{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.biological-pathway","code":"thing-q4915012","url":"https://ver.cy/models/thing/q4915012/","name":"biological pathway","alternateNames":["anticoagulation","cellular pathway","transcriptional pathway","dispersal pathway","tumor invasion pathway","classic metabolic pathway","disease pathway","drug pathway","regulatory pathway","signaling pathway"],"kind":"thing","status":"published","version":"0.2.0-wave.5","language":"en","classifiers":{"family":"Thing Registry","category":"Activities and processes","entryKind":"thing","plane":"ACT","domain":["ACT.PRC"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"A set of interconnected molecular reactions and interactions in a cell or organism, such as metabolic, signalling or gene-regulatory pathways, delineated as a model for studying how biomolecules work together to produce a function.","purpose":"Let an agent describe biological pathways, find them in curated databases with identifiers, and explain their components and roles in health and disease.","scope":{"in":[],"out":[],"boundaries":[]},"distinguishingFeatures":["A model: manually curated or computationally inferred, with boundaries set by each database and purpose.","Metabolic pathways transform molecules; signalling pathways transmit information; regulatory pathways control gene expression.","The same pathway can be represented differently in different databases."],"structure":{"bundles":[{"id":"identity","name":"Identity","description":"Which pathway.","layers":[{"id":"database-record","name":"Database record","description":"Database and ID.","findings":[{"id":"pathway-record","name":"Pathway record","description":"Database, ID and version.","questions":[{"text":"Which database record describes the pathway?","kind":"provenance"},{"text":"Which version and species?","kind":"provenance"}]}]},{"id":"kind","name":"Kind","description":"Metabolic, signalling, regulatory.","findings":[{"id":"pathway-kind","name":"Pathway kind","description":"Kind.","questions":[{"text":"What kind of pathway is it?","kind":"definition"},{"text":"Which process does it serve?","kind":"definition"}]}]}]},{"id":"components","name":"Components","description":"Parts and steps.","layers":[{"id":"participants","name":"Participants","description":"Genes, proteins, metabolites.","findings":[{"id":"participant","name":"Participant","description":"Molecule and role.","questions":[{"text":"Which molecules take part?","kind":"provenance"},{"text":"In which roles?","kind":"definition"}]}]},{"id":"reactions","name":"Reactions","description":"Steps and interactions.","findings":[{"id":"reaction","name":"Reaction","description":"Reaction, direction, catalysts and regulators, compartment and cell context, experimental or inferred evidence.","questions":[{"text":"Which reactions make up the pathway?","kind":"provenance"},{"text":"What evidence supports each?","kind":"provenance"}]}]}]},{"id":"analysis","name":"Analysis","description":"Using pathways in data analysis.","layers":[{"id":"enrichment","name":"Enrichment","description":"Pathway enrichment.","findings":[{"id":"enrichment-result","name":"Enrichment result","description":"Method and statistics.","questions":[{"text":"Which method and database version were used?","kind":"provenance"},{"text":"What correction for multiple testing?","kind":"measurement"}]}]},{"id":"modelling","name":"Modelling","description":"Quantitative models.","findings":[{"id":"model","name":"Model","description":"Format and parameters.","questions":[{"text":"Is there a quantitative model?","kind":"provenance"},{"text":"In which format?","kind":"provenance"}]}]}]},{"id":"biomedical-relevance","name":"Biomedical relevance","description":"Disease and drugs.","layers":[{"id":"disease","name":"Disease","description":"Pathway in disease.","findings":[{"id":"disease-link","name":"Disease link","description":"Disease and evidence.","questions":[{"text":"Which diseases involve the pathway?","kind":"provenance"},{"text":"What is the evidence?","kind":"provenance"}]}]},{"id":"drugs","name":"Drugs","description":"Drug targets.","findings":[{"id":"drug-target","name":"Drug target","description":"Drug and target.","questions":[{"text":"Which drugs act on the pathway?","kind":"provenance"},{"text":"At which step?","kind":"provenance"}]}]}]}]},"agentConduct":{"may":["describe