Transfer data#
Here, we’ll show how to load one instance for reading data and use another to write data.
Setup#
!lamin init --storage ./test-transfer --schema bionty
✅ saved: User(uid='DzTjkKse', handle='testuser1', name='Test User1', updated_at=2023-12-08 11:34:47 UTC)
✅ saved: Storage(uid='l1oSwB6u', root='/home/runner/work/lamindb/lamindb/docs/test-transfer', type='local', updated_at=2023-12-08 11:34:47 UTC, created_by_id=1)
💡 loaded instance: testuser1/test-transfer
💡 did not register local instance on hub
import lamindb as ln
import lnschema_bionty as lb
lb.settings.organism = "human"
ln.settings.verbosity = "hint"
💡 lamindb instance: testuser1/test-transfer
ln.track()
💡 notebook imports: lamindb==0.63.4 lnschema_bionty==0.35.3
💡 saved: Transform(uid='ITeOtm7bhtdqz8', name='Transfer data', short_name='transfer', version='0', type=notebook, updated_at=2023-12-08 11:34:50 UTC, created_by_id=1)
💡 saved: Run(uid='xfnpWRr7yTOcVTM4sQli', run_at=2023-12-08 11:34:50 UTC, transform_id=1, created_by_id=1)
Query cellxgene#
Query a dataset from the public laminlabs/cellxgene LaminDB instance that connects to data from the CZ CELLxGENE (for more info, see here):
# get a QuerySet containing all files in cellxgene
files = ln.File.using("laminlabs/cellxgene")
files.df().head()
| uid | storage_id | key | suffix | accessor | description | version | size | hash | hash_type | transform_id | run_id | initial_version_id | visibility | key_is_virtual | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||
| 1029 | 6IYilXiyiTxZYMCJ2TnY | 2 | cell-census/2023-07-25/h5ads/2fb24a91-55b9-4cc... | .h5ad | AnnData | High Resolution Slide-seqV2 Spatial Transcript... | None | 8856712 | BXH-IIW1Et1CyugN0DMroQ-2 | md5-n | 11.0 | 16.0 | None | 1 | False | 2023-11-28 22:45:38.554629+00:00 | 1 |
| 872 | vEw6vGy47Zi0Qj6T6YJr | 2 | cell-census/2023-07-25/h5ads/0041b9c3-6a49-4bf... | .h5ad | AnnData | Tabula Sapiens | None | 198592773 | 0tEolD_cGXenPjobh1M8Gw-24 | md5-n | 11.0 | 16.0 | None | 1 | False | 2023-11-28 22:44:26.759174+00:00 | 1 |
| 873 | dptYEcjH6o3p9Vy1qZAp | 2 | cell-census/2023-07-25/h5ads/00476f9f-ebc1-4b7... | .h5ad | AnnData | Human Brain Cell Atlas v1.0 | None | 131643578 | HCQOV1VHonILymJHLkcNdg-16 | md5-n | 11.0 | 16.0 | None | 1 | False | 2023-11-28 22:44:27.440055+00:00 | 1 |
| 875 | bittNWi0gJTdcJ0pm9Jo | 2 | cell-census/2023-07-25/h5ads/00ff600e-6e2e-4d7... | .h5ad | AnnData | Single-cell analysis of human B cell maturatio... | None | 5919670 | PxGgTrFmiCh6AMwiu1fHWw | md5 | 11.0 | 16.0 | None | 1 | False | 2023-11-28 22:44:28.116237+00:00 | 1 |
| 876 | HQPT59lX80spJyfKXDC5 | 2 | cell-census/2023-07-25/h5ads/01209dce-3575-4be... | .h5ad | AnnData | Single-cell transcriptomics of human T cells r... | None | 312536917 | zAlluOa2WUIWvs2jkXKvkQ-38 | md5-n | 11.0 | 16.0 | None | 1 | False | 2023-11-28 22:44:28.784784+00:00 | 1 |
Filter or search the queryset:
file = files.filter(description__icontains="tabula sapiens").first()
file
