{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.chemogenomics","code":"thing-q907610","url":"https://ver.cy/models/thing/q907610/","name":"chemogenomics","alternateNames":[],"kind":"thing","status":"published","version":"0.1.0-research.1","language":"en","classifiers":{"family":"Thing Registry","category":"Activities and processes","entryKind":"thing","plane":"ACT","domain":["ACT.ACT"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"Chemogenomics is the systematic study of relationships between small-molecule chemical structures and gene products or genetically defined biological responses, used to connect chemical activity with biological function.","purpose":"Enable an agent to recognise a chemogenomics investigation, assess the evidence connecting chemical perturbations to biological targets and genomic context, and select justified next experiments.","scope":{"in":["Operational definitions of chemogenomics and the scope of a particular investigation","Selection and coverage of compound collections, target families and genomic backgrounds","Generation and integration of compound-target activity and chemical perturbation evidence","Inference of target associations, selectivity and context-dependent biological effects","Validation priorities and conditions for reusing chemogenomic conclusions"],"out":["Complete substance identity, synthesis and manufacturing records owned by chemical substance models","Reference genome annotation and comprehensive gene-function catalogues","General assay equipment operation and laboratory infrastructure","Clinical prescribing and patient-specific pharmacogenomic decisions","Full medicinal chemistry optimisation and drug development programmes"],"boundaries":[]},"distinguishingFeatures":["An instance must specify how chemical perturbations are systematically related to targets or genomic context; an isolated compound potency measurement does not establish that scope.","A genomics study without a chemical perturbation or chemical-target association component lacks the chemical dimension required by this model.","A phenotypic screen qualifies within the adopted scope only when its design or interpretation connects responses to targets, pathways or genomic variation.","Patient genotype associations with drug response belong primarily to pharmacogenomics; any overlap must identify the chemical-target mapping question being addressed.","Chemical genetics may supply perturbation methods, but the investigation must state what systematic coverage or integration justifies calling its activity chemogenomics."],"structure":{"bundles":[{"id":"chemogenomic-question-and-boundaries","name":"Chemogenomic question and boundaries","description":"Establishes what chemical-biological relationship the investigation seeks to resolve and why it falls within chemogenomics.","layers":[{"id":"operational-definition","name":"Operational definition","description":"Records the adopted usage and the evidence needed to recognise an instance.","findings":[{"id":"adopted-chemogenomics-usage","name":"Adopted chemogenomics usage","description":"Record whose definition is used and whether it centres on target-space profiling, genomic perturbation responses or their integration.","questions":[{"text":"What explicit definition makes this investigation an instance of chemogenomics?","id":"adopted-chemogenomics-usage-q01","kind":"definition"},{"text":"Which source or research community supplies that definition?","id":"adopted-chemogenomics-usage-q02","kind":"provenance"}]}]},{"id":"mapping-objective","name":"Mapping objective","description":"Defines the relationships sought and the boundary of the investigation.","findings":[{"id":"chemical-biological-inference-unit","name":"Chemical-biological inference unit","description":"Specify whether the intended conclusion concerns a compound-target pair, target-family profile or genotype-dependent perturbation response.","questions":[{"text":"What relationship is the investigation designed to establish, and at what biological resolution?","id":"chemical-biological-inference-unit-q01","kind":"definition"},{"text":"Which adjacent questions about chemical genetics, pharmacogenomics or drug optimisation are outside this investigation?","id":"chemical-biological-inference-unit-q02","kind":"boundary"}]}]}]},{"id":"chemical-and-biological-space","name":"Chemical and biological space","description":"Describes the perturbations and biological systems selected for systematic comparison.","layers":[{"id":"chemical-collection-design","name":"Chemical collection design","description":"Captures compound selection, identity and suitability as experimental perturbations.","findings":[{"id":"compound-selection-and-integrity","name":"Compound selection and integrity","description":"Record the collection's selection rationale, chemical diversity and sample-level identity or quality limitations.","questions":[{"text":"Were compounds selected for scaffold diversity, known target coverage, probe quality or another