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

💡 connected lamindb: testuser1/test-scrna

ln.settings.transform.stem_uid = "agayZTonayqA"
ln.settings.transform.version = "1"
ln.track()

💡 notebook imports: bionty==0.42.9 lamindb==0.70.3

💡 saved: Transform(uid='agayZTonayqA5zKv', name='Query artifacts', key='scrna3', version='1', type='notebook', updated_at=2024-04-22 10:42:39 UTC, created_by_id=1)

💡 saved: Run(uid='rNG4PQngawr8BlTAwa9R', transform_id=3, created_by_id=1)

Query artifacts by provenance metadata

users = ln.User.lookup()

ln.Transform.filter(created_by=users.testuser1).search("scrna")

	uid	score
name
scRNA-seq	Nv48yAceNSh85zKv	90.0
Standardize and append a batch of data	ManDYgmftZ8C5zKv	45.0
Query artifacts	agayZTonayqA5zKv	36.0

transform = ln.Transform.filter(uid="Nv48yAceNSh85zKv").one()

ln.Artifact.filter(transform=transform).df()

	uid	storage_id	key	suffix	accessor	description	version	size	hash	hash_type	n_objects	n_observations	transform_id	run_id	visibility	key_is_virtual	created_at	updated_at	created_by_id
id
1	Tshv8ZcuQUs1VfprMZ55	1	None	.h5ad	AnnData	Human immune cells from Conde22	None	57612943	9sXda5E7BYiVoDOQkTC0KB	sha1-fl	None	1648	1	1	1	True	2024-04-22 10:42:03.415587+00:00	2024-04-22 10:42:06.762408+00:00	1

Query artifacts by biological metadata

organism = bt.Organism.lookup()
tissues = bt.Tissue.lookup()

query = ln.Artifact.filter(
    organism=organism.human,
    tissues=tissues.bone_marrow,
)

query.df()

	uid	key	suffix	accessor	description	version	size	hash	hash_type	n_objects	n_observations	visibility	key_is_virtual	created_at	updated_at	storage_id	transform_id	run_id	created_by_id
id

Inspect artifact metadata

query_set = ln.Artifact.filter().all()

artifact1, artifact2 = query_set[0], query_set[1]

artifact1.describe()

Artifact(uid='Tshv8ZcuQUs1VfprMZ55', suffix='.h5ad', accessor='AnnData', description='Human immune cells from Conde22', size=57612943, hash='9sXda5E7BYiVoDOQkTC0KB', hash_type='sha1-fl', n_observations=1648, visibility=1, key_is_virtual=True, updated_at=2024-04-22 10:42:06 UTC)

Provenance:
  📎 storage: Storage(uid='KwQeXzq5', root='/home/runner/work/lamin-usecases/lamin-usecases/docs/test-scrna', type='local')
  📎 transform: Transform(uid='Nv48yAceNSh85zKv', name='scRNA-seq', key='scrna', version='1', type='notebook')
  📎 run: Run(uid='IINE0MbPjgvFpAUeyzBH', started_at=2024-04-22 10:40:11 UTC, is_consecutive=True)
  📎 created_by: User(uid='DzTjkKse', handle='testuser1', name='Test User1')
  📎 input_of (core.Run): ['2024-04-22 10:42:13 UTC']
Features:
  var: FeatureSet(uid='LF1XYQjNoUipLfEEALoP', n=36503, type='number', registry='bionty.Gene')
    'LINC02731', 'RALA', 'EPB41L2', 'DNMBP-AS1', 'USP1', 'TLR10', 'ZKSCAN3', 'LINC00654', 'NEMF', 'INTS6', 'KXD1-AS1', 'MICOS13', 'WDR35-DT', 'UBXN8', 'CASP4', 'LINC02253', 'COMMD5', 'ACVR1C', 'KIF5B', 'CHKB', ...
  obs: FeatureSet(uid='cz0e1Iz4dZSe91DZy0we', n=4, registry='core.Feature')
    🔗 donor (12, core.ULabel): '637C', 'A35', 'A29', 'A37', '640C', 'A36', 'A52', '582C', 'D496', '621B', ...
    🔗 tissue (17, bionty.Tissue): 'blood', 'spleen', 'liver', 'bone marrow', 'ileum', 'thoracic lymph node', 'omentum', 'duodenum', 'lung', 'sigmoid colon', ...
    🔗 cell_type (32, bionty.CellType): 'group 3 innate lymphoid cell', 'plasma cell', 'plasmacytoid dendritic cell', 'CD4-positive helper T cell', 'regulatory T cell', 'naive thymus-derived CD4-positive, alpha-beta T cell', 'megakaryocyte', 'dendritic cell, human', 'T follicular helper cell', 'effector memory CD4-positive, alpha-beta T cell', ...
    🔗 assay (3, bionty.ExperimentalFactor): '10x 5' v1', '10x 3' v3', '10x 5' v2'
Labels:
  📎 tissues (17, bionty.Tissue): 'blood', 'spleen', 'liver', 'bone marrow', 'ileum', 'thoracic lymph node', 'omentum', 'duodenum', 'lung', 'sigmoid colon', ...
  📎 cell_types (32, bionty.CellType): 'group 3 innate lymphoid cell', 'plasma cell', 'plasmacytoid dendritic cell', 'CD4-positive helper T cell', 'regulatory T cell', 'naive thymus-derived CD4-positive, alpha-beta T cell', 'megakaryocyte', 'dendritic cell, human', 'T follicular helper cell', 'effector memory CD4-positive, alpha-beta T cell', ...
  📎 experimental_factors (3, bionty.ExperimentalFactor): '10x 5' v1', '10x 3' v3', '10x 5' v2'
  📎 ulabels (12, core.ULabel): '637C', 'A35', 'A29', 'A37', '640C', 'A36', 'A52', '582C', 'D496', '621B', ...