File(uid='vEw6vGy47Zi0Qj6T6YJr', key='cell-census/2023-07-25/h5ads/0041b9c3-6a49-4bf7-8514-9bc7190067a7.h5ad', suffix='.h5ad', accessor='AnnData', description='Tabula Sapiens', size=198592773, hash='0tEolD_cGXenPjobh1M8Gw-24', hash_type='md5-n', visibility=1, key_is_virtual=False, updated_at=2023-11-28 22:44:26 UTC, storage_id=2, transform_id=11, run_id=16, created_by_id=1)
All associated features and labels:
file.describe()
File(uid='vEw6vGy47Zi0Qj6T6YJr', key='cell-census/2023-07-25/h5ads/0041b9c3-6a49-4bf7-8514-9bc7190067a7.h5ad', suffix='.h5ad', accessor='AnnData', description='Tabula Sapiens', size=198592773, hash='0tEolD_cGXenPjobh1M8Gw-24', hash_type='md5-n', visibility=1, key_is_virtual=False, updated_at=2023-11-28 22:44:26 UTC)
Provenance:
🗃️ storage: Storage(uid='oIYGbD74', root='s3://cellxgene-data-public', type='s3', region='us-west-2', updated_at=2023-10-16 15:04:08 UTC, created_by_id=1)
📔 transform: Transform(uid='pNa7RdI26sp4z8', name='Register files from Census release 2023-07-25', short_name='census-release-2023-07-25', version='0', type='notebook', updated_at=2023-11-29 13:53:43 UTC, latest_report_id=1724, source_file_id=1723, created_by_id=1)
👣 run: Run(uid='ZYgsnqK5v2hPmFlS0kfG', run_at=2023-11-29 13:52:08 UTC, is_consecutive=False, transform_id=11, created_by_id=1, report_id=1724)
👤 created_by: User(uid='kmvZDIX9', handle='sunnyosun', name='Sunny Sun', updated_at=2023-11-28 21:14:48 UTC)
Features:
obs: FeatureSet(uid='kwKICViF5O3QjHdg0nov', name='obs features', n=9, type='category', registry='core.Feature', hash='Bx10EzvDxdlAVjqVKdKC', updated_at=2023-11-29 09:28:28 UTC, created_by_id=1)
🔗 assay (2, bionty.ExperimentalFactor): 'Smart-seq2', '10x 3' v3'
🔗 cell_type (24, bionty.CellType): 'cell of skeletal muscle', 'melanocyte', 'T cell', 'CD8-positive, alpha-beta memory T cell', 'CD4-positive, alpha-beta memory T cell', 'mature NK T cell', 'Langerhans cell', 'macrophage', 'plasma cell', 'CD4-positive helper T cell', ...
🔗 development_stage (2, bionty.DevelopmentalStage): '33-year-old human stage', '59-year-old human stage'
🔗 disease (1, bionty.Disease): 'normal'
🔗 donor_id (2, core.ULabel): 'TSP14', 'TSP10'
🔗 self_reported_ethnicity (2, bionty.Ethnicity): 'Hispanic or Latin American', 'European'
🔗 sex (1, bionty.Phenotype): 'male'
🔗 suspension_type (1, core.ULabel): 'cell'
🔗 tissue (1, bionty.Tissue): 'skin of body'
external: FeatureSet(uid='zIgncie4AywRKgLmKHUW', name='external features', n=2, type='category', registry='core.Feature', hash='5E4xD6tOhDB5EOnLx3tv', updated_at=2023-11-29 09:28:20 UTC, created_by_id=1)
🔗 organism (1, bionty.Organism): 'human'
🔗 collection (1, core.ULabel): 'Tabula Sapiens'
var: FeatureSet(uid='9z67jXKNlUMC6GwUMSeK', n=58604, type='number', registry='bionty.Gene', hash='PYHHJaMHHiM5sl5vPQbu', updated_at=2023-11-29 13:18:47 UTC, created_by_id=1)
'DDX11L1', 'WASH7P', 'MIR6859-1', 'MIR1302-2HG', 'MIR1302-2', 'FAM138A', 'OR4G4P', 'OR4G11P', 'OR4F5', 'None', 'None', 'CICP27', 'None', 'None', 'None', 'None', 'RNU6-1100P', 'None', 'DDX11L17', 'WASH9P', ...
