# Data dictionary

`data/processed/omniflic_nkp46.csv` and `omniclic_nkp46.csv` share the same 30-column schema. Each row represents a unique VH/VL sequence combination within one platform.

| Field | Meaning |
|---|---|
| `sample_id` | Platform plus a hash of the VH/VL sequences; key used to align data and embeddings |
| `clone_id` | Selected original clone identifier; identical OmniFlic sequences prefer `Rat_`, while OmniClic excludes `_v2` and the `50 / 0050_v2` group |
| `VH` | Complete heavy-chain variable-domain amino acid sequence |
| `VL` | Fixed light-chain variable-domain sequence for the platform |
| `KD_M` | Original SPR equilibrium dissociation constant of the selected record, in M |
| `pKD` | Regression label, `-log10(KD_M)` |
| `platform` | `OmniFlic` or `OmniClic` |
| `measurement_count` | Number of original measurements used for the label; one for every released sample |
| `pKD_min`, `pKD_max` | Range of retained pKD measurements; both equal `pKD` in the current release |
| `source_table` | Patent table containing the source KD |
| `vh_seq_id`, `vl_seq_id` | SEQ IDs in the filed ST.26 XML; multiple IDs, when present, are separated by `|` |
| `CDRH1`, `CDRH2`, `CDRH3` | VH CDR amino acid sequences under IMGT numbering |
| `V_gene`, `J_gene` | Closest amino acid reference gene assignments; tied candidates separated by `;` |
| `V_allele_candidates`, `J_allele_candidates` | AntPack's tied allele candidates in the original output format |
| `V_identity`, `J_identity` | Amino acid identity fractions for the inferred V/J matches |
| `numbering_identity` | Identity fraction for AntPack's numbering alignment |
| `annotation_warning` | Numbering-tool warning; empty when no warning is present |
| `numbering_imgt` | JSON array mapping each VH residue to its IMGT position, including insertion codes |
| `annotation_source` | Annotation tool/version, numbering scheme, and reference species |
| `numbering_start`, `numbering_end` | IMGT positions of the first and last VH residues; 1 and 128 in the main datasets |
| `family_id` | Connected-component ID under the configured V/J, CDRH3-length, and edit-distance rules |
| `fold_id` | Fixed outer test-fold ID, 0-4; a family belongs to one fold. The remaining four folds directly serve as inner validation folds |

Hugging Face metadata explicitly stores `clone_id` and `vh_seq_id` as strings. When reading local CSVs with pandas, use `dtype={"clone_id": str, "vh_seq_id": str}` to preserve identifiers as text.

## Source and exclusion tables

`data/raw/measurements.csv` retains all 415 original clone records. `clone_to_sample.csv` adds the corresponding `sample_id`, original `pKD`, the `included` flag, and `exclusion_reason`. An excluded record can share `sample_id` with a selected record while retaining `included=false`. Both tables preserve patent sequence IDs, PDF pages, OCR coordinates, and original KD text.

`excluded_measurements.csv` contains eight OmniClic `_v2` records (`excluded_clone_id_suffix`) and 31 OmniFlic numeric-ID measurements replaced by corresponding `Rat_` records (`superseded_by_preferred_clone_id_prefix`). The latter cover 30 sequence groups; `18464` and `9468` are both replaced by `Rat_108`.

The released OmniFlic task contains 138 `Rat_` records and 75 numeric-ID records. OmniClic contains 161 non-`_v2` records. Every label uses its selected record's original KD.

`excluded.csv` contains two excluded deduplicated sequences and their annotations: `Gen_1`, whose VH lacks the IMGT framework terminus (`incomplete_VH_IMGT_terminal_positions`), and OmniClic `50` (`excluded_sequence_group`). The latter records the removal of the complete `50 / 0050_v2` group; `_v2` is also recorded in `excluded_measurements.csv`. Sequence-group exclusions are applied after partition assignment so the remaining samples retain their family and fold IDs.

## Sequence and embedding files

FASTA headers match the CSV `sample_id` values. A custom embedding NPZ contains a one-dimensional string array `sample_ids` and an `N x D` numeric matrix `embeddings`; the evaluator aligns rows by `sample_id`.