Transfer data¶
Here, we’ll show how to transfer data from another instance into the current instance.
!lamin init --storage ./test-transfer --schema bionty
💡 connected lamindb: anonymous/test-transfer
import lamindb as ln
ln.settings.transform.stem_uid = "ITeOtm7bhtdq"
ln.settings.transform.version = "1"
ln.track()
💡 connected lamindb: anonymous/test-transfer
💡 notebook imports: lamindb==0.72.1
💡 saved: Transform(version='1', uid='ITeOtm7bhtdq5zKv', name='Transfer data', key='transfer', type='notebook', updated_at=2024-05-23 11:19:58 UTC, created_by_id=1)
💡 saved: Run(uid='kMHOTvUTwJbqVyKYsHQN', transform_id=1, created_by_id=1)
All artifacts in the laminlabs/cellxgene clone of CZ CELLxGENE (for more info, see cellxgene):
artifacts = ln.Artifact.using("laminlabs/cellxgene")
artifacts.df().head()
Show code cell output
| version | created_at | created_by_id | updated_at | uid | storage_id | key | suffix | accessor | description | size | hash | hash_type | n_objects | n_observations | transform_id | run_id | visibility | key_is_virtual | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||
| 1717 | 2023-07-25 | 2023-11-28 21:46:39.659067+00:00 | 1 | 2024-01-24 07:05:41.771446+00:00 | 6GM0siRkIUISUwpFb54A | 2 | cell-census/2023-07-25/h5ads/ff12e239-9292-4d2... | .h5ad | AnnData | Pla_HDBR9518710 | 21993955 | PFgOHr86dGrEOrPELpKvrQ-3 | md5-n | None | 1216.0 | 11.0 | 16.0 | 1 | False |
| 1613 | 2023-07-25 | 2023-11-28 21:46:33.371255+00:00 | 1 | 2024-01-24 07:05:43.770581+00:00 | qnlBU5a6OR46Zkku1gEl | 2 | cell-census/2023-07-25/h5ads/dfe8e072-94a7-415... | .h5ad | AnnData | WS_PLA_S9101764 | 39725919 | -2OE3CsXIxegNGOQO7cJVw-5 | md5-n | None | 3568.0 | 11.0 | 16.0 | 1 | False |
| 1497 | 2023-07-25 | 2023-11-28 21:46:26.369149+00:00 | 1 | 2024-01-24 07:05:45.247888+00:00 | w6UNsyZp0eTrl3Uz15Wl | 2 | cell-census/2023-07-25/h5ads/c1568274-2af2-4cd... | .h5ad | AnnData | WS_PLA_S9101769 | 34328778 | oaxWjROHsHneVVf7VgcoaA-5 | md5-n | None | 3130.0 | 11.0 | 16.0 | 1 | False |
| 1434 | 2023-07-25 | 2023-11-28 21:46:22.575516+00:00 | 1 | 2024-01-24 07:05:45.699596+00:00 | txst3MWWFtvPGcYOR145 | 2 | cell-census/2023-07-25/h5ads/ab326369-b63c-48d... | .h5ad | AnnData | primary_trophoblast_organoid | 530799215 | 2i7cuX3r562-mfIK8GYAyA-64 | md5-n | None | 26853.0 | 11.0 | 16.0 | 1 | False |
| 979 | 2023-07-25 | 2023-11-28 21:45:55.034851+00:00 | 1 | 2024-01-24 07:15:09.559452+00:00 | Vd2uGOTQOwleGdFRlEOp | 2 | cell-census/2023-07-25/h5ads/1fe63353-9e75-482... | .h5ad | AnnData | Heart - A single-cell transcriptomic atlas cha... | 148387585 | 4keMLCOrr6OP70fPvE0TIQ-18 | md5-n | None | 8613.0 | 11.0 | 16.0 | 1 | False |
Query or search the queryset:
artifact = artifacts.filter(description__icontains="tabula sapiens").first()
artifact
Show code cell output
