Census release 2023-12-15 (LTS)¶
import lamindb as ln
import lnschema_bionty as lb
from cellxgene_lamin import get_datasets_from_cxg, get_collections_from_cxg
💡 lamindb instance: laminlabs/cellxgene
census_version = "2023-12-15"
s3path = f"s3://cellxgene-data-public/cell-census/{census_version}/h5ads"
ln.UPath(s3path)
S3Path('s3://cellxgene-data-public/cell-census/2023-12-15/h5ads')
ln.UPath(s3path).view_tree()
h5ads (0 sub-directories & 1113 files with suffixes '.h5ad'):
├── 00099d5e-154f-4a7a-aa8d-fa30c8c0c43c.h5ad
├── 0041b9c3-6a49-4bf7-8514-9bc7190067a7.h5ad
├── 00476f9f-ebc1-4b72-b541-32f912ce36ea.h5ad
├── 00e5dedd-b9b7-43be-8c28-b0e5c6414a62.h5ad
├── 00ff600e-6e2e-4d76-846f-0eec4f0ae417.h5ad
├── 01209dce-3575-4bed-b1df-129f57fbc031.h5ad
...
ln.context.track()
💡 notebook imports: cellxgene_lamin==0.0.1 lamindb==0.67.2 lnschema_bionty==0.39.0
💡 saved: Transform(uid='G69jtgzKO0eJ5zKv', name='Census release 2023-12-15 (LTS)', short_name='cencus-release-2023-12-15-LTS', version='1', type=notebook, updated_at=2024-01-30 09:07:36 UTC, created_by_id=1)
💡 saved: Run(uid='bfvbF0TJVEuW4HALTilN', run_at=2024-01-30 09:07:36 UTC, transform_id=19, created_by_id=1)
💡 tracked pip freeze > /Users/sunnysun/Library/Caches/lamindb/run_env_pip_bfvbF0TJVEuW4HALTilN.txt
Get all datasets and associated metadata using cellxgene REST API:
cxg_datasets = get_datasets_from_cxg()
len(cxg_datasets)
1188
cxg_datasets[0].keys()
dict_keys(['assay', 'assets', 'cell_count', 'cell_type', 'citation', 'collection_doi', 'collection_id', 'collection_name', 'collection_version_id', 'dataset_id', 'dataset_version_id', 'development_stage', 'disease', 'donor_id', 'explorer_url', 'is_primary_data', 'mean_genes_per_cell', 'organism', 'primary_cell_count', 'processing_status', 'published_at', 'revised_at', 'schema_version', 'self_reported_ethnicity', 'sex', 'suspension_type', 'tissue', 'title', 'tombstone', 'x_approximate_distribution'])
Register artifacts¶
artifacts = ln.Artifact.from_dir(s3path)
ln.save(artifacts)
❗ this creates one artifact per file in the directory - you might simply call ln.Artifact(dir) to get one artifact for the entire directory
artifacts = ln.Artifact.filter(key__contains=census_version).all()
len(artifacts)
1113
artifacts.update(version=census_version)
1113
for cxg_dataset in cxg_datasets:
artifact = artifacts.filter(key__contains=cxg_dataset["dataset_id"]).one_or_none()
if artifact is not None:
artifact.n_observations = cxg_dataset["cell_count"]
artifact.description = cxg_dataset["title"]
artifact.save()
artifacts_20230725 = ln.Artifact.filter(key__contains="2023-07-25").all()
artifacts_20230725.count()
850
for artifact in artifacts:
dataset_id = artifact.key.split("/")[-1]
artifact_20230725 = artifacts_20230725.filter(
key__endswith=dataset_id
).one_or_none()
if artifact_20230725 is not None:
artifact.add_to_version_family(artifact_20230725, version=census_version)
Show code cell output
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✅ updated uid from mTThtrC98ja03wGSFA4G to YTYeoSEsXTxvFSdf3ZkZ!
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✅ updated uid from 3IGzrsguuHABMCb4L9jL to 3GktMKv7NFZfOtzTO37t!
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✅ updated uid from q3N8RTYbpVmLckhA14r6 to KAHDMhL7KC7aHUNAhkar!
✅ updated uid from gHVv3CHPzx7Kslfdu4dM to BtGLeSFvjUjCldgGelwt!
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✅ updated uid from ReJ2vo3wudBCqMOSIXh3 to DPHpKfWvz1iPV9YX89vZ!
✅ updated uid from oUmeVa8IckeQvlAFLhJb to 8p7XTuhjWwSpzRWWKNZE!
✅ updated uid from M7xoaLqoUwiTaiVmtMq4 to hKyQa62JLSaE8UlFseoq!
✅ updated uid from NL7KFUGB3utEsvtTlTKZ to BTHskNWGFg0iJwixoSGY!
✅ updated uid from A4JgGwTo7H5quckrd9H4 to 4XeJhfSD3dptyqoSUHDx!
✅ updated uid from fDDgVfLmVZKNAdWt07xY to 3SSFIz287j3aUMHWQwOJ!
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✅ updated uid from QSUOjsglKICKAnD2iP2h to pnQX4jvkj3eFWGOzekiO!
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✅ updated uid from kwnPVvQ9OPaeZkDHHyLV to lMLp2Aj9tTGXaRtjSQDZ!
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✅ updated uid from Xq6TTQPUSmNDFdHqJz8R to 2HoqnnMXeQtWwrLoFIUy!
✅ updated uid from ccjn4ml6wFi65BKwEcUH to jkeQwS8gamxdOVE56qAj!
✅ updated uid from QbMXpTg8cfV30wfFFelH to 4LP6iYPWOKjBuJLb49tY!
✅ updated uid from dBi9UBfZB4zLTCgJdtzw to NwFOBmT6emiJaeyrpdUO!
✅ updated uid from 635VXAEl6dPWqeajIGaN to AyKamhQmdQRufk8SC1iR!
✅ updated uid from 4UdE334dCgOh0n5xk4ix to LJnjzUJCEG3BkiIUMqz8!
Register metadata¶
Register new features and parent labels¶
from cellxgene_lamin._features import OBS_FEATURES, EXT_FEATURES, register_feature_set
obs_feature_set = ln.FeatureSet.filter(name="obs features").one_or_none()
if obs_feature_set is None:
obs_feature_set = register_feature_set(artifacts, "obs")
ext_feature_set = ln.FeatureSet.filter(name="external metadata").one_or_none()
if ext_feature_set is None:
ext_feature_set = register_feature_set(artifacts, "ext")
features = ln.Feature.lookup()
organisms¶
from cellxgene_lamin._organism import register_organisms, annotate_organisms
register_organisms(cxg_datasets)
Link collections and organisms to artifacts:
annotate_organisms(artifacts, cxg_datasets)
ontologies¶
Register all ontology ids:
from cellxgene_lamin._ontology import register_ontology_ids
register_ontology_ids(cxg_datasets)
Show code cell output
registering assay
registering cell_type
✅ loaded 752 CellType records matching ontology_id: 'CL:0019003', 'CL:1000494', 'CL:0000708', 'CL:0009089', 'CL:1000850', 'CL:0009111', 'CL:0000055', 'CL:1000309', 'CL:0000890', 'CL:1001045', 'CL:0000394', 'CL:0000553', 'CL:0000123', 'CL:0002145', 'CL:0002085', 'CL:1000223', 'CL:1000692', 'CL:0000084', 'CL:0000485', 'CL:0000066', ...
✅ created 20 CellType records from Bionty matching ontology_id: 'CL:0000459', 'CL:0000753', 'CL:0000754', 'CL:0000756', 'CL:0000757', 'CL:0000758', 'CL:0000759', 'CL:0000760', 'CL:0000761', 'CL:0000917', 'CL:0002102', 'CL:0002626', 'CL:0002672', 'CL:0004213', 'CL:0004214', 'CL:0004215', 'CL:0004216', 'CL:0011031', 'CL:1000042', 'CL:4023161'
❗ now recursing through parents: this only happens once, but is much slower than bulk saving
💡 you can switch this off via: lb.settings.auto_save_parents = False
💡 also saving parents of CellType(uid='15Fmigot', name='noradrenergic cell', ontology_id='CL:0000459', synonyms='noradrenaline secreting cell|norepinephrin secreting cell|norepinephrine secreting cell', description='A Cell Capable Of Producting Norepiniphrine. Norepiniphrine Is A Catecholamine With Multiple Roles Including As A Hormone And A Neurotransmitter. In Addition, Epiniphrine Is Synthesized From Norepiniphrine By The Actions Of The Phenylethanolamine N-Methyltransferase Enzyme.', updated_at=2024-01-15 07:18:43 UTC, public_source_id=48, created_by_id=1)
💡 also saving parents of CellType(uid='5QdiFSqz', name='type 1 cone bipolar cell (sensu Mus)', ontology_id='CL:0000753', synonyms='DB1 cone bipolar cell', description='An Off-Bipolar Neuron Found In The Retina And Having Connections With Cone Photoreceptors Cells And Neurons In The Outer Half Of The Inner Plexiform Layer. The Cell Body Of These Cells Is In The Middle Of The Inner Plexiform Layer. The Dendritic Tree Is Stout And The Axon Terminates In Sublamina 1. The Axonal Terminal Is Wide And Has Only A Few Varicosities.', updated_at=2024-01-15 07:18:43 UTC, public_source_id=48, created_by_id=1)
✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0000752'
💡 also saving parents of CellType(uid='nK9fhvk3', name='cone retinal bipolar cell', ontology_id='CL:0000752', description='A Bipolar Neuron Found In The Retina And Having Connections With Cone Photoreceptor Cells And Neurons In The Inner Plexiform Layer.', updated_at=2024-01-15 07:18:44 UTC, public_source_id=48, created_by_id=1)
💡 also saving parents of CellType(uid='16lJK1l3', name='type 2 cone bipolar cell (sensu Mus)', ontology_id='CL:0000754', synonyms='FMB cone bipolar cell', description='An Off-Bipolar Neuron Found In The Retina And Having Connections With Cone Photoreceptors Cells And Neurons In The Outer Half Of The Inner Plexiform Layer. The Dendritic Tree Is Not Well Filled And The Dendrites Are More Delicate Than In Type 1 Cells. The Axon Terminal Is Bushier And Exhibits A Dense Plexus Of Varicosities In The Inner Part Of Sublamina 1 (Ghosh Et Al., 2004). It Can Be Differentiated From Other Retinal Bipolar Neurons By Its Expression Of Marker Genes: Neto1, Lhx3 And Irx-6 (Shekhar, 2016).', updated_at=2024-01-15 07:18:43 UTC, public_source_id=48, created_by_id=1)
💡 also saving parents of CellType(uid='5bskGP7s', name='type 4 cone bipolar cell (sensu Mus)', ontology_id='CL:0000756', synonyms='DB3 cone bipolar cell', description='An Off-Bipolar Neuron Found In The Retina And Having Connections With Cone Photoreceptors Cells And Neurons In The Outer Half Of The Inner Plexiform Layer. The Cell Has A Diffuse Axon Terminal With Varicosities In Sublaminae 1 And 2 Of The Inner Plexiform Layer.', updated_at=2024-01-15 07:18:43 UTC, public_source_id=48, created_by_id=1)
💡 also saving parents of CellType(uid='5m55ukEt', name='type 5 cone bipolar cell (sensu Mus)', ontology_id='CL:0000757', synonyms='DB4 cone bipolar cell', description='An On-Bipolar Neuron Found In The Retina And Having Connections With Cone Photoreceptors Cells And Neurons In The Inner Half Of The Inner Plexiform Layer. The Axon Terminal Is Restricted To Sublamina 3 Of The Inner Plexiform Layer. It Is Narrowly Stratified And Branched. The Dendritic Tree Has Many Delicate Branches.', updated_at=2024-01-15 07:18:43 UTC, public_source_id=48, created_by_id=1)
💡 also saving parents of CellType(uid='RHTDqjIk', name='type 6 cone bipolar cell (sensu Mus)', ontology_id='CL:0000758', synonyms='DB5 cone bipolar cell', description='An On-Bipolar Neuron Found In The Retina And Having Connections With Cone Photoreceptors Cells And Neurons In The Inner Half Of The Inner Plexiform Layer. The Cell Has A Loose, Delicate Axon Terminal That Opens In Sublamina 3 Of The Inner Plexiform Layer And Descends Into Sublamina 4.', updated_at=2024-01-15 07:18:43 UTC, public_source_id=48, created_by_id=1)
💡 also saving parents of CellType(uid='1FSe7Fgv', name='type 7 cone bipolar cell (sensu Mus)', ontology_id='CL:0000759', synonyms='IMB cone bipolar cell', description='An On-Bipolar Neuron Found In The Retina And Having Connections With Cone Photoreceptors Cells And Neurons In The Inner Half Of The Inner Plexiform Layer. The Axon Terminal Is Narrowly Stratified And Are Found Just Below A Calretinin-Expressing Band In Sublamina 4 Of The Inner Plexiform Layer.', updated_at=2024-01-15 07:18:43 UTC, public_source_id=48, created_by_id=1)
💡 also saving parents of CellType(uid='2fwQAWrK', name='type 8 cone bipolar cell (sensu Mus)', ontology_id='CL:0000760', synonyms='DB6 cone bipolar cell', description='An On-Bipolar Neuron Found In The Retina And Having Connections With Cone Photoreceptors Cells And Neurons In The Inner Half Of The Inner Plexiform Layer. This Cell Has The Widest Dendritic Field And The Widest Axon Terminal Of All Retinal Bipolar Cells. The Axon Terminal Is Delicate And Stratified Through Sublaminae 4 And 5 Of The Inner Plexiform Layer.', updated_at=2024-01-15 07:18:43 UTC, public_source_id=48, created_by_id=1)
💡 also saving parents of CellType(uid='3MDP6uCq', name='type 9 cone bipolar cell (sensu Mus)', ontology_id='CL:0000761', synonyms='BB cone bipolar cell', description='An On-Bipolar Neuron Found In The Retina And Having Connections With Cone Photoreceptors Cells And Neurons In The Inner Half Of The Inner Plexiform Layer. The Dendritic Tree Is Wide And The Dendritic Convergence Indicates Cone Selectivity. The Axon Terminal Is Sparsely Branched And Terminates In Sublamina 5 Of The Inner Plexiform Layer.', updated_at=2024-01-15 07:18:43 UTC, public_source_id=48, created_by_id=1)
💡 also saving parents of CellType(uid='4AQr9CRo', name='Tc1 cell', ontology_id='CL:0000917', synonyms='Tc1 T lymphocyte|Tc1 T-cell|Tc1 T cell|T-cytotoxic T cell type 1|CD8-positive Th1 cell|Tc1 CD8+ T cell|Th1 CD8-positive T cell|Tc1 T-lymphocyte|Th1 non-TFH CD8-positive T cell', description='A Cd8-Positive, Alpha-Beta Positive T Cell That Has The Phenotype T-Bet-Positive, Eomesodermin-Positive, Cxcr3-Positive, Ccr6-Negative, And Is Capable Of Producing Interferon-Gamma.', updated_at=2024-01-15 07:18:43 UTC, public_source_id=48, created_by_id=1)
💡 also saving parents of CellType(uid='6uy4Hmew', name='CD38-negative naive B cell', ontology_id='CL:0002102', synonyms='CD38- naive B cell|CD38- naive B-lymphocyte|CD38- naive B-cell|CD38-negative naive B lymphocyte|CD38-negative naive B-cell|CD38- naive B lymphocyte|CD38-negative naive B-lymphocyte', description='A Cd38-Negative Naive B Cell Is A Mature B Cell That Has The Phenotype Cd38-Negative, Surface Igd-Positive, Surface Igm-Positive, And Cd27-Negative, That Has Not Yet Been Activated By Antigen In The Periphery.', updated_at=2024-01-15 07:18:43 UTC, public_source_id=48, created_by_id=1)
💡 also saving parents of CellType(uid='1awEFhiW', name='immature astrocyte', ontology_id='CL:0002626', synonyms='immature astrocytic glia', description='An Immature Astrocyte.', updated_at=2024-01-15 07:18:43 UTC, public_source_id=48, created_by_id=1)
💡 also saving parents of CellType(uid='2DATbWD2', name='retinal progenitor cell', ontology_id='CL:0002672', description='A Multi-Fate Stem Cell That Can Give Rise To Different Retinal Cell Types Including Rod And Cone Cells.', updated_at=2024-01-15 07:18:43 UTC, public_source_id=48, created_by_id=1)
💡 also saving parents of CellType(uid='eS0b73VF', name='type 3a cone bipolar cell', ontology_id='CL:0004213', description='A Type Of Type 3 Cone Bipolar Cell With Distinctive Curly Dendrites.', updated_at=2024-01-15 07:18:43 UTC, public_source_id=48, created_by_id=1)
✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0000755'
💡 also saving parents of CellType(uid='7Nwix97c', name='type 3 cone bipolar cell (sensu Mus)', ontology_id='CL:0000755', synonyms='DB2 cone bipolar cell', description='An Off-Bipolar Neuron Found In The Retina And Having Connections With Cone Photoreceptors Cells And Neurons In The Outer Half Of The Inner Plexiform Layer. The Dendritic Tree Is Delicate And The Dendritic Tips Appear Small When Compared With Type 1 Cells. The Axon Terminal Is Stratified And Restricted To Sublamina 2 Of The Inner Plexiform Layer.', updated_at=2024-01-15 07:18:46 UTC, public_source_id=48, created_by_id=1)
💡 also saving parents of CellType(uid='54NyoAxX', name='type 3b cone bipolar cell', ontology_id='CL:0004214', description='A Type Of Type 3 Cone Bipolar Cell With Distinctive Crescent-Shaped Dendrites.', updated_at=2024-01-15 07:18:43 UTC, public_source_id=48, created_by_id=1)
💡 also saving parents of CellType(uid='1tUGQcMy', name='type 5a cone bipolar cell', ontology_id='CL:0004215', description='A Type 5 Cone Bipolar Cell With Narrowly Stratified Post Synaptic Terminals.', updated_at=2024-01-15 07:18:43 UTC, public_source_id=48, created_by_id=1)
💡 also saving parents of CellType(uid='59K8GEoD', name='type 5b cone bipolar cell', ontology_id='CL:0004216', description='A Type 5 Cone Bipolar Cell With Diffuse Axonal Branches.', updated_at=2024-01-15 07:18:43 UTC, public_source_id=48, created_by_id=1)
💡 also saving parents of CellType(uid='r810TTDw', name='monocyte-derived dendritic cell', ontology_id='CL:0011031', synonyms='MDDC cell', description='A Dendritic Cell That Develops From A Monocyte.', updated_at=2024-01-15 07:18:43 UTC, public_source_id=48, created_by_id=1)
💡 also saving parents of CellType(uid='4vjvlFED', name='forebrain neuroblast', ontology_id='CL:1000042', updated_at=2024-01-15 07:18:43 UTC, public_source_id=48, created_by_id=1)
💡 also saving parents of CellType(uid='011iVJMd', name='unipolar brush cell', ontology_id='CL:4023161', description='An Excitatory Glutamatergic Interneuron Found In The Granular Layer Of The Cerebellar Cortex And Also In The Granule Cell Domain Of The Cochlear Nucleus. Unipolar Brush Cells Have A Round Or Oval Cell Body With Usually A Single Short Dendrite That Ends In A Brush-Like Tuft Of Short Dendrites Unique To Them Known As Dendrioles.', updated_at=2024-01-15 07:18:43 UTC, public_source_id=48, created_by_id=1)
registering development_stage
✅ loaded 228 DevelopmentalStage records matching ontology_id: 'MmusDv:0000034', 'MmusDv:0000052', 'HsapDv:0000242', 'HsapDv:0000060', 'HsapDv:0000121', 'HsapDv:0000238', 'HsapDv:0000119', 'HsapDv:0000216', 'HsapDv:0000096', 'HsapDv:0000179', 'MmusDv:0000089', 'HsapDv:0000208', 'MmusDv:0000057', 'HsapDv:0000068', 'HsapDv:0000103', 'HsapDv:0000183', 'HsapDv:0000029', 'HsapDv:0000148', 'HsapDv:0000237', 'MmusDv:0000051', ...