explicit objective?","id":"compound-selection-and-integrity-q01","kind":"provenance"},{"text":"What identity, purity, solubility and stability evidence supports interpreting the tested samples as the intended perturbations?","id":"compound-selection-and-integrity-q02","kind":"measurement"}]}]},{"id":"target-and-genomic-coverage","name":"Target and genomic coverage","description":"Captures the biological comparison space and its unobserved regions.","findings":[{"id":"tested-biological-universe","name":"Tested biological universe","description":"Record target identities, constructs and genomic backgrounds against an explicitly bounded intended universe.","questions":[{"text":"Which targets, isoforms, species and genomic backgrounds were included, and why?","id":"tested-biological-universe-q01","kind":"provenance"},{"text":"What fraction of the intended compound-target or compound-background combinations was tested, and which regions remain unobserved?","id":"tested-biological-universe-q02","kind":"measurement"}]}]}]},{"id":"perturbation-evidence-and-comparability","name":"Perturbation evidence and comparability","description":"Preserves what each assay observed and determines whether observations support joint interpretation.","layers":[{"id":"assay-observation","name":"Assay observation","description":"Connects responses to endpoints, exposure conditions and biological systems.","findings":[{"id":"endpoint-and-exposure-context","name":"Endpoint and exposure context","description":"Record the measured phenomenon, concentration dependence, exposure duration and experimental context.","questions":[{"text":"Does the endpoint measure binding, biochemical function, cellular engagement, phenotype or genomic response?","id":"endpoint-and-exposure-context-q01","kind":"definition"},{"text":"What doses, exposure times, replicates and response limits support the reported activity or inactivity?","id":"endpoint-and-exposure-context-q02","kind":"measurement"}]}]},{"id":"evidence-quality-and-harmonisation","name":"Evidence quality and harmonisation","description":"Addresses assay interference, inconsistent identifiers and incompatible measurements.","findings":[{"id":"comparison-eligibility","name":"Comparison eligibility","description":"Record controls and transformations that justify comparing observations while retaining censored, conflicting and missing results.","questions":[{"text":"What controls address aggregation, reporter interference, general cytotoxicity or other plausible non-target explanations?","id":"comparison-eligibility-q01","kind":"measurement"},{"text":"Which observations can be compared directly, and which require stratification because endpoints or conditions differ?","id":"comparison-eligibility-q02","kind":"boundary"},{"text":"How are original records, identifier mappings and normalisation steps traceable to the resulting activity profile?","id":"comparison-eligibility-q03","kind":"provenance"}]}]}]},{"id":"target-and-mechanism-inference","name":"Target and mechanism inference","description":"Connects perturbation profiles to candidate targets and explanations of biological effects.","layers":[{"id":"target-attribution","name":"Target attribution","description":"Separates candidate associations from evidence that a target mediates an observed response.","findings":[{"id":"association-to-causal-explanation","name":"Association to causal explanation","description":"Record support and competing explanations for assigning a target or pathway to a chemical perturbation.","questions":[{"text":"Which target assignments come from direct experiments, profile similarity, genetic interactions or computational prediction?","id":"association-to-causal-explanation-q01","kind":"provenance"},{"text":"What engagement, resistance, rescue or orthogonal perturbation evidence would distinguish the proposed mechanism from alternatives?","id":"association-to-causal-explanation-q02","kind":"action"}]}]},{"id":"selectivity-and-context-dependence","name":"Selectivity and context dependence","description":"Assesses multiple-target activity and the dependence of biological responses on genomic context.","findings":[{"id":"bounded-selectivity-and-genotype-effects","name":"Bounded selectivity and genotype effects","description":"Record selectivity within the tested panel and separate genomic associations from explanations involving exposure, expression or other context.","questions":[{"text":"Against which tested targets and at which concentrations is the compound considered selective or multi-target active?","id":"bounded-selectivity-and-genotype-effects-q01","kind":"measurement"},{"text":"What evidence separates a genotype-dependent response from differences in target expression, uptake, metabolism or general sensitivity?","id":"bounded-selectivity-and-genotype-effects-q02","kind":"boundary"}]}]}]},{"id":"prediction-validation-and-next-experiments","name":"Prediction, validation and next experiments","description":"Defines when computational associations