pathways with database identifiers"],"mustNot":["present pathway models as complete reality","give medical advice from pathway data"],"requiresHuman":[]},"ethics":{"considerations":["accuracy","open data"],"affectedParties":["researchers"]},"owners":{"steward":"nobody as a concept; each database curates its own pathway models","roles":[],"masterSystems":["Reactome","KEGG","WikiPathways"]},"relations":[{"target":"Q2996394","type":"parent","note":"registry parent class"},{"target":"biological process model","type":"related","note":"model"},{"target":"biochemical reaction","type":"contains","note":"steps"},{"target":"pathway database","type":"related","note":"Reactome, KEGG, WikiPathways"},{"target":"Gene Ontology biological process","type":"related","note":"annotation"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.biological-pathway","Wikidata: Q4915012 (https://www.wikidata.org/wiki/Q4915012)","Reactome stable ID: R-HSA-<number>, optionally .<version> human pathways; check the record type is Pathway","KEGG pathway ID: map##### or hsa#####","WikiPathways ID: WP<number>, for example WP732 revision recorded separately"]},"properties":{"applicability":"not-applicable","items":[]},"recognition":{"applicability":"optional","items":["Shown as diagrams of molecules connected by reactions and interactions"]},"capabilities":{"applicability":"required","items":["identify a pathway and its database records","list components and steps","explain pathway enrichment analysis in general terms","link pathways to diseases and drugs with sources"]},"hazards":{"applicability":"required","items":["Over-interpreting enrichment results","Mixing pathway versions and species"]},"interfaces":{"applicability":"required","items":["BioPAX and SBGN exchange and notation standards","Systems Biology Markup Language (SBML)"]},"context":{"applicability":"required","items":["Organising knowledge of molecular mechanisms for research, drug discovery and data analysis.","metabolic pathway","signalling pathway","gene-regulatory pathway","disease pathway"]}},"sources":[{"title":"Q4915012","url":"https://www.wikidata.org/wiki/Q4915012","note":"identity of the registry item, labels and sitelinks"},{"title":"Biological pathway","url":"https://en.wikipedia.org/wiki/Biological_pathway","note":"general description of the subject"},{"title":"Biological Pathways Fact Sheet","url":"https://www.genome.gov/about-genomics/fact-sheets/Biological-Pathways-Fact-Sheet","note":"Definition, metabolic and regulatory kinds, interconnected boundaries and disease and drug research applications."},{"title":"Explain the identifiers associated with entities and events","url":"https://release.reactome.org/documentation/faq/37-general-website/201-identifiers","note":"Stable identifier structure, versions, species codes and manually annotated versus computationally inferred events."},{"title":"KEGG PATHWAY Database","url":"https://www.genome.jp/kegg/pathway.html","note":"Pathway categories, reference and organism-specific maps, and prefix-plus-five-digit identifiers."},{"title":"WikiPathways identifier registry","url":"https://www.bioregistry.io/registry/wikipathways","note":"Variable-length WikiPathways identifiers and revision-qualified forms."},{"title":"BioPAX Level 3 Documentation","url":"https://www.biopax.org/release/biopax-level3-documentation.pdf","note":"Pathway exchange, molecular context and the complementary roles of BioPAX, SBGN and SBML."},{"title":"SBML Specifications","url":"https://sbml.org/documents/specifications/","note":"SBML as a model representation standard, including quantitative and qualitative model types."}],"openQuestions":["The registry merges specific processes and ecological dispersal pathways; they need registry corrections."],"resources":{"spec":"/models/things/publications/thing-q4915012/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q4915012/spec.json"],"providers":["Claude"],"researchStatus":"unreviewed","generatedAt":"2026-10-21T20:24:21Z","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":{"_gate":"Published through the thing publication gate 1.0 on 2026-10-21T20:39:55+00:00: completeness 1.00; sense: Wikidata description; 7 live sources; review by codex: pass","interaction.properties":"A molecular model has no physical properties."},"score":1.0}}