Query & integrate data¶
import lamindb as ln
import bionty as bt
ln.track("wukchS8V976U0000")
→ connected lamindb: testuser1/test-facs
→ created Transform('wukchS8V976U0000', key='facs3.ipynb'), started new Run('1Y4BdZan40xkSA80') at 2025-10-30 19:02:32 UTC
→ notebook imports: bionty==1.8.1 lamindb==1.15a1
Inspect the CellMarker registry 
¶
Inspect your aggregated cell marker registry as a DataFrame:
bt.CellMarker.to_dataframe().head()
Show code cell output
| uid | name | synonyms | description | gene_symbol | ncbi_gene_id | uniprotkb_id | is_locked | created_at | branch_id | space_id | created_by_id | run_id | source_id | organism_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 41 | 67ZpJGSKNFyE | CD14|19 | None | None | None | None | None | False | 2025-10-30 19:02:26.322000+00:00 | 1 | 1 | 1 | 2 | NaN | 1 |
| 40 | 31nZfqQo8yZg | CD103 | None | ITGAE | 3682 | P38570 | False | 2025-10-30 19:02:26.311000+00:00 | 1 | 1 | 1 | 2 | 12.0 | 1 | |
| 39 | 1iLDs6cZIpxj | CD69 | None | CD69 | 969 | Q07108 | False | 2025-10-30 19:02:26.311000+00:00 | 1 | 1 | 1 | 2 | 12.0 | 1 | |
| 38 | 525YfNUB967z | CD49B | None | ITGA2 | 3673 | P17301 | False | 2025-10-30 19:02:26.311000+00:00 | 1 | 1 | 1 | 2 | 12.0 | 1 | |
| 37 | 3IPMBjs68Vy1 | CXCR4 | None | CXCR4 | 7852 | P61073 | False | 2025-10-30 19:02:26.311000+00:00 | 1 | 1 | 1 | 2 | 12.0 | 1 |
Search for a marker (synonyms aware):
bt.CellMarker.search("PD-1").to_dataframe().head(2)
Show code cell output
| uid | name | synonyms | description | gene_symbol | ncbi_gene_id | uniprotkb_id | is_locked | created_at | branch_id | space_id | created_by_id | run_id | source_id | organism_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 29 | 33vFR1q26vnM | PD1 | PID1|PD-1|PD 1 | None | PDCD1 | 5133 | A0A0M3M0G7 | False | 2025-10-30 19:02:14.305000+00:00 | 1 | 1 | 1 | 1 | 12 | 1 |
Look up markers with auto-complete:
markers = bt.CellMarker.lookup()
markers.cd8
Show code cell output
CellMarker(uid='1xRpnOHIkdyE', name='CD8', synonyms='', description=None, gene_symbol='CD8A', ncbi_gene_id='925', uniprotkb_id='P01732', branch_id=1, space_id=1, created_by_id=1, run_id=1, source_id=12, organism_id=1, created_at=2025-10-30 19:02:14 UTC, is_locked=False)
Query artifacts by markers ¶
Query panels and collections based on markers, e.g., which collections have 'CD8' in the flow panel:
panels_with_cd8 = ln.FeatureSet.filter(cell_markers=markers.cd8).all()
ln.Artifact.filter(feature_sets__in=panels_with_cd8).to_dataframe()
Show code cell output
| uid | key | description | suffix | kind | otype | size | hash | n_files | n_observations | version | is_latest | is_locked | created_at | branch_id | space_id | storage_id | run_id | schema_id | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||||||
| 2 | CNYtRlJCCNsU1Ln50000 | None | Oetjen18_t1 | .h5ad | dataset | AnnData | 46546520 | BkQOx3xp3OR4FoOq4CsuJA | None | 241552 | None | True | False | 2025-10-30 19:02:26.849000+00:00 | 1 | 1 | 1 | 2 | None | 1 |
| 1 | ETOh6WcbRg6ggd8P0000 | None | Alpert19 | .h5ad | dataset | AnnData | 33450144 | pQFB5xL-IDMLc9WgaYGJlg | None | 166537 | None | True | False | 2025-10-30 19:02:17.726000+00:00 | 1 | 1 | 1 | 1 | None | 1 |
Access registries:
features = ln.Feature.lookup()
Find shared cell markers between two files:
artifacts = ln.Artifact.filter(feature_sets__in=panels_with_cd8).list()
Show code cell output
/tmp/ipykernel_3948/1674707202.py:1: DeprecationWarning: Use to_list instead of list, list will be removed in the future.
artifacts = ln.Artifact.filter(feature_sets__in=panels_with_cd8).list()
shared_markers = artifacts[0].features["var"] & artifacts[1].features["var"]
shared_markers.list("name")
Show code cell output
/tmp/ipykernel_3948/1629185003.py:1: DeprecationWarning: Use slots[slot].members instead of __getitem__, __getitem__ will be removed in the future.
shared_markers = artifacts[0].features["var"] & artifacts[1].features["var"]
/tmp/ipykernel_3948/1629185003.py:2: DeprecationWarning: Use to_list instead of list, list will be removed in the future.
shared_markers.list("name")
['Cd4', 'CD8', 'CD3', 'CD27', 'Ccr7', 'CD45RA']