Query cellxgene-census using TileDB-SOMA

The first guide queried metadata and h5ad artifacts directly through LaminDB.

This guide uses the TileDB-SOMA API to run similar queries.

Setup

Load your LaminDB instance for storing queried data:

!lamin init --storage ./test-cellxgene --schema bionty

💡 connected lamindb: testuser1/test-cellxgene

import lamindb as ln
import bionty as bt
import cellxgene_census

census_version = "2023-07-25"

💡 connected lamindb: testuser1/test-cellxgene

Create lookup objects

We use metadata records in the laminlabs/cellxgene instance to generate lookups:

source = "laminlabs/cellxgene"
human = "homo_sapiens"

features = ln.Feature.using(source).lookup(return_field="name")
assays = bt.ExperimentalFactor.using(source).lookup(return_field="name")
cell_types = bt.CellType.using(source).lookup(return_field="name")
tissues = bt.Tissue.using(source).lookup(return_field="name")
ulabels = ln.ULabel.using(source).lookup()
suspension_types = ulabels.is_suspension_type.children.all().lookup(return_field="name")

Query data

value_filter = (
    f'{features.tissue} == "{tissues.brain}" and {features.cell_type} in'
    f' ["{cell_types.microglial_cell}", "{cell_types.neuron}"] and'
    f' {features.suspension_type} == "{suspension_types.cell}" and {features.assay} =='
    f' "{assays.ln_10x_3_v3}"'
)

value_filter

'tissue == "brain" and cell_type in ["microglial cell", "neuron"] and suspension_type == "cell" and assay == "10x 3\' v3"'

%%time

with cellxgene_census.open_soma(census_version=census_version) as census:
    # Reads SOMADataFrame as a slice
    cell_metadata = census["census_data"][human].obs.read(value_filter=value_filter)

    # Concatenates results to pyarrow.Table
    cell_metadata = cell_metadata.concat()

    # Converts to pandas.DataFrame
    cell_metadata = cell_metadata.to_pandas()

CPU times: user 4.33 s, sys: 1.66 s, total: 6 s
Wall time: 5.41 s

cell_metadata.shape

(66418, 21)

cell_metadata.head()

	soma_joinid	dataset_id	assay	assay_ontology_term_id	cell_type	cell_type_ontology_term_id	development_stage	development_stage_ontology_term_id	disease	disease_ontology_term_id	...	is_primary_data	self_reported_ethnicity	self_reported_ethnicity_ontology_term_id	sex	sex_ontology_term_id	suspension_type	tissue	tissue_ontology_term_id	tissue_general	tissue_general_ontology_term_id
0	29071956	c888b684-6c51-431f-972a-6c963044cef0	10x 3' v3	EFO:0009922	microglial cell	CL:0000129	68-year-old human stage	HsapDv:0000162	glioblastoma	MONDO:0018177	...	False	unknown	unknown	female	PATO:0000383	cell	brain	UBERON:0000955	brain	UBERON:0000955
1	29071957	c888b684-6c51-431f-972a-6c963044cef0	10x 3' v3	EFO:0009922	microglial cell	CL:0000129	68-year-old human stage	HsapDv:0000162	glioblastoma	MONDO:0018177	...	False	unknown	unknown	female	PATO:0000383	cell	brain	UBERON:0000955	brain	UBERON:0000955
2	29071964	c888b684-6c51-431f-972a-6c963044cef0	10x 3' v3	EFO:0009922	microglial cell	CL:0000129	68-year-old human stage	HsapDv:0000162	glioblastoma	MONDO:0018177	...	False	unknown	unknown	female	PATO:0000383	cell	brain	UBERON:0000955	brain	UBERON:0000955
3	29071966	c888b684-6c51-431f-972a-6c963044cef0	10x 3' v3	EFO:0009922	microglial cell	CL:0000129	68-year-old human stage	HsapDv:0000162	glioblastoma	MONDO:0018177	...	False	unknown	unknown	female	PATO:0000383	cell	brain	UBERON:0000955	brain	UBERON:0000955
4	29071967	c888b684-6c51-431f-972a-6c963044cef0	10x 3' v3	EFO:0009922	microglial cell	CL:0000129	68-year-old human stage	HsapDv:0000162	glioblastoma	MONDO:0018177	...	False	unknown	unknown	female	PATO:0000383	cell	brain	UBERON:0000955	brain	UBERON:0000955

