Issues

• B-ALL relapse vs diagnosis mutation frequencies: agent pools four ALL studies instead of comparing

  bug
  cBioPortal/cbioportal-mcp#164 · Filter by author inodb opened on Sep 29, 2026
  2

• Different subtype counts for the same question across attempts (brca_mbcproject_2022)

  bug
  cBioPortal/cbioportal-mcp#163 · Filter by author inodb opened on Sep 29, 2026
  2

• Median age reported from bottom-coded ages (TARGET osteosarcoma: 241/293 ages are exactly 18)

  bug
  cBioPortal/cbioportal-mcp#162 · Filter by author inodb opened on Sep 29, 2026
  2

• Agent says there is no H&E data without checking resource tables (regression of #58)

  bug
  cBioPortal/cbioportal-mcp#161 · Filter by author inodb opened on Sep 29, 2026

• Longitudinal-data study query has multiple errors but the agent still declares success

  cBioPortal/cbioportal-mcp#101 · Filter by author inodb opened on Aug 5, 2026
  1

• Agent can't answer "which studies use separate outcomes files" — no source-file provenance in DB

  cBioPortal/cbioportal-mcp#98 · Filter by author inodb opened on Aug 5, 2026

• Agent returns empty responses to repeated "calculate median expression" queries

  cBioPortal/cbioportal-mcp#93 · Filter by author inodb opened on Aug 5, 2026
  1

• Add auth for local deployments of cbioportal/mcp study permissions etc.

  cBioPortal/cbioportal-mcp#81 · Filter by author ForisKuang opened on Jul 8, 2026

• Agent drifts into out-of-scope territory (paper analysis, methodology critique, presentation outlines, complex external code)

  cBioPortal/cbioportal-mcp#69 · Filter by author inodb opened on Jun 5, 2026

• Agent over-interprets flawed premises instead of flagging the contradiction (TP53-out-of-nowhere, MAP2K1 codon 105, etc.)

  cBioPortal/cbioportal-mcp#67 · Filter by author inodb opened on Jun 5, 2026

• Agent doesn't handle TERT promoter mutations as a special case (queries all TERT alterations)

  cBioPortal/cbioportal-mcp#65 · Filter by author inodb opened on Jun 5, 2026

• cBioDBAgent misses results when clinical attribute_value differs only in case (e.g. 'GERMLINE' vs 'Germline')

  cBioPortal/cbioportal-mcp#56 · Filter by author inodb opened on May 21, 2026

• cBioDBAgent sample counts + frequencies don't match cBioPortal study view

  cBioPortal/cbioportal-mcp#53 · Filter by author inodb opened on May 18, 2026
  1

• cBioDBAgent picks wrong study + returns table for oncoprint requests

  cBioPortal/cbioportal-mcp#51 · Filter by author inodb opened on May 18, 2026

• Surface other cBioPortal instances (pedcbioportal, GENIE) when asked-for cohort lives elsewhere

  cBioPortal/cbioportal-mcp#42 · Filter by author inodb opened on May 12, 2026

• Bot incorrectly says a study does not exist when it does (study lookup gap)

  cBioPortal/cbioportal-mcp#80 · Filter by author inodb opened on May 12, 2026
  1

• Unclear error message when complex multi-criteria cohort queries fail

  cBioPortal/cbioportal-mcp#35 · Filter by author inodb opened on Apr 16, 2026

• Markdown table column headings don't match data columns

  cBioPortal/cbioportal-mcp#29 · Filter by author inodb opened on Apr 9, 2026

• Bot promises capabilities it cannot deliver (KM plots, CSV export)

  cBioPortal/cbioportal-mcp#28 · Filter by author inodb opened on Apr 9, 2026

• Clarify ambiguous gene symbols instead of silently aggregating (e.g. CD3)

  cBioPortal/cbioportal-mcp#37 · Filter by author inodb opened on Apr 9, 2026

• Use current OncoTree codes, not deprecated ones (GBM → GB)

  cBioPortal/cbioportal-mcp#36 · Filter by author inodb opened on Apr 9, 2026
  1

• Bot should describe data submission process when asked how to add data

  cBioPortal/cbioportal-mcp#26 · Filter by author inodb opened on Mar 23, 2026

• Bot should not answer clinical questions using only LLM knowledge

  cBioPortal/cbioportal-mcp#24 · Filter by author inodb opened on Mar 23, 2026
  1

• Bot should quickly respond when asked about data types not stored in cBioPortal

  cBioPortal/cbioportal-mcp#21 · Filter by author inodb opened on Mar 16, 2026
  1

• Add guide for germline variant studies in cBioPortal

  cBioPortal/cbioportal-mcp#20 · Filter by author inodb opened on Mar 16, 2026