tool_id	title	category	audience	execution_state	primary_question	suitability_rule	web_route	api_routes	next_handoff	failure_states	responsible_use
TOOL-GENE-RESOLVER-1.0	Gene Resolver	IDENTITY	biologist | data steward | model developer	LIVE_WEB_WORKFLOW	Which canonical gene does this symbol, alias, previous symbol or identifier resolve to?	Suitable for identifier normalization and navigation; not a biological inference engine.	/resource/search	/resource/api/v1.1/identifier_mapping.json | /resource/api/v1/search_index.json	Open the canonical Gene object | /resource/genes/	IDENTIFIER_NOT_FOUND: No released mapping key matches the input. | AMBIGUOUS_ALIAS: The alias cannot be assigned safely to one canonical symbol.	Do not interpret successful identity resolution as evidence of disease relevance.
TOOL-EVIDENCE-COMPARATOR-1.0	Evidence Comparator	EVIDENCE	biologist | translational researcher	LIVE_WEB_WORKFLOW	How do several genes differ across evidence dimensions without forcing a winner?	Suitable for side-by-side evidence inspection; not suitable for therapeutic ranking.	/resource/compare	/resource/api/v1.3/research-objects/registry.json	Turn a gap into a Study Card | /resource/planner	GENE_NOT_ASSESSED: A dimension has no released evidence for one or more genes. | COMPARISON_NOT_FROZEN: The requested set has no immutable comparison object.	Do not convert a comparison into a clinical or therapeutic recommendation.
TOOL-PROCESS-INSPECTOR-1.0	Process Inspector	MECHANISM	biologist | experimental scientist	LIVE_READ_ONLY	Which observed, contextual or hypothesized edges connect a candidate to a DMD process?	Suitable for mechanism navigation and experiment design; not a causal simulator.	/resource/process/	/resource/api/v1.1/perturbation_cascade_network.json | /resource/api/v1.1/human_myoblast_perturbation_network.json	Design the missing-edge study | /resource/planner	EDGE_NOT_VALIDATED_IN_DMD: The edge is contextual or hypothesized rather than a validated DMD transition.	Do not describe a pathway edge as a predicted cell-state transition unless a registered model and matched truth support it.
TOOL-MODEL-AUDITOR-1.0	Model Auditor	MODEL	model developer | reviewer	LIVE_READ_ONLY	What exact task ran, against which baselines, and why did the gate pass, fail or stop?	Suitable for audit and model selection within the frozen task; external reputation is not accepted as local performance.	/resource/models/	/resource/api/v1.1/model_run_registry.json | /resource/api/v1.1/model_run.schema.json	Inspect benchmark gates | /resource/benchmarks	PARTIAL_REPRODUCTION_RECEIPT: Code, container, data digest or seed receipt is missing. | TASK_CONTEXT_MISMATCH: The run context does not qualify the requested disease prediction.	Completed does not mean calibrated for DMD, therapeutic use or clinical use.
TOOL-METHOD-NAVIGATOR-1.0	Method Navigator	METHOD	biologist | model developer | reviewer	LIVE_READ_ONLY	Which model family, permanent baselines and evaluation layers fit this frozen biological task?	Suitable for method selection and review; it does not execute a model or transfer literature performance into NMD-VCell.	/resource/technology-methods/	/resource/api/v1.1/technical_method_registry.json	Audit an executed ModelRun | /resource/models/	TASK_NOT_FROZEN: The biological unit, output or generalization axis is undefined. | TRUTH_CONTEXT_MISSING: No matched outcome exists for the requested disease and cell state. | BASELINE_NOT_REGISTERED: The advanced model has no task-compatible simple comparator.	Source-reported capability is a method reference, not a local benchmark result or DMD validation.
TOOL-EXPERIMENT-PLANNER-1.0	Experiment Planner	EXPERIMENT	experimental scientist | translational researcher	LIVE_DRAFT_BUILDER	What prospective study would resolve the current decision-blocking evidence gap?	Suitable for drafting a falsifiable study; the output is not a registered protocol or prediction.	/resource/planner	/resource/api/v1.1/registered_studies.json	Review registry lifecycle | /resource/registry	UNKNOWN_GENE: The candidate cannot be resolved to the released identifier map. | INCOMPLETE_STUDY_CONTRACT: Context, comparator, endpoint or decision rule is missing.	A draft Study Card must not be represented as an approved or executed experiment.
TOOL-OUTCOME-REGISTRY-1.0	Outcome Registry Inspector	OUTCOME	reviewer | data steward | experimental scientist	LIVE_READ_ONLY_EMPTY_REGISTRY	Has a draft study become registered, predicted, measured and returned to the evidence graph?	Suitable for lifecycle audit. The currently empty registries are a truthful state, not missing UI content.	/resource/registry	/resource/api/v1.1/registered_studies.json | /resource/api/v1.1/experimental_outcomes.json	Return to Evidence Atlas | /resource/diseases/	NO_REGISTERED_OBJECT: No immutable study, prediction or outcome exists for the identifier. | OUTCOME_NOT_RETURNED: A registered study lacks a measured outcome or evidence-graph return.	Do not fabricate outcome rows or infer efficacy from an empty registry.