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==0.72.0
💡 saved: Transform(version='1', uid='ITeOtm7bhtdq5zKv', name='Transfer data', key='transfer', type='notebook', updated_at=2024-05-19 23:23:47 UTC, created_by_id=1)
💡 saved: Run(uid='2p2lniLMEfAJ17sAgDnP', 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=2024-05-19 23:23:50 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=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=2024-05-19 23:23:50 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)
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='2p2lniLMEfAJ17sAgDnP', started_at=2024-05-19 23:23:47 UTC, is_consecutive=True)
Features:
obs: FeatureSet(uid='v23mrGPPa7kNQOWkwENG', 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='bJ5fNpyl4SWuW2yfsSfP', 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 | 2024-05-19 23:23:50.593044+00:00 | 1 | 2024-05-19 23:23:50.593090+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 | 2024-05-19 23:23:50.969037+00:00 | 1 | 1 | 2024-05-19 23:23:50.969078+00:00 | 9s20Imh64bYU | suspension_type | cat[ULabel] | None | MUST be 'cell', 'nucleus', or 'na' | None |
| 10 | 2024-05-19 23:23:50.968914+00:00 | 1 | 1 | 2024-05-19 23:23:50.968955+00:00 | 69RQ1pVPEo3o | tissue_type | cat[ULabel] | None | MUST be 'tissue', 'organoid', or 'cell culture' | None |
| 9 | 2024-05-19 23:23:50.968786+00:00 | 1 | 1 | 2024-05-19 23:23:50.968830+00:00 | wCbvLeKe2rv8 | organism | cat[bionty.Organism] | None | None | None |
| 8 | 2024-05-19 23:23:50.968641+00:00 | 1 | 1 | 2024-05-19 23:23:50.968682+00:00 | MB1hKtGaQiqV | tissue | cat[bionty.Tissue] | None | None | None |
| 7 | 2024-05-19 23:23:50.968518+00:00 | 1 | 1 | 2024-05-19 23:23:50.968558+00:00 | Xcti9JkM9uvG | sex | cat[bionty.Phenotype] | None | None | None |
| 6 | 2024-05-19 23:23:50.968395+00:00 | 1 | 1 | 2024-05-19 23:23:50.968435+00:00 | DbVAV4BaQXAh | self_reported_ethnicity | cat[bionty.Ethnicity] | None | None | None |
| 5 | 2024-05-19 23:23:50.968271+00:00 | 1 | 1 | 2024-05-19 23:23:50.968312+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 | 2024-05-19 23:23:50.980517+00:00 | 1 | None | v23mrGPPa7kNQOWkwENG | None | 11 | None | Feature | FqF5x0w1rGBjZBGzh-Qr |
| 2 | 2024-05-19 23:24:47.738572+00:00 | 1 | None | bJ5fNpyl4SWuW2yfsSfP | 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 | 2p2lniLMEfAJ17sAgDnP | 1 | 2024-05-19 23:23:47.743254+00:00 | None | 1 | None | None | True | None | None | 2024-05-19 23:23:47.743399+00:00 |
Storage
| created_at | created_by_id | run_id | updated_at | uid | root | description | type | region | instance_uid | |
|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||
| 2 | 2024-05-19 23:23:50.590555+00:00 | 1 | 1.0 | 2024-05-19 23:23:50.590638+00:00 | oIYGbD74 | s3://cellxgene-data-public | None | s3 | us-west-2 | None |
| 1 | 2024-05-19 23:23:45.500976+00:00 | 1 | NaN | 2024-05-19 23:23:45.501049+00:00 | 2KF2KZTM2CoJ | /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 | 2024-05-19 23:23:47.736697+00:00 | 2024-05-19 23:23:47.736762+00:00 | 1 |
ULabel
| created_at | created_by_id | run_id | updated_at | uid | name | description | reference | reference_type | |