❗ did not create DevelopmentalStage records for 3 non-validated ontology_ids: 'MmusDv:0000025', 'MmusDv:0000041', 'MmusDv:0000092'
✅ created 3 DevelopmentalStage records from Bionty matching ontology_id: 'MmusDv:0000041', 'MmusDv:0000025', 'MmusDv:0000092'
registered 3 records: [DevelopmentalStage(uid='6jNHUvWd', name='unknown', ontology_id='MmusDv:0000041', public_source_id=44, created_by_id=1), DevelopmentalStage(uid='4vN31Q5K', name='Theiler stage 18', ontology_id='MmusDv:0000025', synonyms='E10.5-11.25|TS18', description='Organogenesis Stage During Which The Lens Vesicle Gradually Closes And The Nasal Pits Start To Form. The Rapid Growth Of The Brain Is Striking.', public_source_id=44, created_by_id=1), DevelopmentalStage(uid='3wDLorw8', name='postpartum stage', ontology_id='MmusDv:0000092', description='Mouse Developmental Stage That Covers The Period From Birth Until Late Adulthood.', public_source_id=44, created_by_id=1)]
❗ now recursing through parents: this only happens once, but is much slower than bulk saving
💡 you can switch this off via: lb.settings.auto_save_parents = False
💡 also saving parents of DevelopmentalStage(uid='6jNHUvWd', name='unknown', ontology_id='MmusDv:0000041', updated_at=2024-01-15 07:18:49 UTC, public_source_id=44, created_by_id=1)
💡 also saving parents of DevelopmentalStage(uid='4vN31Q5K', name='Theiler stage 18', ontology_id='MmusDv:0000025', synonyms='E10.5-11.25|TS18', description='Organogenesis Stage During Which The Lens Vesicle Gradually Closes And The Nasal Pits Start To Form. The Rapid Growth Of The Brain Is Striking.', updated_at=2024-01-15 07:18:49 UTC, public_source_id=44, created_by_id=1)
💡 also saving parents of DevelopmentalStage(uid='3wDLorw8', name='postpartum stage', ontology_id='MmusDv:0000092', description='Mouse Developmental Stage That Covers The Period From Birth Until Late Adulthood.', updated_at=2024-01-15 07:18:49 UTC, public_source_id=44, created_by_id=1)
registering disease
✅ loaded 91 Disease records matching ontology_id: 'MONDO:0009061', 'MONDO:0005027', 'MONDO:0003573', 'MONDO:0001627', 'MONDO:0004849', 'MONDO:0008433', 'MONDO:0004335', 'MONDO:0004691', 'MONDO:0004514', 'MONDO:0005575', 'MONDO:0013662', 'MONDO:0005021', 'MONDO:0005005', 'MONDO:0005011', 'MONDO:0002052', 'MONDO:0007472', 'MONDO:0002120', 'MONDO:0003050', 'MONDO:0100096', 'MONDO:0600025', ...
✅ created 8 Disease records from Bionty matching ontology_id: 'MONDO:0000819', 'MONDO:0004781', 'MONDO:0004989', 'MONDO:0005252', 'MONDO:0005453', 'MONDO:0005494', 'MONDO:0021115', 'MONDO:0021116'
❗ now recursing through parents: this only happens once, but is much slower than bulk saving
💡 you can switch this off via: lb.settings.auto_save_parents = False
💡 also saving parents of Disease(uid='2g6pBHyD', name='anencephaly', ontology_id='MONDO:0000819', synonyms='anencephalus', description='A Rare Neural Tube Defect During Pregnancy, Resulting In The Absence Of A Large Portion Of The Brain And Skull In The Fetus.', updated_at=2024-01-15 07:18:51 UTC, public_source_id=49, created_by_id=1)
✅ loaded 1 Disease record matching ontology_id: 'MONDO:0003847'
✅ created 1 Disease record from Bionty matching ontology_id: 'MONDO:0002320'
💡 also saving parents of Disease(uid='2t0kJzgY', name='congenital nervous system disorder', ontology_id='MONDO:0002320', synonyms='congenital abnormality of the nervous system|congenital neurologic anomaly|congenital nervous system disorder', description='An Abnormality Of The Nervous System That Is Present At Birth Or Detected In The Neonatal Period.', updated_at=2024-01-15 07:18:53 UTC, public_source_id=49, created_by_id=1)
💡 also saving parents of Disease(uid='5j7A7XYG', name='acute myocardial infarction', ontology_id='MONDO:0004781', synonyms='myocardial infarction (disease), acute|acute myocardial infarction (disease)', description='Necrosis Of The Myocardium, As A Result Of Interruption Of The Blood Supply To The Area. It Is Characterized By A Severe And Rapid Onset Of Symptoms That May Include Chest Pain, Often Radiating To The Left Arm And Left Side Of The Neck, Dyspnea, Sweating, And Palpitations.', updated_at=2024-01-15 07:18:51 UTC, public_source_id=49, created_by_id=1)
💡 also saving parents of Disease(uid='1yX8SwAD', name='breast carcinoma', ontology_id='MONDO:0004989', synonyms='mammary carcinoma|breast carcinoma|carcinoma of the breast|carcinoma of breast', description='A Carcinoma That Arises From Epithelial Cells Of The Breast', updated_at=2024-01-15 07:18:51 UTC, public_source_id=49, created_by_id=1)
💡 also saving parents of Disease(uid='4rqQ6I6U', name='heart failure', ontology_id='MONDO:0005252', synonyms='insufficiency, Cardiac|cardiac failure|heart failure|cardiac insufficiency|failure, heart', description='Inability Of The Heart To Pump Blood At An Adequate Rate To Meet Tissue Metabolic Requirements. Clinical Symptoms Of Heart Failure Include: Unusual Dyspnea On Light Exertion, Recurrent Dyspnea Occurring In The Supine Position, Fluid Retention Or Rales, Jugular Venous Distension, Pulmonary Edema On Physical Exam, Or Pulmonary Edema On Chest X-Ray Presumed To Be Cardiac Dysfunction.', updated_at=2024-01-15 07:18:51 UTC, public_source_id=49, created_by_id=1)
💡 also saving parents of Disease(uid='76nVPrn5', name='congenital heart disease', ontology_id='MONDO:0005453', synonyms='congenital anomaly of heart|congenital heart defects|congenital heart defect|heart defect', description='A Heart Disease That Is Present At Birth. Representative Examples Include Atrial Septal Defect, Ventricular Septal Defect, Tetralogy Of Fallot, And Patent Foramen Ovale.', updated_at=2024-01-15 07:18:51 UTC, public_source_id=49, created_by_id=1)
✅ loaded 1 Disease record matching ontology_id: 'MONDO:0005267'
✅ created 1 Disease record from Bionty matching ontology_id: 'MONDO:0024239'
💡 also saving parents of Disease(uid='7c9IFE6d', name='congenital anomaly of cardiovascular system', ontology_id='MONDO:0024239', synonyms='congenital Abnormality of the circulatory system|congenital anomaly of cardiovascular system|congenital cardiovascular Abnormality|disorder of cardiovascular system development|congenital cardiovascular anomaly|cardiovascular system development disease', description='A Disease That Has Its Basis In The Disruption Of Cardiovascular System Development.', updated_at=2024-01-15 07:18:54 UTC, public_source_id=49, created_by_id=1)
💡 also saving parents of Disease(uid='2g3vdh4F', name='triple-negative breast carcinoma', ontology_id='MONDO:0005494', synonyms='triple-negative breast cancer|triple-negative breast carcinoma|triple-receptor negative breast cancer', description='An Invasive Breast Carcinoma Which Is Negative For Expression Of Estrogen Receptor (Er), Progesterone Receptor (Pr), And Human Epidermal Growth Factor Receptor 2 (Her2).', updated_at=2024-01-15 07:18:51 UTC, public_source_id=49, created_by_id=1)
✅ created 3 Disease records from Bionty matching ontology_id: 'MONDO:0000616', 'MONDO:0006513', 'MONDO:0000618'
💡 also saving parents of Disease(uid='2OGAtYpX', name='progesterone-receptor negative breast cancer', ontology_id='MONDO:0000616', updated_at=2024-01-15 07:18:55 UTC, public_source_id=49, created_by_id=1)
✅ created 1 Disease record from Bionty matching ontology_id: 'MONDO:0006116'
💡 also saving parents of Disease(uid='rpYSjunF', name='breast carcinoma by gene expression profile', ontology_id='MONDO:0006116', synonyms='breast carcinoma by gene expression profile', description='A Header Term That Includes The Following Breast Carcinoma Subtypes Determined By Gene Expression Profiling: Luminal A Breast Carcinoma, Luminal B Breast Carcinoma, Her2 Positive Breast Carcinoma, Basal-Like Breast Carcinoma, Triple-Negative Breast Carcinoma, And Normal Breast-Like Subtype Of Breast Carcinoma.', updated_at=2024-01-15 07:18:57 UTC, public_source_id=49, created_by_id=1)
💡 also saving parents of Disease(uid='1FdMycA0', name='estrogen-receptor negative breast cancer', ontology_id='MONDO:0006513', synonyms='ER- breast cancer', description='A Subtype Of Breast Cancer That Is Estrogen-Receptor Negative', updated_at=2024-01-15 07:18:55 UTC, public_source_id=49, created_by_id=1)
💡 also saving parents of Disease(uid='1UsnNL28', name='Her2-receptor negative breast cancer', ontology_id='MONDO:0000618', updated_at=2024-01-15 07:18:55 UTC, public_source_id=49, created_by_id=1)
💡 also saving parents of Disease(uid='7N4DbHPa', name='luminal B breast carcinoma', ontology_id='MONDO:0021115', synonyms='Luminal B|Luminal B breast carcinoma|Luminal B estrogen receptor positive subtype of breast carcinoma|Luminal B breast cancer|Luminal B subtype of breast carcinoma', description='A Biologic Subset Of Breast Carcinoma Defined By Low To Moderate Expression Of Genes Characteristic Of Luminal Epithelial Cells Including Estrogen Receptor (Er), And High Expression Of Ggh, Laptm4B, And Ccne1. This Subtype Of Breast Cancer Is Associated With A Good Prognosis, Although Not As Favorable As The Luminal A Subtype.', updated_at=2024-01-15 07:18:51 UTC, public_source_id=49, created_by_id=1)
✅ created 1 Disease record from Bionty matching ontology_id: 'MONDO:0004990'
💡 also saving parents of Disease(uid='Me1FU1fo', name='breast tumor luminal A or B', ontology_id='MONDO:0004990', synonyms='breast tumor luminal|luminal breast cancer', description='Subsets Of Breast Carcinoma Defined By Expression Of Genes Characteristic Of Luminal Epithelial Cells.', updated_at=2024-01-15 07:18:58 UTC, public_source_id=49, created_by_id=1)
💡 also saving parents of Disease(uid='6L0xexcA', name='luminal A breast carcinoma', ontology_id='MONDO:0021116', synonyms='Luminal A breast carcinoma|Luminal A estrogen receptor positive subtype of breast carcinoma|Luminal A breast cancer|Luminal A subtype of breast carcinoma|Luminal A', description='A Biologic Subset Of Breast Carcinoma Defined By High Expression Of Genes Characteristic Of Luminal Epithelial Cells, Including Estrogen Receptor (Er), Estrogen Regulated Protein Liv-1, And The Transcription Factors Hepatocyte Nuclear Factor 3, Hnf3A, Xbp1, And Gata 3. This Subtype Of Breast Cancer Is Associated With A Good Prognosis.', updated_at=2024-01-15 07:18:51 UTC, public_source_id=49, created_by_id=1)
registering self_reported_ethnicity
✅ loaded 28 Ethnicity records matching ontology_id: 'unknown', 'HANCESTRO:0017', 'HANCESTRO:0590', 'HANCESTRO:0462', 'HANCESTRO:0009', 'HANCESTRO:0463', 'HANCESTRO:0010', 'HANCESTRO:0568', 'HANCESTRO:0025', 'HANCESTRO:0019', 'HANCESTRO:0008', 'HANCESTRO:0588', 'HANCESTRO:0383', 'HANCESTRO:0321', 'HANCESTRO:0027', 'HANCESTRO:0005', 'HANCESTRO:0595', 'HANCESTRO:0016', 'HANCESTRO:0015', 'HANCESTRO:0021', ...
✅ created 2 Ethnicity records from Bionty matching ontology_id: 'HANCESTRO:0597', 'HANCESTRO:0598'
❗ did not create Ethnicity records for 2 non-validated ontology_ids: 'HANCESTRO:0005,HANCESTRO:0008', 'HANCESTRO:0013,HANCESTRO:0014'
❗ now recursing through parents: this only happens once, but is much slower than bulk saving
💡 you can switch this off via: lb.settings.auto_save_parents = False
💡 also saving parents of Ethnicity(uid='7RNCY3yC', name='Singaporean Malay', ontology_id='HANCESTRO:0597', description='Includes Individuals Who Either Self-Report Or Have Been Described By Authors As Singaporean Malay.', updated_at=2024-01-15 07:19:00 UTC, public_source_id=45, created_by_id=1)
💡 also saving parents of Ethnicity(uid='011BKLRZ', name='Singaporean Indian', ontology_id='HANCESTRO:0598', description='Includes Individuals Who Either Self-Report Or Have Been Described By Authors As Singaporean Indian.', updated_at=2024-01-15 07:19:00 UTC, public_source_id=45, created_by_id=1)
registered 2 records: [Ethnicity(uid='8t2kwFPT', name='Native American,Hispanic or Latin American', ontology_id='HANCESTRO:0013,HANCESTRO:0014', created_by_id=1), Ethnicity(uid='76lLnODz', name='European,Asian', ontology_id='HANCESTRO:0005,HANCESTRO:0008', created_by_id=1)]
registering sex
registering tissue
✅ loaded 356 Tissue records matching ontology_id: 'UBERON:0002067', 'UBERON:0002113', 'UBERON:0002115', 'UBERON:0001925', 'UBERON:0001225', 'UBERON:0001293', 'UBERON:0002382', 'UBERON:0001295', 'UBERON:0001393', 'UBERON:0001159', 'UBERON:0002810', 'UBERON:0004167', 'UBERON:0001707', 'UBERON:0001366', 'UBERON:0002299', 'UBERON:0001471', 'UBERON:0002420', 'UBERON:0039167', 'UBERON:0000004', 'UBERON:0002108', ...
✅ created 6 Tissue records from Bionty matching ontology_id: 'UBERON:0002129', 'UBERON:0002132', 'UBERON:0002245', 'UBERON:0004070', 'UBERON:0014648', 'UBERON:0019207'
❗ did not create Tissue records for 12 non-validated ontology_ids: 'CL:0000010', 'CL:0000082', 'CL:0000084', 'CL:0000115', 'CL:0000351', 'CL:0002322', 'CL:0002327', 'CL:0002328', 'CL:0002334', 'CL:0002335', 'CL:0002633', 'CL:0010003'
❗ now recursing through parents: this only happens once, but is much slower than bulk saving
💡 you can switch this off via: lb.settings.auto_save_parents = False
💡 also saving parents of Tissue(uid='3PjakEs6', name='cerebellar cortex', ontology_id='UBERON:0002129', synonyms='cortex of cerebellar hemisphere', description='The Superficial Gray Matter Of The Cerebellum. It Consists Of Three Main Layers, The Molecular Layer, The Purkinje Cell Layer And The Granule Cell Layer.', updated_at=2024-01-15 07:19:04 UTC, public_source_id=47, created_by_id=1)
✅ created 1 Tissue record from Bionty matching ontology_id: 'UBERON:0019263'
💡 also saving parents of Tissue(uid='49MXa4pd', name='gray matter of hindbrain', ontology_id='UBERON:0019263', synonyms='gray matter of the hindbrain', updated_at=2024-01-15 07:19:05 UTC, public_source_id=47, created_by_id=1)
💡 also saving parents of Tissue(uid='487THodN', name='dentate nucleus', ontology_id='UBERON:0002132', synonyms='lateral nucleus of cerebellum|lateral cerebellar nucleus|dentate cerebellar nucleus', description='The Largest And Most Lateral Of The Deep Cerebellum Nuclei; It Receives Axons Of Purkinje Cells In The Lateral Cerebellar Hemisphere (Neocerebellum) And Receives Its Afferents From The Premotor Cortex And The Supplementary Motor Cortex Through The Pontocerebellar System, And Its Efferents Project Through The Superior Cerebellar Peduncle And Is A Major Source Of Its Fibers.', updated_at=2024-01-15 07:19:04 UTC, public_source_id=47, created_by_id=1)
✅ created 1 Tissue record from Bionty matching ontology_id: 'UBERON:0008995'
💡 also saving parents of Tissue(uid='5ycRhxnh', name='nucleus of cerebellar nuclear complex', ontology_id='UBERON:0008995', synonyms='deep cerebellar nucleus|cerebellar nucleus', description='Four Accumulations Of Gray Substance Embedded In The White Substance Of The Cerebellum, Comprising The Nucleus Dentatus, Nucleus Emboliformis, Nucleus Globosus, And Nucleus Fastigii.', updated_at=2024-01-15 07:19:07 UTC, public_source_id=47, created_by_id=1)
💡 also saving parents of Tissue(uid='47CtdZAI', name='cerebellar hemisphere', ontology_id='UBERON:0002245', synonyms='cerebellum hemisphere|hemispherium cerebelli [H II - H X]|cerebellar hemisphere|hemispherium cerebelli [hII-hX]|hemisphere of cerebellum [H II - H X]|hemisphere of cerebellum', description='A Paired Regions Of The Cerebellum That Lie Outside And Lateral To The Central Vermis[Mp]. The Cerebellum Consists Of Three Parts, A Median And Two Lateral, Which Are Continuous With Each Other, And Are Substantially The Same In Structure. The Median Portion Is Constricted, And Is Called The Vermis, From Its Annulated Appearance Which It Owes To The Transverse Ridges And Furrows Upon It; The Lateral Expanded Portions Are Named The Hemispheres. The Lateral Hemisphere Is Considered The Portion Of The Cerebellum To Develop Most Recently. [Wp,Unvetted].', updated_at=2024-01-15 07:19:04 UTC, public_source_id=47, created_by_id=1)
💡 also saving parents of Tissue(uid='3RMLZOKz', name='cerebellum vermis lobule', ontology_id='UBERON:0004070', synonyms='lobule of vermis', description='The Region Of A Cerebellar Lobule That Resides In The Central Section Of The Cerebellum Between The Two Hemispheres.', updated_at=2024-01-15 07:19:04 UTC, public_source_id=47, created_by_id=1)
💡 also saving parents of Tissue(uid='3r1l5rzE', name='hemisphere part of cerebellar posterior lobe', ontology_id='UBERON:0014648', synonyms='hemispherium lobus posterior|hemisphere of posterior lobe|hemisphere of posterior lobe of cerebellum', description='A Multi-Tissue Structure That Is Part Of A Cerebellar Hemisphere And Is Part Of A Posterior Lobe Of Cerebellum.', updated_at=2024-01-15 07:19:04 UTC, public_source_id=47, created_by_id=1)
💡 also saving parents of Tissue(uid='1q7DYk8z', name='chorioretinal region', ontology_id='UBERON:0019207', synonyms='retinachoroid|retinachoroidal region|chorioretina|choroid and retina', description='The Part Of The Eye That Consists Of Both The Retina And The Optic Choroid.', updated_at=2024-01-15 07:19:04 UTC, public_source_id=47, created_by_id=1)
registered 12 records: [Tissue(uid='22LvKd01', name='T cell', ontology_id='CL:0000084', created_by_id=1), Tissue(uid='1ERsVqRf', name='embryonic stem cell', ontology_id='CL:0002322', created_by_id=1), Tissue(uid='48whgmiD', name='epithelial cell of alveolus of lung', ontology_id='CL:0010003', created_by_id=1), Tissue(uid='5F4YNEUS', name='mammary gland epithelial cell', ontology_id='CL:0002327', created_by_id=1), Tissue(uid='1J6s4gSi', name='endothelial cell', ontology_id='CL:0000115', created_by_id=1), Tissue(uid='XS6m3PvU', name='cultured cell', ontology_id='CL:0000010', created_by_id=1), Tissue(uid='1LzSyCsJ', name='respiratory basal cell', ontology_id='CL:0002633', created_by_id=1), Tissue(uid='4IRoehoY', name='preadipocyte', ontology_id='CL:0002334', created_by_id=1), Tissue(uid='8dEt6lpw', name='brown preadipocyte', ontology_id='CL:0002335', created_by_id=1), Tissue(uid='2mqTx1qQ', name='epithelial cell of lung', ontology_id='CL:0000082', created_by_id=1), Tissue(uid='7MscrSDl', name='trophoblast cell', ontology_id='CL:0000351', created_by_id=1), Tissue(uid='MJYdRbdq', name='bronchial epithelial cell', ontology_id='CL:0002328', created_by_id=1)]
donors and suspension_types¶
from cellxgene_lamin._labels import register_ulabels
register_ulabels(cxg_datasets, "donor_id")
registered 205 donor_ids
register_ulabels(cxg_datasets, "suspension_type")
registered 0 suspension_types
Annotate artifacts with obs metadata¶
from cellxgene_lamin._features import FEATURE_TO_ACCESSOR
features = ln.Feature.lookup()
for idx, cxg_dataset in enumerate(cxg_datasets):
if idx % 100 == 0:
print(f"annotating dataset {idx} of {len(cxg_datasets)}")
artifact = artifacts.filter(key__contains=cxg_dataset["dataset_id"]).one_or_none()
if artifact is None:
continue
for field, terms in cxg_dataset.items():
if field not in FEATURE_TO_ACCESSOR:
continue
accessor, orm = FEATURE_TO_ACCESSOR.get(field)
if field in ["donor_id", "suspension_type", "tissue_type"]:
records = orm.from_values(terms, field="name")
if len(records) > 0:
# stratify by feature so that link tables records are written
artifact.labels.add(records, feature=getattr(features, field))
else:
records = orm.from_values(
[i["ontology_term_id"] for i in terms], field="ontology_id"
)
if len(records) > 0:
getattr(artifact, accessor).add(*records)
# clean up the 2 "unknowns" in DevelopmentalStage
lb.DevelopmentalStage.filter(name="unknown").exclude(ontology_id="unknown").delete()
annotating dataset 0 of 1163
annotating dataset 100 of 1163
annotating dataset 200 of 1163
annotating dataset 300 of 1163
annotating dataset 400 of 1163
annotating dataset 500 of 1163
annotating dataset 600 of 1163
annotating dataset 700 of 1163
annotating dataset 800 of 1163
annotating dataset 900 of 1163
annotating dataset 1000 of 1163
annotating dataset 1100 of 1163
Validate and register genes¶
from cellxgene_lamin._gene import register_genes
Register all genes for each organism:
register_genes()
registering homo_sapiens genes
❗ did not create Gene records for 147 non-validated ensembl_gene_ids: 'ENSG00000112096', 'ENSG00000137808', 'ENSG00000161149', 'ENSG00000182230', 'ENSG00000203812', 'ENSG00000204092', 'ENSG00000205485', 'ENSG00000212951', 'ENSG00000215271', 'ENSG00000221995', 'ENSG00000224739', 'ENSG00000224745', 'ENSG00000225178', 'ENSG00000225932', 'ENSG00000226377', 'ENSG00000226380', 'ENSG00000226403', 'ENSG00000227021', 'ENSG00000227220', 'ENSG00000227902', ...