Artifact(version='2023-07-25', updated_at=2024-01-24 07:05:50 UTC, uid='7JWPBDDaO3v4bsarcj50', key='cell-census/2023-07-25/h5ads/f01bdd17-4902-40f5-86e3-240d66dd2587.h5ad', suffix='.h5ad', accessor='AnnData', description='Tabula Sapiens - Salivary_Gland', size=575121838, hash='4DpycNCrKc_Q_pEYmPXZRw-69', hash_type='md5-n', n_observations=27199, visibility=1, key_is_virtual=False, created_by_id=1, storage_id=2, transform_id=11, run_id=16)
Save the artifact to the default instance:
artifact.save()
Show code cell output
obs
var
❗ now recursing through parents: this only happens once, but is much slower than bulk saving
❗ now recursing through parents: this only happens once, but is much slower than bulk saving
❗ now recursing through parents: this only happens once, but is much slower than bulk saving
❗ did not create Disease record for 1 non-validated ontology_id: 'PATO:0000461'
❗ now recursing through parents: this only happens once, but is much slower than bulk saving
❗ did not create Phenotype records for 2 non-validated ontology_ids: 'PATO:0000384', 'PATO:0000383'
❗ now recursing through parents: this only happens once, but is much slower than bulk saving
Artifact(version='2023-07-25', updated_at=2024-05-23 11:20:00 UTC, uid='7JWPBDDaO3v4bsarcj50', key='cell-census/2023-07-25/h5ads/f01bdd17-4902-40f5-86e3-240d66dd2587.h5ad', suffix='.h5ad', accessor='AnnData', description='Tabula Sapiens - Salivary_Gland', size=575121838, hash='4DpycNCrKc_Q_pEYmPXZRw-69', hash_type='md5-n', n_observations=27199, visibility=1, key_is_virtual=False, created_by_id=1, storage_id=2, transform_id=1, run_id=1)
All features & labels have been transferred, the data itself is still on CZ’s S3:
artifact.describe()
Show code cell output
Artifact(version='2023-07-25', updated_at=2024-05-23 11:20:00 UTC, uid='7JWPBDDaO3v4bsarcj50', key='cell-census/2023-07-25/h5ads/f01bdd17-4902-40f5-86e3-240d66dd2587.h5ad', suffix='.h5ad', accessor='AnnData', description='Tabula Sapiens - Salivary_Gland', size=575121838, hash='4DpycNCrKc_Q_pEYmPXZRw-69', hash_type='md5-n', n_observations=27199, visibility=1, key_is_virtual=False)
Provenance:
📎 created_by: User(uid='00000000', handle='anonymous')
📎 storage: uid='oIYGbD74', root='s3://cellxgene-data-public', type='s3', region='us-west-2')
📎 transform: Transform(version='1', uid='ITeOtm7bhtdq5zKv', name='Transfer data', key='transfer', type='notebook')
📎 run: Run(uid='kMHOTvUTwJbqVyKYsHQN', started_at=2024-05-23 11:19:58 UTC, is_consecutive=True)
Features:
obs: FeatureSet(uid='fwPyhthEifqtRuO0InkI', n=11, registry='Feature')
🔗 assay (11, cat[bionty.ExperimentalFactor]): 'Smart-seq2', '10x 3' v3'
🔗 cell_type (11, cat[bionty.CellType]): 'monocyte', 'myoepithelial cell', 'CD4-positive, alpha-beta T cell', 'endothelial cell of lymphatic vessel', 'duct epithelial cell', 'endothelial cell of hepatic sinusoid', 'pericyte', 'adventitial cell', 'basal cell', 'neutrophil'
🔗 development_stage (11, cat[bionty.DevelopmentalStage]): '59-year-old human stage', '69-year-old human stage'
🔗 disease (11, cat[bionty.Disease]): 'normal'
🔗 donor_id (11, cat[ULabel]): 'TSP14', 'TSP7'
🔗 self_reported_ethnicity (11, cat[bionty.Ethnicity]): 'European'