Labels:
🏷️ organism (1, bionty.Organism): 'human'
🏷️ tissues (1, bionty.Tissue): 'skin of body'
🏷️ cell_types (24, bionty.CellType): 'cell of skeletal muscle', 'melanocyte', 'T cell', 'CD8-positive, alpha-beta memory T cell', 'CD4-positive, alpha-beta memory T cell', 'mature NK T cell', 'Langerhans cell', 'macrophage', 'plasma cell', 'CD4-positive helper T cell', ...
🏷️ diseases (1, bionty.Disease): 'normal'
🏷️ phenotypes (1, bionty.Phenotype): 'male'
🏷️ experimental_factors (2, bionty.ExperimentalFactor): 'Smart-seq2', '10x 3' v3'
🏷️ developmental_stages (2, bionty.DevelopmentalStage): '33-year-old human stage', '59-year-old human stage'
🏷️ ethnicities (2, bionty.Ethnicity): 'Hispanic or Latin American', 'European'
🏷️ ulabels (4, core.ULabel): 'Tabula Sapiens', 'TSP14', 'TSP10', 'cell'
The file id on the remote source database is:
file.id
872
The file transform on the remote source database is:
file.transform
Transform(uid='pNa7RdI26sp4z8', name='Register files from Census release 2023-07-25', short_name='census-release-2023-07-25', version='0', type='notebook', updated_at=2023-11-29 13:53:43 UTC, latest_report_id=1724, source_file_id=1723, created_by_id=1)
The file was created on the remote source database by this user:
file.created_by
User(uid='kmvZDIX9', handle='sunnyosun', name='Sunny Sun', updated_at=2023-11-28 21:14:48 UTC)
file.storage
Storage(uid='oIYGbD74', root='s3://cellxgene-data-public', type='s3', region='us-west-2', updated_at=2023-10-16 15:04:08 UTC, created_by_id=1)
Save the dataset to our default instance:
file.save()
💡 saving from instance laminlabs/cellxgene to default instance: File(uid='vEw6vGy47Zi0Qj6T6YJr', key='cell-census/2023-07-25/h5ads/0041b9c3-6a49-4bf7-8514-9bc7190067a7.h5ad', suffix='.h5ad', accessor='AnnData', description='Tabula Sapiens', size=198592773, hash='0tEolD_cGXenPjobh1M8Gw-24', hash_type='md5-n', visibility=1, key_is_virtual=False, updated_at=2023-11-28 22:44:26 UTC, storage_id=2, transform_id=11, run_id=16, created_by_id=1)
💡 saving from instance laminlabs/cellxgene to default instance: Storage(uid='oIYGbD74', root='s3://cellxgene-data-public', type='s3', region='us-west-2', updated_at=2023-10-16 15:04:08 UTC, created_by_id=1)
💡 transfer features
💡 saving from instance laminlabs/cellxgene to default instance: Feature(uid='tSNzi7e6BWnu', name='assay', type='category', registries='bionty.ExperimentalFactor', updated_at=2023-11-28 21:49:31 UTC, created_by_id=1)
💡 saving from instance laminlabs/cellxgene to default instance: Feature(uid='CBDJHomBrUIJ', name='cell_type', type='category', registries='bionty.CellType', updated_at=2023-11-28 21:49:31 UTC, created_by_id=1)
💡 saving from instance laminlabs/cellxgene to default instance: Feature(uid='Up1fqy1APH21', name='development_stage', type='category', registries='bionty.DevelopmentalStage', updated_at=2023-11-28 21:49:31 UTC, created_by_id=1)
💡 saving from instance laminlabs/cellxgene to default instance: Feature(uid='UnTz4XK8XGd0', name='disease', type='category', registries='bionty.Disease', updated_at=2023-11-28 21:49:31 UTC, created_by_id=1)
💡 saving from instance laminlabs/cellxgene to default instance: Feature(uid='xbMGSIMHV67J', name='donor_id', type='category', registries='core.ULabel', updated_at=2023-11-28 21:49:31 UTC, created_by_id=1)
