{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.wm-liv-016","code":"wm-liv-016-biological-pathway-process","url":"https://ver.cy/models/wm-liv-016-biological-pathway-process/","name":"Biological Pathway / Process","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":["biological","pathway","process","phy.liv.mol"],"facets":{}},"whatItIs":"A biological pathway is a reusable description of a molecular or cellular process: an ordered set of reactions, interactions and regulatory steps among genes, proteins and small molecules that produce a biological function. It is a curated model of how a process works in a taxon, not a measurement in one sample and not the whole organism.","purpose":"Reusable molecular and cellular process context","scope":{"in":[],"out":[],"boundaries":[]},"distinguishingFeatures":["It is a curated, reusable model of a process, not an observation in a single sample or experiment.","It connects many genes, proteins and metabolites; a single gene or protein has its own model.","Phenotypes and diseases may result from pathway changes but are described in their own models.","Its taxonomic scope must be stated, because pathways are often inferred across species."],"structure":{"bundles":[{"id":"LIV016-B1","name":"Pathway identity","description":"Which process is described and for which organisms.","layers":[{"id":"LIV016-B1-L1","name":"Definition and scope","description":"The process the pathway represents and its taxonomic scope.","findings":[{"id":"LIV016-F01","name":"Pathway reference","description":"The pathway with its database identifier, name and version.","questions":[{"text":"Which pathway database and identifier define this pathway?","id":"LIV016-Q01"},{"text":"Which version or release of the pathway is used?","id":"LIV016-Q02"}]},{"id":"LIV016-F02","name":"Taxonomic scope","description":"The organisms for which the pathway is curated or inferred.","questions":[{"text":"For which species is the pathway curated?","id":"LIV016-Q03"},{"text":"Was it inferred from another species by orthology, and from which?","id":"LIV016-Q04"}]}]}]},{"id":"LIV016-B2","name":"Pathway content","description":"The participants and steps that make up the process.","layers":[{"id":"LIV016-B2-L1","name":"Participants","description":"Genes, proteins, complexes and small molecules in the pathway.","findings":[{"id":"LIV016-F03","name":"Participant list","description":"Each participant with its identifier in a reference database.","questions":[{"text":"Which genes, proteins and metabolites take part, by reference identifier?","id":"LIV016-Q05"},{"text":"Are participants given as specific forms, such as modified proteins or complexes?","id":"LIV016-Q06"}]}]},{"id":"LIV016-B2-L2","name":"Reactions and regulation","description":"The steps, their order and the regulation acting on them.","findings":[{"id":"LIV016-F04","name":"Reaction steps","description":"Reactions or interactions with inputs, outputs, catalysts and regulators.","questions":[{"text":"Which reactions make up the pathway, and in what order?","id":"LIV016-Q07"},{"text":"Which participants catalyse or regulate each step?","id":"LIV016-Q08"}]}]}]},{"id":"LIV016-B3","name":"Evidence","description":"How the pathway knowledge is supported.","layers":[{"id":"LIV016-B3-L1","name":"Curation and evidence","description":"The literature and experimental evidence behind each step.","findings":[{"id":"LIV016-F05","name":"Supporting evidence","description":"The publications and evidence codes that support each step.","questions":[{"text":"Which publications support each step, and with what kind of evidence?","id":"LIV016-Q09"},{"text":"Who curated the pathway, and when was it last reviewed?","id":"LIV016-Q10"}]}]}]}]},"agentConduct":{"may":["Look up pathways and their participants by reference identifiers.","Map experimental results onto pathways for interpretation.","Report which steps of a pathway are supported by which evidence.","Flag pathways inferred by orthology rather than curated for the species."],"mustNot":["Present an inferred pathway as experimentally established for the species.","Merge pathways from different databases without keeping their identifiers and versions.","Give guidance for enhancing the harmfulness or transmissibility of pathogens.","Use pathway analysis results as a clinical diagnosis.","Strip curator attribution or licence terms from pathway data."],"requiresHuman":["Using pathway analysis to support a clinical or regulatory decision.","Publishing a new or changed curated pathway.","Resolving conflicting evidence between curation sources."]},"ethics":{"considerations":["Pathway knowledge drives drug discovery, and errors can mislead research for years.","Some pathway knowledge on pathogens is dual-use and needs responsible handling.","Curators' work should be credited and licences respected."],"affectedParties":["Researchers and curators","Patients affected by research based on pathway models","Pathway database maintainers"]},"owners":{"steward":"A curated pathway knowledge base or research consortium that maintains the pathway and its evidence.","roles":[],"masterSystems":["Curated pathway databases","Gene and protein reference databases"]},"relations":[{"target":"WM-LIV-002","type":"parent"}],"interaction":{"identity":{"applicability":"required","items":["A pathway is identified by its stable identifier in a pathway database, with version.","Participants are identified by reference identifiers such as gene, protein and chemical entity identifiers.","Process terms can be mapped to Gene Ontology biological process terms."]},"properties":{"applicability":"not-applicable","items":[]},"recognition":{"applicability":"optional","items":["A pathway record names a process, a set of participants with identifiers and a taxonomic scope.","Often confused with a gene set without reactions, or with an interaction network without order."]},"capabilities":{"applicability":"required","items":["Pathways can be queried by participant, process term or species.","Experimental data can be overlaid on pathways for enrichment analysis.","Pathways can be exchanged between tools in standard formats."]},"hazards":{"applicability":"required","items":["Misinterpretation of enrichment results as causal evidence.","Propagation of errors from inferred pathways into downstream research.","Dual-use misuse of pathogen pathway knowledge."]},"interfaces":{"applicability":"required","items":["BioPAX for pathway data exchange.","Systems Biology Markup Language (SBML) for computational models.","Gene Ontology for biological process terms."]},"context":{"applicability":"required","items":["Used in molecular biology, systems biology, drug discovery and the interpretation of omics data.","Pathway knowledge is curated in public databases with their own licences."]}},"sources":[{"title":"Gene Ontology, Gene Ontology Consortium","url":"https://geneontology.org/"},{"title":"BioPAX Biological Pathway Exchange, BioPAX community"},{"title":"Reactome pathway knowledgebase","url":"https://reactome.org/"}],"openQuestions":["Planned model: boundary questions, research and every section remain to be written."],"resources":{"spec":"https://ver.cy/models/wm-liv-016-biological-pathway-process/spec.yaml","agents":"https://ver.cy/models/wm-liv-016-biological-pathway-process/AGENTS.md"},"provenance":{"origin":"planned (registry candidate)","builtFrom":["models/runtime-index.json","ver-cy/world-models/card-supplements/wm-liv-016-biological-pathway-process.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 pathway is an abstract model of a process, not a physical object with measurable properties.","_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}}