artifact1.view_lineage()

artifact2.describe()

Artifact(uid='2rM782zVcyLx46qGM2EU', suffix='.h5ad', accessor='AnnData', description='10x reference adata', size=857752, hash='0Fozmib89XWbFoD6hSq5yA', hash_type='md5', n_observations=70, visibility=1, key_is_virtual=True, updated_at=2024-04-22 10:42:32 UTC)

Provenance:
  📎 storage: Storage(uid='KwQeXzq5', root='/home/runner/work/lamin-usecases/lamin-usecases/docs/test-scrna', type='local')
  📎 transform: Transform(uid='ManDYgmftZ8C5zKv', name='Standardize and append a batch of data', key='scrna2', version='1', type='notebook')
  📎 run: Run(uid='dB2PAgeaKiIqmwXpzyDG', started_at=2024-04-22 10:42:13 UTC, is_consecutive=True)
  📎 created_by: User(uid='DzTjkKse', handle='testuser1', name='Test User1')
Features:
  var: FeatureSet(uid='QTZfL7djujTuGfD3Kf5T', n=754, type='number', registry='bionty.Gene')
    'IMPDH2', 'ILF3-DT', 'PMVK', 'LEPROTL1', 'MZB1', 'SPINT2', 'EVL', 'LY9', 'ELOVL5', 'OGG1', 'PAXX', 'CD33', 'IGLL1', 'EIF1B', 'TLN1', 'MYO5A', 'PPP2R5C', 'PBXIP1', 'GATA3', 'STMN1', ...
  obs: FeatureSet(uid='8gZ1gzgpX0BJIpLsfG1a', n=1, registry='core.Feature')
    🔗 cell_type (9, bionty.CellType): 'CD8-positive, CD25-positive, alpha-beta regulatory T cell', 'CD38-positive naive B cell', 'effector memory CD4-positive, alpha-beta T cell, terminally differentiated', 'B cell, CD19-positive', 'CD16-positive, CD56-dim natural killer cell, human', 'CD4-positive, alpha-beta T cell', 'cytotoxic T cell', 'dendritic cell', 'CD14-positive, CD16-negative classical monocyte'
Labels:
  📎 cell_types (9, bionty.CellType): 'CD8-positive, CD25-positive, alpha-beta regulatory T cell', 'CD38-positive naive B cell', 'effector memory CD4-positive, alpha-beta T cell, terminally differentiated', 'B cell, CD19-positive', 'CD16-positive, CD56-dim natural killer cell, human', 'CD4-positive, alpha-beta T cell', 'cytotoxic T cell', 'dendritic cell', 'CD14-positive, CD16-negative classical monocyte'

artifact2.view_lineage()

Compare features

Here we compute shared genes:

artifact1_genes = artifact1.features["var"]
artifact2_genes = artifact2.features["var"]

shared_genes = artifact1_genes & artifact2_genes
len(shared_genes)

749

shared_genes.list("symbol")[:10]

['HES4',
 'TNFRSF4',
 'SSU72',
 'PARK7',
 'RBP7',
 'SRM',
 'MAD2L2',
 'AGTRAP',
 'TNFRSF1B',
 'EFHD2']

Compare cell types

artifact1_celltypes = artifact1.cell_types.all()
artifact2_celltypes = artifact2.cell_types.all()

shared_celltypes = artifact1_celltypes & artifact2_celltypes
shared_celltypes_names = shared_celltypes.list("name")
shared_celltypes_names

['CD16-positive, CD56-dim natural killer cell, human']

Load the individual artifacts

We could either load the artifacts into memory or access them in backed mode through .backed() to lazily load their content.

Let’s load them into memory:

adata1 = artifact1.load()
adata2 = artifact2.load()

We can now subset the two collections by shared cell types:

adata1_subset = adata1[adata1.obs["cell_type"].isin(shared_celltypes_names)]
adata2_subset = adata2[adata2.obs["cell_type"].isin(shared_celltypes_names)]