Extraction flags

12 values
Extraction schema (list)Merge step
Flags the extractor attaches to a row; the merge step adds encoding-artifact-healed and mesh-not-in-candidates.
2. No biomarker in the text (classic chemotherapy, anti-angiogenesis without biomarker gating) → biomarker_name="none", alteration_type="none", biomarker_detail="n/a", diagnostic_criterion="n/a", scoring_system="n/a", test_method=[] (empty list — no diagnostic test applies). Flag "no-biomarker" and "non-targeted-therapy".
2a. A hereditary tumour syndrome named as the population (von Hippel-Lindau disease, neurofibromatosis type 1, tuberous sclerosis complex) is a clinical diagnosis, not a biomarker: biomarker_name="none", alteration_type="none", scoring_system="n/a", test_method=[]. Put the syndrome into tumor_type (e.g. "VHL disease-associated renal cell carcinoma") and patient_eligibility, and flag "no-biomarker" but NOT "non-targeted-therapy". Record a germline biomarker only when the text names the alteration itself (e.g. "germline BRCA1/2 mutations").
3. Primary negative biomarker (e.g. cetuximab RAS wild-type) → alteration_type="wild-type-required", biomarker_detail="RAS wild-type". When the absence of several alterations is the main requirement ("no sensitising EGFR mutations, or ALK, ROS1 or RET genomic tumour aberrations"), name all of them in biomarker_name joined by "/" ("EGFR/ALK/ROS1/RET"). Secondary negative (e.g. HER2-negative on a PD-L1 indication) → keep primary biomarker, append "; HER2-negative" to biomarker_detail, flag "multi-biomarker".
5. Do NOT invent thresholds. "Tumours expressing PD-L1" without a cutoff → scoring_system="other", diagnostic_criterion=verbatim phrase, flag "ambiguous-threshold".
8. If uncertain on an enum, pick the closest and flag. Never leave blanks.
FlagRowsSource
ambiguous-threshold3Extractor
multi-biomarker56Extractor
compound-sentence51Extractor
negative-biomarker43Extractor
no-biomarker346Extractor
encoding-artifact0Extractor
tumor-agnostic6Extractor
histology-specific39Extractor
prior-therapy-required309Extractor
age-restricted79Extractor
non-targeted-therapy188Extractor
encoding-artifact-healed48Merge step