|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||
| 4 | 2024-05-19 23:25:33.386768+00:00 | 1 | 1 | 2024-05-19 23:25:33.386841+00:00 | WzKPMCXX | cell | None | None | None |
| 3 | 2024-05-19 23:25:33.198863+00:00 | 1 | 1 | 2024-05-19 23:25:33.198933+00:00 | orwn0HKG | tissue | None | None | None |
| 2 | 2024-05-19 23:25:23.301819+00:00 | 1 | 1 | 2024-05-19 23:25:23.301862+00:00 | 1s9HrDbk | TSP7 | None | None | None |
| 1 | 2024-05-19 23:25:23.301666+00:00 | 1 | 1 | 2024-05-19 23:25:23.301740+00:00 | HVoqm0bp | TSP14 | None | None | None |
User
| uid | handle | name | created_at | updated_at | |
|---|---|---|---|---|---|
| id | |||||
| 1 | 00000000 | anonymous | None | 2024-05-19 23:23:45.495522+00:00 | 2024-05-19 23:23:45.495556+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 | |||||||||||
| 78 | 2024-05-19 23:25:20.069132+00:00 | 1 | None | 2024-05-19 23:25:20.069208+00:00 | 7glBbUDw | protein secreting cell | CL:0000154 | None | None | None | 21 |
| 77 | 2024-05-19 23:25:19.456920+00:00 | 1 | None | 2024-05-19 23:25:19.456997+00:00 | 1uUQwGAL | endo-epithelial cell | CL:0002076 | None | None | An Epithelial Cell Derived From Endoderm. | 21 |
| 76 | 2024-05-19 23:25:18.797349+00:00 | 1 | None | 2024-05-19 23:25:18.797425+00:00 | 4eEkKmdU | secretory cell | CL:0000151 | None | None | A Cell That Specializes In Controlled Release ... | 21 |
| 75 | 2024-05-19 23:25:18.299904+00:00 | 1 | None | 2024-05-19 23:25:18.299944+00:00 | 6o2T6eYX | epithelial cell of alimentary canal | CL:0002251 | None | None | An Epithelial Cell Of The Musculomembranous Di... | 21 |
| 74 | 2024-05-19 23:25:18.299764+00:00 | 1 | None | 2024-05-19 23:25:18.299806+00:00 | 4cUGHo42 | exocrine cell | CL:0000152 | None | None | A Cell Of An Exocrine Gland; I.E. A Gland That... | 21 |
| 73 | 2024-05-19 23:25:18.299583+00:00 | 1 | None | 2024-05-19 23:25:18.299658+00:00 | 41jKWil4 | glandular epithelial cell | CL:0000150 | None | None | A Specialized Epithelial Cell That Is Capable ... | 21 |
| 72 | 2024-05-19 23:25:17.701629+00:00 | 1 | None | 2024-05-19 23:25:17.701671+00:00 | 4CcnyLVr | acinar cell | CL:0000622 | None | acinic cell|acinous cell | A Secretory Cell That Is Grouped Together With... | 21 |
DevelopmentalStage
| created_at | created_by_id | run_id | updated_at | uid | name | ontology_id | abbr | synonyms | description | public_source_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||
| 3 | 2024-05-19 23:25:21.263898+00:00 | 1 | None | 2024-05-19 23:25:21.263975+00:00 | 7k1A0zkT | human life cycle stage | HsapDv:0000000 | None | developmental stage | A Spatiotemporal Region Encompassing Some Part... | 52 |
| 2 | 2024-05-19 23:25:20.681768+00:00 | 1 | None | 2024-05-19 23:25:20.681809+00:00 | 5q64GXx1 | 69-year-old human stage | HsapDv:0000163 | None | None | Adult Stage That Refers To An Adult Who Is Ove... | 52 |
| 1 | 2024-05-19 23:25:20.681590+00:00 | 1 | None | 2024-05-19 23:25:20.681662+00:00 | 2zxrb1Pu | 59-year-old human stage | HsapDv:0000153 | None | None | Middle Aged Stage That Refers To An Adult Who ... | 52 |
Disease