💡 saving from instance laminlabs/cellxgene to default instance: Feature(uid='DbVAV4BaQXAh', name='self_reported_ethnicity', type='category', registries='bionty.Ethnicity', updated_at=2023-11-28 21:49:31 UTC, created_by_id=1)
💡 saving from instance laminlabs/cellxgene to default instance: Feature(uid='Xcti9JkM9uvG', name='sex', type='category', registries='bionty.Phenotype', updated_at=2023-11-28 21:49:31 UTC, created_by_id=1)
💡 saving from instance laminlabs/cellxgene to default instance: Feature(uid='9s20Imh64bYU', name='suspension_type', type='category', registries='core.ULabel', updated_at=2023-11-28 21:49:31 UTC, created_by_id=1)
💡 saving from instance laminlabs/cellxgene to default instance: Feature(uid='MB1hKtGaQiqV', name='tissue', type='category', registries='bionty.Tissue', updated_at=2023-11-28 21:49:31 UTC, created_by_id=1)
✅ 9 terms (100.00%) are validated for name
💡 saving from instance laminlabs/cellxgene to default instance: Feature(uid='wCbvLeKe2rv8', name='organism', type='category', registries='bionty.Organism', updated_at=2023-11-28 21:49:35 UTC, created_by_id=1)
💡 saving from instance laminlabs/cellxgene to default instance: Feature(uid='PXHsNgXtfekm', name='collection', type='category', registries='core.ULabel', updated_at=2023-11-28 21:49:35 UTC, created_by_id=1)
✅ 2 terms (100.00%) are validated for name
✅ 58604 terms (100.00%) are validated for uid
💡 transfer labels
💡 transferring assay
💡 transferring cell_type
💡 transferring development_stage
💡 transferring disease
💡 transferring donor_id
💡 transferring self_reported_ethnicity
💡 transferring sex
💡 transferring suspension_type
💡 transferring tissue
💡 transferring organism
💡 transferring collection
All features & labels have been transferred and now the file record points to the current database:
file.describe()
File(uid='vEw6vGy47Zi0Qj6T6YJr', key='cell-census/2023-07-25/h5ads/0041b9c3-6a49-4bf7-8514-9bc7190067a7.h5ad', suffix='.h5ad', accessor='AnnData', description='Tabula Sapiens', size=198592773, hash='0tEolD_cGXenPjobh1M8Gw-24', hash_type='md5-n', visibility=1, key_is_virtual=False, updated_at=2023-12-08 11:35:02 UTC)
Provenance:
🗃️ storage: Storage(uid='oIYGbD74', root='s3://cellxgene-data-public', type='s3', region='us-west-2', updated_at=2023-12-08 11:35:02 UTC, created_by_id=1)
📔 transform: Transform(uid='ITeOtm7bhtdqz8', name='Transfer data', short_name='transfer', version='0', type='notebook', updated_at=2023-12-08 11:34:50 UTC, created_by_id=1)
👣 run: Run(uid='xfnpWRr7yTOcVTM4sQli', run_at=2023-12-08 11:34:50 UTC, transform_id=1, created_by_id=1)
👤 created_by: User(uid='DzTjkKse', handle='testuser1', name='Test User1', updated_at=2023-12-08 11:34:47 UTC)
Features:
obs: FeatureSet(uid='kwKICViF5O3QjHdg0nov', n=9, registry='core.Feature', hash='Bx10EzvDxdlAVjqVKdKC', updated_at=2023-12-08 11:35:02 UTC, created_by_id=1)
🔗 assay (2, bionty.ExperimentalFactor): 'Smart-seq2', '10x 3' v3'
🔗 cell_type (24, bionty.CellType): 'cell of skeletal muscle', 'melanocyte', 'T cell', 'CD8-positive, alpha-beta memory T cell', 'CD4-positive, alpha-beta memory T cell', 'mature NK T cell', 'Langerhans cell', 'macrophage', 'plasma cell', 'CD4-positive helper T cell', ...
