@pikaa-ai/pikaa 0.2.5 → 0.3.1

package/skills/hypothesis-generation/assets/hypothesis_record_template.json

@@ -0,0 +1,331 @@
+{
+  "schema_version": "2.0",
+  "project_id": "HG-SYN-001",
+  "status": "draft",
+  "updated_on": "2026-07-23",
+  "human_owner": "Accountable human investigator",
+  "observation": {
+    "statement": "In a synthetic demonstration dataset, units measured after condition X had a different mean value of outcome Y than units measured after the comparator condition.",
+    "provenance": "Synthetic demonstration only; no human, animal, clinical, proprietary, or security-sensitive data.",
+    "source_ids": [
+      "SRC-SYN-001"
+    ],
+    "uncertainties": [
+      "The synthetic pattern could reflect the generating process, selection, measurement, or random variation."
+    ]
+  },
+  "research_question": {
+    "statement": "In the synthetic target system, what is the effect of assigning condition X rather than the comparator on outcome Y after one measurement interval?",
+    "framework": "PICO",
+    "question_type": "causal",
+    "population_or_system": "Synthetic independent units meeting the declared eligibility rule",
+    "intervention_or_exposure": "Assignment to synthetic condition X",
+    "comparator": "Assignment to the synthetic comparator condition",
+    "outcome": "Validated synthetic outcome Y",
+    "timeframe": "One prespecified measurement interval"
+  },
+  "hypotheses": [
+    {
+      "hypothesis_id": "H1",
+      "statement": "Condition X changes outcome Y through the proposed synthetic process M.",
+      "mechanism": "Condition X changes intermediate M before outcome Y is measured.",
+      "status": "candidate",
+      "source_ids": [
+        "SRC-SYN-001"
+      ],
+      "assumptions": [
+        "The synthetic assignment and measurement procedures operate as declared."
+      ],
+      "boundary_conditions": [
+        "The candidate is limited to the declared synthetic units and one-interval horizon."
+      ],
+      "uncertainties": [
+        "The intermediate may be a marker rather than a mediator."
+      ],
+      "prediction_ids": [
+        "P1"
+      ],
+      "rival_hypothesis_ids": [
+        "H2"
+      ]
+    },
+    {
+      "hypothesis_id": "H2",
+      "statement": "The observed difference in outcome Y is produced by a synthetic measurement drift rather than process M.",
+      "mechanism": "A time-linked offset changes the recorded outcome without changing the target construct.",
+      "status": "candidate",
+      "source_ids": [
+        "SRC-SYN-001"
+      ],
+      "assumptions": [
+        "The synthetic measurement offset is not removed by calibration."
+      ],
+      "boundary_conditions": [
+        "The candidate applies only to measurements from the affected synthetic acquisition period."
+      ],
+      "uncertainties": [
+        "The size and stability of any offset are unknown."
+      ],
+      "prediction_ids": [
+        "P2"
+      ],
+      "rival_hypothesis_ids": [
+        "H1"
+      ]
+    }
+  ],
+  "causal_estimands": [
+    {
+      "estimand_id": "E1",
+      "linked_hypothesis_ids": [
+        "H1"
+      ],
+      "population": "Synthetic eligible units",
+      "intervention_or_exposure": "Assignment to condition X",
+      "comparator": "Assignment to comparator",
+      "outcome": "Outcome Y measured with method M-OUTCOME",
+      "time_horizon": "One measurement interval",
+      "population_summary": "Difference in population mean outcome Y",
+      "intercurrent_event_strategy": "Not applicable in the synthetic demonstration",
+      "identification_assumptions": [
+        "Random assignment, no interference, consistent treatment versions, and valid outcome measurement."