🔗 sex (11, cat[bionty.Phenotype]): 'male', 'female'
🔗 tissue (11, cat[bionty.Tissue]): 'sublingual gland', 'parotid gland'
🔗 organism (11, cat[bionty.Organism]): 'human'
🔗 tissue_type (11, cat[ULabel]): 'tissue'
🔗 suspension_type (11, cat[ULabel]): 'cell'
var: FeatureSet(uid='yCr7u7NXs01e8YykgWiA', n=58604, dtype='number', registry='bionty.Gene')
'RNF145', 'RNU4ATAC2P', 'LINC01847', 'ADRA1B', 'GAPDHP40', 'TTC1', 'FAM200C', 'None', 'LINC02159', 'GABRA1', 'LINC01202', 'CCNG1', 'HMMR', 'RN7SKP60', 'RPL21P59', 'RPLP0P9', 'WWC1', 'MIR103A1', 'SLIT3-AS1', 'MIR585'
Labels:
📎 organisms (1, bionty.Organism): 'human'
📎 tissues (2, bionty.Tissue): 'sublingual gland', 'parotid gland'
📎 cell_types (24, bionty.CellType): 'monocyte', 'myoepithelial cell', 'CD4-positive, alpha-beta T cell', 'endothelial cell of lymphatic vessel', 'duct epithelial cell', 'endothelial cell of hepatic sinusoid', 'pericyte', 'adventitial cell', 'basal cell', 'neutrophil'
📎 diseases (1, bionty.Disease): 'normal'
📎 phenotypes (2, bionty.Phenotype): 'male', 'female'
📎 experimental_factors (2, bionty.ExperimentalFactor): 'Smart-seq2', '10x 3' v3'
📎 developmental_stages (2, bionty.DevelopmentalStage): '59-year-old human stage', '69-year-old human stage'
📎 ethnicities (1, bionty.Ethnicity): 'European'
📎 ulabels (4, ULabel): 'TSP14', 'TSP7', 'tissue', 'cell'
The database is populated correspondingly.
ln.view()
Show code cell output
****************
* module: core *
****************
Artifact
| version | created_at | created_by_id | updated_at | uid | storage_id | key | suffix | accessor | description | size | hash | hash_type | n_objects | n_observations | transform_id | run_id | visibility | key_is_virtual | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||
| 1 | 2023-07-25 | 2024-05-23 11:20:00.338581+00:00 | 1 | 2024-05-23 11:20:00.338635+00:00 | 7JWPBDDaO3v4bsarcj50 | 2 | cell-census/2023-07-25/h5ads/f01bdd17-4902-40f... | .h5ad | AnnData | Tabula Sapiens - Salivary_Gland | 575121838 | 4DpycNCrKc_Q_pEYmPXZRw-69 | md5-n | None | 27199 | 1 | 1 | 1 | False |
Feature
| created_at | created_by_id | run_id | updated_at | uid | name | dtype | unit | description | synonyms | |
|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||
| 11 | 2024-05-23 11:20:00.463091+00:00 | 1 | 1 | 2024-05-23 11:20:00.463131+00:00 | 9s20Imh64bYU | suspension_type | cat[ULabel] | None | MUST be 'cell', 'nucleus', or 'na' | None |
| 10 | 2024-05-23 11:20:00.462969+00:00 | 1 | 1 | 2024-05-23 11:20:00.463009+00:00 | 69RQ1pVPEo3o | tissue_type | cat[ULabel] | None | MUST be 'tissue', 'organoid', or 'cell culture' | None |
| 9 | 2024-05-23 11:20:00.462848+00:00 | 1 | 1 | 2024-05-23 11:20:00.462888+00:00 | wCbvLeKe2rv8 | organism | cat[bionty.Organism] | None | None | None |
| 8 | 2024-05-23 11:20:00.462725+00:00 | 1 | 1 | 2024-05-23 11:20:00.462766+00:00 | MB1hKtGaQiqV | tissue | cat[bionty.Tissue] | None | None | None |