🔗 development_stage (2, bionty.DevelopmentalStage): '33-year-old human stage', '59-year-old human stage'
🔗 disease (1, bionty.Disease): 'normal'
🔗 donor_id (2, core.ULabel): 'TSP14', 'TSP10'
🔗 self_reported_ethnicity (2, bionty.Ethnicity): 'Hispanic or Latin American', 'European'
🔗 sex (1, bionty.Phenotype): 'male'
🔗 suspension_type (1, core.ULabel): 'cell'
🔗 tissue (1, bionty.Tissue): 'skin of body'
external: FeatureSet(uid='zIgncie4AywRKgLmKHUW', n=2, registry='core.Feature', hash='5E4xD6tOhDB5EOnLx3tv', updated_at=2023-12-08 11:35:02 UTC, created_by_id=1)
🔗 organism (1, bionty.Organism): 'human'
🔗 collection (1, core.ULabel): 'Tabula Sapiens'
var: FeatureSet(uid='9z67jXKNlUMC6GwUMSeK', n=58604, type='number', registry='bionty.Gene', hash='PYHHJaMHHiM5sl5vPQbu', updated_at=2023-12-08 11:35:48 UTC, created_by_id=1)
'DDX11L1', 'WASH7P', 'MIR6859-1', 'MIR1302-2HG', 'MIR1302-2', 'FAM138A', 'OR4G4P', 'OR4G11P', 'OR4F5', 'None', 'None', 'CICP27', 'None', 'None', 'None', 'None', 'RNU6-1100P', 'None', 'DDX11L17', 'WASH9P', ...
Labels:
🏷️ organism (1, bionty.Organism): 'human'
🏷️ tissues (1, bionty.Tissue): 'skin of body'
🏷️ cell_types (24, bionty.CellType): 'cell of skeletal muscle', 'melanocyte', 'T cell', 'CD8-positive, alpha-beta memory T cell', 'CD4-positive, alpha-beta memory T cell', 'mature NK T cell', 'Langerhans cell', 'macrophage', 'plasma cell', 'CD4-positive helper T cell', ...
🏷️ diseases (1, bionty.Disease): 'normal'
🏷️ phenotypes (1, bionty.Phenotype): 'male'
🏷️ experimental_factors (2, bionty.ExperimentalFactor): 'Smart-seq2', '10x 3' v3'
🏷️ developmental_stages (2, bionty.DevelopmentalStage): '33-year-old human stage', '59-year-old human stage'
🏷️ ethnicities (2, bionty.Ethnicity): 'Hispanic or Latin American', 'European'
🏷️ ulabels (4, core.ULabel): 'TSP14', 'TSP10', 'cell', 'Tabula Sapiens'
All ids and related attributes have been adjusted:
file.id
1
file.created_by
User(uid='DzTjkKse', handle='testuser1', name='Test User1', updated_at=2023-12-08 11:34:47 UTC)
file.transform
Transform(uid='ITeOtm7bhtdqz8', name='Transfer data', short_name='transfer', version='0', type='notebook', updated_at=2023-12-08 11:34:50 UTC, created_by_id=1)
And the database is populated correspondingly:
Show code cell content
ln.view()
****************
* module: core *
****************
Feature
| uid | name | type | unit | description | registries | synonyms | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||
| 11 | PXHsNgXtfekm | collection | category | None | None | core.ULabel | None | 2023-12-08 11:35:02.849746+00:00 | 1 |
| 10 | wCbvLeKe2rv8 | organism | category | None | None | bionty.Organism | None | 2023-12-08 11:35:02.849684+00:00 | 1 |
| 9 | MB1hKtGaQiqV | tissue | category | None | None | bionty.Tissue | None | 2023-12-08 11:35:02.683748+00:00 | 1 |
| 8 | 9s20Imh64bYU | suspension_type | category | None | None | core.ULabel | None | 2023-12-08 11:35:02.683694+00:00 | 1 |
| 7 | Xcti9JkM9uvG | sex | category | None | None | bionty.Phenotype | None | 2023-12-08 11:35:02.683641+00:00 | 1 |
| 6 | DbVAV4BaQXAh | self_reported_ethnicity | category | None | None | bionty.Ethnicity | None | 2023-12-08 11:35:02.683588+00:00 | 1 |
| 5 | xbMGSIMHV67J | donor_id | category | None | None | core.ULabel | None | 2023-12-08 11:35:02.683533+00:00 | 1 |
FeatureSet
| uid | name | n | type | registry | hash | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|
| id | ||||||||
