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")
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→ connected lamindb: testuser1/test-scrna
→ created Transform('agayZTonayqA0000'), started new Run('AEGxhIUn...') at 2025-05-08 07:33:25 UTC
→ notebook imports: bionty==1.3.2 lamindb==1.5.0
Query artifacts by provenance metadata¶
Query the transform, e.g., by key:
transform = ln.Transform.get(key="scrna.ipynb")
transform
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Transform(uid='Nv48yAceNSh80000', is_latest=True, key='scrna.ipynb', description='scRNA-seq', type='notebook', hash='N9bsgXXEvwah50XKpKewGg', space_id=1, created_by_id=1, created_at=2025-05-08 07:32:20 UTC)
Query the artifact:
ln.Artifact.filter(transform=transform).df()
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| 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_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||||||
| 1 | N1mEcYOuezEzvHsx0000 | datasets/conde22.h5ad | None | .h5ad | dataset | AnnData | 57612943 | t_YJQpYrAyAGhs7Ir68zKj | None | 1648 | sha1-fl | True | False | 1 | 1 | 3 | None | True | 1 | 2025-05-08 07:32:58.528000+00:00 | 1 | None | 1 |
Query artifacts by biological metadata¶
tissues = bt.Tissue.lookup()
query = ln.Artifact.filter(
tissues=tissues.blood,
)
query.df()
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| 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_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||||||
| 1 | N1mEcYOuezEzvHsx0000 | datasets/conde22.h5ad | None | .h5ad | dataset | AnnData | 57612943 | t_YJQpYrAyAGhs7Ir68zKj | None | 1648 | sha1-fl | True | False | 1 | 1 | 3 | None | True | 1 | 2025-05-08 07:32:58.528000+00:00 | 1 | None | 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()
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Artifact .h5ad/AnnData ├── General │ ├── .uid = 'N1mEcYOuezEzvHsx0000' │ ├── .key = 'datasets/conde22.h5ad' │ ├── .size = 57612943 │ ├── .hash = 't_YJQpYrAyAGhs7Ir68zKj' │ ├── .n_observations = 1648 │ ├── .path = /home/runner/work/lamin-usecases/lamin-usecases/docs/test-scrna/.lamindb/N1mEcYOuezEzvHsx0000.h5ad │ ├── .created_by = testuser1 (Test User1) │ ├── .created_at = 2025-05-08 07:32:58 │ └── .transform = 'scRNA-seq' ├── Dataset features │ ├── obs • 4 [Feature] │ │ assay cat[bionty.ExperimentalF… 10x 3' v3, 10x 5' v1, 10x 5' v2 │ │ cell_type cat[bionty.CellType] CD16-negative, CD56-bright natural kille… │ │ tissue cat[bionty.Tissue] blood, bone marrow, caecum, duodenum, il… │ │ donor str │ └── var.T • 36503 [bionty.Gene.ensembl_gen… └── Labels └── .tissues bionty.Tissue blood, thoracic lymph node, spleen, lung… .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()
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artifact2.describe()
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Artifact .h5ad/AnnData ├── General │ ├── .uid = 'DqTotMzB8ylFsZRB0001' │ ├── .size = 857336 │ ├── .hash = 'GK721a-L-fGDI8kXefKMtA' │ ├── .n_observations = 70 │ ├── .path = /home/runner/work/lamin-usecases/lamin-usecases/docs/test-scrna/.lamindb/DqTotMzB8ylFsZRB0001.h5ad │ ├── .created_by = testuser1 (Test User1) │ ├── .created_at = 2025-05-08 07:33:19 │ └── .transform = 'Standardize and append a dataset' ├── 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 mon… │ cell_type_untrusted cat[bionty.CellType] B cell, CD19-positive, CD14-positive mon… └── Labels └── .cell_types bionty.CellType CD8-positive, alpha-beta memory T cell, …
artifact2.view_lineage()
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