and experimental conclusions can guide further work.","layers":[{"id":"predictive-evaluation","name":"Predictive evaluation","description":"Records the task, evaluation design and applicability of models trained on chemogenomic evidence.","findings":[{"id":"generalisation-and-leakage","name":"Generalisation and leakage","description":"For computational components, record whether evaluation tests new pairs, new chemical scaffolds, new targets or new biological contexts.","questions":[{"text":"Does evaluation hold out related scaffolds, homologous targets or shared experimental sources when required by the intended use?","id":"generalisation-and-leakage-q01","kind":"measurement"},{"text":"How are untested pairs distinguished from measured negatives, and how does that choice affect reported performance?","id":"generalisation-and-leakage-q02","kind":"measurement"},{"text":"For which chemical and biological regions is predictive reliability still unevaluated?","id":"generalisation-and-leakage-q03","kind":"boundary"}]}]},{"id":"experimental-decision","name":"Experimental decision","description":"Translates evidence gaps into experiments and bounded reuse decisions.","findings":[{"id":"discriminating-validation-plan","name":"Discriminating validation plan","description":"Record the next test most likely to resolve a consequential uncertainty and the outcomes that would change the conclusion.","questions":[{"text":"Which next compound, target, genomic background or orthogonal assay would best distinguish the leading explanations?","id":"discriminating-validation-plan-q01","kind":"action"},{"text":"What result would justify accepting, narrowing or rejecting the proposed association, and what uncertainty would remain?","id":"discriminating-validation-plan-q02","kind":"action"}]}]}]},{"id":"evidence-and-external-alignment","name":"Evidence and external alignment","description":"What the world already says about this thing, gathered so the model can be checked against it.","layers":[{"id":"reported-evidence","name":"Reported evidence","description":"Findings from the breadth pass, kept separate from the structural claims.","findings":[{"id":"evidence-confidence-notes","name":"Check these first","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these check these first hold for the sense of chemogenomics this model covers, and on what evidence?","id":"evidence-confidence-notes-q01","kind":"provenance"}]},{"id":"evidence-kinds","name":"Kinds and varieties","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these kinds and varieties hold for the sense of chemogenomics this model covers, and on what evidence?","id":"evidence-kinds-q01","kind":"provenance"}]},{"id":"evidence-identifiers","name":"Identifiers and schemes","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these identifiers and schemes hold for the sense of chemogenomics this model covers, and on what evidence?","id":"evidence-identifiers-q01","kind":"provenance"}]},{"id":"evidence-real-world-use","name":"Real-world use","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these real-world use hold for the sense of chemogenomics this model covers, and on what evidence?","id":"evidence-real-world-use-q01","kind":"provenance"}]},{"id":"evidence-measurements","name":"Typical measurements","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these typical measurements hold for the sense of chemogenomics this model covers, and on what evidence?","id":"evidence-measurements-q01","kind":"provenance"}]},{"id":"evidence-failure-modes-and-hazards","name":"Failure modes and hazards","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these failure modes and hazards hold for the sense of chemogenomics this model covers, and on what evidence?","id":"evidence-failure-modes-and-hazards-q01","kind":"provenance"}]},{"id":"evidence-neighbours","name":"Neighbouring kinds and how to tell them apart","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these neighbouring kinds and how to tell them apart hold for the sense of chemogenomics this model covers, and on what evidence?","id":"evidence-neighbours-q01","kind":"provenance"}]}]}]}]},"agentConduct":{"may":["Explain chemogenomics and how it links chemical structures to biological targets.","Analyse public screening data for research the user is authorized to conduct."],"mustNot":["Help identify or design compounds intended to harm people.","Present screening hits as safe or effective medicines.","Use or share proprietary or patient-linked data without authorization."],"requiresHuman":["Publishing findings with clear potential for misuse."]