| 3 | 9z67jXKNlUMC6GwUMSeK | None | 58604 | number | bionty.Gene | PYHHJaMHHiM5sl5vPQbu | 2023-12-08 11:35:48.409740+00:00 | 1 |
| 2 | zIgncie4AywRKgLmKHUW | None | 2 | None | core.Feature | 5E4xD6tOhDB5EOnLx3tv | 2023-12-08 11:35:02.862394+00:00 | 1 |
| 1 | kwKICViF5O3QjHdg0nov | None | 9 | None | core.Feature | Bx10EzvDxdlAVjqVKdKC | 2023-12-08 11:35:02.696146+00:00 | 1 |
File
| uid | storage_id | key | suffix | accessor | description | version | size | hash | hash_type | transform_id | run_id | initial_version_id | visibility | key_is_virtual | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||
| 1 | vEw6vGy47Zi0Qj6T6YJr | 2 | cell-census/2023-07-25/h5ads/0041b9c3-6a49-4bf... | .h5ad | AnnData | Tabula Sapiens | None | 198592773 | 0tEolD_cGXenPjobh1M8Gw-24 | md5-n | 1 | 1 | None | 1 | False | 2023-12-08 11:35:02.235956+00:00 | 1 |
Run
| uid | transform_id | run_at | created_by_id | report_id | is_consecutive | reference | reference_type | |
|---|---|---|---|---|---|---|---|---|
| id | ||||||||
| 1 | xfnpWRr7yTOcVTM4sQli | 1 | 2023-12-08 11:34:50.144665+00:00 | 1 | None | None | None | None |
Storage
| uid | root | type | region | updated_at | created_by_id | |
|---|---|---|---|---|---|---|
| id | ||||||
| 2 | oIYGbD74 | s3://cellxgene-data-public | s3 | us-west-2 | 2023-12-08 11:35:02.233848+00:00 | 1 |
| 1 | l1oSwB6u | /home/runner/work/lamindb/lamindb/docs/test-tr... | local | None | 2023-12-08 11:34:47.524383+00:00 | 1 |
Transform
| uid | name | short_name | version | type | latest_report_id | source_file_id | reference | reference_type | initial_version_id | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||
| 1 | ITeOtm7bhtdqz8 | Transfer data | transfer | 0 | notebook | None | None | None | None | None | 2023-12-08 11:34:50.141484+00:00 | 1 |
ULabel
| uid | name | description | reference | reference_type | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|
| id | |||||||
| 4 | SayoR6hp | Tabula Sapiens | 10.1126/science.abl4896 | e5f58829-1a66-40b5-a624-9046778e74f5 | collection_id | 2023-12-08 11:35:57.361716+00:00 | 1 |
| 3 | WzKPMCXX | cell | None | None | None | 2023-12-08 11:35:55.752282+00:00 | 1 |
| 2 | QYcbDNfa | TSP10 | None | None | None | 2023-12-08 11:35:54.210714+00:00 | 1 |
| 1 | HVoqm0bp | TSP14 | None | None | None | 2023-12-08 11:35:54.210660+00:00 | 1 |
User
| uid | handle | name | updated_at | |
|---|---|---|---|---|
| id | ||||
| 1 | DzTjkKse | testuser1 | Test User1 | 2023-12-08 11:34:47.519802+00:00 |
******************
* module: bionty *
******************
BiontySource
| uid | entity | organism | currently_used | source | source_name | version | url | md5 | source_website | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||
| 51 | rsbG | BioSample | all | True | ncbi | NCBI BioSample attributes | 2023-09 | s3://bionty-assets/df_all__ncbi__2023-09__BioS... | 918db9bd1734b97c596c67d9654a4126 | https://www.ncbi.nlm.nih.gov/biosample/docs/at... | 2023-12-08 11:34:47.608421+00:00 | 1 |
| 50 | clid | Ethnicity | human | True | hancestro | Human Ancestry Ontology | 3.0 | https://github.com/EBISPOT/hancestro/raw/3.0/h... | 76dd9efda9c2abd4bc32fc57c0b755dd | https://github.com/EBISPOT/hancestro | 2023-12-08 11:34:47.608358+00:00 | 1 |
| 49 | JIKv | DevelopmentalStage | mouse | True | mmusdv | Mouse Developmental Stages | 2020-03-10 | http://aber-owl.net/media/ontologies/MMUSDV/9/... | 5bef72395d853c7f65450e6c2a1fc653 | https://github.com/obophenotype/developmental-... | 2023-12-08 11:34:47.608294+00:00 | 1 |
