Query artifacts¶
Here, we’ll query artifacts and inspect their metadata.
This guide can be skipped if you are only interested in how to leverage the overall collection.
import lamindb as ln
import bionty as bt
ln.track("agayZTonayqA")
Show code cell output
→ connected lamindb: testuser1/test-scrna
→ created Transform('agayZTonayqA0000'), started new Run('7QvW7mYW...') at 2025-07-08 11:03:09 UTC
→ notebook imports: bionty==1.6.0 lamindb==1.7.1
Query artifacts by provenance metadata¶
Query the transform, e.g., by key:
transform = ln.Transform.get(key="scrna.ipynb")
transform
Show code cell output
Transform(uid='Nv48yAceNSh80000', is_latest=True, key='scrna.ipynb', description='scRNA-seq', type='notebook', hash='IrEQsLuzw-3-3td1Pd778w', branch_id=1, space_id=1, created_by_id=1, created_at=2025-07-08 11:01:39 UTC)
Query the artifact:
ln.Artifact.filter(transform=transform).df()
Show code cell output
| uid | key | description | suffix | kind | otype | size | hash | n_files | n_observations | _hash_type | _key_is_virtual | _overwrite_versions | space_id | storage_id | schema_id | version | is_latest | run_id | created_at | created_by_id | _aux | branch_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||||||
| 1 | 2AJSQbtyNKdIU9tk0000 | datasets/conde22.h5ad | None | .h5ad | dataset | AnnData | 57612943 | t_YJQpYrAyAGhs7Ir68zKj | None | 1648 | sha1-fl | True | False | 1 | 1 | 3 | None | True | 1 | 2025-07-08 11:02:38.377000+00:00 | 1 | {'af': {'0': True}} | 1 |
Query artifacts by biological metadata¶
tissues = bt.Tissue.lookup()
query = ln.Artifact.filter(
tissues=tissues.blood,
)
query.df()
Show code cell output
| uid | key | description | suffix | kind | otype | size | hash | n_files | n_observations | _hash_type | _key_is_virtual | _overwrite_versions | space_id | storage_id | schema_id | version | is_latest | run_id | created_at | created_by_id | _aux | branch_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||||||
| 1 | 2AJSQbtyNKdIU9tk0000 | datasets/conde22.h5ad | None | .h5ad | dataset | AnnData | 57612943 | t_YJQpYrAyAGhs7Ir68zKj | None | 1648 | sha1-fl | True | False | 1 | 1 | 3 | None | True | 1 | 2025-07-08 11:02:38.377000+00:00 | 1 | {'af': {'0': True}} | 1 |
Inspect artifact metadata¶
Query all artifacts that measured the “cell_type” feature:
query_set = ln.Artifact.filter(feature_sets__features__name="cell_type").all()
artifact1, artifact2 = query_set[0], query_set[1]
artifact1.describe()
Show code cell output
Artifact .h5ad · AnnData · dataset ├── General │ ├── uid: 2AJSQbtyNKdIU9tk0000 hash: t_YJQpYrAyAGhs7Ir68zKj │ ├── size: 54.9 MB n_observations: 1648 │ ├── space: all branch: main │ ├── created_at: 2025-07-08 11:02:38 created_by: testuser1 (Test User1) │ ├── key: datasets/conde22.h5ad │ ├── storage location / path: │ │ /home/runner/work/lamin-usecases/lamin-usecases/docs/test-scrna/.lamindb/2AJSQbtyNKdIU9tk0000.h5ad │ └── transform: scrna.ipynb ├── Dataset features │ ├── obs • 4 [Feature] │ │ assay cat[bionty.ExperimentalFactor] 10x 3' v3, 10x 5' v1, 10x 5' v2 │ │ cell_type cat[bionty.CellType] CD16-negative, CD56-bright natural kill… │ │ tissue cat[bionty.Tissue] blood, bone marrow, caecum, duodenum, i… │ │ donor str │ └── var.T • 36283 [bionty.Gene.ensembl_gene_id] └── Labels └── .tissues bionty.Tissue blood, thoracic lymph node, spleen, lun… .cell_types bionty.CellType classical monocyte, T follicular helper… .experimental_factors bionty.ExperimentalFactor 10x 3' v3, 10x 5' v2, 10x 5' v1
artifact1.view_lineage()
Show code cell output
artifact2.describe()
Show code cell output
Artifact .h5ad · AnnData · dataset ├── General │ ├── uid: se0IcLB1kiNnExJ80001 hash: GK721a-L-fGDI8kXefKMtA │ ├── size: 837.2 KB n_observations: 70 │ ├── space: all branch: main │ ├── created_at: 2025-07-08 11:03:02 created_by: testuser1 (Test User1) │ ├── storage location / path: │ │ /home/runner/work/lamin-usecases/lamin-usecases/docs/test-scrna/.lamindb/se0IcLB1kiNnExJ80001.h5ad │ ├── description: 10x reference adata, trusted cell type annotation │ └── transform: scrna2.ipynb ├── Dataset features │ ├── var • 754 [bionty.Gene] │ │ HES4 float │ │ TNFRSF4 float │ │ SSU72 float │ │ PARK7 float │ │ RBP7 float │ │ SRM float │ │ MAD2L2 float │ │ AGTRAP float │ │ TNFRSF1B float │ │ EFHD2 float │ │ NECAP2 float │ │ HP1BP3 float │ │ C1QA float │ │ C1QB float │ │ HNRNPR float │ │ GALE float │ │ STMN1 float │ │ CD52 float │ │ FGR float │ │ ATP5IF1 float │ └── obs • 2 [Feature] │ cell_type cat[bionty.CellType] B cell, CD19-positive, CD14-positive mo… │ cell_type_untrusted cat[bionty.CellType] B cell, CD19-positive, CD14-positive mo… └── Labels └── .cell_types bionty.CellType CD8-positive, alpha-beta memory T cell,…
artifact2.view_lineage()
Show code cell output