+      ]
+    }
+  ],
+  "predictions": [
+    {
+      "prediction_id": "P1",
+      "hypothesis_id": "H1",
+      "statement": "Under matched acquisition conditions, assignment to X will precede a change in intermediate M and then outcome Y.",
+      "observable": "Ordered changes in intermediate M and outcome Y",
+      "conditions": "Synthetic units are randomly assigned and measured with calibrated instruments.",
+      "expected_pattern": "Intermediate M changes before outcome Y in X but not comparator units.",
+      "falsifier": "Outcome Y changes without the prespecified change in intermediate M under a successful manipulation and valid measurements.",
+      "rival_hypothesis_ids": [
+        "H2"
+      ],
+      "measurement_ids": [
+        "M-INTERMEDIATE",
+        "M-OUTCOME"
+      ],
+      "analysis_ids": [
+        "A1"
+      ]
+    },
+    {
+      "prediction_id": "P2",
+      "hypothesis_id": "H2",
+      "statement": "A reference quantity measured in the same acquisition period will show a similar offset even though process M cannot affect it.",
+      "observable": "Offset in the negative-control reference quantity",
+      "conditions": "The same acquisition and calibration workflow is used.",
+      "expected_pattern": "The reference quantity and outcome Y shift together by acquisition period.",
+      "falsifier": "The reference quantity remains stable while outcome Y changes reproducibly across independently calibrated periods.",
+      "rival_hypothesis_ids": [
+        "H1"
+      ],
+      "measurement_ids": [
+        "M-NEGATIVE-CONTROL",
+        "M-OUTCOME"
+      ],
+      "analysis_ids": [
+        "A2"
+      ]
+    }
+  ],
+  "alternative_explanations": [
+    {
+      "alternative_id": "ALT1",
+      "statement": "Synthetic selection into the analyzed set creates the observed difference.",
+      "linked_hypothesis_ids": [
+        "H1",
+        "H2"
+      ],
+      "risk_types": [
+        "selection_bias"
+      ],
+      "discriminating_prediction_ids": [
+        "P1",
+        "P2"
+      ]
+    }
+  ],
+  "null_hypotheses": [
+    {
+      "null_id": "N1",
+      "statement": "The population mean of outcome Y is equal under assignment to X and comparator at the prespecified horizon.",
+      "linked_prediction_ids": [
+        "P1"
+      ],
+      "rejection_or_compatibility_rule": "Use the prespecified interval estimate and decision rule in analysis A1; do not equate failure to reject with equivalence."
+    },
+    {
+      "null_id": "N2",
+      "statement": "The synthetic negative-control reference mean is equal across acquisition periods.",
+      "linked_prediction_ids": [
+        "P2"
+      ],
+      "rejection_or_compatibility_rule": "Use analysis A2 as a bias diagnostic; failure to reject does not prove absence of drift when precision or reference sensitivity is insufficient."
+    }
+  ],
+  "negative_controls": [
+    {
+      "control_id": "NC1",
+      "control_type": "negative_outcome",
+      "rationale": "The reference quantity cannot be changed by process M but shares the synthetic acquisition workflow.",
+      "expected_result": "No difference by assigned condition after accounting for acquisition period.",
+      "failure_implication": "A non-null control result raises concern about acquisition, selection, or analysis bias.",
+      "linked_prediction_ids": [
+        "P2"
+      ]
+    }
+  ],
+  "operationalizations": [
+    {
+      "measurement_id": "M-INTERMEDIATE",
+      "construct": "Synthetic intermediate M",
+      "variable": "m_value",
+      "role": "mediator",
+      "operational_definition": "Calibrated continuous synthetic measurement at the prespecified early time.",
+      "instrument_or_method": "Deterministic synthetic measurement procedure",
+      "unit": "synthetic units",
+      "timing": "Early prespecified time",
+      "population_or_system": "Synthetic eligible units",
+      "validity_evidence_source_ids": [
+        "SRC-SYN-001"
+      ],
+      "reliability_plan": "Repeat the deterministic check on an independent synthetic batch.",
+      "missingness_plan": "Report missingness by assignment and use the prespecified sensitivity analysis.",
+      "blinding_or_masking": "Synthetic analyst label is masked until validation completes.",
+      "threshold_rationale": "No threshold; analyze the continuous measurement."
+    },
+    {
+      "measurement_id": "M-OUTCOME",
+      "construct": "Synthetic outcome Y",
+      "variable": "y_value",
+      "role": "outcome",
+      "operational_definition": "Calibrated continuous synthetic outcome at one interval.",
+      "instrument_or_method": "Deterministic synthetic measurement procedure",
+      "unit": "synthetic units",
+      "timing": "One prespecified measurement interval",
+      "population_or_system": "Synthetic eligible units",
+      "validity_evidence_source_ids": [
+        "SRC-SYN-001"
+      ],
+      "reliability_plan": "Verify calibration and repeatability before unmasking assignment.",
+      "missingness_plan": "Report reasons and analyze under the prespecified primary and sensitivity assumptions.",
+      "blinding_or_masking": "Outcome acquisition and validation are masked to assignment.",
+      "threshold_rationale": "No threshold; estimate the continuous mean contrast."
+    },
+    {
+      "measurement_id": "M-NEGATIVE-CONTROL",
+      "construct": "Synthetic reference quantity",
+      "variable": "reference_value",
+      "role": "negative_control",
+      "operational_definition": "Stable synthetic reference measured in the same acquisition workflow.",
+      "instrument_or_method": "Deterministic synthetic reference procedure",
+      "unit": "synthetic reference units",
+      "timing": "Concurrent with outcome Y",
+      "population_or_system": "Synthetic acquisition batches",
+      "validity_evidence_source_ids": [
+        "SRC-SYN-001"
+      ],
+      "reliability_plan": "Check repeatability across synthetic batches.",
+      "missingness_plan": "Treat a missing reference as an acquisition-quality failure.",
+      "blinding_or_masking": "Reference processing is independent of assignment labels.",
+      "threshold_rationale": "Use the prespecified calibration tolerance."