❗ 147 terms (0.20%) are not validated for ensembl_gene_id: ENSG00000269933, ENSG00000261737, ENSG00000259834, ENSG00000256374, ENSG00000263464, ENSG00000203812, ENSG00000272196, ENSG00000272880, ENSG00000284299, ENSG00000270188, ENSG00000287116, ENSG00000237133, ENSG00000224739, ENSG00000227902, ENSG00000239467, ENSG00000272551, ENSG00000280374, ENSG00000284741, ENSG00000236886, ENSG00000229352, ...
registering mus_musculus genes
❗ did not create Gene records for 135 non-validated ensembl_gene_ids: 'ENSMUSG00000022591', 'ENSMUSG00000045506', 'ENSMUSG00000053706', 'ENSMUSG00000053861', 'ENSMUSG00000066378', 'ENSMUSG00000066810', 'ENSMUSG00000066936', 'ENSMUSG00000067085', 'ENSMUSG00000067122', 'ENSMUSG00000067292', 'ENSMUSG00000067627', 'ENSMUSG00000067929', 'ENSMUSG00000068181', 'ENSMUSG00000069518', 'ENSMUSG00000072693', 'ENSMUSG00000073290', 'ENSMUSG00000073291', 'ENSMUSG00000073682', 'ENSMUSG00000074210', 'ENSMUSG00000074302', ...
❗ 135 terms (0.20%) are not validated for ensembl_gene_id: ENSMUSG00000022591, ENSMUSG00000094127, ENSMUSG00000066936, ENSMUSG00000116275, ENSMUSG00000091312, ENSMUSG00000098794, ENSMUSG00000079353, ENSMUSG00000096240, ENSMUSG00000079286, ENSMUSG00000085431, ENSMUSG00000075015, ENSMUSG00000075014, ENSMUSG00000078091, ENSMUSG00000075006, ENSMUSG00000079175, ENSMUSG00000079171, ENSMUSG00000079170, ENSMUSG00000079169, ENSMUSG00000090353, ENSMUSG00000100963, ...
registering synthetic_construct genes
❗ loading non-default source inside a LaminDB instance
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
❗ did not create Gene records for 92 non-validated ensembl_gene_ids: 'ERCC-00002', 'ERCC-00003', 'ERCC-00004', 'ERCC-00009', 'ERCC-00012', 'ERCC-00013', 'ERCC-00014', 'ERCC-00016', 'ERCC-00017', 'ERCC-00019', 'ERCC-00022', 'ERCC-00024', 'ERCC-00025', 'ERCC-00028', 'ERCC-00031', 'ERCC-00033', 'ERCC-00034', 'ERCC-00035', 'ERCC-00039', 'ERCC-00040', ...
❗ 92 terms (100.00%) are not validated for ensembl_gene_id: ERCC-00002, ERCC-00003, ERCC-00004, ERCC-00009, ERCC-00012, ERCC-00013, ERCC-00014, ERCC-00016, ERCC-00017, ERCC-00019, ERCC-00022, ERCC-00024, ERCC-00025, ERCC-00028, ERCC-00031, ERCC-00033, ERCC-00034, ERCC-00035, ERCC-00039, ERCC-00040, ...
registering severe_acute_respiratory_syndrome_coronavirus_2 genes
❗ loading non-default source inside a LaminDB instance
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
❗ did not create Gene records for 12 non-validated ensembl_gene_ids: 'ENSSASG00005000002', 'ENSSASG00005000003', 'ENSSASG00005000004', 'ENSSASG00005000006', 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000005', 'ENSSASG00005000013'
❗ 12 terms (100.00%) are not validated for ensembl_gene_id: ENSSASG00005000002, ENSSASG00005000003, ENSSASG00005000004, ENSSASG00005000006, ENSSASG00005000010, ENSSASG00005000007, ENSSASG00005000011, ENSSASG00005000009, ENSSASG00005000012, ENSSASG00005000008, ENSSASG00005000005, ENSSASG00005000013
Link metadata to individual artifacts¶
annotate with genes measured in each artifact:
organisms = lb.Organism.lookup(field=lb.Organism.scientific_name)
for idx, artifact in enumerate(artifacts):
if idx % 100 == 0:
print(f"annotating dataset {idx} of {len(artifacts)}")
adata_backed = artifact.backed()
var_names = adata_backed.var_names
organism_record = artifact.organism.first()
if organism_record is None:
print(f"No organism found for artifact: {artifact}")
continue
genes = lb.Gene.from_values(
var_names, field=lb.Gene.ensembl_gene_id, organism=organism_record
)
if len(genes) == 0 and var_names[0].startswith("ENSG"):
genes += lb.Gene.from_values(
var_names, field=lb.Gene.ensembl_gene_id, organism="human"
)
if len(var_names[var_names.str.startswith("ERCC")]) > 0:
genes += lb.Gene.from_values(
var_names,
field=lb.Gene.ensembl_gene_id,
organism=organisms.synthetic_construct,
)
if len(var_names[var_names.str.startswith("ENSSASG")]) > 0:
genes += lb.Gene.from_values(
var_names,
field=lb.Gene.ensembl_gene_id,
organism=organisms.severe_acute_respiratory_syndrome_coronavirus_2,
)
var_feature_set_artifact = ln.FeatureSet(genes, type="number")
var_feature_set_artifact.save()
artifact.feature_sets.add(
var_feature_set_artifact, through_defaults={"slot": "var"}
)
Show code cell output
annotating dataset 0 of 1113
✅ loaded: FeatureSet(uid='qztydaKUhnRp4zHzXUXd', n=30933, type='number', registry='bionty.Gene', hash='bMTbQNmrQxHwjX4k3XGh', updated_at=2024-01-15 08:00:19 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 08:02:07 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:01:41 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:04:03 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 19149 non-validated ensembl_gene_ids: 'ENSG00000162063', 'ENSG00000162062', 'ENSG00000198951', 'ENSG00000163121', 'ENSG00000105829', 'ENSG00000081237', 'ENSG00000134153', 'ENSG00000134152', 'ENSG00000173728', 'ENSG00000035687', 'ENSG00000166961', 'ENSG00000172689', 'ENSG00000110104', 'ENSG00000179397', 'ENSG00000149506', 'ENSG00000125384', 'ENSG00000168229', 'ENSG00000183579', 'ENSG00000166548', 'ENSG00000181234', ...
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 08:04:31 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 08:03:00 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:05:12 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:04:06 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:12:20 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:12:23 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 12591 non-validated ensembl_gene_ids: 'ENSG00000121410', 'ENSG00000148584', 'ENSG00000175899', 'ENSG00000166535', 'ENSG00000184389', 'ENSG00000128274', 'ENSG00000081760', 'ENSG00000188984', 'ENSG00000109576', 'ENSG00000103591', 'ENSG00000115977', 'ENSG00000087884', 'ENSG00000127837', 'ENSG00000129673', 'ENSG00000131043', 'ENSG00000205002', 'ENSG00000090861', 'ENSG00000124608', 'ENSG00000157426', 'ENSG00000149313', ...
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 13623 non-validated ensembl_gene_ids: 'ENSG00000121410', 'ENSG00000148584', 'ENSG00000175899', 'ENSG00000166535', 'ENSG00000184389', 'ENSG00000128274', 'ENSG00000118017', 'ENSG00000081760', 'ENSG00000188984', 'ENSG00000109576', 'ENSG00000103591', 'ENSG00000115977', 'ENSG00000087884', 'ENSG00000127837', 'ENSG00000129673', 'ENSG00000131043', 'ENSG00000205002', 'ENSG00000090861', 'ENSG00000124608', 'ENSG00000157426', ...
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 13155 non-validated ensembl_gene_ids: 'ENSG00000121410', 'ENSG00000175899', 'ENSG00000166535', 'ENSG00000184389', 'ENSG00000128274', 'ENSG00000081760', 'ENSG00000188984', 'ENSG00000109576', 'ENSG00000103591', 'ENSG00000115977', 'ENSG00000087884', 'ENSG00000127837', 'ENSG00000129673', 'ENSG00000131043', 'ENSG00000090861', 'ENSG00000124608', 'ENSG00000157426', 'ENSG00000149313', 'ENSG00000008311', 'ENSG00000275700', ...
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 08:05:00 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 08:09:31 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 08:13:22 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='b0ZrJY5hy4EPHqCA7d9p', n=37073, type='number', registry='bionty.Gene', hash='_CRP0gN53PfyaubI4Piw', updated_at=2024-01-15 08:07:41 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:05:55 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:14:23 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:14:28 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MLFo2ZBXvibkOyBR9UOR', n=32922, type='number', registry='bionty.Gene', hash='2A2lU2b4wuSFwJEYynxn', updated_at=2024-01-15 08:06:16 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 08:13:13 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='1q6Bb6Y1sAQOXk17GLPB', n=33178, type='number', registry='bionty.Gene', hash='CVYdOrA6H1bRgzke8eH9', updated_at=2024-01-15 08:10:04 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 08:05:04 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:14:33 UTC, created_by_id=1)
✅ loaded 32551 Gene records matching ensembl_gene_id: 'ENSG00000121410', 'ENSG00000268895', 'ENSG00000148584', 'ENSG00000175899', 'ENSG00000245105', 'ENSG00000166535', 'ENSG00000256661', 'ENSG00000256904', 'ENSG00000184389', 'ENSG00000128274', 'ENSG00000118017', 'ENSG00000094914', 'ENSG00000081760', 'ENSG00000114771', 'ENSG00000197953', 'ENSG00000242908', 'ENSG00000188984', 'ENSG00000204518', 'ENSG00000109576', 'ENSG00000158122', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 32551 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 08:17:57 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 08:21:03 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MLFo2ZBXvibkOyBR9UOR', n=32922, type='number', registry='bionty.Gene', hash='2A2lU2b4wuSFwJEYynxn', updated_at=2024-01-15 08:15:14 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 08:15:18 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='qztydaKUhnRp4zHzXUXd', n=30933, type='number', registry='bionty.Gene', hash='bMTbQNmrQxHwjX4k3XGh', updated_at=2024-01-15 08:02:03 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='hrgirrsFM5UrBy2uqZpB', n=21069, type='number', registry='bionty.Gene', hash='r2zgtMrdBUKvKDVcWL1O', updated_at=2024-01-15 08:10:34 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='raT5X81gwJTAVJCLf4Vy', n=32826, type='number', registry='bionty.Gene', hash='QhlSiI1A7kijxjwi55do', updated_at=2024-01-15 08:11:18 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:12:27 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:24:09 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 08:21:07 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 08:24:47 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:24:12 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 10782 non-validated ensembl_gene_ids: 'ENSG00000148584', 'ENSG00000081760', 'ENSG00000188984', 'ENSG00000109576', 'ENSG00000103591', 'ENSG00000115977', 'ENSG00000087884', 'ENSG00000127837', 'ENSG00000131043', 'ENSG00000090861', 'ENSG00000124608', 'ENSG00000157426', 'ENSG00000149313', 'ENSG00000008311', 'ENSG00000275700', 'ENSG00000181409', 'ENSG00000183044', 'ENSG00000165029', 'ENSG00000144452', 'ENSG00000179869', ...
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 08:21:16 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 08:13:31 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:24:54 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 08:25:40 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:19:51 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:25:44 UTC, created_by_id=1)
annotating dataset 100 of 1113
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:27:10 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='fu1QNLhxofpI7ogRyLmk', n=28590, type='number', registry='bionty.Gene', hash='dIdZSLH_fsEHq1zk-uoI', updated_at=2024-01-15 08:26:28 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:27:19 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 08:25:32 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:27:31 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:28:16 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='y4tQYNGVyXyn75E25n3q', n=17811, type='number', registry='bionty.Gene', hash='KQjXFSi5CZIOSvQFuk1g', updated_at=2024-01-15 08:28:38 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MLFo2ZBXvibkOyBR9UOR', n=32922, type='number', registry='bionty.Gene', hash='2A2lU2b4wuSFwJEYynxn', updated_at=2024-01-15 08:21:12 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MLFo2ZBXvibkOyBR9UOR', n=32922, type='number', registry='bionty.Gene', hash='2A2lU2b4wuSFwJEYynxn', updated_at=2024-01-15 08:34:02 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='qztydaKUhnRp4zHzXUXd', n=30933, type='number', registry='bionty.Gene', hash='bMTbQNmrQxHwjX4k3XGh', updated_at=2024-01-15 08:22:41 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='7bByOf9OLV0FmGYJQHsM', n=17985, type='number', registry='bionty.Gene', hash='ndk2sUwm_Yixh-QM6k2v', updated_at=2024-01-15 08:30:18 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='raT5X81gwJTAVJCLf4Vy', n=32826, type='number', registry='bionty.Gene', hash='QhlSiI1A7kijxjwi55do', updated_at=2024-01-15 08:23:33 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 08:30:23 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='eZ0mQH25SXgqjofpZk0E', n=34088, type='number', registry='bionty.Gene', hash='YCufLSczD70l408yrOq-', updated_at=2024-01-15 08:30:28 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:30:35 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:36:52 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:36:55 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 08:29:40 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 08:32:02 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 08:36:45 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='nQ51YKqBhB0ILDbanXVr', n=36503, type='number', registry='bionty.Gene', hash='xtVNbbhs3ty63qs-rwKZ', updated_at=2024-01-15 08:29:49 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='fu1QNLhxofpI7ogRyLmk', n=28590, type='number', registry='bionty.Gene', hash='dIdZSLH_fsEHq1zk-uoI', updated_at=2024-01-15 08:27:25 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:33:13 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 08:37:19 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MLFo2ZBXvibkOyBR9UOR', n=32922, type='number', registry='bionty.Gene', hash='2A2lU2b4wuSFwJEYynxn', updated_at=2024-01-15 08:34:06 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='QQjhZ67Kjz2k0t3WE2OB', n=19492, type='number', registry='bionty.Gene', hash='umcQPNUERZ7V2Gu2lQoT', updated_at=2024-01-15 08:36:18 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='mlt8Tz3VeDs7InXyvkwV', n=60452, type='number', registry='bionty.Gene', hash='qNH4duNQv7Yki2rlogva', updated_at=2024-01-15 08:03:06 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:36:59 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:42:27 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 11653 non-validated ensembl_gene_ids: 'ENSG00000148584', 'ENSG00000166535', 'ENSG00000184389', 'ENSG00000128274', 'ENSG00000081760', 'ENSG00000188984', 'ENSG00000109576', 'ENSG00000103591', 'ENSG00000115977', 'ENSG00000087884', 'ENSG00000127837', 'ENSG00000129673', 'ENSG00000131043', 'ENSG00000090861', 'ENSG00000124608', 'ENSG00000157426', 'ENSG00000149313', 'ENSG00000008311', 'ENSG00000275700', 'ENSG00000181409', ...
✅ loaded: FeatureSet(uid='nQ51YKqBhB0ILDbanXVr', n=36503, type='number', registry='bionty.Gene', hash='xtVNbbhs3ty63qs-rwKZ', updated_at=2024-01-15 08:37:23 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:37:32 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:43:53 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='nQ51YKqBhB0ILDbanXVr', n=36503, type='number', registry='bionty.Gene', hash='xtVNbbhs3ty63qs-rwKZ', updated_at=2024-01-15 08:42:49 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='qztydaKUhnRp4zHzXUXd', n=30933, type='number', registry='bionty.Gene', hash='bMTbQNmrQxHwjX4k3XGh', updated_at=2024-01-15 08:36:15 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MLFo2ZBXvibkOyBR9UOR', n=32922, type='number', registry='bionty.Gene', hash='2A2lU2b4wuSFwJEYynxn', updated_at=2024-01-15 08:38:29 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='qztydaKUhnRp4zHzXUXd', n=30933, type='number', registry='bionty.Gene', hash='bMTbQNmrQxHwjX4k3XGh', updated_at=2024-01-15 08:44:08 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='mlt8Tz3VeDs7InXyvkwV', n=60452, type='number', registry='bionty.Gene', hash='qNH4duNQv7Yki2rlogva', updated_at=2024-01-15 08:41:56 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:42:30 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:48:21 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:48:25 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:48:28 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 19149 non-validated ensembl_gene_ids: 'ENSG00000162063', 'ENSG00000162062', 'ENSG00000198951', 'ENSG00000163121', 'ENSG00000105829', 'ENSG00000081237', 'ENSG00000134153', 'ENSG00000134152', 'ENSG00000173728', 'ENSG00000035687', 'ENSG00000166961', 'ENSG00000172689', 'ENSG00000110104', 'ENSG00000179397', 'ENSG00000149506', 'ENSG00000125384', 'ENSG00000168229', 'ENSG00000183579', 'ENSG00000166548', 'ENSG00000181234', ...
