The regime in force and what it allows.", "questions": [ { "id": "rights-record-q01", "text": "What rights subsist in biological database, in which jurisdictions, and until when?", "kind": "definition" }, { "id": "rights-record-q02", "text": "Which acts are permitted without further permission, and which must an agent refuse?", "kind": "action" } ] } ] } ] }, { "id": "provenance-and-evidence", "name": "Provenance, evidence and time", "description": "Where every claim about a biological database came from and when it held.", "rationale": "A claim without a source and a time cannot be superseded, only overwritten, and an agent that overwrites loses the ability to explain itself.", "layers": [ 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"evidence", "event time", "knowledge time" ] }, { "id": "preferred-name-and-aliases-q03", "text": "What may an agent decide or do once the name of a biological database is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "stable-identifiers", "name": "Stable identifiers and external keys", "description": "Identifiers that keep pointing at this kind of thing across systems and languages.", "questions": [ { "id": "stable-identifiers-q01", "text": "What identifies and describes an identifier for a biological database, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stable-identifiers-q02", "text": "Who or what asserted this about an identifier for a biological database, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stable-identifiers-q03", "text": "What may an agent decide or do once an identifier for a biological database is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "classification-and-granularity", "name": "Classification and granularity", "description": "Where a biological database sits among kinds, and how finely a task needs to cut it.", "findings": [ { "id": "kind-and-parents", "name": "Kind, parents and neighbouring kinds", "description": "The classes this thing belongs to and the ones it is next to.", "questions": [ { "id": "kind-and-parents-q01", "text": "What identifies and describes the kind of a biological database, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "kind-and-parents-q02", "text": "Who or what asserted this about the kind of a biological database, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "kind-and-parents-q03", "text": "What may an agent decide or do once the kind of a biological database is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "distinguishing-features", "name": "Distinguishing features", "description": "What separates a biological database from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a biological database, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "distinguishing-features-q02", "text": "Who or what asserted this about what distinguishes a biological database, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "distinguishing-features-q03", "text": "What may an agent decide or do once what distinguishes a biological database is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "state-and-lifecycle", "name": "State and lifecycle", "description": "The states a biological database passes through and the events that move it between them.", "rationale": "Most decisions about a thing depend on what state it is in now, which is a claim with a time on it, not a property.", "layers": [ { "id": "lifecycle-stages", "name": "Lifecycle stages", "description": "From coming into existence to ceasing to be one of these.", "findings": [ { "id": "stages-and-transitions", "name": "Stages and transitions", "description": "The stages worth naming and what moves a biological database between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a biological database, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stages-and-transitions-q02", "text": "Who or what asserted this about the lifecycle of a biological database, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stages-and-transitions-q03", "text": "What may an agent decide or do once the lifecycle of a biological database is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "observations-and-status", "name": "Observations and current status", "description": "What is observed about a biological database, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a biological database is recorded so that it can be superseded rather than overwritten.", "questions": [ { "id": "observation-record-q01", "text": "What identifies and describes an observation of a biological database, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "observation-record-q02", "text": "Who or what asserted this about an observation of a biological database, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "observation-record-q03", "text": "What may an agent decide or do once an observation of a biological database is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "content-and-access", "name": "Content, encoding and access", "description": "What a biological database says, how it is encoded and who may read it.", "rationale": "An informational thing carries content that can be copied, versioned and withheld, none of which its physical carrier explains.", "layers": [ { "id": "content-and-encoding", "name": "Content and encoding", "description": "The content itself, its format and its language.", "findings": [ { "id": "content-and-format", "name": "Content, format and language", "description": "What a biological database contains and in what form it is held.", "questions": [ { "id": "content-and-format-q01", "text": "What identifies and describes the content of a biological database, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "content-and-format-q02", "text": "Who or what asserted this about the content of a biological database, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "content-and-format-q03", "text": "What