+    }
+  ],
+  "analysis_plan": {
+    "analyses": [
+      {
+        "analysis_id": "A1",
+        "prediction_ids": [
+          "P1"
+        ],
+        "estimand_ids": [
+          "E1"
+        ],
+        "analysis_population": "All randomized synthetic eligible units under the declared estimand strategy",
+        "method": "Estimate the prespecified mean contrast with its uncertainty interval.",
+        "effect_or_summary_measure": "Difference in population means",
+        "uncertainty_method": "Prespecified interval estimate under the declared independent-unit assumptions",
+        "missing_data_plan": "Primary declared assumption plus a bounded sensitivity analysis",
+        "multiplicity_plan": "A1 is the sole confirmatory contrast; all additional contrasts are exploratory.",
+        "sensitivity_analyses": [
+          "Repeat under the prespecified alternative missingness assumption."
+        ],
+        "decision_rule": "Interpret compatibility with predicted patterns and rivals; do not select a hypothesis automatically.",
+        "exploratory_or_confirmatory": "confirmatory"
+      },
+      {
+        "analysis_id": "A2",
+        "prediction_ids": [
+          "P2"
+        ],
+        "estimand_ids": [],
+        "analysis_population": "All synthetic acquisition batches with valid reference measurements",
+        "method": "Estimate reference shifts by acquisition period and assigned condition.",
+        "effect_or_summary_measure": "Difference in reference means",
+        "uncertainty_method": "Prespecified interval estimate",
+        "missing_data_plan": "Report and exclude acquisition failures according to the locked quality rule.",
+        "multiplicity_plan": "Negative-control analysis is interpreted as a bias diagnostic, not a candidate-selection score.",
+        "sensitivity_analyses": [
+          "Repeat after excluding the prespecified failed-calibration batch category."
+        ],
+        "decision_rule": "A non-null reference shift triggers investigation and limits causal interpretation.",
+        "exploratory_or_confirmatory": "confirmatory"
+      }
+    ],
+    "harking_control": "Freeze this record before viewing the target synthetic outcomes and label later candidates or analyses exploratory.",
+    "deviation_reporting": "Preserve the original plan and log each deviation with date, rationale, decision owner, result-awareness status, and interpretive impact."
+  },
+  "evidence": {
+    "ledger_path": "local-evidence-ledger.csv",
+    "source_ids": [
+      "SRC-SYN-001"
+    ],
+    "search_boundary_id": "SEARCH-SYN-001",
+    "evidence_limitations": [
+      "The bundled row is synthetic and demonstrates structure only."
+    ]
+  },
+  "risk_register": {
+    "confounding": [
+      "Synthetic assignment failure or implementation differences could act as common causes."
+    ],
+    "selection_bias": [
+      "Post-assignment exclusion could make analyzed groups non-comparable."
+    ],
+    "collider_bias": [
+      "Restricting analysis to a jointly caused quality indicator could open bias."
+    ],
+    "reverse_causation": [
+      "Temporal ordering is built into the synthetic design but must be verified."
+    ],
+    "measurement_bias": [
+      "Acquisition-period drift could change recorded outcome Y."
+    ],
+    "other": [
+      "Random variation and model misspecification remain possible."
+    ]
+  },
+  "ethics_and_feasibility": {
+    "human_subjects_gate": "not_applicable",
+    "animal_research_gate": "not_applicable",
+    "biosafety_gate": "not_applicable",
+    "dual_use_gate": "not_applicable",
+    "regulatory_gate": "not_applicable",
+    "data_governance_gate": "approved",
+    "feasibility_status": "feasible_for_planning",
+    "required_reviews": [],
+    "unresolved_blocks": []
+  },
+  "ai_use": {
+    "used": false,
+    "sensitive_or_unpublished_data_sent_externally": false,
+    "local_policy_checked": true,
+    "citation_verification_required": true,
+    "human_accountable": true,
+    "diversity_mitigation": "Generate independent rivals before any authorized AI-assisted expansion and retain human-origin candidates."
