Issues

• Standard full text embeds the negation cue, so negated findings map to the wrong term

  berntpopp/phentrieve#472 · Filter by author janpower opened on Oct 30, 2026

• LLM pipeline silently drops findings mapped to non-phenotypic terms

  berntpopp/phentrieve#471 · Filter by author janpower opened on Oct 30, 2026

• Local checks fail with a local data dir and on Windows

  berntpopp/phentrieve#470 · Filter by author janpower opened on Oct 30, 2026

• Full-text receipt strings are hardcoded in English

  berntpopp/phentrieve#469 · Filter by author janpower opened on Oct 30, 2026

• Standard retrieval ranks subtypes above Seizure for "Recurrent seizures"

  berntpopp/phentrieve#468 · Filter by author janpower opened on Oct 30, 2026
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• PII check flags a false name on hyphenated clinical text

  berntpopp/phentrieve#467 · Filter by author janpower opened on Oct 30, 2026

• Esc does not close the reset dialog or the tutorial

  berntpopp/phentrieve#466 · Filter by author janpower opened on Oct 30, 2026

• Reloading a /?text= deep link submits the query again

  berntpopp/phentrieve#465 · Filter by author janpower opened on Oct 30, 2026

• Case workspace drawer blocks adding further terms

  berntpopp/phentrieve#464 · Filter by author janpower opened on Oct 30, 2026
  1

• Standard backend: normal and non-English findings have no highlight

  berntpopp/phentrieve#463 · Filter by author janpower opened on Oct 30, 2026

• LLM full text: soft hyphens and line-break hyphens lose findings and highlights

  berntpopp/phentrieve#462 · Filter by author janpower opened on Oct 30, 2026
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• REST LLM path returns 500 when PHENTRIEVE_LLM_BASE_URL is set

  berntpopp/phentrieve#461 · Filter by author janpower opened on Oct 30, 2026

• Frontend: other-person, family-history and temporality data are not shown (a note can report 0 findings)

  berntpopp/phentrieve#460 · Filter by author janpower opened on Oct 30, 2026

• Standard assertion detection inverts negation: "ruled out" affirmed, "cannot be ruled out" negated

  berntpopp/phentrieve#459 · Filter by author janpower opened on Oct 30, 2026

• Full-text: language 'Auto' is never sent, API always processes as English (regression for German UI since v0.30.0)

  bug
  berntpopp/phentrieve#458 · Filter by author janpower opened on Oct 29, 2026

• Evaluate: does extracted HPO rank the right disease? (VarLens v2 scorer, soft profiles)

  enhancementresearch
  berntpopp/phentrieve#451 · Filter by author berntpopp opened on Oct 27, 2026
  1

  

• Cleanup: remove about 1,000 lines of unused evaluation modules and three CLI options that do nothing

  enhancement
  berntpopp/phentrieve#414 · Filter by author berntpopp opened on Oct 27, 2026
  

• LLM full-text: attribution offsets break on non-ASCII text, always pick the first occurrence, and trust unchecked model offsets

  bug
  berntpopp/phentrieve#411 · Filter by author berntpopp opened on Oct 27, 2026
  1

  

• Standard pipeline: negation of coordinated lists and family experiencer are lost

  bug
  berntpopp/phentrieve#400 · Filter by author berntpopp opened on Oct 27, 2026

• Phenopacket export: uncertain exported as observed, temporality lost, opposite-polarity twins, per-chunk duplicates

  bug
  berntpopp/phentrieve#399 · Filter by author berntpopp opened on Oct 27, 2026

• LLM mapping prompt: no guidance on term specificity between ancestor and descendant candidates

  berntpopp/phentrieve#380 · Filter by author janpower opened on Oct 16, 2026

• LLM phase-1 prompt: negation scope rule too narrow for coordinated findings

  berntpopp/phentrieve#379 · Filter by author janpower opened on Oct 16, 2026
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• LLM two-phase prompts: few-shot examples are defined but never sent

  berntpopp/phentrieve#378 · Filter by author janpower opened on Oct 16, 2026
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• LLM phase 1: fragmented negated coordination triggers runaway evidence_text repetition; recovery retries identical requests at the output cap

  berntpopp/phentrieve#375 · Filter by author janpower opened on Oct 16, 2026

• Grounded two-phase LLM extraction drops negation context and overrides correct ConText assertions

  berntpopp/phentrieve#325 · Filter by author janpower opened on Jul 28, 2026