✅ loaded: FeatureSet(uid='rbYnYuUQ0IZvoEBeBzkk', n=19149, type='number', registry='bionty.Gene', hash='CKLjeNBt3B8FbTigegnE', updated_at=2024-01-15 08:04:11 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 19149 non-validated ensembl_gene_ids: 'ENSG00000162063', 'ENSG00000162062', 'ENSG00000198951', 'ENSG00000163121', 'ENSG00000105829', 'ENSG00000081237', 'ENSG00000134153', 'ENSG00000134152', 'ENSG00000173728', 'ENSG00000035687', 'ENSG00000166961', 'ENSG00000172689', 'ENSG00000110104', 'ENSG00000179397', 'ENSG00000149506', 'ENSG00000125384', 'ENSG00000168229', 'ENSG00000183579', 'ENSG00000166548', 'ENSG00000181234', ...
✅ loaded: FeatureSet(uid='rbYnYuUQ0IZvoEBeBzkk', n=19149, type='number', registry='bionty.Gene', hash='CKLjeNBt3B8FbTigegnE', updated_at=2024-01-15 08:48:36 UTC, created_by_id=1)
annotating dataset 200 of 1113
✅ loaded: FeatureSet(uid='XI7g9POS6rVy5LpNtyBr', n=33784, type='number', registry='bionty.Gene', hash='iQyVIpS3b2NM0T5vfKiR', updated_at=2024-01-15 08:18:02 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 08:37:39 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:43:59 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:50:22 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 08:48:50 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 08:37:04 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSmfNtwb7z2JXF0lS7U7', n=33452, type='number', registry='bionty.Gene', hash='5jCxqPjo4OEBPABmA2TC', updated_at=2024-01-15 08:16:27 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:48:32 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:54:35 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:54:39 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 13003 non-validated ensembl_gene_ids: 'ENSG00000121410', 'ENSG00000148584', 'ENSG00000175899', 'ENSG00000166535', 'ENSG00000184389', 'ENSG00000128274', 'ENSG00000118017', 'ENSG00000081760', 'ENSG00000188984', 'ENSG00000109576', 'ENSG00000103591', 'ENSG00000115977', 'ENSG00000087884', 'ENSG00000127837', 'ENSG00000129673', 'ENSG00000131043', 'ENSG00000205002', 'ENSG00000090861', 'ENSG00000124608', 'ENSG00000157426', ...
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 13194 non-validated ensembl_gene_ids: 'ENSG00000121410', 'ENSG00000148584', 'ENSG00000175899', 'ENSG00000166535', 'ENSG00000184389', 'ENSG00000128274', 'ENSG00000081760', 'ENSG00000188984', 'ENSG00000109576', 'ENSG00000103591', 'ENSG00000115977', 'ENSG00000087884', 'ENSG00000127837', 'ENSG00000129673', 'ENSG00000131043', 'ENSG00000090861', 'ENSG00000124608', 'ENSG00000157426', 'ENSG00000149313', 'ENSG00000008311', ...
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 08:51:53 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 08:50:58 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:50:28 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:55:33 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:55:38 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:55:44 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:55:49 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:56:00 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:56:05 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:56:10 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='1q6Bb6Y1sAQOXk17GLPB', n=33178, type='number', registry='bionty.Gene', hash='CVYdOrA6H1bRgzke8eH9', updated_at=2024-01-15 08:17:32 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='hrgirrsFM5UrBy2uqZpB', n=21069, type='number', registry='bionty.Gene', hash='r2zgtMrdBUKvKDVcWL1O', updated_at=2024-01-15 08:30:15 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 08:55:27 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='eZ0mQH25SXgqjofpZk0E', n=34088, type='number', registry='bionty.Gene', hash='YCufLSczD70l408yrOq-', updated_at=2024-01-15 08:36:48 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:54:43 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:59:47 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:59:51 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 08:59:10 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='nQ51YKqBhB0ILDbanXVr', n=36503, type='number', registry='bionty.Gene', hash='xtVNbbhs3ty63qs-rwKZ', updated_at=2024-01-15 08:44:04 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MLFo2ZBXvibkOyBR9UOR', n=32922, type='number', registry='bionty.Gene', hash='2A2lU2b4wuSFwJEYynxn', updated_at=2024-01-15 08:44:30 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vs8t8QYozeuIMRUPp3Pr', n=60602, type='number', registry='bionty.Gene', hash='ndNn8HvX4z14ERuFVvC9', updated_at=2024-01-15 08:19:16 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 08:56:16 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:01:56 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:02:02 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 08:59:58 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='Wnyv7NtEFxzKpPDMzN52', n=25090, type='number', registry='bionty.Gene', hash='Y8IR1h2pCbIgVgkRaKod', updated_at=2024-01-15 08:44:36 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 08:45:09 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='1q6Bb6Y1sAQOXk17GLPB', n=33178, type='number', registry='bionty.Gene', hash='CVYdOrA6H1bRgzke8eH9', updated_at=2024-01-15 08:58:15 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='7bByOf9OLV0FmGYJQHsM', n=17985, type='number', registry='bionty.Gene', hash='ndk2sUwm_Yixh-QM6k2v', updated_at=2024-01-15 08:36:37 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='NDEvxx6xwstARjkqRxmO', n=57717, type='number', registry='bionty.Gene', hash='ZwbMidUCZMGy-SL-F2t8', updated_at=2024-01-15 08:48:56 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:02:07 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:04:43 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:04:48 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:04:54 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='Wnyv7NtEFxzKpPDMzN52', n=25090, type='number', registry='bionty.Gene', hash='Y8IR1h2pCbIgVgkRaKod', updated_at=2024-01-15 09:03:03 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 08:55:24 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 09:03:14 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 09:05:59 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSmfNtwb7z2JXF0lS7U7', n=33452, type='number', registry='bionty.Gene', hash='5jCxqPjo4OEBPABmA2TC', updated_at=2024-01-15 08:52:32 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='7bByOf9OLV0FmGYJQHsM', n=17985, type='number', registry='bionty.Gene', hash='ndk2sUwm_Yixh-QM6k2v', updated_at=2024-01-15 09:03:38 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:02:19 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:08:12 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='eZ0mQH25SXgqjofpZk0E', n=34088, type='number', registry='bionty.Gene', hash='YCufLSczD70l408yrOq-', updated_at=2024-01-15 08:59:13 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 08:59:55 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 09:08:27 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 12555 non-validated ensembl_gene_ids: 'ENSG00000148584', 'ENSG00000175899', 'ENSG00000166535', 'ENSG00000184389', 'ENSG00000128274', 'ENSG00000081760', 'ENSG00000188984', 'ENSG00000109576', 'ENSG00000103591', 'ENSG00000115977', 'ENSG00000087884', 'ENSG00000127837', 'ENSG00000129673', 'ENSG00000131043', 'ENSG00000205002', 'ENSG00000090861', 'ENSG00000124608', 'ENSG00000157426', 'ENSG00000149313', 'ENSG00000008311', ...
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 09:05:49 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 09:09:20 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 08:37:12 UTC, created_by_id=1)
annotating dataset 300 of 1113
✅ loaded: FeatureSet(uid='nQ51YKqBhB0ILDbanXVr', n=36503, type='number', registry='bionty.Gene', hash='xtVNbbhs3ty63qs-rwKZ', updated_at=2024-01-15 09:00:05 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='fu1QNLhxofpI7ogRyLmk', n=28590, type='number', registry='bionty.Gene', hash='dIdZSLH_fsEHq1zk-uoI', updated_at=2024-01-15 08:37:27 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:04:59 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:10:45 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 09:09:34 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 09:13:39 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='1q6Bb6Y1sAQOXk17GLPB', n=33178, type='number', registry='bionty.Gene', hash='CVYdOrA6H1bRgzke8eH9', updated_at=2024-01-15 09:03:31 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='1q6Bb6Y1sAQOXk17GLPB', n=33178, type='number', registry='bionty.Gene', hash='CVYdOrA6H1bRgzke8eH9', updated_at=2024-01-15 09:13:51 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:08:16 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:14:28 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 09:08:31 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 09:14:36 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 09:14:40 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 09:14:43 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 09:13:48 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='OtcZlqF2wTYJ3nVaSD2C', n=27345, type='number', registry='bionty.Gene', hash='fjvAeV_nR2DDy2qfDoDM', updated_at=2024-01-15 08:30:06 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:14:33 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='IUwxKgaQzZ7pEwDA2h2Y', n=32870, type='number', registry='bionty.Gene', hash='2B70wf2vWmVtlM-jxAt_', updated_at=2024-01-15 08:43:20 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:10:51 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:16:20 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:16:26 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 09:09:27 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 09:06:11 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='7bByOf9OLV0FmGYJQHsM', n=17985, type='number', registry='bionty.Gene', hash='ndk2sUwm_Yixh-QM6k2v', updated_at=2024-01-15 09:07:47 UTC, created_by_id=1)
✅ loaded 33221 Gene records matching ensembl_gene_id: 'ENSG00000204381', 'ENSG00000095059', 'ENSG00000172638', 'ENSG00000198369', 'ENSG00000259417', 'ENSG00000281248', 'ENSG00000228787', 'ENSG00000253982', 'ENSG00000186298', 'ENSG00000239482', 'ENSG00000172346', 'ENSG00000240211', 'ENSG00000136834', 'ENSG00000152518', 'ENSG00000260011', 'ENSG00000237914', 'ENSG00000167394', 'ENSG00000249152', 'ENSG00000182447', 'ENSG00000248746', ...
❗ did not create Gene records for 7 non-validated ensembl_gene_ids: 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 7 Gene records matching ensembl_gene_id: 'ENSSASG00005000007', 'ENSSASG00005000010', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000009', 'ENSSASG00005000006', 'ENSSASG00005000008'
❗ did not create Gene records for 33221 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='gwSVPQJp7nujJg8qV8MG', n=30666, type='number', registry='bionty.Gene', hash='C-5IHu9bL0i5zdi3f6IM', updated_at=2024-01-15 09:07:52 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 09:14:47 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 09:20:10 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 19149 non-validated ensembl_gene_ids: 'ENSG00000162063', 'ENSG00000162062', 'ENSG00000198951', 'ENSG00000163121', 'ENSG00000105829', 'ENSG00000081237', 'ENSG00000134153', 'ENSG00000134152', 'ENSG00000173728', 'ENSG00000035687', 'ENSG00000166961', 'ENSG00000172689', 'ENSG00000110104', 'ENSG00000179397', 'ENSG00000149506', 'ENSG00000125384', 'ENSG00000168229', 'ENSG00000183579', 'ENSG00000166548', 'ENSG00000181234', ...
✅ loaded: FeatureSet(uid='rbYnYuUQ0IZvoEBeBzkk', n=19149, type='number', registry='bionty.Gene', hash='CKLjeNBt3B8FbTigegnE', updated_at=2024-01-15 08:48:41 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MLFo2ZBXvibkOyBR9UOR', n=32922, type='number', registry='bionty.Gene', hash='2A2lU2b4wuSFwJEYynxn', updated_at=2024-01-15 09:00:09 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 09:17:15 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 09:20:27 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 09:16:02 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='nQ51YKqBhB0ILDbanXVr', n=36503, type='number', registry='bionty.Gene', hash='xtVNbbhs3ty63qs-rwKZ', updated_at=2024-01-15 09:09:38 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:16:32 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:20:56 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:21:02 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='gwSVPQJp7nujJg8qV8MG', n=30666, type='number', registry='bionty.Gene', hash='C-5IHu9bL0i5zdi3f6IM', updated_at=2024-01-15 09:19:31 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:16:10 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:21:15 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:21:44 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='hrgirrsFM5UrBy2uqZpB', n=21069, type='number', registry='bionty.Gene', hash='r2zgtMrdBUKvKDVcWL1O', updated_at=2024-01-15 08:58:39 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='raT5X81gwJTAVJCLf4Vy', n=32826, type='number', registry='bionty.Gene', hash='QhlSiI1A7kijxjwi55do', updated_at=2024-01-15 08:36:41 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 09:20:13 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 12545 non-validated ensembl_gene_ids: 'ENSG00000121410', 'ENSG00000175899', 'ENSG00000166535', 'ENSG00000184389', 'ENSG00000128274', 'ENSG00000081760', 'ENSG00000188984', 'ENSG00000109576', 'ENSG00000103591', 'ENSG00000115977', 'ENSG00000087884', 'ENSG00000127837', 'ENSG00000129673', 'ENSG00000131043', 'ENSG00000090861', 'ENSG00000124608', 'ENSG00000157426', 'ENSG00000149313', 'ENSG00000008311', 'ENSG00000275700', ...
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 09:20:39 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 09:24:33 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 09:20:46 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 09:25:25 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:23:39 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='nQ51YKqBhB0ILDbanXVr', n=36503, type='number', registry='bionty.Gene', hash='xtVNbbhs3ty63qs-rwKZ', updated_at=2024-01-15 09:20:50 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:21:07 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:25:47 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:25:54 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='Wnyv7NtEFxzKpPDMzN52', n=25090, type='number', registry='bionty.Gene', hash='Y8IR1h2pCbIgVgkRaKod', updated_at=2024-01-15 09:05:42 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='nQ51YKqBhB0ILDbanXVr', n=36503, type='number', registry='bionty.Gene', hash='xtVNbbhs3ty63qs-rwKZ', updated_at=2024-01-15 09:25:41 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 09:17:25 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='7bByOf9OLV0FmGYJQHsM', n=17985, type='number', registry='bionty.Gene', hash='ndk2sUwm_Yixh-QM6k2v', updated_at=2024-01-15 09:18:43 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='raT5X81gwJTAVJCLf4Vy', n=32826, type='number', registry='bionty.Gene', hash='QhlSiI1A7kijxjwi55do', updated_at=2024-01-15 09:23:48 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 09:24:13 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:25:37 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='qVXNacutwIepiNrQ6naX', n=19782, type='number', registry='bionty.Gene', hash='aKVwTNpn9O6MlImFDi8s', updated_at=2024-01-15 09:00:13 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='IUwxKgaQzZ7pEwDA2h2Y', n=32870, type='number', registry='bionty.Gene', hash='2B70wf2vWmVtlM-jxAt_', updated_at=2024-01-15 09:16:14 UTC, created_by_id=1)
annotating dataset 400 of 1113
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:25:59 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:30:54 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:30:59 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:31:06 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:31:12 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 12871 non-validated ensembl_gene_ids: 'ENSG00000175899', 'ENSG00000166535', 'ENSG00000184389', 'ENSG00000128274', 'ENSG00000081760', 'ENSG00000188984', 'ENSG00000109576', 'ENSG00000103591', 'ENSG00000115977', 'ENSG00000087884', 'ENSG00000127837', 'ENSG00000129673', 'ENSG00000131043', 'ENSG00000090861', 'ENSG00000124608', 'ENSG00000157426', 'ENSG00000149313', 'ENSG00000008311', 'ENSG00000275700', 'ENSG00000181409', ...
✅ loaded: FeatureSet(uid='gwSVPQJp7nujJg8qV8MG', n=30666, type='number', registry='bionty.Gene', hash='C-5IHu9bL0i5zdi3f6IM', updated_at=2024-01-15 09:21:11 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='gwSVPQJp7nujJg8qV8MG', n=30666, type='number', registry='bionty.Gene', hash='C-5IHu9bL0i5zdi3f6IM', updated_at=2024-01-15 09:31:40 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 09:25:18 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 09:27:33 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='1q6Bb6Y1sAQOXk17GLPB', n=33178, type='number', registry='bionty.Gene', hash='CVYdOrA6H1bRgzke8eH9', updated_at=2024-01-15 09:13:58 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 09:29:56 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 19149 non-validated ensembl_gene_ids: 'ENSG00000162063', 'ENSG00000162062', 'ENSG00000198951', 'ENSG00000163121', 'ENSG00000105829', 'ENSG00000081237', 'ENSG00000134153', 'ENSG00000134152', 'ENSG00000173728', 'ENSG00000035687', 'ENSG00000166961', 'ENSG00000172689', 'ENSG00000110104', 'ENSG00000179397', 'ENSG00000149506', 'ENSG00000125384', 'ENSG00000168229', 'ENSG00000183579', 'ENSG00000166548', 'ENSG00000181234', ...
✅ loaded: FeatureSet(uid='rbYnYuUQ0IZvoEBeBzkk', n=19149, type='number', registry='bionty.Gene', hash='CKLjeNBt3B8FbTigegnE', updated_at=2024-01-15 09:20:17 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='XI7g9POS6rVy5LpNtyBr', n=33784, type='number', registry='bionty.Gene', hash='iQyVIpS3b2NM0T5vfKiR', updated_at=2024-01-15 08:48:46 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:30:40 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='nQ51YKqBhB0ILDbanXVr', n=36503, type='number', registry='bionty.Gene', hash='xtVNbbhs3ty63qs-rwKZ', updated_at=2024-01-15 09:27:23 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:35:09 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='IUwxKgaQzZ7pEwDA2h2Y', n=32870, type='number', registry='bionty.Gene', hash='2B70wf2vWmVtlM-jxAt_', updated_at=2024-01-15 09:30:47 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MLFo2ZBXvibkOyBR9UOR', n=32922, type='number', registry='bionty.Gene', hash='2A2lU2b4wuSFwJEYynxn', updated_at=2024-01-15 09:20:22 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:35:27 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:36:09 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:36:42 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MLFo2ZBXvibkOyBR9UOR', n=32922, type='number', registry='bionty.Gene', hash='2A2lU2b4wuSFwJEYynxn', updated_at=2024-01-15 09:35:36 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 09:32:43 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 09:32:52 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 09:37:47 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='1q6Bb6Y1sAQOXk17GLPB', n=33178, type='number', registry='bionty.Gene', hash='CVYdOrA6H1bRgzke8eH9', updated_at=2024-01-15 09:34:10 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='hrgirrsFM5UrBy2uqZpB', n=21069, type='number', registry='bionty.Gene', hash='r2zgtMrdBUKvKDVcWL1O', updated_at=2024-01-15 09:23:43 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='mlt8Tz3VeDs7InXyvkwV', n=60452, type='number', registry='bionty.Gene', hash='qNH4duNQv7Yki2rlogva', updated_at=2024-01-15 08:48:18 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 09:34:53 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 09:39:14 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 09:39:17 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='XI7g9POS6rVy5LpNtyBr', n=33784, type='number', registry='bionty.Gene', hash='iQyVIpS3b2NM0T5vfKiR', updated_at=2024-01-15 09:35:02 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:31:17 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:39:59 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:40:05 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:40:12 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='gwSVPQJp7nujJg8qV8MG', n=30666, type='number', registry='bionty.Gene', hash='C-5IHu9bL0i5zdi3f6IM', updated_at=2024-01-15 09:31:45 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='gwSVPQJp7nujJg8qV8MG', n=30666, type='number', registry='bionty.Gene', hash='C-5IHu9bL0i5zdi3f6IM', updated_at=2024-01-15 09:40:22 UTC, created_by_id=1)
✅ loaded 40995 Gene records matching ensembl_gene_id: 'ENSMUSG00000035722', 'ENSMUSG00000105265', 'ENSMUSG00000042976', 'ENSMUSG00000060904', 'ENSMUSG00000108523', 'ENSMUSG00000088318', 'ENSMUSG00000029684', 'ENSMUSG00000048794', 'ENSMUSG00000048031', 'ENSMUSG00000092323', 'ENSMUSG00000078886', 'ENSMUSG00000026077', 'ENSMUSG00000114130', 'ENSMUSG00000027330', 'ENSMUSG00000118421', 'ENSMUSG00000065340', 'ENSMUSG00000114588', 'ENSMUSG00000061022', 'ENSMUSG00000013584', 'ENSMUSG00000081459', ...
❗ did not create Gene records for 85 non-validated ensembl_gene_ids: 'ERCC-00002', 'ERCC-00003', 'ERCC-00004', 'ERCC-00009', 'ERCC-00012', 'ERCC-00013', 'ERCC-00014', 'ERCC-00016', 'ERCC-00019', 'ERCC-00022', 'ERCC-00024', 'ERCC-00025', 'ERCC-00028', 'ERCC-00031', 'ERCC-00033', 'ERCC-00034', 'ERCC-00035', 'ERCC-00039', 'ERCC-00040', 'ERCC-00041', ...