+  }
+}

package/skills/hypothesis-generation/assets/operationalization_template.json

@@ -0,0 +1,56 @@
+{
+  "schema_version": "2.0",
+  "checklist_id": "OP-SYN-001",
+  "record_id": "HG-SYN-001",
+  "human_reviewer": "Qualified measurement reviewer pending",
+  "items": [
+    {
+      "measurement_id": "M-OUTCOME",
+      "applicability": "applicable",
+      "construct_defined": true,
+      "variable_role": "outcome",
+      "operational_definition_recorded": true,
+      "population_scope_recorded": true,
+      "unit_or_categories_recorded": true,
+      "timing_recorded": true,
+      "instrument_or_method_recorded": true,
+      "validity_evidence_source_ids": [
+        "SRC-SYN-001"
+      ],
+      "validity_applicability_reviewed": false,
+      "reliability_or_repeatability_plan_recorded": true,
+      "calibration_or_quality_control_status": "planned",
+      "measurement_invariance_or_comparability_status": "unresolved",
+      "masking_status": "planned",
+      "missingness_plan_recorded": true,
+      "threshold_or_cutpoint_status": "not_applicable",
+      "limitations_recorded": true,
+      "human_review_status": "pending",
+      "note": "Synthetic example. A qualified human must determine whether the validity evidence applies to the target system."
+    },
+    {
+      "measurement_id": "M-NEGATIVE-CONTROL",
+      "applicability": "applicable",
+      "construct_defined": true,
+      "variable_role": "negative_control",
+      "operational_definition_recorded": true,
+      "population_scope_recorded": true,
+      "unit_or_categories_recorded": true,
+      "timing_recorded": true,
+      "instrument_or_method_recorded": true,
+      "validity_evidence_source_ids": [
+        "SRC-SYN-001"
+      ],
+      "validity_applicability_reviewed": false,
+      "reliability_or_repeatability_plan_recorded": true,
+      "calibration_or_quality_control_status": "planned",
+      "measurement_invariance_or_comparability_status": "not_applicable",
+      "masking_status": "not_applicable",
+      "missingness_plan_recorded": true,
+      "threshold_or_cutpoint_status": "planned",
+      "limitations_recorded": true,
+      "human_review_status": "pending",
+      "note": "Synthetic example. Confirm that the target mechanism cannot affect this control and that relevant bias pathways are shared."
+    }
+  ]
+}

package/skills/hypothesis-generation/assets/prediction_rival_matrix_template.csv

@@ -0,0 +1,3 @@
+prediction_id,hypothesis_id,rival_hypothesis_ids,conditions,observable,expected_if_focal,expected_if_rivals,falsifier,indeterminate_result,boundary_conditions,measurement_ids,negative_control_ids,analysis_ids,uncertainty
+P1,H1,H2,"Random assignment, successful manipulation, calibrated measurements, and masked validation","Ordering of synthetic intermediate M and outcome Y","Intermediate M changes before outcome Y in condition X","H2 predicts no condition-specific intermediate change and a shift shared with the reference quantity","Outcome Y changes without the prespecified intermediate change after successful manipulation and valid measurement","Manipulation or measurement check fails, or uncertainty is too large to distinguish the patterns","Synthetic eligible units over one prespecified interval",M-INTERMEDIATE;M-OUTCOME,NC1,A1,"Magnitude is not assumed; the planned interval and measurement resolution determine whether patterns are distinguishable"
+P2,H2,H1,"Matched synthetic acquisition and calibration workflow","Shift in the synthetic negative-control reference quantity","Reference quantity and outcome Y shift together by acquisition period","H1 predicts outcome Y changes without a corresponding reference shift","Reference quantity is stable across independently calibrated periods while outcome Y changes reproducibly by assignment","Reference measurement fails or acquisition periods do not overlap assigned conditions","Synthetic acquisition batches covered by the declared calibration process",M-NEGATIVE-CONTROL;M-OUTCOME,NC1,A2,"A control shift can have causes other than the stated measurement-drift rival"

package/skills/hypothesis-generation/assets/preregistration_scaffold_template.md

@@ -0,0 +1,137 @@
+# Preregistration scaffold: {{PROJECT_ID}}
+
+> **UNREGISTERED DRAFT — NOT AN APPROVAL OR SCIENTIFIC ENDORSEMENT**
+>
+> Generated locally on {{GENERATED_ON}} from a validated structural record. Complete repository-specific fields, obtain required human/ethics/safety/regulatory review, and verify every statement before registration.
+
+## 1. Administrative record
+
+- Project ID: {{PROJECT_ID}}
+- Accountable human owner: {{HUMAN_OWNER}}
+- Record status: {{RECORD_STATUS}}
+- Record updated: {{UPDATED_ON}}
+- Registration repository and identifier: [TO COMPLETE]
+- Registration timestamp: [TO COMPLETE]
+- Study status and prior access to target data: [TO COMPLETE]
+- Roles, funding, conflicts, sponsor role: [TO COMPLETE]
+
+## 2. Authorization and oversight gates
+
+{{ETHICS_AND_FEASIBILITY}}
+
+- Human/animal/biosafety/dual-use/data/regulatory determinations and identifiers: [TO COMPLETE]
+- Local policy and jurisdiction checked on: [TO COMPLETE]
+- Unresolved work must not begin until the responsible authority clears it.