may an agent decide or do once the content of a biological database is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "access-and-rights", "name": "Access, rights and retention", "description": "Who may read, copy or change it, and for how long it is kept.", "findings": [ { "id": "access-rules", "name": "Access rules and retention", "description": "The permissions attached to a biological database and the period it survives.", "questions": [ { "id": "access-rules-q01", "text": "What identifies and describes access to a biological database, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "access-rules-q02", "text": "Who or what asserted this about access to a biological database, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "access-rules-q03", "text": "What may an agent decide or do once access to a biological database is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "work-and-manifestation", "name": "Work, version and copy", "description": "Which level of biological database a statement is about.", "rationale": "The work, the edition, the file and the copy in hand are four things; rights and content attach to different ones.", "layers": [ { "id": "levels", "name": "Levels of the thing", "description": "Work, expression, manifestation and item, in plain terms.", "findings": [ { "id": "level-rules", "name": "What belongs at each level", "description": "Which facts hold for the work and which only for one copy.", "questions": [ { "id": "level-rules-q01", "text": "For biological database, which facts belong to the work itself, which to a version, and which to a single copy?", "kind": "boundary" }, { "id": "level-rules-q02", "text": "What identifier exists at each level, and which one is being cited?", "kind": "definition" } ] } ] }, { "id": "versions", "name": "Versions, editions and variants", "description": "How versions differ and which is canonical to whom.", "findings": [ { "id": "version-record", "name": "Versions and canonicity", "description": "Differences that matter and who calls one authoritative.", "questions": [ { "id": "version-record-q01", "text": "Which versions or editions of biological database exist, and how do they differ substantively?", "kind": "definition" }, { "id": "version-record-q02", "text": "Who treats which version as authoritative, and for what purpose?", "kind": "provenance" } ] } ] } ] }, { "id": "authorship-and-rights", "name": "Authorship, rights and permitted use", "description": "Who made biological database and what may be done with it.", "rationale": "Rights are jurisdictional, time-limited and attached to a level, and an agent that ignores that will copy what it may not.", "layers": [ { "id": "authorship", "name": "Authorship and contribution", "description": "Who contributed what, and in what capacity.", "findings": [ { "id": "contribution-record", "name": "Contributors and roles", "description": "The people and bodies behind it, with their roles.", "questions": [ { "id": "contribution-record-q01", "text": "Who authored or contributed to biological database, in what roles, and how is that attested?", "kind": "provenance" }, { "id": "contribution-record-q02", "text": "Where authorship is disputed or anonymous, what is recorded instead?", "kind": "boundary" } ] } ] }, { "id": "rights", "name": "Rights and permissions", "description": "Which rights subsist, where, until when, and what they permit.", "findings": [ { "id": "rights-record", "name": "Rights, term and permitted acts", "description": "The regime in force and what it allows.", "questions": [ { "id": "rights-record-q01", "text": "What rights subsist in biological database, in which jurisdictions, and until when?", "kind": "definition" }, { "id": "rights-record-q02", "text": "Which acts are permitted without further permission, and which must an agent refuse?", "kind": "action" } ] } ] } ] }, { "id": "provenance-and-evidence", "name": "Provenance, evidence and time", "description": "Where every claim about a biological database came from and when it held.", "rationale": "A claim without a source and a time cannot be superseded, only overwritten, and an agent that overwrites loses the ability to explain itself.", "layers": [ { "id": "source-and-authority", "name": "Source and authority", "description": "Who said it, on what evidence, and how strongly.", "findings": [ { "id": "claim-provenance", "name": "Claim provenance and confidence", "description": "The authority behind each claim about a biological database and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a biological database, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "claim-provenance-q02", "text": "Who or what asserted this about a claim about a biological database, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "claim-provenance-q03", "text": "What may an agent decide or do once a claim about a biological database is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "time-and-versions", "name": "Time, versions and supersession", "description": "When a claim was true, when it was learnt, and what replaced it.", "findings": [ { "id": "validity-and-supersession", "name": "Validity period and supersession", "description": "How an old claim about a biological database is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a biological database, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "validity-and-supersession-q02", "text": "Who or what asserted this about the validity of a claim about a biological database, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "validity-and-supersession-q03", "text": "What may an agent decide or do once the validity of a claim about a biological database is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 6, "layers": 12, "findings": 14, "questions": 38 } } } }