| 48 | 7JhT | DevelopmentalStage | human | True | hsapdv | Human Developmental Stages | 2020-03-10 | http://aber-owl.net/media/ontologies/HSAPDV/11... | 52181d59df84578ed69214a5cb614036 | https://github.com/obophenotype/developmental-... | 2023-12-08 11:34:47.608230+00:00 | 1 |
| 47 | chfO | Drug | all | True | dron | Drug Ontology | 2023-03-10 | https://data.bioontology.org/ontologies/DRON/s... | 75e86011158fae76bb46d96662a33ba3 | https://bioportal.bioontology.org/ontologies/DRON | 2023-12-08 11:34:47.608166+00:00 | 1 |
| 46 | fxHJ | BFXPipeline | all | True | lamin | Bioinformatics Pipeline | 1.0.0 | s3://bionty-assets/bfxpipelines.json | a7eff57a256994692fba46e0199ffc94 | https://lamin.ai | 2023-12-08 11:34:47.608103+00:00 | 1 |
| 45 | DiJI | Pathway | all | False | pw | Pathway Ontology | 7.79 | https://data.bioontology.org/ontologies/PW/sub... | 02e2337bb1ab7cc4332ef6acc4cbdfa6 | https://www.ebi.ac.uk/ols/ontologies/pw | 2023-12-08 11:34:47.608039+00:00 | 1 |
CellType
| uid | name | ontology_id | abbr | synonyms | description | bionty_source_id | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||
| 24 | yZiIM84A | smooth muscle cell | CL:0000192 | None | smooth muscle fiber|SMCs|myocytes, smooth muscle | A Non-Striated, Elongated, Spindle-Shaped Cell... | 21 | 2023-12-08 11:35:52.656665+00:00 | 1 |
| 23 | X458vtJX | naive B cell | CL:0000788 | None | naive B-cell|naive B-lymphocyte|naive B lympho... | A Naive B Cell Is A Mature B Cell That Has The... | 21 | 2023-12-08 11:35:52.656612+00:00 | 1 |
| 22 | gXOMeVM0 | CD1c-positive myeloid dendritic cell | CL:0002399 | None | None | A Myeloid Dendritic Cell Found In The Blood Th... | 21 | 2023-12-08 11:35:52.656558+00:00 | 1 |
| 21 | baEuJabx | CD8-positive, alpha-beta cytotoxic T cell | CL:0000794 | None | CD8-positive, alpha-beta cytotoxic T-cell|CD8-... | A Cd8-Positive, Alpha-Beta T Cell That Is Capa... | 21 | 2023-12-08 11:35:52.656504+00:00 | 1 |
| 20 | dRUgw2Fo | CD141-positive myeloid dendritic cell | CL:0002394 | None | None | A Myeloid Dendritic Cell Found In The Blood, L... | 21 | 2023-12-08 11:35:52.656451+00:00 | 1 |
| 19 | i20ionW5 | mast cell | CL:0000097 | None | labrocyte|histaminocyte|mastocyte | A Cell That Is Found In Almost All Tissues Con... | 21 | 2023-12-08 11:35:52.656398+00:00 | 1 |
| 18 | 1njHag0v | naive thymus-derived CD4-positive, alpha-beta ... | CL:0000895 | None | T.4Nve.Sp|naive thymus-derived CD4-positive, a... | An Antigen Inexperienced Cd4-Positive, Alpha-B... | 21 | 2023-12-08 11:35:52.656344+00:00 | 1 |
DevelopmentalStage
| uid | name | ontology_id | abbr | synonyms | description | bionty_source_id | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||
| 2 | 07H1120C | 59-year-old human stage | HsapDv:0000153 | None | None | Middle Aged Stage That Refers To An Adult Who ... | 48 | 2023-12-08 11:35:53.185181+00:00 | 1 |
| 1 | dUUOE2r0 | 33-year-old human stage | HsapDv:0000127 | None | None | Adult Stage That Refers To An Adult Who Is Ove... | 48 | 2023-12-08 11:35:53.185122+00:00 | 1 |
Disease
| uid | name | ontology_id | abbr | synonyms | description | bionty_source_id | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||
| 1 | 4r2nqggf | normal | PATO:0000461 | None | None | A Quality Inhering In A Bearer By Virtue Of Th... | 43 | 2023-12-08 11:35:53.699191+00:00 | 1 |
Ethnicity