5 rows × 21 columns

Create AnnData

%%time

with cellxgene_census.open_soma(census_version=census_version) as census:
    adata = cellxgene_census.get_anndata(
        census=census,
        organism=human,
        obs_value_filter=value_filter,
        column_names={
            "obs": [
                features.assay,
                features.cell_type,
                features.tissue,
                features.disease,
                features.suspension_type,
            ]
        },
    )

CPU times: user 36.1 s, sys: 11.3 s, total: 47.4 s
Wall time: 29.8 s

adata.var = adata.var.set_index("feature_id")

adata

AnnData object with n_obs × n_vars = 66418 × 60664
    obs: 'assay', 'cell_type', 'tissue', 'disease', 'suspension_type'
    var: 'soma_joinid', 'feature_name', 'feature_length'

adata.var.head()

	soma_joinid	feature_name	feature_length
feature_id
ENSG00000121410	0	A1BG	3999
ENSG00000268895	1	A1BG-AS1	3374
ENSG00000148584	2	A1CF	9603
ENSG00000175899	3	A2M	6318
ENSG00000245105	4	A2M-AS1	2948

adata.obs.head()

	assay	cell_type	tissue	disease	suspension_type
0	10x 3' v3	microglial cell	brain	glioblastoma	cell
1	10x 3' v3	microglial cell	brain	glioblastoma	cell
2	10x 3' v3	microglial cell	brain	glioblastoma	cell
3	10x 3' v3	microglial cell	brain	glioblastoma	cell
4	10x 3' v3	microglial cell	brain	glioblastoma	cell

Register the queried AnnData

ln.transform.stem_uid = "6oq3VJy5yxIU"
ln.transform.version = "0"
ln.track()

💡 notebook imports: bionty==0.42.9 cellxgene-census==1.13.0 lamindb==0.71.0

💡 saved: Transform(uid='6oq3VJy5yxIU6K79', name='Query cellxgene-census using TileDB-SOMA', key='query-census', version='0', type='notebook', updated_at=2024-05-01 18:50:02 UTC, created_by_id=1)

💡 saved: Run(uid='mhqsIeOhVxpOWa3WLqrG', transform_id=1, created_by_id=1)

Register genes and features:

bt.settings.organism = "human"

genes = bt.Gene.from_values(adata.var_names, field=bt.Gene.ensembl_gene_id)
ln.save(genes)

features = ln.Feature.from_df(adata.obs)
ln.save(features)

❗ did not create Gene records for 147 non-validated ensembl_gene_ids: 'ENSG00000256222', 'ENSG00000273301', 'ENSG00000272370', 'ENSG00000112096', 'ENSG00000256427', 'ENSG00000228906', 'ENSG00000277077', 'ENSG00000272551', 'ENSG00000239446', 'ENSG00000273370', 'ENSG00000261773', 'ENSG00000280095', 'ENSG00000261963', 'ENSG00000261534', 'ENSG00000268955', 'ENSG00000273923', 'ENSG00000279765', 'ENSG00000287388', 'ENSG00000260461', 'ENSG00000227902', ...

Register the AnnData object:

artifact = ln.Artifact.from_anndata(
    adata,
    description=(
        "microglial and neuron cell data from 10x 3' v3 in brain queried from Census"
    ),
)

artifact.save()

Artifact(uid='RbANRPl53UcoG9W8lLna', suffix='.h5ad', accessor='AnnData', description='microglial and neuron cell data from 10x 3' v3 in brain queried from Census', size=674995866, hash='v8QkSfHA4jUocUskUyBSzl', hash_type='sha1-fl', visibility=1, key_is_virtual=True, updated_at=2024-05-01 18:50:23 UTC, storage_id=1, transform_id=1, run_id=1, created_by_id=1)

Link validated metadata:

artifact.features.add_from_anndata(var_field=bt.Gene.ensembl_gene_id)

❗    147 terms (0.20%) are not validated for ensembl_gene_id: ENSG00000285162, ENSG00000276814, ENSG00000282080, ENSG00000237513, ENSG00000239467, ENSG00000236886, ENSG00000273576, ENSG00000256427, ENSG00000272040, ENSG00000278198, ENSG00000273496, ENSG00000279765, ENSG00000224739, ENSG00000226380, ENSG00000285106, ENSG00000272551, ENSG00000237133, ENSG00000272267, ENSG00000271870, ENSG00000227902, ...

features_remote = ln.Feature.using(source).lookup().dict()
features = ln.Feature.lookup().dict()

for col, orm in {
    "assay": bt.ExperimentalFactor,
    "cell_type": bt.CellType,
    "tissue": bt.Tissue,
    "disease": bt.Disease,
    "suspension_type": ln.ULabel,
}.items():
    labels = orm.from_values(adata.obs[col])
    if len(labels) > 0:
        ln.save(labels)
    else:
        labels = [orm(name=name) for name in adata.obs[col].unique()]
        ln.save(labels)
    artifact.labels.add(labels, features.get(col))