+
+## 3. Search boundary and evidence
+
+{{EVIDENCE_BOUNDARY}}
+
+- Attach the completed search-boundary record and evidence ledger.
+- “Not located within this boundary” does not establish universal absence or novelty.
+- Verify every citation and claim-to-source link against the primary source.
+
+## 4. Frozen observation
+
+{{OBSERVATION}}
+
+- Units, preprocessing, exclusions, missingness, and uncertainty: [TO COMPLETE]
+- Whether expected or selected after inspection: [TO COMPLETE]
+
+## 5. Research question and claim type
+
+{{RESEARCH_QUESTION}}
+
+## 6. Candidate hypotheses and mechanisms
+
+{{HYPOTHESES}}
+
+All listed hypotheses remain candidates. This scaffold does not rank or select one.
+
+## 7. Causal estimand(s), if applicable
+
+{{ESTIMANDS}}
+
+- Target-trial/design analogue and identification logic: [TO COMPLETE]
+- Confounding, selection, collider, measurement, reverse-causation, positivity, and interference assumptions: [TO COMPLETE]
+
+## 8. Predictions, rivals, and falsification
+
+{{PREDICTIONS}}
+
+- Indeterminate and mixed-mechanism outcomes: [TO COMPLETE]
+- Assumption/manipulation checks required before interpreting a challenge: [TO COMPLETE]
+
+## 9. Null hypotheses and controls
+
+{{NULLS_AND_CONTROLS}}
+
+- Positive/procedural-control details: [TO COMPLETE]
+- Why each negative control cannot operate through the target mechanism and which bias pathways it shares: [TO COMPLETE]
+
+## 10. Operationalization and measurement validity
+
+{{OPERATIONALIZATIONS}}
+
+- Validity applicability, reliability/repeatability, calibration, detection limits, masking, missingness, invariance/comparability, and limitations: [TO COMPLETE]
+
+## 11. Design
+
+- Target population/system and sampling frame: [TO COMPLETE]
+- Experimental/observational unit and analysis unit: [TO COMPLETE]
+- Eligibility, recruitment/selection, and exclusions: [TO COMPLETE]
+- Intervention/exposure and comparator versions: [TO COMPLETE]
+- Allocation, randomization, concealment, and masking: [TO COMPLETE]
+- Measurement schedule and quality control: [TO COMPLETE]
+- Sample-size, precision, or information rationale with sensitivity to assumptions: [TO COMPLETE]
+- Stopping, attrition, and missing-outcome plan: [TO COMPLETE]
+- Replication, transport, and external-validation plan: [TO COMPLETE]
+
+## 12. Analysis plan
+
+{{ANALYSES}}
+
+- Software, environment, versions, and seeds where applicable: [TO COMPLETE]
+- Assumption diagnostics and model checks: [TO COMPLETE]
+- Full multiplicity family across hypotheses, outcomes, timepoints, subgroups, models, and looks: [TO COMPLETE]
+- Confirmatory versus exploratory outputs: [TO COMPLETE]
+
+## 13. Data, code, materials, and retention
+
+- Provenance and versioning: [TO COMPLETE]
+- Data/code/material availability or justified restriction: [TO COMPLETE]
+- Consent, privacy, community governance, intellectual property, export-control, biosafety, and dual-use limits: [TO COMPLETE]
+- Approved storage, access, retention, and deletion: [TO COMPLETE]
+
+## 14. AI and tool assistance
+
+{{AI_USE}}
+
+- Named tools/versions and material influence: [TO COMPLETE IF PERMITTED]
+- Verification and disclosure plan: [TO COMPLETE]
+- Sensitive or unpublished information must remain local unless explicitly authorized for a named service and scope.
+
+## 15. Deviations and amendments
+
+{{DEVIATION_PLAN}}
+
+For each deviation record:
+
+- date;
+- affected section and IDs;
+- original plan;
+- change and rationale;
+- decision owner;
+- whether target results were known;
+- expected interpretive impact;
+- whether the original analysis will still be reported.
+
+## 16. Human sign-off
+
+- Domain expert: [NAME / DATE / STATUS]
+- Measurement expert: [NAME / DATE / STATUS]
+- Methodologist/statistician: [NAME / DATE / STATUS]
+- Ethics/safety/data/regulatory authorities as applicable: [NAME / DATE / STATUS]
+- Accountable investigator: [NAME / DATE / STATUS]
+
+No signature turns a hypothesis into fact. Interpret results with uncertainty, rivals, boundary conditions, controls, and replication evidence.