},"ethics":{"considerations":["Data linking chemicals to biological effects can serve medicine or harm.","Overstating early results misleads patients and investors."],"affectedParties":["Patients","Researchers","The public"]},"owners":{"steward":"Nobody owns the field; data owners and research institutions answer for each project.","roles":[],"masterSystems":[]},"relations":[{"target":"Q3516872","type":"parent","note":"registry parent class"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.chemogenomics","Wikidata: Q907610 (https://www.wikidata.org/wiki/Q907610)"]},"properties":{"applicability":"not-applicable","items":["Operational scope: Target-family mapping; broad compound-target profiling; genomic-context perturbation; integrated scope; explicitly defined alternative","Chemical collection coverage: Number of tested compounds and represented scaffolds, with scaffold definition and intended chemical-space denominator","Biological coverage: Number and fraction of intended targets, target families or genomic backgrounds evaluated, with denominator","Compound-target observation status: Untested; tested inconclusive; active under stated conditions; inactive within assay limits; computationally predicted","Activity endpoint: Endpoint-specific values such as Kd, Ki, IC50 or EC50 in mol/L, or defined response and fitness measures with units and conditions","Experimental context: Links to species, target construct, genotype, cell system, dose, exposure duration and assay protocol","Target-attribution status: Unassigned; predicted; associated; experimentally supported; supported by convergent causal evidence; conflicting","Selectivity assessment: Explicit metric, tested comparator panel, activity thresholds and uncertainty; otherwise not assessable","Predictive applicability: Within evaluated chemical and biological domain; chemical extrapolation; biological extrapolation; both; undetermined"]},"recognition":{"applicability":"not-applicable","items":[]},"capabilities":{"applicability":"required","items":["Classify an investigation against its explicit operational definition of chemogenomics.","Identify missing compound-target tests and underrepresented genomic backgrounds.","Compare activity profiles while preserving endpoint and assay-context differences.","Rank candidate target explanations and identify evidence that could distinguish them.","Prioritise orthogonal assays, target-engagement measurements or genetic perturbations.","Constrain reuse of measured and predicted associations to their supported contexts."]},"hazards":{"applicability":"required","items":["Off-target activity can lead investigators to assign a biological response to the wrong gene product.","Poor compound characterization or inconsistent assays can produce misleading associations between chemical structure and biological function.","Results from a limited experimental system can support unjustified conclusions about other organisms or clinical effects."]},"interfaces":{"applicability":"not-applicable","items":[]},"context":{"applicability":"required","items":["Chemogenomics is used in molecular biology and drug discovery to relate small-molecule activity to gene products and genetically defined biological responses.","Investigations combine chemical screening with genomic information to propose targets, compare response patterns and guide experiments testing biological function."]}},"sources":[{"title":"Wikidata item Q907610: chemogenomics","url":"https://www.wikidata.org/wiki/Q907610","note":"identity and sense of the item"},{"title":"Wikipedia: Chemogenomics","url":"https://en.wikipedia.org/wiki/Chemogenomics","note":"general description of the item"}],"openQuestions":["Which published definitions and research communities should anchor this registry entry's treatment of target-centric chemogenomics and genomic perturbation approaches?","Does an existing Vercy world model already cover this activity, requiring a registry link rather than a separate publication?","What minimum systematic coverage distinguishes a chemogenomics investigation from an isolated chemical genetics experiment or target assay?","Which evidence standards should govern target attribution when biochemical binding, cellular engagement and genetic perturbation results disagree?","Which benchmarks and uncertainty measures are appropriate for sparse compound-target maps whose missing observations are shaped by prior research choices?"],"resources":{"spec":"/models/things/publications/thing-q907610/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q907610/spec.json"],"providers":["Codex"],"researchStatus":"unreviewed","generatedAt":"2026-09-12T08:35:42Z","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":"not-applicable","interaction.capabilities":"filled","interaction.hazards":"filled","interaction.interfaces":"not-applicable","interaction.context":"filled","sources":"filled"},"notes":{"_gate":"Published through the thing publication gate 1.0 on 2026-10-07T10:10:33+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass","interaction.properties":"Plane ACT: no invented physical properties.","interaction.interfaces":"No single standard, law or official classification applies specifically to chemogenomics as a technique independently of its experimental setting.","interaction.recognition":"Chemogenomics is an investigative technique that cannot be identified by visual appearance alone."},"score":1.0}}