Protocol

CIViC evidence-direction retrieval, March 2026

Compare expected CIViC evidence-direction labels for exact molecular-profile, disease and therapy triplets. Exclude No Evidence from performance aggregation; distinguish support, non-support, contradictory and absent evidence. Micro-average significance labels within evidence types.

3 evaluations · 162 results

Overview

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

3 recorded evaluations, 162 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

3 evaluations · 162 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	0.83 overall_accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP: integrating large language models with the Clinical Interpretations of Variants in Cancer · Fig1c Overall Accuracy; Section 3
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	0.84 diagnostic_micro_f1 F1 score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP: integrating large language models with the Clinical Interpretations of Variants in Cancer · Figure 1c, diagnostic row, agent column
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	0 diagnostic_negative_f1 F1 score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP supplementary methods and complete Tables 1–3 · Supplementary Table 3, Diagnostic / Negative, f1
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	0 diagnostic_negative_precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP supplementary methods and complete Tables 1–3 · Supplementary Table 3, Diagnostic / Negative, precision
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	0 diagnostic_negative_recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP supplementary methods and complete Tables 1–3 · Supplementary Table 3, Diagnostic / Negative, recall
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	0.94 diagnostic_positive_f1 F1 score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP supplementary methods and complete Tables 1–3 · Supplementary Table 3, Diagnostic / Positive, f1
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	0.89 diagnostic_positive_precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP supplementary methods and complete Tables 1–3 · Supplementary Table 3, Diagnostic / Positive, precision
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	1 diagnostic_positive_recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP supplementary methods and complete Tables 1–3 · Supplementary Table 3, Diagnostic / Positive, recall
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	1 functional_dominant_negative_f1 F1 score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP supplementary methods and complete Tables 1–3 · Supplementary Table 3, Functional / Dominant Negative, f1
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	1 functional_dominant_negative_precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP supplementary methods and complete Tables 1–3 · Supplementary Table 3, Functional / Dominant Negative, precision
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	1 functional_dominant_negative_recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP supplementary methods and complete Tables 1–3 · Supplementary Table 3, Functional / Dominant Negative, recall
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	0.88 functional_micro_f1 F1 score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP: integrating large language models with the Clinical Interpretations of Variants in Cancer · Figure 1c, functional row, agent column
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	0.67 functional_gain_of_function_f1 F1 score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP supplementary methods and complete Tables 1–3 · Supplementary Table 3, Functional / Gain of Function, f1
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	0.75 functional_gain_of_function_precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP supplementary methods and complete Tables 1–3 · Supplementary Table 3, Functional / Gain of Function, precision
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	0.6 functional_gain_of_function_recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP supplementary methods and complete Tables 1–3 · Supplementary Table 3, Functional / Gain of Function, recall
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	0.92 functional_loss_of_function_f1 F1 score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP supplementary methods and complete Tables 1–3 · Supplementary Table 3, Functional / Loss of Function, f1
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	0.86 functional_loss_of_function_precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP supplementary methods and complete Tables 1–3 · Supplementary Table 3, Functional / Loss of Function, precision
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	1 functional_loss_of_function_recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP supplementary methods and complete Tables 1–3 · Supplementary Table 3, Functional / Loss of Function, recall
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	1 functional_unaltered_function_f1 F1 score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP supplementary methods and complete Tables 1–3 · Supplementary Table 3, Functional / Unaltered Function, f1
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	1 functional_unaltered_function_precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP supplementary methods and complete Tables 1–3 · Supplementary Table 3, Functional / Unaltered Function, precision
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	1 functional_unaltered_function_recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP supplementary methods and complete Tables 1–3 · Supplementary Table 3, Functional / Unaltered Function, recall
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	0.91 micro_f1 F1 score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP: integrating large language models with the Clinical Interpretations of Variants in Cancer · Fig1c Micro F1; Section 3
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	0.96 oncogenic_micro_f1 F1 score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP: integrating large language models with the Clinical Interpretations of Variants in Cancer · Figure 1c, oncogenic row, agent column
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	0.96 oncogenic_oncogenicity_f1 F1 score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP supplementary methods and complete Tables 1–3 · Supplementary Table 3, Oncogenic / Oncogenicity, f1
Configuration: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation	Protocol: CIViC evidence-direction retrieval, March 2026 Dataset: CIViC 100 molecular-profile/disease/therapy triplets, March 2026	0.92 oncogenic_oncogenicity_precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CIViC agent retrieval Not reported Aggregation: Not reported CIViC MCP supplementary methods and complete Tables 1–3 · Supplementary Table 3, Oncogenic / Oncogenicity, precision

Source checking is not independent reproduction. Release 2026-09-30-e37e3ab1284d.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Evaluation design

Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.