package/skills/hypothesis-generation/assets/search_boundary_template.json

@@ -0,0 +1,23 @@
+{
+  "schema_version": "2.0",
+  "search_boundary_id": "SEARCH-SYN-001",
+  "searched_on": "2026-07-23",
+  "searched_by": "Accountable human or authorized research assistant",
+  "purpose": "Demonstrate a bounded, traceable search record for a synthetic hypothesis package.",
+  "databases_or_indexes": [
+    "Synthetic index for format demonstration"
+  ],
+  "queries": [
+    "synthetic condition X outcome Y mechanism",
+    "synthetic condition X alternative explanation measurement drift"
+  ],
+  "date_limits": "No date restriction in the synthetic demonstration.",
+  "language_limits": "Synthetic English records only.",
+  "inclusion_scope": "Sources bearing on the observation, candidate process, measurement, rivals, and methods.",
+  "exclusion_scope": "No real scientific sources were screened in this synthetic template.",
+  "known_limitations": [
+    "This is a schema example and cannot support novelty, priority, or an evidence claim."
+  ],
+  "last_result_screened_or_stop_rule": "Replace with the actual result depth, saturation rule, or protocol completion statement.",
+  "novelty_status": "not_assessed"
+}

package/skills/hypothesis-generation/assets/source_ledger.csv

@@ -0,0 +1,37 @@
+source_id,organization,title,version_or_date,source_type,url,verified_on,status,notes
+SRC-NIH-RIGOR,National Institutes of Health,Guidance: Rigor and Reproducibility in Grant Applications,Page updated 2024-10-16,official guidance,https://grants.nih.gov/policy-and-compliance/policy-topics/reproducibility/guidance,2026-07-23,current_official,"Scientific premise, rigorous design, biological variables, resource authentication, and transparency"
+SRC-NIH-REPLICATION,National Institutes of Health,Strengthening Replication and Reproducibility of NIH-funded Research,Page reviewed 2026-06-22,official initiative,https://www.nih.gov/replicationandreproducibility,2026-07-23,current_official,"Agency-wide replication and reproducibility initiative; policy implementation may continue to evolve"
+SRC-COCHRANE-PICO,Cochrane,Handbook Chapter 2: Determining the scope of the review and the questions it will address,Current handbook chapter,official handbook,https://www.cochrane.org/authors/handbooks-and-manuals/handbook/current/chapter-02,2026-07-23,current_official,"PICO for intervention reviews, protocol-stage definition, synthesis-level distinctions, and stakeholder input"
+SRC-PICO-ORIGINAL,Richardson et al.,The well-built clinical question: a key to evidence-based decisions,Published 1995-11-01,primary methods article,https://www.acpjournals.org/doi/10.7326/ACPJC-1995-123-3-A12,2026-07-23,foundational_primary,"Original four-part well-built clinical-question article; DOI 10.7326/ACPJC-1995-123-3-A12"
+SRC-FINER-1988,Hulley and Cummings,Designing Clinical Research: An Epidemiologic Approach,First edition 1988,foundational book metadata,https://books.google.com/books/about/Designing_Clinical_Research.html?id=hKdpAAAAMAAJ,2026-07-23,historical_metadata_limited,"Earliest FINER-attributed source located in this search; bibliographic preview confirms edition metadata but the search did not prove first printed use or coinage"
+SRC-FINER-CURRENT,Werner and Willis,Back to the basics: guidance for formulating good research questions,Published 2023-10-12,current methods article,https://pmc.ncbi.nlm.nih.gov/articles/PMC11129835/,2026-07-23,current_primary,"Current discussion of FINER as a practical question-appraisal framework; novelty requires literature review"
+SRC-PLATT-1964,John R. Platt,Strong Inference,Published 1964-10-16,primary methods essay,https://www.science.org/doi/10.1126/science.146.3642.347,2026-07-23,foundational_primary,"Multiple alternatives, crucial experiments, and iterative exclusion; DOI 10.1126/science.146.3642.347"
+SRC-COS-PREREG,Center for Open Science,Preregistration,Current official page,official guidance,https://www.cos.io/initiatives/prereg,2026-07-23,current_official,"Separates planned from unplanned work and requires transparent changes; exploration remains valid"
+SRC-OSF-REG,Center for Open Science / OSF,Welcome to Registrations and Preregistrations,Current 2026 help page,official implementation guidance,https://help.osf.io/article/330-welcome-to-registrations,2026-07-23,current_official,"Timestamped plans, template guidance, analysis details, and anticipated deviations"
+SRC-COS-RR,Center for Open Science,Registered Reports,Current official initiative page,official guidance,https://www.cos.io/initiatives/registered-reports,2026-07-23,current_official,"Results-blind protocol review and in-principle acceptance; verify the target journal policy"
