torchcell.datasets.scerevisiae.smith2006.FattyAcidSmith2006Dataset

class FattyAcidSmith2006Dataset(root: str = 'data/torchcell/env_chemgen_smith2006', io_workers: int = 0, transform: Callable[[...], Any] | None = None, pre_transform: Callable[[...], Any] | None = None, **kwargs: Any)

Bases: ExperimentDataset

Smith 2006 fatty-acid clear-zone env x geno -> ordinal response dataset.

organism: ClassVar[Organism] = 'scerevisiae'

each loader declares its own, the build’s organism switch reads it off the class (dataset_organism), and a loader that forgot it is refused by name instead of inheriting an organism it may not have.

Type:

The host organism every record describes. Annotated here WITHOUT a value

property experiment_class: type[Experiment]

Experiment schema class produced by this dataset.

property reference_class: type[ExperimentReference]

Experiment-reference schema class produced by this dataset.

property raw_file_names: list[str]

The mirrored Supplementary Table 1 .xls (per-strain ordinal score table).

download() → None

Link the mirror file into raw/ after verifying it against XLS_SHA256.

The mirror plus the XLS_SHA256 pin is canonical; the Europe PMC URL is retrieval metadata that deposit_raw_mirror records, never a live build dependency. The manifest is the retrieval record and must carry the pin, else ManifestPinMismatchError names both digests.

process() → None

Parse the ordinal score table into per-(strain, condition) records; write LMDB.

preprocess_raw(df: Any, preprocess: dict[str, Any] | None = None) → Any

Preprocessing is handled inside process() for this dataset.

create_experiment() → None

Experiment construction is handled inline in process() for this dataset.