| created_at | created_by_id | run_id | updated_at | uid | name | ontology_id | abbr | synonyms | description | public_source_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||
| 1 | 2024-05-19 23:25:23.105335+00:00 | 1 | 1 | 2024-05-19 23:25:23.105415+00:00 | 6IZiH6X8 | normal | PATO:0000461 | None | None | A Quality Inhering In A Bearer By Virtue Of Th... | 47 |
Ethnicity
| created_at | created_by_id | run_id | updated_at | uid | name | ontology_id | abbr | synonyms | description | public_source_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||
| 2 | 2024-05-19 23:25:24.501992+00:00 | 1 | None | 2024-05-19 23:25:24.502065+00:00 | 6Tnv21Sw | ancestry category | HANCESTRO:0004 | None | ancestral group | Population Category Defined Using Ancestry Inf... | 54 |
| 1 | 2024-05-19 23:25:23.919755+00:00 | 1 | None | 2024-05-19 23:25:23.919827+00:00 | 15mGvAtW | European | HANCESTRO:0005 | None | Caucasian|white | Includes Individuals Who Either Self-Report Or... | 54 |
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 | 2024-05-19 23:24:56.819240+00:00 | 1 | None | 2024-05-19 23:24:56.819319+00:00 | 6JvKxplX | 10x technology | EFO:0008995 | None | 10x Genomics|10x single cell library construction | 10X Is A "Synthetic Long-Read" Technology And ... | None | None | None | 39 |
| 8 | 2024-05-19 23:24:56.189653+00:00 | 1 | None | 2024-05-19 23:24:56.189733+00:00 | 1SAR2Y26 | 10x transcription profiling | EFO:0030080 | None | None | The 10X-Based Single-Cell Technology That Sequ... | None | None | None | 39 |
| 7 | 2024-05-19 23:24:55.539307+00:00 | 1 | None | 2024-05-19 23:24:55.539392+00:00 | 2kXleO7C | 10x 3' transcription profiling | EFO:0030003 | None | None | 10X 3' Transcription Profiling Is The 10X-Base... | None | None | None | 39 |
| 6 | 2024-05-19 23:24:55.017735+00:00 | 1 | None | 2024-05-19 23:24:55.017813+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 | 39 |
| 5 | 2024-05-19 23:24:54.269531+00:00 | 1 | None | 2024-05-19 23:24:54.269611+00:00 | 1wLRxESw | assay by molecule | EFO:0002772 | None | None | None | None | None | None | 39 |
| 4 | 2024-05-19 23:24:53.745642+00:00 | 1 | None | 2024-05-19 23:24:53.745682+00:00 | 1x8VaVN0 | Smart-like | EFO:0010184 | None | None | Library Construction Method Using The Smart (S... | None | None | None | 39 |
| 3 | 2024-05-19 23:24:53.745425+00:00 | 1 | None | 2024-05-19 23:24:53.745504+00:00 | 789nVHwo | RNA assay | EFO:0001457 | None | None | An Assay With Input Rna | RNA assay | None | None | 39 |
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 | 2024-05-19 23:24:43.458528+00:00 | 1 | 1 | 2024-05-19 23:24:43.458568+00:00 | 70hEAyHdv2mf | None | None | ENSG00000272085 | lncRNA | novel transcript | 1 | 9 | ||
| 58603 | 2024-05-19 23:24:43.458365+00:00 | 1 | 1 | 2024-05-19 23:24:43.458404+00:00 | 7fhcZHrnbaY1 | None | None | ENSG00000253424 | lncRNA | novel transcript | 1 | 9 | ||
| 58602 | 2024-05-19 23:24:43.458200+00:00 | 1 | 1 | 2024-05-19 23:24:43.458240+00:00 | 2QvvJOfXjXPd | None | None | ENSG00000253449 | lncRNA | novel transcript | 1 | 9 | ||