| 7 | 2024-05-23 11:20:00.462603+00:00 | 1 | 1 | 2024-05-23 11:20:00.462644+00:00 | Xcti9JkM9uvG | sex | cat[bionty.Phenotype] | None | None | None |
| 6 | 2024-05-23 11:20:00.462480+00:00 | 1 | 1 | 2024-05-23 11:20:00.462520+00:00 | DbVAV4BaQXAh | self_reported_ethnicity | cat[bionty.Ethnicity] | None | None | None |
| 5 | 2024-05-23 11:20:00.462358+00:00 | 1 | 1 | 2024-05-23 11:20:00.462399+00:00 | xbMGSIMHV67J | donor_id | cat[ULabel] | None | None | None |
FeatureSet
| created_at | created_by_id | run_id | uid | name | n | dtype | registry | hash | |
|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||
| 1 | 2024-05-23 11:20:00.475164+00:00 | 1 | 1 | fwPyhthEifqtRuO0InkI | None | 11 | None | Feature | FqF5x0w1rGBjZBGzh-Qr |
| 2 | 2024-05-23 11:20:56.133985+00:00 | 1 | 1 | yCr7u7NXs01e8YykgWiA | None | 58604 | number | bionty.Gene | vGM2j-OZYfQ4-9KsK75K |
Run
| uid | transform_id | started_at | finished_at | created_by_id | report_id | environment_id | is_consecutive | reference | reference_type | created_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||
| 1 | kMHOTvUTwJbqVyKYsHQN | 1 | 2024-05-23 11:19:58.097546+00:00 | None | 1 | None | None | True | None | None | 2024-05-23 11:19:58.097680+00:00 |
Storage
| created_at | created_by_id | run_id | updated_at | uid | root | description | type | region | instance_uid | |
|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||
| 2 | 2024-05-23 11:20:00.335988+00:00 | 1 | 1.0 | 2024-05-23 11:20:00.336078+00:00 | oIYGbD74 | s3://cellxgene-data-public | None | s3 | us-west-2 | None |
| 1 | 2024-05-23 11:19:55.699923+00:00 | 1 | NaN | 2024-05-23 11:19:55.700005+00:00 | NDVg4jXq4W9l | /home/runner/work/lamindb/lamindb/docs/test-tr... | None | local | None | 1FHu5eE0uxm4 |
Transform
| version | uid | name | key | description | type | latest_report_id | source_code_id | reference | reference_type | created_at | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||
| 1 | 1 | ITeOtm7bhtdq5zKv | Transfer data | transfer | None | notebook | None | None | None | None | 2024-05-23 11:19:58.090274+00:00 | 2024-05-23 11:19:58.090320+00:00 | 1 |
ULabel
| created_at | created_by_id | run_id | updated_at | uid | name | description | reference | reference_type | |
|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||
| 4 | 2024-05-23 11:22:14.021677+00:00 | 1 | 1 | 2024-05-23 11:22:14.021756+00:00 | WzKPMCXX | cell | None | None | None |
| 3 | 2024-05-23 11:22:13.964810+00:00 | 1 | 1 | 2024-05-23 11:22:13.964894+00:00 | orwn0HKG | tissue | None | None | None |
| 2 | 2024-05-23 11:21:56.741559+00:00 | 1 | 1 | 2024-05-23 11:21:56.741603+00:00 | 1s9HrDbk | TSP7 | None | None | None |
| 1 | 2024-05-23 11:21:56.741400+00:00 | 1 | 1 | 2024-05-23 11:21:56.741478+00:00 | HVoqm0bp | TSP14 | None | None | None |
User
| uid | handle | name | created_at | updated_at | |
|---|---|---|---|---|---|
| id | |||||
| 1 | 00000000 | anonymous | None | 2024-05-23 11:19:55.694690+00:00 | 2024-05-23 11:19:55.694727+00:00 |
******************
* module: bionty *
