Pipeline

CIViC fixed-schema evidence retrieval evaluation workflow

Published fixed-triplet evidence-direction workflow with tool-assisted and unaided configurations; no clinical validation claim.

3 evaluations · 162 results

Overview

Published fixed-triplet evidence-direction workflow with tool-assisted and unaided configurations; no clinical validation claim.

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

Evaluations and results

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

Filter evaluations

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.

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How it works, versions and access

Versions and evaluated configurations

ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation · variant of
GPT-5 2025-08-07 alone, CIViC March 2026 · variant of
GPT-5 2025-08-07 with CIViC MCP, March 2026 · variant of

Strengths, limitations and unresolved questions

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

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

0 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-30-e37e3ab1284d
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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-pipeline-civic-retrieval

areas: dna-genomes
contexts: clinical_research
source locator: Supplementary implementation and Agent Mode evaluation methods
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

Related records

variant of: ChatGPT Agent Mode, 2–7 March 2026 CIViC evaluation
variant of: GPT-5 2025-08-07 alone, CIViC March 2026
variant of: GPT-5 2025-08-07 with CIViC MCP, March 2026

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