+SRC-SPIRIT-2025,SPIRIT-CONSORT Group,SPIRIT 2025 statement: updated guideline for protocols of randomised trials,Published 2025-04-28,primary reporting guideline,https://www.bmj.com/content/389/bmj-2024-081477,2026-07-23,current_primary,"34 minimum protocol items; supersedes SPIRIT 2013; DOI 10.1136/bmj-2024-081477"
+SRC-CONSORT-2025,SPIRIT-CONSORT Group,CONSORT 2025 statement: updated guideline for reporting randomised trials,Published 2025-04-14,primary reporting guideline,https://www.bmj.com/content/389/bmj-2024-081123,2026-07-23,current_primary,"30-item result-reporting guideline with open-science, harms, outcomes, intervention, and change-reporting updates"
+SRC-ICH-E9R1,International Council for Harmonisation,ICH E9(R1) Addendum on Estimands and Sensitivity Analysis in Clinical Trials,Step 4 2019; implemented 2020,official statistical guidance,https://database.ich.org/sites/default/files/E9-R1_Step4_Guideline_2019_1203.pdf,2026-07-23,current_official,"Defines estimand as the precise treatment-effect target and aligns planning, design, analysis, sensitivity, and interpretation"
+SRC-WHATIF,Hernán and Robins,Causal Inference: What If,2020 citation; latest author-hosted revision linked 2025-11-21,foundational methods book,https://miguelhernan.org/whatifbook,2026-07-23,current_author_source,"Causal questions, counterfactuals, interventions, confounding, selection, causal diagrams, measurement, and target-trial emulation"
+SRC-NEG-CONTROL,Lipsitch Tchetgen Tchetgen and Cohen,Negative controls: a tool for detecting confounding and bias in observational studies,Published 2010-05,primary methods article,https://pubmed.ncbi.nlm.nih.gov/20335814/,2026-07-23,foundational_primary,"Negative exposure and outcome controls; DOI 10.1097/EDE.0b013e3181d61eeb"
+SRC-HARKING,Norbert L. Kerr,HARKing: hypothesizing after the results are known,Published 1998,primary methods article,https://pubmed.ncbi.nlm.nih.gov/15647155/,2026-07-23,foundational_primary,"Defines presenting a post hoc hypothesis as if a priori; DOI 10.1207/s15327957pspr0203_4"
+SRC-ASA-PVALUE,American Statistical Association,ASA Statement on Statistical Significance and P-Values,Released 2016-03-07,professional statistical statement,https://www.amstat.org/asa/files/pdfs/P-ValueStatement.pdf,2026-07-23,current_official,"Thresholds alone do not support scientific conclusions; p-values do not measure hypothesis truth or effect importance; full reporting is required"
+SRC-NASEM-RR,National Academies of Sciences Engineering and Medicine,Reproducibility and Replicability in Science,Published 2019-05-07,consensus report,https://www.nationalacademies.org/read/25303,2026-07-23,current_authoritative,"Defines reproducibility using same data/code and replicability using new data; DOI 10.17226/25303"
+SRC-TOP,Center for Open Science collaborators,Promoting an open research culture,Published 2015-06-26,primary transparency framework,https://www.science.org/doi/10.1126/science.aab2374,2026-07-23,current_primary,"Transparency and Openness Promotion guidelines; apply with privacy, consent, governance, and security limits"
+SRC-NIH-DMS,National Institutes of Health,Data Management and Sharing Policy,Effective 2023-01-25,official policy,https://sharing.nih.gov/data-management-and-sharing-policy,2026-07-23,current_official,"Prospective data-management and sharing planning for covered NIH-funded research; sharing remains subject to justified limits"
+SRC-NIST-GENAI,National Institute of Standards and Technology,Artificial Intelligence Risk Management Framework: Generative Artificial Intelligence Profile,NIST AI 600-1 July 2024; page updated 2026-04-08,official risk framework,https://www.nist.gov/publications/artificial-intelligence-risk-management-framework-generative-artificial-intelligence,2026-07-23,current_official,"Confabulation, privacy, harmful bias/homogenization, information integrity, dangerous recommendations, and human-AI configuration"
+SRC-DOSHI-HAUSER,Doshi and Hauser,Generative AI enhances individual creativity but reduces the collective diversity of novel content,Published 2024-07-12,primary research,https://www.science.org/doi/10.1126/sciadv.adn5290,2026-07-23,current_primary,"AI-assisted stories were more similar in this experiment; do not generalize beyond the studied task without evidence"
+SRC-UNESCO-AI,UNESCO,Recommendation on the Ethics of Artificial Intelligence,Adopted 2021; official page current 2026,international recommendation,https://www.unesco.org/en/artificial-intelligence/recommendation-ethics,2026-07-23,current_official,"Human rights, privacy, accountability, transparency, diversity, and human oversight"