******************
CellType
| created_at | created_by_id | run_id | updated_at | uid | name | ontology_id | abbr | synonyms | description | public_source_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||
| 77 | 2024-05-23 11:21:51.743793+00:00 | 1 | 1 | 2024-05-23 11:21:51.743882+00:00 | 1uUQwGAL | endo-epithelial cell | CL:0002076 | None | None | An Epithelial Cell Derived From Endoderm. | 29 |
| 76 | 2024-05-23 11:21:50.794989+00:00 | 1 | 1 | 2024-05-23 11:21:50.795034+00:00 | 6o2T6eYX | epithelial cell of alimentary canal | CL:0002251 | None | None | An Epithelial Cell Of The Musculomembranous Di... | 29 |
| 75 | 2024-05-23 11:21:50.794795+00:00 | 1 | 1 | 2024-05-23 11:21:50.794880+00:00 | 4cUGHo42 | exocrine cell | CL:0000152 | None | None | A Cell Of An Exocrine Gland; I.E. A Gland That... | 29 |
| 74 | 2024-05-23 11:21:49.690183+00:00 | 1 | 1 | 2024-05-23 11:21:49.690268+00:00 | 4eEkKmdU | secretory cell | CL:0000151 | None | None | A Cell That Specializes In Controlled Release ... | 29 |
| 73 | 2024-05-23 11:21:48.790783+00:00 | 1 | 1 | 2024-05-23 11:21:48.790827+00:00 | 7glBbUDw | protein secreting cell | CL:0000154 | None | None | None | 29 |
| 72 | 2024-05-23 11:21:48.790580+00:00 | 1 | 1 | 2024-05-23 11:21:48.790665+00:00 | 41jKWil4 | glandular epithelial cell | CL:0000150 | None | None | A Specialized Epithelial Cell That Is Capable ... | 29 |
| 71 | 2024-05-23 11:21:47.724931+00:00 | 1 | 1 | 2024-05-23 11:21:47.724982+00:00 | dcsPbfKc | salivary gland glandular cell | CL:1001596 | None | None | Glandular Cell Of Salivary Gland. Example: Ser... | 29 |
DevelopmentalStage
| created_at | created_by_id | run_id | updated_at | uid | name | ontology_id | abbr | synonyms | description | public_source_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||
| 3 | 2024-05-23 11:21:53.942485+00:00 | 1 | 1 | 2024-05-23 11:21:53.942572+00:00 | 7k1A0zkT | human life cycle stage | HsapDv:0000000 | None | developmental stage | A Spatiotemporal Region Encompassing Some Part... | 70 |
| 2 | 2024-05-23 11:21:52.899813+00:00 | 1 | 1 | 2024-05-23 11:21:52.899858+00:00 | 5q64GXx1 | 69-year-old human stage | HsapDv:0000163 | None | None | Adult Stage That Refers To An Adult Who Is Ove... | 70 |
| 1 | 2024-05-23 11:21:52.899618+00:00 | 1 | 1 | 2024-05-23 11:21:52.899702+00:00 | 2zxrb1Pu | 59-year-old human stage | HsapDv:0000153 | None | None | Middle Aged Stage That Refers To An Adult Who ... | 70 |
Disease
| created_at | created_by_id | run_id | updated_at | uid | name | ontology_id | abbr | synonyms | description | public_source_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||
| 1 | 2024-05-23 11:21:56.682158+00:00 | 1 | 1 | 2024-05-23 11:21:56.682245+00:00 | 6IZiH6X8 | normal | PATO:0000461 | None | None | A Quality Inhering In A Bearer By Virtue Of Th... | 63 |
Ethnicity
| created_at | created_by_id | run_id | updated_at | uid | name | ontology_id | abbr | synonyms | description | public_source_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||
