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README.md

@@ -122,9 +122,9 @@ per-class F1 scores of 0.95 (low-risk), 0.74 (moderate), and 0.49
 
 | Table | Description |
 |-------|-------------|
-| `oligos.csv` | Oligonucleotide identifiers, target genes, modality, 5'-to-3' sequence, sequence length, control assignment, source role |
+| `oligos.csv` | Oligonucleotide identifiers, target genes, modality, 5'-to-3' sequence, sequence length, `is_administered_oligo` flag, control assignment, source role |
 | `chemical_modifications.csv` | Aggregate chemistry per oligo: sugar chemistry, backbone class, phosphorothioate fraction, modification pattern, GalNAc conjugation, purity, characterization-method metadata |
-| `oligo_modification_positions.csv` | **Position-level** chemical modifications: per-position base, sugar modification, backbone linkage, region (e.g., gapmer wing/gap, siRNA seed region), terminal conjugate, and provenance |
+| `oligo_modification_positions.csv` | Position-level chemical modifications: per-position base, sugar modification, backbone linkage, region (e.g., gapmer wing/gap, siRNA seed region), terminal conjugate, and provenance |
 | `biophysical_properties.csv` | Predicted Tm, ΔG, GC content, off-target hybridization burden, sequence-derived risk fields |
 | `dose_exposure.csv` | Dose/concentration, exposure duration, treatment frequency, exposure normalization |
 | `assays.csv` | Model system, cell model, species/human-proxy flag, organoid/MPS status, replicate count, assay type |
@@ -189,18 +189,18 @@ The full calibration specification is recorded in
   non-trivial classification problem with both common and rare strata;
   it is not a claim about wet-lab oligonucleotide toxicity prevalence.
 - Of the 1,120 rows in `oligos.csv`, 1,089 represent oligos with
-  explicit sequences (`sequence_length > 0`) and 31 represent context
-  records without an administered oligo: vehicle/mock controls,
-  clinical risk-score contexts, extracellular-vesicle delivery
-  contexts, small-molecule rescue contexts, and non-administered
-  injury-model contexts. These context records carry an
-  `oligo_modality` value that explicitly indicates they are not
-  administered oligos (e.g., `vehicle_mock`,
-  `context_not_administered_oligo`,
+  explicit sequences and 31 represent context records without an
+  administered oligo: vehicle/mock controls, clinical risk-score
+  contexts, extracellular-vesicle delivery contexts, small-molecule
+  rescue contexts, and non-administered injury-model contexts. Each
+  row carries an `is_administered_oligo` boolean column for
+  unambiguous filtering. Users restricting analysis to sequence-bearing
+  oligos should filter on `is_administered_oligo == True` (equivalent
+  to `sequence_length > 0`). Context records additionally carry an
+  `oligo_modality` value that explicitly identifies their non-oligo
+  nature (e.g., `vehicle_mock`, `context_not_administered_oligo`,
   `extracellular_vesicle_context_not_oligo`,
-  `clinical-risk-score-context`). Users restricting analysis to
-  sequence-bearing oligos should filter on `sequence_length > 0` or on
-  the modality field.
+  `clinical-risk-score-context`).
 - Original source PDFs are not redistributed; sources are identified
   through title-level metadata only.