lamindb#

A data framework for biology.

LaminDB helps you manage data batches with two basic registries:

File()

Files: data batches (blobs & array shards).

Dataset()

Datasets: collections of data batches.

Four registries track provenance of data batches:

Transform()

Transforms of files & datasets.

Run()

Runs of transforms.

User()

Users.

Storage()

Storage locations.

Three registries validate & contextualize:

ULabel()

Universal label ontology.

Feature()

Dimensions of measurement.

FeatureSet()

Jointly measured sets of features.

You can also access data directly via paths:

UPath(*args, **kwargs)

Paths: low-level key-value access to files & objects.

Functions:

track([transform, new_run, reference, ...])

Track global Transform & Run for a notebook or pipeline.

view([n, schema, registries])

View latest metadata state.

save(records[, ignore_conflicts])

Bulk save to registries & storage.

Modules & settings:

settings

Global Settings.

setup

Setup & configure LaminDB.

dev

Developer API.