Benchmarks

CIViC MCP 2026 evidence-retrieval evaluation

These source-backed links do not make different protocols or scores interchangeable.

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

Author-reported evaluations: 3

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

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Conventional reference

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Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums

Coverage is derived from release 2026-09-30-e37e3ab1284d. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

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Strengths, limitations and unresolved questions

Applicable tests and references

Applicability is distinct from a completed evaluation.

Browser Agent Mode retrieval baseline · source_supported
Unaided GPT-5 retrieval baseline · source_supported
Equal-effort EGFR manual lookup baseline (proposed) · proposed

Evidence

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Evidence table

Inspect claims, sources and review details

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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

2 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-30-e37e3ab1284d
Property and statement	Original source and location	Review and provenance
Relationship: part of uc-clinical-20260930-benchmark-civic-study Individual claims	CIViC MCP: integrating large language models with the Clinical Interpretations of Variants in Cancer Original source ↗ Figure1c; Supplementary Tables1–3 and implementation methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Final article corrected and typeset 12 August 2026 Retrieved: 2026-09-30T21:24:15Z	source checked automated source review · 2026-09-30 Audit details Transcription from inspected primary source. No execution, independent replication or human scientific review. Field: `links:part_of:uc-clinical-20260930-benchmark-civic-study` Claim: uc-clinical-20260930-membership-civic-retrieval-protocol Source artifact SHA-256: `1bebf491323f252d27539a73da04fab4dacf7e3f83b531ee9262645f79e40bad` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Relationship: part of uc-clinical-20260930-benchmark-civic-study Individual claims	CIViC MCP supplementary methods and complete Tables 1–3 Original source ↗ Figure1c; Supplementary Tables1–3 and implementation methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: vbag209_supplementary_data.docx, final article supplement Retrieved: 2026-09-30T21:25:48Z	source checked automated source review · 2026-09-30 Audit details Transcription from inspected primary source. No execution, independent replication or human scientific review. Field: `links:part_of:uc-clinical-20260930-benchmark-civic-study` Claim: uc-clinical-20260930-membership-civic-retrieval-protocol Source artifact SHA-256: `857b272f9f29b9cb35d4fba7f424ef31d664d8acf8a23475c7c626a452b2e9e6` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

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Release 2026-09-30-e37e3ab1284d · Record review: source checked

1 source records and release history

CIViC MCP supplementary methods and complete Tables 1–3 · Original source · vbag209_supplementary_data.docx, final article supplement

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Technical metadata and extraction receipts

Stable ID: uc-clinical-20260930-civic-retrieval-protocol

areas: dna-genomes
contexts: clinical_research
protocol: Compare expected CIViC evidence-direction labels for exact molecular-profile, disease and therapy triplets. Exclude No Evidence from performance aggregation; distinguish support, non-support, contradictory and absent evidence. Micro-average significance labels within evidence types.
review: method: automated_source_review; reviewer: Codex clinical coverage worker; date: 2026-09-30; note: Transcription from inspected primary source. No execution, independent replication or human scientific review.; source id: uc-clinical-20260930-source-civic-supp
limitations: Pan-cancer retrieval task; no measured EGFR-mutant advanced NSCLC subgroup.; No treatment-line, prior-therapy, jurisdiction or complete primary-literature recall benchmark.; Live March 2026 CIViC source; current reruns may differ.; Supplement describes four outcomes although body says three.; UI Agent Mode model/version and concurrent timings differ from API configurations.

Related records

part of: CIViC MCP 2026 evidence-retrieval evaluation
applicable to: Browser Agent Mode retrieval baseline
applicable to: Unaided GPT-5 retrieval baseline
applicable to: Equal-effort EGFR manual lookup baseline (proposed)
protocol: CIViC agent retrieval
protocol: CIViC alone retrieval
protocol: CIViC mcp retrieval
subject: Published study membership: CIViC evidence-direction retrieval, March 2026

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