| uid | name | ontology_id | abbr | synonyms | description | bionty_source_id | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||
| 2 | lLDMbq0l | European | HANCESTRO:0005 | None | Caucasian|white | Includes Individuals Who Either Self-Report Or... | 50 | 2023-12-08 11:35:54.724848+00:00 | 1 |
| 1 | dAsSCPeM | Hispanic or Latin American | HANCESTRO:0014 | None | None | Includes Individuals Who Either Self-Report Or... | 50 | 2023-12-08 11:35:54.724789+00:00 | 1 |
ExperimentalFactor
| uid | name | ontology_id | abbr | synonyms | description | molecule | instrument | measurement | bionty_source_id | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||
| 2 | Vep0itYq | 10x 3' v3 | EFO:0009922 | None | 10X 3' v3 | 10X 3' V3 Is The Third Version Of The 10X Sequ... | None | None | None | 36 | 2023-12-08 11:35:52.129460+00:00 | 1 |
| 1 | 4TdYPFrL | Smart-seq2 | EFO:0008931 | None | None | Switch Mechanism At The 5’ End Of Rna Template... | RNA assay | None | None | 36 | 2023-12-08 11:35:52.129392+00:00 | 1 |
Gene
| uid | symbol | stable_id | ensembl_gene_id | ncbi_gene_ids | biotype | description | synonyms | organism_id | bionty_source_id | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||
| 58604 | QK7YN7GDVfmA | WI2-89031B12.1 | None | ENSG00000261773 | None | None | None | None | 1 | 9 | 2023-12-08 11:35:44.006282+00:00 | 1 |
| 58603 | DrlkqGl08Pi1 | LINC01402 | None | ENSG00000228139 | None | None | None | None | 1 | 9 | 2023-12-08 11:35:44.006221+00:00 | 1 |
| 58602 | F2C8IxXWetl6 | RP13-216E22.4 | None | ENSG00000228906 | None | None | None | None | 1 | 9 | 2023-12-08 11:35:44.006160+00:00 | 1 |
| 58601 | 0QZj2iFlPs8F | MTRNR2L10 | None | ENSG00000256045 | None | None | None | None | 1 | 9 | 2023-12-08 11:35:44.006098+00:00 | 1 |
| 58600 | jq0I7JHu9T4i | RP1-76B20.12 | None | ENSG00000239446 | None | None | None | None | 1 | 9 | 2023-12-08 11:35:44.006037+00:00 | 1 |
| 58599 | Ok7cuO0Iu0Ij | CH17-476P10.1 | None | ENSG00000285762 | None | None | None | None | 1 | 9 | 2023-12-08 11:35:44.005976+00:00 | 1 |
| 58598 | cS30j3l0TzuC | TUBA3FP | None | ENSG00000161149 | None | None | None | None | 1 | 9 | 2023-12-08 11:35:44.005914+00:00 | 1 |
Organism
| uid | name | ontology_id | scientific_name | bionty_source_id | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|
| id | |||||||
| 1 | EeBGvIYd | human | NCBITaxon:9606 | homo_sapiens | 1 | 2023-12-08 11:34:49.585049+00:00 | 1 |
Phenotype
| uid | name | ontology_id | abbr | synonyms | description | bionty_source_id | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||
| 1 | Pl1UiuS0 | male | PATO:0000384 | None | None | A Biological Sex Quality Inhering In An Indivi... | 43 | 2023-12-08 11:35:55.239111+00:00 | 1 |
Tissue
| uid | name | ontology_id | abbr | synonyms | description | bionty_source_id | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||
| 1 | C2mTxgy8 | skin of body | UBERON:0002097 | None | entire skin|skin organ | The Organ Covering The Body That Consists Of T... | 25 | 2023-12-08 11:35:56.267040+00:00 | 1 |
Show code cell content
# clean up test instance
!lamin delete --force test-transfer
!rm -r test-transfer
💡 deleting instance testuser1/test-transfer
✅ deleted instance settings file: /home/runner/.lamin/instance--testuser1--test-transfer.env
✅ instance cache deleted
✅ deleted '.lndb' sqlite file
❗ consider manually deleting your stored data: /home/runner/work/lamindb/lamindb/docs/test-transfer