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 85 Gene records matching ensembl_gene_id: 'ERCC-00170', 'ERCC-00092', 'ERCC-00042', 'ERCC-00062', 'ERCC-00130', 'ERCC-00044', 'ERCC-00136', 'ERCC-00164', 'ERCC-00079', 'ERCC-00054', 'ERCC-00076', 'ERCC-00137', 'ERCC-00168', 'ERCC-00163', 'ERCC-00067', 'ERCC-00077', 'ERCC-00081', 'ERCC-00144', 'ERCC-00025', 'ERCC-00031', ...
❗ did not create Gene records for 40995 non-validated ensembl_gene_ids: 'ENSMUSG00000000001', 'ENSMUSG00000000003', 'ENSMUSG00000000028', 'ENSMUSG00000000031', 'ENSMUSG00000000037', 'ENSMUSG00000000049', 'ENSMUSG00000000056', 'ENSMUSG00000000058', 'ENSMUSG00000000078', 'ENSMUSG00000000085', 'ENSMUSG00000000088', 'ENSMUSG00000000093', 'ENSMUSG00000000094', 'ENSMUSG00000000103', 'ENSMUSG00000000120', 'ENSMUSG00000000125', 'ENSMUSG00000000126', 'ENSMUSG00000000127', 'ENSMUSG00000000131', 'ENSMUSG00000000134', ...
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 09:37:37 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 09:37:57 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSmfNtwb7z2JXF0lS7U7', n=33452, type='number', registry='bionty.Gene', hash='5jCxqPjo4OEBPABmA2TC', updated_at=2024-01-15 09:06:43 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='qztydaKUhnRp4zHzXUXd', n=30933, type='number', registry='bionty.Gene', hash='bMTbQNmrQxHwjX4k3XGh', updated_at=2024-01-15 08:47:07 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='hrgirrsFM5UrBy2uqZpB', n=21069, type='number', registry='bionty.Gene', hash='r2zgtMrdBUKvKDVcWL1O', updated_at=2024-01-15 09:39:05 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:37:08 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:44:49 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='eZ0mQH25SXgqjofpZk0E', n=34088, type='number', registry='bionty.Gene', hash='YCufLSczD70l408yrOq-', updated_at=2024-01-15 09:08:23 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 09:39:21 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 09:45:03 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:44:54 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 09:25:31 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:45:33 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='gNobLQdZ7eZLJdAorgpT', n=34535, type='number', registry='bionty.Gene', hash='MedmqGl6jXsdR0gE2Ha2', updated_at=2024-01-15 08:13:49 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='qztydaKUhnRp4zHzXUXd', n=30933, type='number', registry='bionty.Gene', hash='bMTbQNmrQxHwjX4k3XGh', updated_at=2024-01-15 09:43:47 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:45:46 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:40:18 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:46:14 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:46:20 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='qztydaKUhnRp4zHzXUXd', n=30933, type='number', registry='bionty.Gene', hash='bMTbQNmrQxHwjX4k3XGh', updated_at=2024-01-15 09:46:01 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='1q6Bb6Y1sAQOXk17GLPB', n=33178, type='number', registry='bionty.Gene', hash='CVYdOrA6H1bRgzke8eH9', updated_at=2024-01-15 09:39:02 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='7bByOf9OLV0FmGYJQHsM', n=17985, type='number', registry='bionty.Gene', hash='ndk2sUwm_Yixh-QM6k2v', updated_at=2024-01-15 09:29:21 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='7bByOf9OLV0FmGYJQHsM', n=17985, type='number', registry='bionty.Gene', hash='ndk2sUwm_Yixh-QM6k2v', updated_at=2024-01-15 09:49:31 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:46:05 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 09:45:06 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 09:50:13 UTC, created_by_id=1)
annotating dataset 500 of 1113
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 09:42:10 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='nQ51YKqBhB0ILDbanXVr', n=36503, type='number', registry='bionty.Gene', hash='xtVNbbhs3ty63qs-rwKZ', updated_at=2024-01-15 09:35:14 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='NDEvxx6xwstARjkqRxmO', n=57717, type='number', registry='bionty.Gene', hash='ZwbMidUCZMGy-SL-F2t8', updated_at=2024-01-15 09:04:38 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:49:39 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vs8t8QYozeuIMRUPp3Pr', n=60602, type='number', registry='bionty.Gene', hash='ndNn8HvX4z14ERuFVvC9', updated_at=2024-01-15 09:00:40 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:46:24 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:52:48 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MLFo2ZBXvibkOyBR9UOR', n=32922, type='number', registry='bionty.Gene', hash='2A2lU2b4wuSFwJEYynxn', updated_at=2024-01-15 09:37:34 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSmfNtwb7z2JXF0lS7U7', n=33452, type='number', registry='bionty.Gene', hash='5jCxqPjo4OEBPABmA2TC', updated_at=2024-01-15 09:42:42 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='1q6Bb6Y1sAQOXk17GLPB', n=33178, type='number', registry='bionty.Gene', hash='CVYdOrA6H1bRgzke8eH9', updated_at=2024-01-15 09:49:27 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='1q6Bb6Y1sAQOXk17GLPB', n=33178, type='number', registry='bionty.Gene', hash='CVYdOrA6H1bRgzke8eH9', updated_at=2024-01-15 09:55:23 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:52:36 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='raT5X81gwJTAVJCLf4Vy', n=32826, type='number', registry='bionty.Gene', hash='QhlSiI1A7kijxjwi55do', updated_at=2024-01-15 09:29:24 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 09:50:22 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 09:51:05 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 09:55:46 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:55:33 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 09:45:41 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 09:56:02 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 09:56:09 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='nQ51YKqBhB0ILDbanXVr', n=36503, type='number', registry='bionty.Gene', hash='xtVNbbhs3ty63qs-rwKZ', updated_at=2024-01-15 09:51:10 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='zpknfmQlZdBKakhMtbpD', n=27574, type='number', registry='bionty.Gene', hash='1zlsddzUI1DxB7sMb7aP', updated_at=2024-01-15 08:18:48 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vs8t8QYozeuIMRUPp3Pr', n=60602, type='number', registry='bionty.Gene', hash='ndNn8HvX4z14ERuFVvC9', updated_at=2024-01-15 09:52:41 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:52:53 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:57:16 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:57:22 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:57:27 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='gwSVPQJp7nujJg8qV8MG', n=30666, type='number', registry='bionty.Gene', hash='C-5IHu9bL0i5zdi3f6IM', updated_at=2024-01-15 09:40:25 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MLFo2ZBXvibkOyBR9UOR', n=32922, type='number', registry='bionty.Gene', hash='2A2lU2b4wuSFwJEYynxn', updated_at=2024-01-15 09:53:51 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 09:55:50 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='McgFD29PHhYholoLyR4k', n=32828, type='number', registry='bionty.Gene', hash='ARCLDKhnI4gX1pJ_bBCH', updated_at=2024-01-15 08:21:21 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSmfNtwb7z2JXF0lS7U7', n=33452, type='number', registry='bionty.Gene', hash='5jCxqPjo4OEBPABmA2TC', updated_at=2024-01-15 09:54:05 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 09:55:55 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:00:11 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:00:16 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='NDEvxx6xwstARjkqRxmO', n=57717, type='number', registry='bionty.Gene', hash='ZwbMidUCZMGy-SL-F2t8', updated_at=2024-01-15 09:52:32 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='iumqrwHQSN4Zl01GrBFZ', n=19298, type='number', registry='bionty.Gene', hash='mB95Lu3kL2FbUmAXcADa', updated_at=2024-01-15 08:50:31 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 09:57:33 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:01:37 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:01:42 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='Wnyv7NtEFxzKpPDMzN52', n=25090, type='number', registry='bionty.Gene', hash='Y8IR1h2pCbIgVgkRaKod', updated_at=2024-01-15 09:26:48 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 09:57:48 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='nQ51YKqBhB0ILDbanXVr', n=36503, type='number', registry='bionty.Gene', hash='xtVNbbhs3ty63qs-rwKZ', updated_at=2024-01-15 09:56:20 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 09:42:21 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='b0ZrJY5hy4EPHqCA7d9p', n=37073, type='number', registry='bionty.Gene', hash='_CRP0gN53PfyaubI4Piw', updated_at=2024-01-15 08:14:18 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='qztydaKUhnRp4zHzXUXd', n=30933, type='number', registry='bionty.Gene', hash='bMTbQNmrQxHwjX4k3XGh', updated_at=2024-01-15 09:48:14 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='QQjhZ67Kjz2k0t3WE2OB', n=19492, type='number', registry='bionty.Gene', hash='umcQPNUERZ7V2Gu2lQoT', updated_at=2024-01-15 08:40:33 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 09:56:16 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='hrgirrsFM5UrBy2uqZpB', n=21069, type='number', registry='bionty.Gene', hash='r2zgtMrdBUKvKDVcWL1O', updated_at=2024-01-15 09:44:18 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:01:22 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 09:55:39 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 13556 non-validated ensembl_gene_ids: 'ENSG00000121410', 'ENSG00000148584', 'ENSG00000175899', 'ENSG00000166535', 'ENSG00000184389', 'ENSG00000128274', 'ENSG00000118017', 'ENSG00000081760', 'ENSG00000188984', 'ENSG00000109576', 'ENSG00000103591', 'ENSG00000115977', 'ENSG00000087884', 'ENSG00000127837', 'ENSG00000129673', 'ENSG00000131043', 'ENSG00000205002', 'ENSG00000090861', 'ENSG00000124608', 'ENSG00000157426', ...
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 13385 non-validated ensembl_gene_ids: 'ENSG00000121410', 'ENSG00000148584', 'ENSG00000175899', 'ENSG00000166535', 'ENSG00000184389', 'ENSG00000128274', 'ENSG00000081760', 'ENSG00000188984', 'ENSG00000109576', 'ENSG00000103591', 'ENSG00000115977', 'ENSG00000087884', 'ENSG00000127837', 'ENSG00000129673', 'ENSG00000131043', 'ENSG00000090861', 'ENSG00000124608', 'ENSG00000157426', 'ENSG00000149313', 'ENSG00000008311', ...
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 10:02:02 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 10:06:21 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='qztydaKUhnRp4zHzXUXd', n=30933, type='number', registry='bionty.Gene', hash='bMTbQNmrQxHwjX4k3XGh', updated_at=2024-01-15 10:03:03 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:01:49 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:06:45 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 10:06:25 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 10:02:19 UTC, created_by_id=1)
✅ loaded 15589 Gene records matching ensembl_gene_id: 'ENSG00000135365', 'ENSG00000278616', 'ENSG00000105401', 'ENSG00000116793', 'ENSG00000136383', 'ENSG00000170323', 'ENSG00000136942', 'ENSG00000006747', 'ENSG00000164209', 'ENSG00000172409', 'ENSG00000143543', 'ENSG00000132464', 'ENSG00000159314', 'ENSG00000173349', 'ENSG00000166148', 'ENSG00000104863', 'ENSG00000135525', 'ENSG00000124256', 'ENSG00000244694', 'ENSG00000196378', ...
❗ did not create Gene records for 81 non-validated ensembl_gene_ids: 'ERCC-00002', 'ERCC-00003', 'ERCC-00004', 'ERCC-00009', 'ERCC-00013', 'ERCC-00014', 'ERCC-00016', 'ERCC-00019', 'ERCC-00022', 'ERCC-00025', 'ERCC-00028', 'ERCC-00031', 'ERCC-00033', 'ERCC-00034', 'ERCC-00035', 'ERCC-00039', 'ERCC-00040', 'ERCC-00041', 'ERCC-00042', 'ERCC-00043', ...
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 81 Gene records matching ensembl_gene_id: 'ERCC-00028', 'ERCC-00168', 'ERCC-00067', 'ERCC-00171', 'ERCC-00130', 'ERCC-00043', 'ERCC-00013', 'ERCC-00085', 'ERCC-00126', 'ERCC-00041', 'ERCC-00034', 'ERCC-00078', 'ERCC-00016', 'ERCC-00095', 'ERCC-00022', 'ERCC-00147', 'ERCC-00039', 'ERCC-00164', 'ERCC-00123', 'ERCC-00062', ...
❗ did not create Gene records for 15589 non-validated ensembl_gene_ids: 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', 'ENSG00000002079', 'ENSG00000002330', ...
✅ loaded: FeatureSet(uid='0Wuzx4VIEIS0s23O4Vs8', n=21757, type='number', registry='bionty.Gene', hash='yUbyuSoQ6nlFbZi-IZLo', updated_at=2024-01-15 08:47:43 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='raT5X81gwJTAVJCLf4Vy', n=32826, type='number', registry='bionty.Gene', hash='QhlSiI1A7kijxjwi55do', updated_at=2024-01-15 09:55:36 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:04:29 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 10:05:04 UTC, created_by_id=1)
annotating dataset 600 of 1113
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 13853 non-validated ensembl_gene_ids: 'ENSG00000121410', 'ENSG00000148584', 'ENSG00000175899', 'ENSG00000166535', 'ENSG00000184389', 'ENSG00000128274', 'ENSG00000118017', 'ENSG00000081760', 'ENSG00000188984', 'ENSG00000109576', 'ENSG00000103591', 'ENSG00000115977', 'ENSG00000087884', 'ENSG00000127837', 'ENSG00000129673', 'ENSG00000131043', 'ENSG00000205002', 'ENSG00000090861', 'ENSG00000124608', 'ENSG00000157426', ...
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 12648 non-validated ensembl_gene_ids: 'ENSG00000121410', 'ENSG00000175899', 'ENSG00000166535', 'ENSG00000184389', 'ENSG00000128274', 'ENSG00000081760', 'ENSG00000188984', 'ENSG00000109576', 'ENSG00000103591', 'ENSG00000115977', 'ENSG00000087884', 'ENSG00000127837', 'ENSG00000129673', 'ENSG00000131043', 'ENSG00000205002', 'ENSG00000090861', 'ENSG00000124608', 'ENSG00000157426', 'ENSG00000149313', 'ENSG00000008311', ...
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:10:34 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MLFo2ZBXvibkOyBR9UOR', n=32922, type='number', registry='bionty.Gene', hash='2A2lU2b4wuSFwJEYynxn', updated_at=2024-01-15 09:57:41 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='gNobLQdZ7eZLJdAorgpT', n=34535, type='number', registry='bionty.Gene', hash='MedmqGl6jXsdR0gE2Ha2', updated_at=2024-01-15 09:45:56 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='Tz1PoCZDpgrdCSjdHenJ', n=25701, type='number', registry='bionty.Gene', hash='ONgbQ6_P8jDMwpxZ2kz4', updated_at=2024-01-15 08:18:33 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='IUwxKgaQzZ7pEwDA2h2Y', n=32870, type='number', registry='bionty.Gene', hash='2B70wf2vWmVtlM-jxAt_', updated_at=2024-01-15 09:35:32 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:06:51 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:12:18 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:12:26 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:11:22 UTC, created_by_id=1)
✅ loaded 40995 Gene records matching ensembl_gene_id: 'ENSMUSG00000035722', 'ENSMUSG00000105265', 'ENSMUSG00000042976', 'ENSMUSG00000060904', 'ENSMUSG00000108523', 'ENSMUSG00000088318', 'ENSMUSG00000029684', 'ENSMUSG00000048794', 'ENSMUSG00000048031', 'ENSMUSG00000092323', 'ENSMUSG00000078886', 'ENSMUSG00000026077', 'ENSMUSG00000114130', 'ENSMUSG00000027330', 'ENSMUSG00000118421', 'ENSMUSG00000065340', 'ENSMUSG00000114588', 'ENSMUSG00000061022', 'ENSMUSG00000013584', 'ENSMUSG00000081459', ...
❗ did not create Gene records for 85 non-validated ensembl_gene_ids: 'ERCC-00002', 'ERCC-00003', 'ERCC-00004', 'ERCC-00009', 'ERCC-00012', 'ERCC-00013', 'ERCC-00014', 'ERCC-00016', 'ERCC-00019', 'ERCC-00022', 'ERCC-00024', 'ERCC-00025', 'ERCC-00028', 'ERCC-00031', 'ERCC-00033', 'ERCC-00034', 'ERCC-00035', 'ERCC-00039', 'ERCC-00040', 'ERCC-00041', ...
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 85 Gene records matching ensembl_gene_id: 'ERCC-00170', 'ERCC-00092', 'ERCC-00042', 'ERCC-00062', 'ERCC-00130', 'ERCC-00044', 'ERCC-00136', 'ERCC-00164', 'ERCC-00079', 'ERCC-00054', 'ERCC-00076', 'ERCC-00137', 'ERCC-00168', 'ERCC-00163', 'ERCC-00067', 'ERCC-00077', 'ERCC-00081', 'ERCC-00144', 'ERCC-00025', 'ERCC-00031', ...
❗ did not create Gene records for 40995 non-validated ensembl_gene_ids: 'ENSMUSG00000000001', 'ENSMUSG00000000003', 'ENSMUSG00000000028', 'ENSMUSG00000000031', 'ENSMUSG00000000037', 'ENSMUSG00000000049', 'ENSMUSG00000000056', 'ENSMUSG00000000058', 'ENSMUSG00000000078', 'ENSMUSG00000000085', 'ENSMUSG00000000088', 'ENSMUSG00000000093', 'ENSMUSG00000000094', 'ENSMUSG00000000103', 'ENSMUSG00000000120', 'ENSMUSG00000000125', 'ENSMUSG00000000126', 'ENSMUSG00000000127', 'ENSMUSG00000000131', 'ENSMUSG00000000134', ...
✅ loaded: FeatureSet(uid='ppSDidiGvsU1yqiHw9sD', n=41080, type='number', registry='bionty.Gene', hash='3DgzAtbbsFZg_s5FG9wG', updated_at=2024-01-15 09:41:48 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 10:07:36 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 10:08:15 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='1q6Bb6Y1sAQOXk17GLPB', n=33178, type='number', registry='bionty.Gene', hash='CVYdOrA6H1bRgzke8eH9', updated_at=2024-01-15 09:55:29 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='hrgirrsFM5UrBy2uqZpB', n=21069, type='number', registry='bionty.Gene', hash='r2zgtMrdBUKvKDVcWL1O', updated_at=2024-01-15 10:03:39 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='hrgirrsFM5UrBy2uqZpB', n=21069, type='number', registry='bionty.Gene', hash='r2zgtMrdBUKvKDVcWL1O', updated_at=2024-01-15 10:14:43 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='raT5X81gwJTAVJCLf4Vy', n=32826, type='number', registry='bionty.Gene', hash='QhlSiI1A7kijxjwi55do', updated_at=2024-01-15 10:10:30 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:13:31 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:14:55 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 10:10:38 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 12513 non-validated ensembl_gene_ids: 'ENSG00000175899', 'ENSG00000166535', 'ENSG00000184389', 'ENSG00000128274', 'ENSG00000081760', 'ENSG00000188984', 'ENSG00000109576', 'ENSG00000103591', 'ENSG00000115977', 'ENSG00000087884', 'ENSG00000127837', 'ENSG00000129673', 'ENSG00000131043', 'ENSG00000090861', 'ENSG00000124608', 'ENSG00000157426', 'ENSG00000149313', 'ENSG00000008311', 'ENSG00000275700', 'ENSG00000181409', ...
