Issues

• Investigate failed LOVD instance URLs from harvest

  text2gene/text2gene2#24 · Filter by author nthmost opened on Apr 10, 2026

• Contact LOVD/LUMC to get unblocked on databases.lovd.nl

  text2gene/text2gene2#23 · Filter by author nthmost opened on Apr 10, 2026

• LOVD implementation: get unblocked + build source against working instances

  text2gene/text2gene2#22 · Filter by author nthmost-orkes opened on Apr 10, 2026
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• HPO phenotype-aware query expansion

  text2gene/text2gene2#21 · Filter by author nthmost opened on Apr 5, 2026

• Orphanet rare disease context for variant queries

  text2gene/text2gene2#20 · Filter by author nthmost opened on Apr 5, 2026

• [Epic] Query expansion — port and extend text2gene's expansion system

  text2gene/text2gene2#18 · Filter by author nthmost opened on Apr 4, 2026

• Reconnect Google CSE with expanded queries

  text2gene/text2gene2#17 · Filter by author nthmost opened on Apr 4, 2026

• Cross-reference expansion: try more HGVS forms in text searches

  text2gene/text2gene2#16 · Filter by author nthmost opened on Apr 4, 2026

• LLM-assisted query expansion for zero-result variants

  text2gene/text2gene2#15 · Filter by author nthmost opened on Apr 4, 2026

• Gene synonym/alias expansion for text-based sources

  text2gene/text2gene2#14 · Filter by author nthmost opened on Apr 4, 2026

• LLM-assisted abstract validation via LiteLLM router

  text2gene/text2gene2#13 · Filter by author nthmost opened on Apr 4, 2026

• PubTator as a validation oracle (replace/augment regex)

  text2gene/text2gene2#12 · Filter by author nthmost opened on Apr 4, 2026

• Full-text validation (PMC + local fulltext corpus)

  text2gene/text2gene2#11 · Filter by author nthmost opened on Apr 4, 2026

• Disease-based PMID discovery via medgen.pubmed + HPO/ClinVar conditions

  text2gene/text2gene2#10 · Filter by author nthmost opened on Apr 4, 2026

• Add gene2pubmed as a confirmation signal

  text2gene/text2gene2#9 · Filter by author nthmost opened on Apr 4, 2026

• Add local ClinVar var_citations as a source

  text2gene/text2gene2#8 · Filter by author nthmost opened on Apr 4, 2026

• EuropePMC query degrades to gene-only for splice-site and p.? variants

  text2gene/text2gene2#5 · Filter by author nthmost-orkes opened on Mar 27, 2026

• Pilot: verify literature results for 5 rare disease variants using metapub fulltext

  text2gene/text2gene2#3 · Filter by author nthmost-orkes opened on Mar 27, 2026

• Benchmark text2gene vs LitVar2 on rare disease variant list

  text2gene/text2gene2#2 · Filter by author nthmost-orkes opened on Mar 27, 2026

• Establish rare disease variant benchmark list (100-200 variants)

  text2gene/text2gene2#1 · Filter by author nthmost-orkes opened on Mar 27, 2026