| 2 | 2024-05-23 11:21:58.887474+00:00 | 1 | 1 | 2024-05-23 11:21:58.887561+00:00 | 6Tnv21Sw | ancestry category | HANCESTRO:0004 | None | ancestral group | Population Category Defined Using Ancestry Inf... | 72 |
| 1 | 2024-05-23 11:21:57.990234+00:00 | 1 | 1 | 2024-05-23 11:21:57.990315+00:00 | 15mGvAtW | European | HANCESTRO:0005 | None | Caucasian|white | Includes Individuals Who Either Self-Report Or... | 72 |
ExperimentalFactor
| created_at | created_by_id | run_id | updated_at | uid | name | ontology_id | abbr | synonyms | description | molecule | instrument | measurement | public_source_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||
| 9 | 2024-05-23 11:21:08.570084+00:00 | 1 | 1 | 2024-05-23 11:21:08.570168+00:00 | 6JvKxplX | 10x technology | EFO:0008995 | None | 10x single cell library construction|10x Genomics | 10X Is A "Synthetic Long-Read" Technology And ... | None | None | None | 51 |
| 8 | 2024-05-23 11:21:07.472749+00:00 | 1 | 1 | 2024-05-23 11:21:07.472873+00:00 | 1SAR2Y26 | 10x transcription profiling | EFO:0030080 | None | None | The 10X-Based Single-Cell Technology That Sequ... | None | None | None | 51 |
| 7 | 2024-05-23 11:21:06.371074+00:00 | 1 | 1 | 2024-05-23 11:21:06.371163+00:00 | 2kXleO7C | 10x 3' transcription profiling | EFO:0030003 | None | None | 10X 3' Transcription Profiling Is The 10X-Base... | None | None | None | 51 |
| 6 | 2024-05-23 11:21:05.300039+00:00 | 1 | 1 | 2024-05-23 11:21:05.300123+00:00 | 1wLRxESw | assay by molecule | EFO:0002772 | None | None | None | None | None | None | 51 |
| 5 | 2024-05-23 11:21:04.042549+00:00 | 1 | 1 | 2024-05-23 11:21:04.042642+00:00 | 5q5okCXl | single cell library construction | EFO:0010183 | None | single cell library preparation|single-cell li... | A Library Preparation Process That Starts From... | None | None | None | 51 |
| 4 | 2024-05-23 11:21:03.104956+00:00 | 1 | 1 | 2024-05-23 11:21:03.105006+00:00 | 789nVHwo | RNA assay | EFO:0001457 | None | None | An Assay With Input Rna | RNA assay | None | None | 51 |
| 3 | 2024-05-23 11:21:03.104665+00:00 | 1 | 1 | 2024-05-23 11:21:03.104759+00:00 | 1x8VaVN0 | Smart-like | EFO:0010184 | None | None | Library Construction Method Using The Smart (S... | None | None | None | 51 |
Gene
| created_at | created_by_id | run_id | updated_at | uid | symbol | stable_id | ensembl_gene_id | ncbi_gene_ids | biotype | description | synonyms | organism_id | public_source_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||
| 58604 | 2024-05-23 11:20:51.956369+00:00 | 1 | 1 | 2024-05-23 11:20:51.956409+00:00 | 70hEAyHdv2mf | None | None | ENSG00000272085 | lncRNA | novel transcript | 1 | 13 | ||
| 58603 | 2024-05-23 11:20:51.956200+00:00 | 1 | 1 | 2024-05-23 11:20:51.956241+00:00 | 7fhcZHrnbaY1 | None | None | ENSG00000253424 | lncRNA | novel transcript | 1 | 13 | ||
| 58602 | 2024-05-23 11:20:51.956031+00:00 | 1 | 1 | 2024-05-23 11:20:51.956072+00:00 | 2QvvJOfXjXPd | None | None | ENSG00000253449 | lncRNA | novel transcript | 1 | 13 | ||