✅ loaded: FeatureSet(uid='XI7g9POS6rVy5LpNtyBr', n=33784, type='number', registry='bionty.Gene', hash='iQyVIpS3b2NM0T5vfKiR', updated_at=2024-01-15 09:39:25 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='nQ51YKqBhB0ILDbanXVr', n=36503, type='number', registry='bionty.Gene', hash='xtVNbbhs3ty63qs-rwKZ', updated_at=2024-01-15 10:02:09 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 10:13:45 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='NDEvxx6xwstARjkqRxmO', n=57717, type='number', registry='bionty.Gene', hash='ZwbMidUCZMGy-SL-F2t8', updated_at=2024-01-15 10:01:28 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:12:31 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:17:09 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:17:15 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MLFo2ZBXvibkOyBR9UOR', n=32922, type='number', registry='bionty.Gene', hash='2A2lU2b4wuSFwJEYynxn', updated_at=2024-01-15 10:11:50 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 10:16:48 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 10:13:55 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='b0ZrJY5hy4EPHqCA7d9p', n=37073, type='number', registry='bionty.Gene', hash='_CRP0gN53PfyaubI4Piw', updated_at=2024-01-15 10:02:58 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 10:03:15 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='1q6Bb6Y1sAQOXk17GLPB', n=33178, type='number', registry='bionty.Gene', hash='CVYdOrA6H1bRgzke8eH9', updated_at=2024-01-15 10:14:17 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='gwSVPQJp7nujJg8qV8MG', n=30666, type='number', registry='bionty.Gene', hash='C-5IHu9bL0i5zdi3f6IM', updated_at=2024-01-15 09:57:37 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4wo5rlRD8Hc0gqX5VLtA', n=20086, type='number', registry='bionty.Gene', hash='UBYbZ3yVyPHF8mG0ZQVm', updated_at=2024-01-15 09:23:51 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 10:15:21 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 10:20:50 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 10:20:54 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 10:20:58 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 10:20:32 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='NDEvxx6xwstARjkqRxmO', n=57717, type='number', registry='bionty.Gene', hash='ZwbMidUCZMGy-SL-F2t8', updated_at=2024-01-15 10:16:53 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='HyHp0niQLqy8SwXEU0pd', n=374, type='number', registry='bionty.Gene', hash='fNqSnsimQJy1SsGdDDKa', updated_at=2024-01-15 10:17:03 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:17:23 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:21:32 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MLFo2ZBXvibkOyBR9UOR', n=32922, type='number', registry='bionty.Gene', hash='2A2lU2b4wuSFwJEYynxn', updated_at=2024-01-15 10:18:04 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yveNyxpzbtAFWc399i9N', n=56445, type='number', registry='bionty.Gene', hash='4jYWNAWDZ672T553Iiq1', updated_at=2024-01-15 09:32:04 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='5uqXu94Y96v2FEsvb70S', n=27275, type='number', registry='bionty.Gene', hash='gLFfUWtEraNOZ_e5oNkj', updated_at=2024-01-15 09:53:26 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 10:18:48 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='b0ZrJY5hy4EPHqCA7d9p', n=37073, type='number', registry='bionty.Gene', hash='_CRP0gN53PfyaubI4Piw', updated_at=2024-01-15 10:19:08 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='hrgirrsFM5UrBy2uqZpB', n=21069, type='number', registry='bionty.Gene', hash='r2zgtMrdBUKvKDVcWL1O', updated_at=2024-01-15 10:14:46 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='hrgirrsFM5UrBy2uqZpB', n=21069, type='number', registry='bionty.Gene', hash='r2zgtMrdBUKvKDVcWL1O', updated_at=2024-01-15 10:24:29 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 10:21:03 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 10:18:09 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:15:00 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 10:21:10 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 10:25:57 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='qztydaKUhnRp4zHzXUXd', n=30933, type='number', registry='bionty.Gene', hash='bMTbQNmrQxHwjX4k3XGh', updated_at=2024-01-15 10:06:29 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='IUwxKgaQzZ7pEwDA2h2Y', n=32870, type='number', registry='bionty.Gene', hash='2B70wf2vWmVtlM-jxAt_', updated_at=2024-01-15 10:12:10 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:21:38 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:26:46 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:26:51 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:26:57 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:27:03 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='WtaXbp9Tj0lccAAe3dXt', n=60185, type='number', registry='bionty.Gene', hash='7F802GqCp1wNErN-wRpx', updated_at=2024-01-15 09:46:31 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:25:49 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MLFo2ZBXvibkOyBR9UOR', n=32922, type='number', registry='bionty.Gene', hash='2A2lU2b4wuSFwJEYynxn', updated_at=2024-01-15 10:22:08 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='Wnyv7NtEFxzKpPDMzN52', n=25090, type='number', registry='bionty.Gene', hash='Y8IR1h2pCbIgVgkRaKod', updated_at=2024-01-15 10:01:54 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='Wnyv7NtEFxzKpPDMzN52', n=25090, type='number', registry='bionty.Gene', hash='Y8IR1h2pCbIgVgkRaKod', updated_at=2024-01-15 10:27:32 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:27:21 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='0Wuzx4VIEIS0s23O4Vs8', n=21757, type='number', registry='bionty.Gene', hash='yUbyuSoQ6nlFbZi-IZLo', updated_at=2024-01-15 10:10:04 UTC, created_by_id=1)
annotating dataset 700 of 1113
✅ loaded: FeatureSet(uid='eZ0mQH25SXgqjofpZk0E', n=34088, type='number', registry='bionty.Gene', hash='YCufLSczD70l408yrOq-', updated_at=2024-01-15 09:44:58 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 19149 non-validated ensembl_gene_ids: 'ENSG00000162063', 'ENSG00000162062', 'ENSG00000198951', 'ENSG00000163121', 'ENSG00000105829', 'ENSG00000081237', 'ENSG00000134153', 'ENSG00000134152', 'ENSG00000173728', 'ENSG00000035687', 'ENSG00000166961', 'ENSG00000172689', 'ENSG00000110104', 'ENSG00000179397', 'ENSG00000149506', 'ENSG00000125384', 'ENSG00000168229', 'ENSG00000183579', 'ENSG00000166548', 'ENSG00000181234', ...
✅ loaded: FeatureSet(uid='rbYnYuUQ0IZvoEBeBzkk', n=19149, type='number', registry='bionty.Gene', hash='CKLjeNBt3B8FbTigegnE', updated_at=2024-01-15 09:34:57 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 19149 non-validated ensembl_gene_ids: 'ENSG00000162063', 'ENSG00000162062', 'ENSG00000198951', 'ENSG00000163121', 'ENSG00000105829', 'ENSG00000081237', 'ENSG00000134153', 'ENSG00000134152', 'ENSG00000173728', 'ENSG00000035687', 'ENSG00000166961', 'ENSG00000172689', 'ENSG00000110104', 'ENSG00000179397', 'ENSG00000149506', 'ENSG00000125384', 'ENSG00000168229', 'ENSG00000183579', 'ENSG00000166548', 'ENSG00000181234', ...
✅ loaded: FeatureSet(uid='rbYnYuUQ0IZvoEBeBzkk', n=19149, type='number', registry='bionty.Gene', hash='CKLjeNBt3B8FbTigegnE', updated_at=2024-01-15 10:29:41 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='qztydaKUhnRp4zHzXUXd', n=30933, type='number', registry='bionty.Gene', hash='bMTbQNmrQxHwjX4k3XGh', updated_at=2024-01-15 10:26:08 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='NDEvxx6xwstARjkqRxmO', n=57717, type='number', registry='bionty.Gene', hash='ZwbMidUCZMGy-SL-F2t8', updated_at=2024-01-15 10:21:16 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='NDEvxx6xwstARjkqRxmO', n=57717, type='number', registry='bionty.Gene', hash='ZwbMidUCZMGy-SL-F2t8', updated_at=2024-01-15 10:31:03 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:27:09 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:31:14 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 10:25:46 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 10:32:00 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 10:22:28 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:29:06 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSmfNtwb7z2JXF0lS7U7', n=33452, type='number', registry='bionty.Gene', hash='5jCxqPjo4OEBPABmA2TC', updated_at=2024-01-15 09:58:30 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:32:37 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='7bByOf9OLV0FmGYJQHsM', n=17985, type='number', registry='bionty.Gene', hash='ndk2sUwm_Yixh-QM6k2v', updated_at=2024-01-15 09:49:33 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='KdRqiYa4fN3UmTnXBMFz', n=23636, type='number', registry='bionty.Gene', hash='e81n2ZeEVsGyF4WYvT6P', updated_at=2024-01-15 09:49:00 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='5s4LzmWoNtPaINt5mmiF', n=17912, type='number', registry='bionty.Gene', hash='hiYwrr1mhSrQnssuOwpR', updated_at=2024-01-15 09:34:35 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:34:17 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 10:25:39 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 10:35:07 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 10:35:10 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 13580 non-validated ensembl_gene_ids: 'ENSG00000121410', 'ENSG00000148584', 'ENSG00000175899', 'ENSG00000166535', 'ENSG00000184389', 'ENSG00000128274', 'ENSG00000118017', 'ENSG00000081760', 'ENSG00000188984', 'ENSG00000109576', 'ENSG00000103591', 'ENSG00000115977', 'ENSG00000087884', 'ENSG00000127837', 'ENSG00000129673', 'ENSG00000131043', 'ENSG00000205002', 'ENSG00000090861', 'ENSG00000124608', 'ENSG00000157426', ...
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:35:04 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 10:26:05 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 10:35:48 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:35:41 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='qztydaKUhnRp4zHzXUXd', n=30933, type='number', registry='bionty.Gene', hash='bMTbQNmrQxHwjX4k3XGh', updated_at=2024-01-15 10:30:18 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='nQ51YKqBhB0ILDbanXVr', n=36503, type='number', registry='bionty.Gene', hash='xtVNbbhs3ty63qs-rwKZ', updated_at=2024-01-15 10:16:03 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:36:00 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:31:19 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:37:06 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:37:14 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='iumqrwHQSN4Zl01GrBFZ', n=19298, type='number', registry='bionty.Gene', hash='mB95Lu3kL2FbUmAXcADa', updated_at=2024-01-15 10:01:32 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 10:32:18 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='9VDriQK8SDCA0gfn58k8', n=22865, type='number', registry='bionty.Gene', hash='MdxKLToEP64ALo8IHi-v', updated_at=2024-01-15 10:19:49 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='hrgirrsFM5UrBy2uqZpB', n=21069, type='number', registry='bionty.Gene', hash='r2zgtMrdBUKvKDVcWL1O', updated_at=2024-01-15 10:24:33 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='7bByOf9OLV0FmGYJQHsM', n=17985, type='number', registry='bionty.Gene', hash='ndk2sUwm_Yixh-QM6k2v', updated_at=2024-01-15 10:34:20 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 10:35:14 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 10:39:11 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 10:39:14 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 10:39:18 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 13178 non-validated ensembl_gene_ids: 'ENSG00000121410', 'ENSG00000148584', 'ENSG00000166535', 'ENSG00000184389', 'ENSG00000128274', 'ENSG00000081760', 'ENSG00000188984', 'ENSG00000109576', 'ENSG00000103591', 'ENSG00000115977', 'ENSG00000087884', 'ENSG00000127837', 'ENSG00000129673', 'ENSG00000131043', 'ENSG00000205002', 'ENSG00000090861', 'ENSG00000124608', 'ENSG00000157426', 'ENSG00000149313', 'ENSG00000008311', ...
✅ loaded: FeatureSet(uid='qztydaKUhnRp4zHzXUXd', n=30933, type='number', registry='bionty.Gene', hash='bMTbQNmrQxHwjX4k3XGh', updated_at=2024-01-15 10:36:04 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:37:21 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:41:17 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:41:24 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:36:58 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='Wnyv7NtEFxzKpPDMzN52', n=25090, type='number', registry='bionty.Gene', hash='Y8IR1h2pCbIgVgkRaKod', updated_at=2024-01-15 10:27:36 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 10:37:35 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MLFo2ZBXvibkOyBR9UOR', n=32922, type='number', registry='bionty.Gene', hash='2A2lU2b4wuSFwJEYynxn', updated_at=2024-01-15 10:27:28 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='qztydaKUhnRp4zHzXUXd', n=30933, type='number', registry='bionty.Gene', hash='bMTbQNmrQxHwjX4k3XGh', updated_at=2024-01-15 10:40:55 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='9VDriQK8SDCA0gfn58k8', n=22865, type='number', registry='bionty.Gene', hash='MdxKLToEP64ALo8IHi-v', updated_at=2024-01-15 10:38:31 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='1q6Bb6Y1sAQOXk17GLPB', n=33178, type='number', registry='bionty.Gene', hash='CVYdOrA6H1bRgzke8eH9', updated_at=2024-01-15 10:20:36 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='hrgirrsFM5UrBy2uqZpB', n=21069, type='number', registry='bionty.Gene', hash='r2zgtMrdBUKvKDVcWL1O', updated_at=2024-01-15 10:38:35 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='KdRqiYa4fN3UmTnXBMFz', n=23636, type='number', registry='bionty.Gene', hash='e81n2ZeEVsGyF4WYvT6P', updated_at=2024-01-15 10:34:23 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:42:52 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='eZ0mQH25SXgqjofpZk0E', n=34088, type='number', registry='bionty.Gene', hash='YCufLSczD70l408yrOq-', updated_at=2024-01-15 10:29:36 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 10:39:21 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 10:45:28 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 10:45:32 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 12593 non-validated ensembl_gene_ids: 'ENSG00000148584', 'ENSG00000175899', 'ENSG00000166535', 'ENSG00000184389', 'ENSG00000128274', 'ENSG00000118017', 'ENSG00000081760', 'ENSG00000188984', 'ENSG00000109576', 'ENSG00000103591', 'ENSG00000115977', 'ENSG00000087884', 'ENSG00000127837', 'ENSG00000129673', 'ENSG00000131043', 'ENSG00000090861', 'ENSG00000124608', 'ENSG00000157426', 'ENSG00000149313', 'ENSG00000008311', ...
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 10:35:56 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='qztydaKUhnRp4zHzXUXd', n=30933, type='number', registry='bionty.Gene', hash='bMTbQNmrQxHwjX4k3XGh', updated_at=2024-01-15 10:44:24 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='qztydaKUhnRp4zHzXUXd', n=30933, type='number', registry='bionty.Gene', hash='bMTbQNmrQxHwjX4k3XGh', updated_at=2024-01-15 10:47:06 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:41:30 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:47:15 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:47:20 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:47:25 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:47:32 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='Wnyv7NtEFxzKpPDMzN52', n=25090, type='number', registry='bionty.Gene', hash='Y8IR1h2pCbIgVgkRaKod', updated_at=2024-01-15 10:42:56 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 10:32:07 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:44:45 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 10:43:07 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 10:48:32 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 10:48:43 UTC, created_by_id=1)
annotating dataset 800 of 1113
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:48:21 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 10:45:36 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 10:50:30 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 12004 non-validated ensembl_gene_ids: 'ENSG00000166535', 'ENSG00000184389', 'ENSG00000128274', 'ENSG00000081760', 'ENSG00000188984', 'ENSG00000109576', 'ENSG00000103591', 'ENSG00000115977', 'ENSG00000087884', 'ENSG00000127837', 'ENSG00000129673', 'ENSG00000131043', 'ENSG00000090861', 'ENSG00000124608', 'ENSG00000157426', 'ENSG00000149313', 'ENSG00000008311', 'ENSG00000275700', 'ENSG00000181409', 'ENSG00000183044', ...
✅ loaded: FeatureSet(uid='9CUNhnUIBqgcXEZ5zMJ1', n=40145, type='number', registry='bionty.Gene', hash='EgWbAB2T8BbVNqo1mEee', updated_at=2024-01-15 09:14:55 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='nQ51YKqBhB0ILDbanXVr', n=36503, type='number', registry='bionty.Gene', hash='xtVNbbhs3ty63qs-rwKZ', updated_at=2024-01-15 10:36:52 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='NDEvxx6xwstARjkqRxmO', n=57717, type='number', registry='bionty.Gene', hash='ZwbMidUCZMGy-SL-F2t8', updated_at=2024-01-15 10:31:08 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:49:49 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:47:37 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:51:14 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:51:20 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:51:28 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='gwSVPQJp7nujJg8qV8MG', n=30666, type='number', registry='bionty.Gene', hash='C-5IHu9bL0i5zdi3f6IM', updated_at=2024-01-15 10:20:42 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:51:09 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 10:48:14 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='r0VTmiNBLfTAggG0jri1', n=28024, type='number', registry='bionty.Gene', hash='A5IBzn_l4ouVq17hsZNd', updated_at=2024-01-15 08:06:55 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='KNa9jc9VGQwIGLhTU0QW', n=46483, type='number', registry='bionty.Gene', hash='fEzLEhnBG1jVRwetijqw', updated_at=2024-01-15 10:54:49 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 33138 non-validated ensembl_gene_ids: 'ENSG00000121410', 'ENSG00000268895', 'ENSG00000148584', 'ENSG00000175899', 'ENSG00000245105', 'ENSG00000166535', 'ENSG00000256661', 'ENSG00000256904', 'ENSG00000256069', 'ENSG00000184389', 'ENSG00000128274', 'ENSG00000118017', 'ENSG00000265544', 'ENSG00000081760', 'ENSG00000250420', 'ENSG00000114771', 'ENSG00000188984', 'ENSG00000204518', 'ENSG00000240602', 'ENSG00000109576', ...
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 16571 non-validated ensembl_gene_ids: 'ENSG00000185220', 'ENSG00000171163', 'ENSG00000171161', 'ENSG00000175137', 'ENSG00000259823', 'ENSG00000162722', 'ENSG00000169224', 'ENSG00000162711', 'ENSG00000196418', 'ENSG00000188295', 'ENSG00000277462', 'ENSG00000153207', 'ENSG00000143653', 'ENSG00000162852', 'ENSG00000162851', 'ENSG00000185420', 'ENSG00000203666', 'ENSG00000153187', 'ENSG00000203667', 'ENSG00000121644', ...
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 15043 non-validated ensembl_gene_ids: 'ENSG00000121410', 'ENSG00000148584', 'ENSG00000175899', 'ENSG00000166535', 'ENSG00000184389', 'ENSG00000128274', 'ENSG00000118017', 'ENSG00000081760', 'ENSG00000114771', 'ENSG00000188984', 'ENSG00000204518', 'ENSG00000109576', 'ENSG00000158122', 'ENSG00000103591', 'ENSG00000115977', 'ENSG00000087884', 'ENSG00000127837', 'ENSG00000129673', 'ENSG00000131043', 'ENSG00000205002', ...
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 31985 non-validated ensembl_gene_ids: 'ENSG00000121410', 'ENSG00000268895', 'ENSG00000148584', 'ENSG00000175899', 'ENSG00000245105', 'ENSG00000166535', 'ENSG00000256661', 'ENSG00000256904', 'ENSG00000256069', 'ENSG00000184389', 'ENSG00000128274', 'ENSG00000118017', 'ENSG00000265544', 'ENSG00000081760', 'ENSG00000250420', 'ENSG00000114771', 'ENSG00000188984', 'ENSG00000204518', 'ENSG00000240602', 'ENSG00000109576', ...