+SRC-UNESCO-OPEN,UNESCO,Recommendation on Open Science,Adopted 2021,international recommendation,https://unesdoc.unesco.org/ark:/48223/pf0000379949,2026-07-23,current_official,"Open-science values and practices with responsibility, inclusiveness, and governance"
+SRC-HHS-COMMON-RULE,U.S. Department of Health and Human Services,Federal Policy for the Protection of Human Subjects (Common Rule),Official page updated 2026-01-15,regulation and policy index,https://www.hhs.gov/ohrp/regulations-and-policy/regulations/common-rule/index.html,2026-07-23,current_official,"45 CFR 46 applicability and agency implementation; obtain an authorized local determination"
+SRC-BELMONT,U.S. Department of Health and Human Services,The Belmont Report,Published 1979,ethical principles report,https://www.hhs.gov/ohrp/regulations-and-policy/belmont-report/index.html,2026-07-23,current_foundational,"Respect for persons, beneficence, and justice"
+SRC-HELSINKI,World Medical Association,WMA Declaration of Helsinki: Ethical Principles for Medical Research Involving Human Participants,Revised October 2024,international ethical declaration,https://www.wma.net/policies-post/wma-declaration-of-helsinki/,2026-07-23,current_official,"Current international medical-research ethics statement; local law and review remain controlling"
+SRC-OLAW-PHS,Office of Laboratory Animal Welfare,Public Health Service Policy on Humane Care and Use of Laboratory Animals,Current official policy page,official animal-welfare policy,https://grants.nih.gov/policy-and-compliance/policy-topics/animal-welfare/laws-regulations/phs-policy,2026-07-23,current_official,"Institutional assurance and IACUC review for covered PHS-conducted or supported animal activities"
+SRC-ARRIVE,NC3Rs / ARRIVE Group,ARRIVE Guidelines 2.0,Published 2020,animal reporting guideline,https://arriveguidelines.org/arrive-guidelines,2026-07-23,current_official,"Reporting guidance for in vivo animal research; not an ethics approval or design-quality certificate"
+SRC-NIH-RSNA,National Institutes of Health,NIH Guidelines for Research Involving Recombinant or Synthetic Nucleic Acid Molecules,April 2024 or latest revision,official biosafety policy,https://osp.od.nih.gov/wp-content/uploads/NIH_Guidelines.htm,2026-07-23,current_official,"Institutional biosafety oversight and covered research categories; verify the latest revision and local applicability"
+SRC-NIH-BIOSEC,NIH Office of Science Policy,Biosafety and Biosecurity Policy,Official page updated 2026-04-09,official policy portal,https://osp.od.nih.gov/policies/biosafety-and-biosecurity-policy,2026-07-23,current_official,"Current NIH biosafety, biosecurity, IBC, transparency, and Executive Order implementation links"
+SRC-BMBL,Centers for Disease Control and Prevention and National Institutes of Health,Biosafety in Microbiological and Biomedical Laboratories,6th edition June 2020,official biosafety guidance,https://www.cdc.gov/labs/bmbl/index.html,2026-07-23,current_official,"Risk assessment and biosafety guidance; use qualified institutional review rather than inferring procedures from this skill"
+SRC-WHO-LIFE,World Health Organization,Global Guidance Framework for the Responsible Use of the Life Sciences,Published 2022-09-13,international guidance,https://www.who.int/publications/i/item/9789240056107,2026-07-23,current_official,"Values, principles, tools, and governance for biorisks and dual-use throughout the research lifecycle"
+SRC-EO-14292,The White House,Executive Order 14292: Improving the Safety and Security of Biological Research,Signed 2025-05-05,executive order,https://www.whitehouse.gov/presidential-actions/2025/05/improving-the-safety-and-security-of-biological-research,2026-07-23,current_official,"Directed revision/replacement of 2024 DURC/PEPP policy and pause/termination actions for covered dangerous gain-of-function research"
+SRC-NIH-NOT-25-112,National Institutes of Health,NOT-OD-25-112: Implementation Update—Improving the Safety and Security of Biological Research,Issued 2025-05,official funding notice,https://grants.nih.gov/grants/guide/notice-files/NOT-OD-25-112.html,2026-07-23,current_official,"States Executive Order definitions superseded NIH's 2024 DURC/PEPP implementation and rescinds NOT-OD-25-061"
+SRC-ASPR-DURC,U.S. Department of Health and Human Services ASPR,Dual Use Research of Concern Oversight Policy Framework,Official page current at verification,official policy status page,https://aspr.hhs.gov/S3/Pages/Dual-Use-Research-of-Concern-Oversight-Policy-Framework.aspx,2026-07-23,current_transition_notice,"At verification, states the 2024 DURC/PEPP policy will be revised or replaced and page will update when revised policy is available"