| 58601 | 2024-05-23 11:20:51.955861+00:00 | 1 | 1 | 2024-05-23 11:20:51.955902+00:00 | 6e9f3nDhfRWs | None | None | ENSG00000253673 | lncRNA | novel transcript | 1 | 13 | ||
| 58600 | 2024-05-23 11:20:51.955692+00:00 | 1 | 1 | 2024-05-23 11:20:51.955732+00:00 | 4ylvxaM60dXB | None | None | ENSG00000253792 | lncRNA | novel transcript | 1 | 13 | ||
| 58599 | 2024-05-23 11:20:51.955522+00:00 | 1 | 1 | 2024-05-23 11:20:51.955563+00:00 | 1gpu6hQGoHVj | None | None | ENSG00000213414 | processed_pseudogene | cell division cycle 37 homolog (S. cerevisiae)... | 1 | 13 | ||
| 58598 | 2024-05-23 11:20:51.955352+00:00 | 1 | 1 | 2024-05-23 11:20:51.955392+00:00 | Z3GXFaLKPXSm | RNU2-48P | None | ENSG00000222626 | snRNA | RNA, U2 small nuclear 48, pseudogene [Source:H... | 1 | 13 |
Organism
| created_at | created_by_id | run_id | updated_at | uid | name | ontology_id | scientific_name | public_source_id | |
|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||
| 1 | 2024-05-23 11:20:05.211268+00:00 | 1 | 1 | 2024-05-23 11:20:05.211359+00:00 | 1dpCL6Td | human | NCBITaxon:9606 | Homo sapiens | 10 |
Phenotype
| created_at | created_by_id | run_id | updated_at | uid | name | ontology_id | abbr | synonyms | description | public_source_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||
| 2 | 2024-05-23 11:22:00.902459+00:00 | 1 | 1 | 2024-05-23 11:22:00.902502+00:00 | 3OV8JZsS | female | PATO:0000383 | None | None | A Biological Sex Quality Inhering In An Indivi... | 63 |
| 1 | 2024-05-23 11:22:00.902269+00:00 | 1 | 1 | 2024-05-23 11:22:00.902354+00:00 | kniZxLLf | male | PATO:0000384 | None | None | A Biological Sex Quality Inhering In An Indivi... | 63 |
PublicSource
| created_at | created_by_id | run_id | updated_at | uid | entity | organism | currently_used | source | source_name | version | url | md5 | source_website | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||
| 73 | 2024-05-23 11:19:55.808168+00:00 | 1 | None | 2024-05-23 11:19:55.808210+00:00 | 5JnV | BioSample | all | True | ncbi | NCBI BioSample attributes | 2023-09 | s3://bionty-assets/df_all__ncbi__2023-09__BioS... | 918db9bd1734b97c596c67d9654a4126 | https://www.ncbi.nlm.nih.gov/biosample/docs/at... |
| 72 | 2024-05-23 11:19:55.807979+00:00 | 1 | None | 2024-05-23 11:19:55.808043+00:00 | 3Tlc | Ethnicity | human | True | hancestro | Human Ancestry Ontology | 3.0 | https://github.com/EBISPOT/hancestro/raw/3.0/h... | 76dd9efda9c2abd4bc32fc57c0b755dd | https://github.com/EBISPOT/hancestro |
| 71 | 2024-05-23 11:19:55.803998+00:00 | 1 | None | 2024-05-23 11:19:55.804035+00:00 | 16tR | DevelopmentalStage | mouse | True | mmusdv | Mouse Developmental Stages | 2020-03-10 | http://aber-owl.net/media/ontologies/MMUSDV/9/... | 5bef72395d853c7f65450e6c2a1fc653 | https://github.com/obophenotype/developmental-... |