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 10:52:13 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 10:50:34 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 10:52:18 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:04:26 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 10:47:01 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='zpknfmQlZdBKakhMtbpD', n=27574, type='number', registry='bionty.Gene', hash='1zlsddzUI1DxB7sMb7aP', updated_at=2024-01-15 09:56:42 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 10:51:33 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='nQ51YKqBhB0ILDbanXVr', n=36503, type='number', registry='bionty.Gene', hash='xtVNbbhs3ty63qs-rwKZ', updated_at=2024-01-15 10:50:59 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='1q6Bb6Y1sAQOXk17GLPB', n=33178, type='number', registry='bionty.Gene', hash='CVYdOrA6H1bRgzke8eH9', updated_at=2024-01-15 10:44:33 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:04:37 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='5s4LzmWoNtPaINt5mmiF', n=17912, type='number', registry='bionty.Gene', hash='hiYwrr1mhSrQnssuOwpR', updated_at=2024-01-15 10:34:59 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MVyjpOpoxSUNds1Xpk63', n=32664, type='number', registry='bionty.Gene', hash='IbnPcVCWAGQ3EKmCnzka', updated_at=2024-01-15 09:19:35 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:07:49 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:08:14 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:08:18 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:08:23 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:08:29 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:08:34 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:08:38 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:08:44 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:08:48 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:08:53 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:08:59 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MVyjpOpoxSUNds1Xpk63', n=32664, type='number', registry='bionty.Gene', hash='IbnPcVCWAGQ3EKmCnzka', updated_at=2024-01-15 11:08:09 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:09:03 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='5s4LzmWoNtPaINt5mmiF', n=17912, type='number', registry='bionty.Gene', hash='hiYwrr1mhSrQnssuOwpR', updated_at=2024-01-15 11:07:53 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:09:12 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:09:21 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:09:25 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:09:32 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:09:36 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:09:40 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:09:46 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:09:51 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:09:55 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:10:00 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='mlt8Tz3VeDs7InXyvkwV', n=60452, type='number', registry='bionty.Gene', hash='qNH4duNQv7Yki2rlogva', updated_at=2024-01-15 09:39:11 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='mlt8Tz3VeDs7InXyvkwV', n=60452, type='number', registry='bionty.Gene', hash='qNH4duNQv7Yki2rlogva', updated_at=2024-01-15 11:10:14 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='mlt8Tz3VeDs7InXyvkwV', n=60452, type='number', registry='bionty.Gene', hash='qNH4duNQv7Yki2rlogva', updated_at=2024-01-15 11:10:20 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='mlt8Tz3VeDs7InXyvkwV', n=60452, type='number', registry='bionty.Gene', hash='qNH4duNQv7Yki2rlogva', updated_at=2024-01-15 11:10:27 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='mlt8Tz3VeDs7InXyvkwV', n=60452, type='number', registry='bionty.Gene', hash='qNH4duNQv7Yki2rlogva', updated_at=2024-01-15 11:10:32 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='mlt8Tz3VeDs7InXyvkwV', n=60452, type='number', registry='bionty.Gene', hash='qNH4duNQv7Yki2rlogva', updated_at=2024-01-15 11:10:40 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='mlt8Tz3VeDs7InXyvkwV', n=60452, type='number', registry='bionty.Gene', hash='qNH4duNQv7Yki2rlogva', updated_at=2024-01-15 11:10:45 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='mlt8Tz3VeDs7InXyvkwV', n=60452, type='number', registry='bionty.Gene', hash='qNH4duNQv7Yki2rlogva', updated_at=2024-01-15 11:10:51 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='eZ0mQH25SXgqjofpZk0E', n=34088, type='number', registry='bionty.Gene', hash='YCufLSczD70l408yrOq-', updated_at=2024-01-15 10:44:49 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dmFYO2ZPmG8F5J6lOIuh', n=24185, type='number', registry='bionty.Gene', hash='hnWAHQIJP5aGHIN5peeE', updated_at=2024-01-15 08:32:34 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 11:04:29 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 11:14:10 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 11:14:13 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 11:14:17 UTC, created_by_id=1)
annotating dataset 900 of 1113
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 11:14:21 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yJkW1pbCGyfFdJ32yvbf', n=27651, type='number', registry='bionty.Gene', hash='aALn7EGvPqdoBJdhQ9QZ', updated_at=2024-01-15 11:14:25 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 19149 non-validated ensembl_gene_ids: 'ENSG00000162063', 'ENSG00000162062', 'ENSG00000198951', 'ENSG00000163121', 'ENSG00000105829', 'ENSG00000081237', 'ENSG00000134153', 'ENSG00000134152', 'ENSG00000173728', 'ENSG00000035687', 'ENSG00000166961', 'ENSG00000172689', 'ENSG00000110104', 'ENSG00000179397', 'ENSG00000149506', 'ENSG00000125384', 'ENSG00000168229', 'ENSG00000183579', 'ENSG00000166548', 'ENSG00000181234', ...
✅ loaded: FeatureSet(uid='rbYnYuUQ0IZvoEBeBzkk', n=19149, type='number', registry='bionty.Gene', hash='CKLjeNBt3B8FbTigegnE', updated_at=2024-01-15 10:30:14 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 19149 non-validated ensembl_gene_ids: 'ENSG00000162063', 'ENSG00000162062', 'ENSG00000198951', 'ENSG00000163121', 'ENSG00000105829', 'ENSG00000081237', 'ENSG00000134153', 'ENSG00000134152', 'ENSG00000173728', 'ENSG00000035687', 'ENSG00000166961', 'ENSG00000172689', 'ENSG00000110104', 'ENSG00000179397', 'ENSG00000149506', 'ENSG00000125384', 'ENSG00000168229', 'ENSG00000183579', 'ENSG00000166548', 'ENSG00000181234', ...
✅ loaded: FeatureSet(uid='rbYnYuUQ0IZvoEBeBzkk', n=19149, type='number', registry='bionty.Gene', hash='CKLjeNBt3B8FbTigegnE', updated_at=2024-01-15 11:14:32 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 19149 non-validated ensembl_gene_ids: 'ENSG00000162063', 'ENSG00000162062', 'ENSG00000198951', 'ENSG00000163121', 'ENSG00000105829', 'ENSG00000081237', 'ENSG00000134153', 'ENSG00000134152', 'ENSG00000173728', 'ENSG00000035687', 'ENSG00000166961', 'ENSG00000172689', 'ENSG00000110104', 'ENSG00000179397', 'ENSG00000149506', 'ENSG00000125384', 'ENSG00000168229', 'ENSG00000183579', 'ENSG00000166548', 'ENSG00000181234', ...
✅ loaded: FeatureSet(uid='rbYnYuUQ0IZvoEBeBzkk', n=19149, type='number', registry='bionty.Gene', hash='CKLjeNBt3B8FbTigegnE', updated_at=2024-01-15 11:14:37 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 19149 non-validated ensembl_gene_ids: 'ENSG00000162063', 'ENSG00000162062', 'ENSG00000198951', 'ENSG00000163121', 'ENSG00000105829', 'ENSG00000081237', 'ENSG00000134153', 'ENSG00000134152', 'ENSG00000173728', 'ENSG00000035687', 'ENSG00000166961', 'ENSG00000172689', 'ENSG00000110104', 'ENSG00000179397', 'ENSG00000149506', 'ENSG00000125384', 'ENSG00000168229', 'ENSG00000183579', 'ENSG00000166548', 'ENSG00000181234', ...
✅ loaded: FeatureSet(uid='rbYnYuUQ0IZvoEBeBzkk', n=19149, type='number', registry='bionty.Gene', hash='CKLjeNBt3B8FbTigegnE', updated_at=2024-01-15 11:14:42 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 19149 non-validated ensembl_gene_ids: 'ENSG00000162063', 'ENSG00000162062', 'ENSG00000198951', 'ENSG00000163121', 'ENSG00000105829', 'ENSG00000081237', 'ENSG00000134153', 'ENSG00000134152', 'ENSG00000173728', 'ENSG00000035687', 'ENSG00000166961', 'ENSG00000172689', 'ENSG00000110104', 'ENSG00000179397', 'ENSG00000149506', 'ENSG00000125384', 'ENSG00000168229', 'ENSG00000183579', 'ENSG00000166548', 'ENSG00000181234', ...
✅ loaded: FeatureSet(uid='rbYnYuUQ0IZvoEBeBzkk', n=19149, type='number', registry='bionty.Gene', hash='CKLjeNBt3B8FbTigegnE', updated_at=2024-01-15 11:14:50 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 19149 non-validated ensembl_gene_ids: 'ENSG00000162063', 'ENSG00000162062', 'ENSG00000198951', 'ENSG00000163121', 'ENSG00000105829', 'ENSG00000081237', 'ENSG00000134153', 'ENSG00000134152', 'ENSG00000173728', 'ENSG00000035687', 'ENSG00000166961', 'ENSG00000172689', 'ENSG00000110104', 'ENSG00000179397', 'ENSG00000149506', 'ENSG00000125384', 'ENSG00000168229', 'ENSG00000183579', 'ENSG00000166548', 'ENSG00000181234', ...
✅ loaded: FeatureSet(uid='rbYnYuUQ0IZvoEBeBzkk', n=19149, type='number', registry='bionty.Gene', hash='CKLjeNBt3B8FbTigegnE', updated_at=2024-01-15 11:14:56 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 19149 non-validated ensembl_gene_ids: 'ENSG00000162063', 'ENSG00000162062', 'ENSG00000198951', 'ENSG00000163121', 'ENSG00000105829', 'ENSG00000081237', 'ENSG00000134153', 'ENSG00000134152', 'ENSG00000173728', 'ENSG00000035687', 'ENSG00000166961', 'ENSG00000172689', 'ENSG00000110104', 'ENSG00000179397', 'ENSG00000149506', 'ENSG00000125384', 'ENSG00000168229', 'ENSG00000183579', 'ENSG00000166548', 'ENSG00000181234', ...
✅ loaded: FeatureSet(uid='rbYnYuUQ0IZvoEBeBzkk', n=19149, type='number', registry='bionty.Gene', hash='CKLjeNBt3B8FbTigegnE', updated_at=2024-01-15 11:15:19 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 19149 non-validated ensembl_gene_ids: 'ENSG00000162063', 'ENSG00000162062', 'ENSG00000198951', 'ENSG00000163121', 'ENSG00000105829', 'ENSG00000081237', 'ENSG00000134153', 'ENSG00000134152', 'ENSG00000173728', 'ENSG00000035687', 'ENSG00000166961', 'ENSG00000172689', 'ENSG00000110104', 'ENSG00000179397', 'ENSG00000149506', 'ENSG00000125384', 'ENSG00000168229', 'ENSG00000183579', 'ENSG00000166548', 'ENSG00000181234', ...
✅ loaded: FeatureSet(uid='rbYnYuUQ0IZvoEBeBzkk', n=19149, type='number', registry='bionty.Gene', hash='CKLjeNBt3B8FbTigegnE', updated_at=2024-01-15 11:15:35 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='9CUNhnUIBqgcXEZ5zMJ1', n=40145, type='number', registry='bionty.Gene', hash='EgWbAB2T8BbVNqo1mEee', updated_at=2024-01-15 10:50:55 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 11:04:33 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 11:16:55 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 11:17:00 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 11:17:04 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 11:17:09 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 15824 non-validated ensembl_gene_ids: 'ENSG00000008018', 'ENSG00000112584', 'ENSG00000198719', 'ENSG00000130023', 'ENSG00000184786', 'ENSG00000130024', 'ENSG00000185127', 'ENSG00000184465', 'ENSG00000186340', 'ENSG00000112562', 'ENSG00000164488', 'ENSG00000153303', 'ENSG00000130396', 'ENSG00000112494', 'ENSG00000166984', 'ENSG00000112486', 'ENSG00000213066', 'ENSG00000026297', 'ENSG00000071242', 'ENSG00000060762', ...
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 11:17:14 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='BpZnavGEUWvVDjYVSzsI', n=30534, type='number', registry='bionty.Gene', hash='lvhPbhp6AW5fSvyzyD8O', updated_at=2024-01-15 10:39:46 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='nQ51YKqBhB0ILDbanXVr', n=36503, type='number', registry='bionty.Gene', hash='xtVNbbhs3ty63qs-rwKZ', updated_at=2024-01-15 11:05:21 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='nQ51YKqBhB0ILDbanXVr', n=36503, type='number', registry='bionty.Gene', hash='xtVNbbhs3ty63qs-rwKZ', updated_at=2024-01-15 11:17:51 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 11:04:44 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='XI7g9POS6rVy5LpNtyBr', n=33784, type='number', registry='bionty.Gene', hash='iQyVIpS3b2NM0T5vfKiR', updated_at=2024-01-15 10:15:59 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:10:05 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:18:42 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:18:45 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='8fZguefWRYrPpKXNvbU4', n=30639, type='number', registry='bionty.Gene', hash='GMKfOSaOS1UZWMP4ybIR', updated_at=2024-01-15 10:03:46 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='qztydaKUhnRp4zHzXUXd', n=30933, type='number', registry='bionty.Gene', hash='bMTbQNmrQxHwjX4k3XGh', updated_at=2024-01-15 10:47:09 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MLFo2ZBXvibkOyBR9UOR', n=32922, type='number', registry='bionty.Gene', hash='2A2lU2b4wuSFwJEYynxn', updated_at=2024-01-15 10:43:11 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='NDEvxx6xwstARjkqRxmO', n=57717, type='number', registry='bionty.Gene', hash='ZwbMidUCZMGy-SL-F2t8', updated_at=2024-01-15 10:51:05 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='qVXNacutwIepiNrQ6naX', n=19782, type='number', registry='bionty.Gene', hash='aKVwTNpn9O6MlImFDi8s', updated_at=2024-01-15 09:30:44 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='qVXNacutwIepiNrQ6naX', n=19782, type='number', registry='bionty.Gene', hash='aKVwTNpn9O6MlImFDi8s', updated_at=2024-01-15 11:22:38 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='qVXNacutwIepiNrQ6naX', n=19782, type='number', registry='bionty.Gene', hash='aKVwTNpn9O6MlImFDi8s', updated_at=2024-01-15 11:22:42 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vs8t8QYozeuIMRUPp3Pr', n=60602, type='number', registry='bionty.Gene', hash='ndNn8HvX4z14ERuFVvC9', updated_at=2024-01-15 09:56:48 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vs8t8QYozeuIMRUPp3Pr', n=60602, type='number', registry='bionty.Gene', hash='ndNn8HvX4z14ERuFVvC9', updated_at=2024-01-15 11:22:50 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dmFYO2ZPmG8F5J6lOIuh', n=24185, type='number', registry='bionty.Gene', hash='hnWAHQIJP5aGHIN5peeE', updated_at=2024-01-15 11:12:18 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:04:54 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:24:37 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:24:42 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:24:48 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:24:55 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:25:00 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:25:05 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:25:11 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:25:17 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:25:22 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:25:28 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:25:33 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:25:39 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:25:44 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:25:50 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:25:54 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:26:00 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:26:06 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:26:13 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:26:18 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:26:24 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:26:30 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:26:36 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:26:42 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:26:47 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:26:53 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:26:58 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:27:04 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:27:09 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:27:15 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:27:21 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:27:26 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:27:31 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:27:36 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:27:41 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:28:05 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:28:11 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:28:17 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='K3qP78lOBD3sLXtSAmFa', n=59357, type='number', registry='bionty.Gene', hash='pKowz66xdpGZox8OCaCm', updated_at=2024-01-15 11:28:23 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MLFo2ZBXvibkOyBR9UOR', n=32922, type='number', registry='bionty.Gene', hash='2A2lU2b4wuSFwJEYynxn', updated_at=2024-01-15 11:20:59 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:18:52 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:29:44 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:29:50 UTC, created_by_id=1)
annotating dataset 1000 of 1113
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:29:54 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MLFo2ZBXvibkOyBR9UOR', n=32922, type='number', registry='bionty.Gene', hash='2A2lU2b4wuSFwJEYynxn', updated_at=2024-01-15 11:29:30 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='yveNyxpzbtAFWc399i9N', n=56445, type='number', registry='bionty.Gene', hash='4jYWNAWDZ672T553Iiq1', updated_at=2024-01-15 10:22:14 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='5uqXu94Y96v2FEsvb70S', n=27275, type='number', registry='bionty.Gene', hash='gLFfUWtEraNOZ_e5oNkj', updated_at=2024-01-15 10:22:17 UTC, created_by_id=1)
✅ loaded 40995 Gene records matching ensembl_gene_id: 'ENSMUSG00000035722', 'ENSMUSG00000105265', 'ENSMUSG00000042976', 'ENSMUSG00000060904', 'ENSMUSG00000108523', 'ENSMUSG00000088318', 'ENSMUSG00000029684', 'ENSMUSG00000048794', 'ENSMUSG00000048031', 'ENSMUSG00000092323', 'ENSMUSG00000078886', 'ENSMUSG00000026077', 'ENSMUSG00000114130', 'ENSMUSG00000027330', 'ENSMUSG00000118421', 'ENSMUSG00000065340', 'ENSMUSG00000114588', 'ENSMUSG00000061022', 'ENSMUSG00000013584', 'ENSMUSG00000081459', ...
❗ did not create Gene records for 85 non-validated ensembl_gene_ids: 'ERCC-00002', 'ERCC-00003', 'ERCC-00004', 'ERCC-00009', 'ERCC-00012', 'ERCC-00013', 'ERCC-00014', 'ERCC-00016', 'ERCC-00019', 'ERCC-00022', 'ERCC-00024', 'ERCC-00025', 'ERCC-00028', 'ERCC-00031', 'ERCC-00033', 'ERCC-00034', 'ERCC-00035', 'ERCC-00039', 'ERCC-00040', 'ERCC-00041', ...
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 85 Gene records matching ensembl_gene_id: 'ERCC-00170', 'ERCC-00092', 'ERCC-00042', 'ERCC-00062', 'ERCC-00130', 'ERCC-00044', 'ERCC-00136', 'ERCC-00164', 'ERCC-00079', 'ERCC-00054', 'ERCC-00076', 'ERCC-00137', 'ERCC-00168', 'ERCC-00163', 'ERCC-00067', 'ERCC-00077', 'ERCC-00081', 'ERCC-00144', 'ERCC-00025', 'ERCC-00031', ...
❗ did not create Gene records for 40995 non-validated ensembl_gene_ids: 'ENSMUSG00000000001', 'ENSMUSG00000000003', 'ENSMUSG00000000028', 'ENSMUSG00000000031', 'ENSMUSG00000000037', 'ENSMUSG00000000049', 'ENSMUSG00000000056', 'ENSMUSG00000000058', 'ENSMUSG00000000078', 'ENSMUSG00000000085', 'ENSMUSG00000000088', 'ENSMUSG00000000093', 'ENSMUSG00000000094', 'ENSMUSG00000000103', 'ENSMUSG00000000120', 'ENSMUSG00000000125', 'ENSMUSG00000000126', 'ENSMUSG00000000127', 'ENSMUSG00000000131', 'ENSMUSG00000000134', ...
✅ loaded: FeatureSet(uid='ppSDidiGvsU1yqiHw9sD', n=41080, type='number', registry='bionty.Gene', hash='3DgzAtbbsFZg_s5FG9wG', updated_at=2024-01-15 10:13:40 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='qztydaKUhnRp4zHzXUXd', n=30933, type='number', registry='bionty.Gene', hash='bMTbQNmrQxHwjX4k3XGh', updated_at=2024-01-15 11:19:42 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='MLFo2ZBXvibkOyBR9UOR', n=32922, type='number', registry='bionty.Gene', hash='2A2lU2b4wuSFwJEYynxn', updated_at=2024-01-15 11:33:50 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='BzUN8XuS90ts2IncDh0l', n=22447, type='number', registry='bionty.Gene', hash='vgmm8Ox-ozdHu3kaHbIE', updated_at=2024-01-15 09:11:55 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 11:17:38 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 11:34:57 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 11:35:05 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 11:35:09 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSpO6yuXCsjxtLTUmQKz', n=36517, type='number', registry='bionty.Gene', hash='3HrkUAoqY_2w7DSjc2g-', updated_at=2024-01-15 11:35:14 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='nv0cgiovC9GSrWf4xwlX', n=28121, type='number', registry='bionty.Gene', hash='M1OnUnfmsBiSVBK5GGlc', updated_at=2024-01-15 09:47:44 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 10:48:53 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 11:35:34 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 11:35:44 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 11:35:55 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 11:36:05 UTC, created_by_id=1)
✅ loaded 33234 Gene records matching ensembl_gene_id: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
❗ did not create Gene records for 10 non-validated ensembl_gene_ids: 'ENSSASG00005000004', 'ENSSASG00005000005', 'ENSSASG00005000006', 'ENSSASG00005000007', 'ENSSASG00005000008', 'ENSSASG00005000009', 'ENSSASG00005000010', 'ENSSASG00005000011', 'ENSSASG00005000012', 'ENSSASG00005000013'
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 10 Gene records matching ensembl_gene_id: 'ENSSASG00005000010', 'ENSSASG00005000007', 'ENSSASG00005000005', 'ENSSASG00005000013', 'ENSSASG00005000006', 'ENSSASG00005000011', 'ENSSASG00005000009', 'ENSSASG00005000012', 'ENSSASG00005000008', 'ENSSASG00005000004'
❗ did not create Gene records for 33234 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='PufaVjTvwxDgLMQ9Z8PL', n=33244, type='number', registry='bionty.Gene', hash='wyOT9DMFVFgLQfxQIAmo', updated_at=2024-01-15 11:36:15 UTC, created_by_id=1)
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ did not create Gene records for 15186 non-validated ensembl_gene_ids: 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001631', 'ENSG00000002016', 'ENSG00000002549', 'ENSG00000002586', 'ENSG00000002587', 'ENSG00000002726', ...