Show code cell output Hide code cell output

❗ now recursing through parents: this only happens once, but is much slower than bulk saving

❗ now recursing through parents: this only happens once, but is much slower than bulk saving

❗ now recursing through parents: this only happens once, but is much slower than bulk saving

❗ now recursing through parents: this only happens once, but is much slower than bulk saving

❗ did not create ULabel record for 1 non-validated name: 'cell'

artifact.describe()

Artifact(uid='RbANRPl53UcoG9W8lLna', suffix='.h5ad', accessor='AnnData', description='microglial and neuron cell data from 10x 3' v3 in brain queried from Census', size=674995866, hash='v8QkSfHA4jUocUskUyBSzl', hash_type='sha1-fl', visibility=1, key_is_virtual=True, updated_at=2024-05-01 18:50:29 UTC)

Provenance:
  📎 storage: Storage(uid='SNvsFGNNBINT', root='/home/runner/work/cellxgene-lamin/cellxgene-lamin/docs/test-cellxgene', type='local', instance_uid='5lZgSHvkhwQL')
  📎 transform: Transform(uid='6oq3VJy5yxIU6K79', name='Query cellxgene-census using TileDB-SOMA', key='query-census', version='0', type='notebook')
  📎 run: Run(uid='mhqsIeOhVxpOWa3WLqrG', started_at=2024-05-01 18:50:02 UTC, is_consecutive=True)
  📎 created_by: User(uid='DzTjkKse', handle='testuser1', name='Test User1')
Features:
  var: FeatureSet(uid='LAldMPaIO8RuFcmadgnr', n=60517, type='number', registry='bionty.Gene')
    'SMCR8', 'RXFP4', 'RLIMP2', 'MIR4477A', 'GIMAP7', 'FKBP1AP1', 'NR1H4', 'CDR2L', 'LINC01746', 'CXCL5', 'COX7BP6', 'TAAR5', 'RNU4ATAC16P', 'RPL18AP2', 'ZNHIT3', 'RN7SL606P', 'RN7SKP235', 'LAP3P1', 'PCDH9-AS2', 'STK38L', ...
  obs: FeatureSet(uid='xVUCP6IE7EIV36vdp7Rz', n=5, registry='core.Feature')
    🔗 assay (1, bionty.ExperimentalFactor): '10x 3' v3'
    🔗 cell_type (2, bionty.CellType): 'microglial cell', 'neuron'
    🔗 tissue (1, bionty.Tissue): 'brain'
    🔗 disease (1, bionty.Disease): 'glioblastoma'
    🔗 suspension_type (1, core.ULabel): 'cell'
Labels:
  📎 tissues (1, bionty.Tissue): 'brain'
  📎 cell_types (2, bionty.CellType): 'microglial cell', 'neuron'
  📎 diseases (1, bionty.Disease): 'glioblastoma'
  📎 experimental_factors (1, bionty.ExperimentalFactor): '10x 3' v3'
  📎 ulabels (1, core.ULabel): 'cell'

artifact.view_lineage()

# clean up test instance
!lamin delete --force test-cellxgene
!rm -r ./test-cellxgene

Show code cell output Hide code cell output

Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.10.14/x64/bin/lamin", line 8, in <module>
    sys.exit(main())
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/rich_click/rich_command.py", line 360, in __call__
    return super().__call__(*args, **kwargs)
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/rich_click/rich_command.py", line 152, in main
    rv = self.invoke(ctx)
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/lamin_cli/__main__.py", line 103, in delete
    return delete(instance, force=force)
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/lamindb_setup/_delete.py", line 140, in delete
    n_objects = check_storage_is_empty(
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/lamindb_setup/core/upath.py", line 814, in check_storage_is_empty
    raise InstanceNotEmpty(message)
lamindb_setup.core.upath.InstanceNotEmpty: Storage /home/runner/work/cellxgene-lamin/cellxgene-lamin/docs/test-cellxgene/.lamindb contains 2 objects ('./lamindb/_is_initialized'  ignored) - delete them prior to deleting the instance
['/home/runner/work/cellxgene-lamin/cellxgene-lamin/docs/test-cellxgene/.lamindb/RbANRPl53UcoG9W8lLna.h5ad', '/home/runner/work/cellxgene-lamin/cellxgene-lamin/docs/test-cellxgene/.lamindb/_is_initialized']