| 70 | 2024-05-23 11:19:55.803847+00:00 | 1 | None | 2024-05-23 11:19:55.803884+00:00 | 7CRn | DevelopmentalStage | human | True | hsapdv | Human Developmental Stages | 2020-03-10 | http://aber-owl.net/media/ontologies/HSAPDV/11... | 52181d59df84578ed69214a5cb614036 | https://github.com/obophenotype/developmental-... |
| 69 | 2024-05-23 11:19:55.803697+00:00 | 1 | None | 2024-05-23 11:19:55.803734+00:00 | 3TI0 | Drug | all | False | dron | Drug Ontology | 2023-03-10 | https://data.bioontology.org/ontologies/DRON/s... | 75e86011158fae76bb46d96662a33ba3 | https://bioportal.bioontology.org/ontologies/DRON |
| 68 | 2024-05-23 11:19:55.803547+00:00 | 1 | None | 2024-05-23 11:19:55.803583+00:00 | 5alK | Drug | all | True | dron | Drug Ontology | 2024-03-02 | https://data.bioontology.org/ontologies/DRON/s... | 84138459de4f65034e979f4e46783747 | https://bioportal.bioontology.org/ontologies/DRON |
| 67 | 2024-05-23 11:19:55.803396+00:00 | 1 | None | 2024-05-23 11:19:55.803432+00:00 | 3rm9 | BFXPipeline | all | True | lamin | Bioinformatics Pipeline | 1.0.0 | s3://bionty-assets/bfxpipelines.json | a7eff57a256994692fba46e0199ffc94 | https://lamin.ai |
Tissue
| created_at | created_by_id | run_id | updated_at | uid | name | ontology_id | abbr | synonyms | description | public_source_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||
| 17 | 2024-05-23 11:22:13.824371+00:00 | 1 | 1 | 2024-05-23 11:22:13.824415+00:00 | 7SvOepT5 | buccal salivary gland | UBERON:0012102 | None | None | A Salivary Gland That Is Part Of A Cheek. | 34 |
| 16 | 2024-05-23 11:22:13.824166+00:00 | 1 | 1 | 2024-05-23 11:22:13.824260+00:00 | 6TiLnvMv | serous gland | UBERON:0000409 | None | None | A Gland In Which The Principal Secretory Cells... | 34 |
| 15 | 2024-05-23 11:22:12.635182+00:00 | 1 | 1 | 2024-05-23 11:22:12.635271+00:00 | 2rlm5wUr | anatomical entity | UBERON:0001062 | None | None | Biological Entity That Is Either An Individual... | 34 |
| 14 | 2024-05-23 11:22:11.713053+00:00 | 1 | 1 | 2024-05-23 11:22:11.713144+00:00 | N039zety | material anatomical entity | UBERON:0000465 | None | None | Anatomical Entity That Has Mass. | 34 |
| 13 | 2024-05-23 11:22:10.620726+00:00 | 1 | 1 | 2024-05-23 11:22:10.620842+00:00 | 5SGM2iq3 | anatomical structure | UBERON:0000061 | None | biological structure|connected biological stru... | Material Anatomical Entity That Is A Single Co... | 34 |
| 12 | 2024-05-23 11:22:09.503594+00:00 | 1 | 1 | 2024-05-23 11:22:09.503683+00:00 | 4o2HviGe | multicellular anatomical structure | UBERON:0010000 | None | multicellular structure | An Anatomical Structure That Has More Than One... | 34 |
| 11 | 2024-05-23 11:22:08.587327+00:00 | 1 | 1 | 2024-05-23 11:22:08.587415+00:00 | 7HJIkVT2 | organ | UBERON:0000062 | None | None | Anatomical Structure That Performs A Specific ... | 34 |
Show code cell content
# clean up test instance
!lamin delete --force test-transfer
!rm -r test-transfer
❗ calling anonymously, will miss private instances
💡 deleting instance anonymous/test-transfer
rm: cannot remove 'test-transfer': No such file or directory