✅ loaded: FeatureSet(uid='b0ZrJY5hy4EPHqCA7d9p', n=37073, type='number', registry='bionty.Gene', hash='_CRP0gN53PfyaubI4Piw', updated_at=2024-01-15 10:23:12 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='vSmfNtwb7z2JXF0lS7U7', n=33452, type='number', registry='bionty.Gene', hash='5jCxqPjo4OEBPABmA2TC', updated_at=2024-01-15 10:32:41 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='6fP4wbyFCff3NPFdwfPJ', n=39117, type='number', registry='bionty.Gene', hash='d-9vIrthY7mOUgotmtBI', updated_at=2024-01-15 10:23:47 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='diNL86QZAzAh2N0Qw1lh', n=22697, type='number', registry='bionty.Gene', hash='trdA4nPv-KQ9xULdAr2k', updated_at=2024-01-15 09:43:52 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='diNL86QZAzAh2N0Qw1lh', n=22697, type='number', registry='bionty.Gene', hash='trdA4nPv-KQ9xULdAr2k', updated_at=2024-01-15 11:51:19 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='uvYQntZUUCHa3pHB1BMx', n=20807, type='number', registry='bionty.Gene', hash='KI-8wjQJszAiUju3lLOD', updated_at=2024-01-15 08:58:08 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='uvYQntZUUCHa3pHB1BMx', n=20807, type='number', registry='bionty.Gene', hash='KI-8wjQJszAiUju3lLOD', updated_at=2024-01-15 11:51:26 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4NUKMvkVtrhccIVqgUfG', n=27370, type='number', registry='bionty.Gene', hash='rHH550YDDJMIYbCL5ZRj', updated_at=2024-01-15 10:33:46 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4NUKMvkVtrhccIVqgUfG', n=27370, type='number', registry='bionty.Gene', hash='rHH550YDDJMIYbCL5ZRj', updated_at=2024-01-15 11:51:35 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='4NUKMvkVtrhccIVqgUfG', n=27370, type='number', registry='bionty.Gene', hash='rHH550YDDJMIYbCL5ZRj', updated_at=2024-01-15 11:51:41 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='dKaTO81QIpXdVcfR4I1J', n=58604, type='number', registry='bionty.Gene', hash='vGM2j-OZYfQ4-9KsK75K', updated_at=2024-01-15 11:18:03 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='1q6Bb6Y1sAQOXk17GLPB', n=33178, type='number', registry='bionty.Gene', hash='CVYdOrA6H1bRgzke8eH9', updated_at=2024-01-15 11:06:03 UTC, created_by_id=1)
✅ loaded 22164 Gene records matching ensembl_gene_id: 'ENSG00000113205', 'ENSG00000204381', 'ENSG00000172995', 'ENSG00000129038', 'ENSG00000207979', 'ENSG00000095059', 'ENSG00000232150', 'ENSG00000112081', 'ENSG00000172638', 'ENSG00000207782', 'ENSG00000178691', 'ENSG00000176601', 'ENSG00000198369', 'ENSG00000112308', 'ENSG00000169727', 'ENSG00000124535', 'ENSG00000117984', 'ENSG00000120963', 'ENSG00000186298', 'ENSG00000172346', ...
❗ did not create Gene records for 92 non-validated ensembl_gene_ids: 'ERCC-00002', 'ERCC-00003', 'ERCC-00004', 'ERCC-00009', 'ERCC-00012', 'ERCC-00013', 'ERCC-00014', 'ERCC-00016', 'ERCC-00017', 'ERCC-00019', 'ERCC-00022', 'ERCC-00024', 'ERCC-00025', 'ERCC-00028', 'ERCC-00031', 'ERCC-00033', 'ERCC-00034', 'ERCC-00035', 'ERCC-00039', 'ERCC-00040', ...
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
❗ no Bionty source found, skipping Bionty validation
❗ loading non-default source inside a LaminDB instance
💡 please consider:
close your instance via `lamin close` and use Bionty stand alone
OR
modify currently_used Gene source in `lnschema_bionty.PublicSource`
✅ loaded 92 Gene records matching ensembl_gene_id: 'ERCC-00097', 'ERCC-00014', 'ERCC-00012', 'ERCC-00157', 'ERCC-00034', 'ERCC-00004', 'ERCC-00165', 'ERCC-00077', 'ERCC-00147', 'ERCC-00075', 'ERCC-00016', 'ERCC-00111', 'ERCC-00067', 'ERCC-00098', 'ERCC-00150', 'ERCC-00156', 'ERCC-00168', 'ERCC-00022', 'ERCC-00044', 'ERCC-00131', ...
❗ did not create Gene records for 22164 non-validated ensembl_gene_ids: 'ENSG00000000003', 'ENSG00000000005', 'ENSG00000000419', 'ENSG00000000457', 'ENSG00000000460', 'ENSG00000000938', 'ENSG00000000971', 'ENSG00000001036', 'ENSG00000001084', 'ENSG00000001167', 'ENSG00000001460', 'ENSG00000001461', 'ENSG00000001497', 'ENSG00000001561', 'ENSG00000001617', 'ENSG00000001626', 'ENSG00000001629', 'ENSG00000001630', 'ENSG00000001631', 'ENSG00000002016', ...
✅ loaded: FeatureSet(uid='4a3TNgtW7Gqo8rjmF6To', n=33234, type='number', registry='bionty.Gene', hash='QxtBB8YlF4P9hZsWN1iG', updated_at=2024-01-15 11:33:39 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='1q6Bb6Y1sAQOXk17GLPB', n=33178, type='number', registry='bionty.Gene', hash='CVYdOrA6H1bRgzke8eH9', updated_at=2024-01-15 11:52:02 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='1q6Bb6Y1sAQOXk17GLPB', n=33178, type='number', registry='bionty.Gene', hash='CVYdOrA6H1bRgzke8eH9', updated_at=2024-01-15 11:52:43 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='1q6Bb6Y1sAQOXk17GLPB', n=33178, type='number', registry='bionty.Gene', hash='CVYdOrA6H1bRgzke8eH9', updated_at=2024-01-15 11:53:28 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='1F7qQ9oHXxohtyCgTEB1', n=30761, type='number', registry='bionty.Gene', hash='OmUhPk5yYF9888WMlYUy', updated_at=2024-01-15 08:47:13 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='0Wuzx4VIEIS0s23O4Vs8', n=21757, type='number', registry='bionty.Gene', hash='yUbyuSoQ6nlFbZi-IZLo', updated_at=2024-01-15 10:29:12 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='hrgirrsFM5UrBy2uqZpB', n=21069, type='number', registry='bionty.Gene', hash='r2zgtMrdBUKvKDVcWL1O', updated_at=2024-01-15 10:44:36 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='hrgirrsFM5UrBy2uqZpB', n=21069, type='number', registry='bionty.Gene', hash='r2zgtMrdBUKvKDVcWL1O', updated_at=2024-01-15 11:54:19 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='hrgirrsFM5UrBy2uqZpB', n=21069, type='number', registry='bionty.Gene', hash='r2zgtMrdBUKvKDVcWL1O', updated_at=2024-01-15 11:54:22 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='hrgirrsFM5UrBy2uqZpB', n=21069, type='number', registry='bionty.Gene', hash='r2zgtMrdBUKvKDVcWL1O', updated_at=2024-01-15 11:54:25 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='hrgirrsFM5UrBy2uqZpB', n=21069, type='number', registry='bionty.Gene', hash='r2zgtMrdBUKvKDVcWL1O', updated_at=2024-01-15 11:54:29 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='7bByOf9OLV0FmGYJQHsM', n=17985, type='number', registry='bionty.Gene', hash='ndk2sUwm_Yixh-QM6k2v', updated_at=2024-01-15 10:38:39 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='hrgirrsFM5UrBy2uqZpB', n=21069, type='number', registry='bionty.Gene', hash='r2zgtMrdBUKvKDVcWL1O', updated_at=2024-01-15 11:54:32 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='hrgirrsFM5UrBy2uqZpB', n=21069, type='number', registry='bionty.Gene', hash='r2zgtMrdBUKvKDVcWL1O', updated_at=2024-01-15 11:54:40 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='hrgirrsFM5UrBy2uqZpB', n=21069, type='number', registry='bionty.Gene', hash='r2zgtMrdBUKvKDVcWL1O', updated_at=2024-01-15 11:54:43 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='hrgirrsFM5UrBy2uqZpB', n=21069, type='number', registry='bionty.Gene', hash='r2zgtMrdBUKvKDVcWL1O', updated_at=2024-01-15 11:54:46 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='7bByOf9OLV0FmGYJQHsM', n=17985, type='number', registry='bionty.Gene', hash='ndk2sUwm_Yixh-QM6k2v', updated_at=2024-01-15 11:54:37 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='hrgirrsFM5UrBy2uqZpB', n=21069, type='number', registry='bionty.Gene', hash='r2zgtMrdBUKvKDVcWL1O', updated_at=2024-01-15 11:54:49 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='7bByOf9OLV0FmGYJQHsM', n=17985, type='number', registry='bionty.Gene', hash='ndk2sUwm_Yixh-QM6k2v', updated_at=2024-01-15 11:54:53 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='7bByOf9OLV0FmGYJQHsM', n=17985, type='number', registry='bionty.Gene', hash='ndk2sUwm_Yixh-QM6k2v', updated_at=2024-01-15 11:54:59 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='7bByOf9OLV0FmGYJQHsM', n=17985, type='number', registry='bionty.Gene', hash='ndk2sUwm_Yixh-QM6k2v', updated_at=2024-01-15 11:55:04 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='7bByOf9OLV0FmGYJQHsM', n=17985, type='number', registry='bionty.Gene', hash='ndk2sUwm_Yixh-QM6k2v', updated_at=2024-01-15 11:55:08 UTC, created_by_id=1)
annotating dataset 1100 of 1113
✅ loaded: FeatureSet(uid='gjfYj8LlCPnQRzVyFb4a', n=35393, type='number', registry='bionty.Gene', hash='QklnEoTGCLGInMFtdP1E', updated_at=2024-01-15 10:29:17 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='KdRqiYa4fN3UmTnXBMFz', n=23636, type='number', registry='bionty.Gene', hash='e81n2ZeEVsGyF4WYvT6P', updated_at=2024-01-15 10:44:39 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='KdRqiYa4fN3UmTnXBMFz', n=23636, type='number', registry='bionty.Gene', hash='e81n2ZeEVsGyF4WYvT6P', updated_at=2024-01-15 11:55:20 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='raT5X81gwJTAVJCLf4Vy', n=32826, type='number', registry='bionty.Gene', hash='QhlSiI1A7kijxjwi55do', updated_at=2024-01-15 10:14:50 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='raT5X81gwJTAVJCLf4Vy', n=32826, type='number', registry='bionty.Gene', hash='QhlSiI1A7kijxjwi55do', updated_at=2024-01-15 11:56:12 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='raT5X81gwJTAVJCLf4Vy', n=32826, type='number', registry='bionty.Gene', hash='QhlSiI1A7kijxjwi55do', updated_at=2024-01-15 11:56:16 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='raT5X81gwJTAVJCLf4Vy', n=32826, type='number', registry='bionty.Gene', hash='QhlSiI1A7kijxjwi55do', updated_at=2024-01-15 11:56:19 UTC, created_by_id=1)
✅ loaded: FeatureSet(uid='QlnhORl0UVuVcpyPNs7W', n=55773, type='number', registry='bionty.Gene', hash='oklP4oPBB4b7pwhj8ZFF', updated_at=2024-01-15 08:53:58 UTC, created_by_id=1)
artifact.describe()
Artifact(uid='4UdE334dCgOh0n5xk4ix', key='cell-census/2023-12-15/h5ads/108c2b65-4ea9-4792-8b5b-451842faf35b.h5ad', suffix='.h5ad', accessor='AnnData', description='Massively multiplex chemical transcriptomics at single-cell resolution - A549', size=342294033, hash='XHxCWnmWNjKufUTzMOeWCw-41', hash_type='md5-n', n_observations=143015, visibility=1, key_is_virtual=False, updated_at=2024-01-11 09:43:51 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='V4AGIdOJcOgj6K79', name='Census release 2023-12-15 (LTS)', short_name='cencus-release-2023-12-15-LTS', version='0', type='notebook', updated_at=2024-01-11 09:06:31 UTC, created_by_id=1)
👣 run: Run(uid='UAAiLAi0BrLvlKnsuvP3', run_at=2024-01-15 07:01:32 UTC, transform_id=17, created_by_id=1)
👤 created_by: User(uid='kmvZDIX9', handle='sunnyosun', name='Sunny Sun', updated_at=2023-12-13 16:23:44 UTC)
Features:
obs: FeatureSet(uid='zAQ6WnmIMDLslhfgdIOt', name='obs metadata', n=10, type='category', registry='core.Feature', hash='CFxuf-VqTFbrkbqPHiY-', updated_at=2023-12-09 16:16:49 UTC, created_by_id=1)
🔗 tissue (1, bionty.Tissue): 'epithelial cell of alveolus of lung'
🔗 tissue_type (0, core.ULabel):
🔗 assay (1, bionty.ExperimentalFactor): 'sci-Plex'
🔗 cell_type (1, bionty.CellType): 'cultured cell'
🔗 development_stage (1, bionty.DevelopmentalStage): 'unknown'
🔗 disease (1, bionty.Disease): 'normal'
🔗 donor_id (1, core.ULabel): 'A549'
🔗 self_reported_ethnicity (1, bionty.Ethnicity): 'unknown'
🔗 sex (1, bionty.Phenotype): 'male'
🔗 suspension_type (1, core.ULabel): 'nucleus'
external: FeatureSet(uid='zIgncie4AywRKgLmKHUW', name='external metadata', n=2, type='category', registry='core.Feature', hash='5E4xD6tOhDB5EOnLx3tv', updated_at=2023-12-20 04:35:20 UTC, created_by_id=1)
🔗 organism (1, bionty.Organism): 'human'
🔗 collection (0, core.ULabel):
var: FeatureSet(uid='QlnhORl0UVuVcpyPNs7W', n=55773, type='number', registry='bionty.Gene', hash='oklP4oPBB4b7pwhj8ZFF', updated_at=2024-01-15 11:57:50 UTC, created_by_id=1)
'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', ...
Labels:
🏷️ organism (1, bionty.Organism): 'human'
🏷️ tissues (1, bionty.Tissue): 'epithelial cell of alveolus of lung'
🏷️ cell_types (1, bionty.CellType): 'cultured cell'
🏷️ diseases (1, bionty.Disease): 'normal'
🏷️ phenotypes (1, bionty.Phenotype): 'male'
🏷️ experimental_factors (1, bionty.ExperimentalFactor): 'sci-Plex'
🏷️ developmental_stages (1, bionty.DevelopmentalStage): 'unknown'
🏷️ ethnicities (1, bionty.Ethnicity): 'unknown'
🏷️ ulabels (2, core.ULabel): 'A549', 'nucleus'
Annotate tissue_type¶
Before CxG schema 4.0, tissue_type column was not annotated, instead “cell culture” or “organoid” was added to the record ontology_id.
register_ulabels(cxg_datasets, "tissue_type")
is_tissue_type = ln.ULabel.filter(name="is_tissue_type").one()
tissue_types = is_tissue_type.children.lookup()
features = ln.Feature.lookup()
organoids = lb.Tissue.filter(ontology_id__contains="organoid").all()
organoids.df()
| uid | name | ontology_id | abbr | synonyms | description | created_at | updated_at | public_source_id | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|
| id |
for record in organoids:
print(record.name)
ontology_id = record.ontology_id.split(" ")[0]
tissue_record = lb.Tissue.from_bionty(ontology_id=ontology_id)
if tissue_record._state.adding:
tissue_record.save()
for f in tissue_record.artifacts.all():
f.labels.add(tissue_types.organoid, features.tissue_type)
organoids.delete()
cell_cultures = lb.Tissue.filter(ontology_id__contains="cell culture").all()
cell_cultures.df()
| uid | name | ontology_id | abbr | synonyms | description | created_at | updated_at | public_source_id | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|
| id |
for record in cell_cultures:
print(record.name)
ontology_id = record.ontology_id.split(" ")[0]
tissue_record = lb.CellType.from_bionty(ontology_id=ontology_id)
if tissue_record._state.adding:
tissue_record.save()
for f in tissue_record.artifacts.all():
f.labels.add(tissue_types.cell_culture, features.tissue_type)
cell_cultures.delete()
Register collections¶
collection = ln.Collection(
artifacts,
name="cellxgene-census",
version=census_version,
is_new_version_of=ln.Collection.filter(
name="cellxgene-census", version="2023-07-25"
).one(),
)
collection.save()
cxg_collections = get_collections_from_cxg()
for collection_meta in cxg_collections:
keys = [
f'cell-census/{census_version}/h5ads/{dataset["dataset_id"]}.h5ad'
for dataset in collection_meta["datasets"]
]
collection_artifacts = artifacts.filter(key__in=keys).all()
if collection_artifacts.count() > 0:
kwargs = dict(
name=collection_meta["name"],
description=collection_meta["doi"],
reference=collection_meta["collection_id"],
reference_type="CELLxGENE Collection ID",
version=census_version,
)
collection_record = ln.Collection(
collection_artifacts,
**kwargs,
)
# if is needed here as .save() errors if collection is already saved
if collection_record._state.adding:
collection_record.save()
Add existing collections to their corresponding version families:
collections = ln.Collection.filter(version=census_version).all()
collections.count()
165
collections_20230725 = ln.Collection.filter(version="2023-07-25").all()
collections_20230725.count()
80
for collection in collections:
collection_20230725 = collections_20230725.filter(
reference=collection.reference
).one_or_none()
if collection_20230725 is not None:
collection.add_to_version_family(collection_20230725, version=census_version)
Show code cell output
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Link metadata to collection¶
collection = ln.Collection.filter(name="cellxgene-census", version=census_version).one()
feature sets:
collection.feature_sets.add(
ln.FeatureSet.filter(name__contains="obs").one(), through_defaults={"slot": "obs"}
)
collection.feature_sets.add(
ln.FeatureSet.filter(name__contains="ext").one(),
through_defaults={"slot": "external"},
)
collection.describe()
Collection(uid='T9xK6Iu5mJCY0lmd832u', name='cellxgene-census', version='2023-12-15', hash='0NB32iVKG5ttaW5XILvG', visibility=1, updated_at=2024-01-11 13:47:39 UTC)
Provenance:
📔 transform: Transform(uid='G69jtgzKO0eJ6K79', name='Census release 2023-12-15 (LTS)', short_name='cencus-release-2023-12-15-LTS', version='0', type='notebook', updated_at=2024-01-11 09:33:35 UTC, created_by_id=1)
👣 run: Run(uid='UAAiLAi0BrLvlKnsuvP3', run_at=2024-01-15 07:01:32 UTC, transform_id=17, created_by_id=1)
👤 created_by: User(uid='kmvZDIX9', handle='sunnyosun', name='Sunny Sun', updated_at=2023-12-13 16:23:44 UTC)
Features:
obs: FeatureSet(uid='zAQ6WnmIMDLslhfgdIOt', name='obs metadata', n=10, type='category', registry='core.Feature', hash='CFxuf-VqTFbrkbqPHiY-', updated_at=2023-12-09 16:16:49 UTC, created_by_id=1)
🔗 tissue (0, bionty.Tissue):
🔗 tissue_type (0, core.ULabel):
🔗 assay (0, bionty.ExperimentalFactor):
🔗 cell_type (0, bionty.CellType):
🔗 development_stage (0, bionty.DevelopmentalStage):
🔗 disease (0, bionty.Disease):
🔗 donor_id (0, core.ULabel):
🔗 self_reported_ethnicity (0, bionty.Ethnicity):
🔗 sex (0, bionty.Phenotype):
🔗 suspension_type (0, core.ULabel):
external: FeatureSet(uid='zIgncie4AywRKgLmKHUW', name='external metadata', n=2, type='category', registry='core.Feature', hash='5E4xD6tOhDB5EOnLx3tv', updated_at=2023-12-20 04:35:20 UTC, created_by_id=1)
🔗 organism (0, bionty.Organism):
🔗 collection (0, core.ULabel):