| 58601 | 2024-05-19 23:24:43.458034+00:00 | 1 | 1 | 2024-05-19 23:24:43.458075+00:00 | 6e9f3nDhfRWs | None | None | ENSG00000253673 | lncRNA | novel transcript | 1 | 9 | ||
| 58600 | 2024-05-19 23:24:43.457872+00:00 | 1 | 1 | 2024-05-19 23:24:43.457911+00:00 | 4ylvxaM60dXB | None | None | ENSG00000253792 | lncRNA | novel transcript | 1 | 9 | ||
| 58599 | 2024-05-19 23:24:43.457709+00:00 | 1 | 1 | 2024-05-19 23:24:43.457748+00:00 | 1gpu6hQGoHVj | None | None | ENSG00000213414 | processed_pseudogene | cell division cycle 37 homolog (S. cerevisiae)... | 1 | 9 | ||
| 58598 | 2024-05-19 23:24:43.457545+00:00 | 1 | 1 | 2024-05-19 23:24:43.457585+00:00 | Z3GXFaLKPXSm | RNU2-48P | None | ENSG00000222626 | snRNA | RNA, U2 small nuclear 48, pseudogene [Source:H... | 1 | 9 |
Organism
| created_at | created_by_id | run_id | updated_at | uid | name | ontology_id | scientific_name | public_source_id | |
|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||
| 1 | 2024-05-19 23:23:57.232604+00:00 | 1 | 1 | 2024-05-19 23:23:57.232697+00:00 | 1dpCL6Td | human | NCBITaxon:9606 | Homo sapiens | 8 |
Phenotype
| created_at | created_by_id | run_id | updated_at | uid | name | ontology_id | abbr | synonyms | description | public_source_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||
| 2 | 2024-05-19 23:25:25.668021+00:00 | 1 | 1 | 2024-05-19 23:25:25.668066+00:00 | 3OV8JZsS | female | PATO:0000383 | None | None | A Biological Sex Quality Inhering In An Indivi... | 47 |
| 1 | 2024-05-19 23:25:25.667829+00:00 | 1 | 1 | 2024-05-19 23:25:25.667912+00:00 | kniZxLLf | male | PATO:0000384 | None | None | A Biological Sex Quality Inhering In An Indivi... | 47 |
PublicSource
| created_at | created_by_id | run_id | updated_at | uid | entity | organism | currently_used | source | source_name | version | url | md5 | source_website | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||
| 55 | 2024-05-19 23:23:45.587948+00:00 | 1 | None | 2024-05-19 23:23:45.587983+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... |
| 54 | 2024-05-19 23:23:45.587801+00:00 | 1 | None | 2024-05-19 23:23:45.587836+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 |
| 53 | 2024-05-19 23:23:45.587654+00:00 | 1 | None | 2024-05-19 23:23:45.587690+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-... |
| 52 | 2024-05-19 23:23:45.587508+00:00 | 1 | None | 2024-05-19 23:23:45.587543+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-... |
| 51 | 2024-05-19 23:23:45.587362+00:00 | 1 | None | 2024-05-19 23:23:45.587398+00:00 | 3TI0 | Drug | all | True | dron | Drug Ontology | 2023-03-10 | https://data.bioontology.org/ontologies/DRON/s... | 75e86011158fae76bb46d96662a33ba3 | https://bioportal.bioontology.org/ontologies/DRON |
| 50 | 2024-05-19 23:23:45.587215+00:00 | 1 | None | 2024-05-19 23:23:45.587251+00:00 | 3rm9 | BFXPipeline | all | True | lamin | Bioinformatics Pipeline | 1.0.0 | s3://bionty-assets/bfxpipelines.json | a7eff57a256994692fba46e0199ffc94 | https://lamin.ai |
| 49 | 2024-05-19 23:23:45.587069+00:00 | 1 | None | 2024-05-19 23:23:45.587104+00:00 | QfYh | Pathway | all | False | pw | Pathway Ontology | 7.79 | https://data.bioontology.org/ontologies/PW/sub... | 02e2337bb1ab7cc4332ef6acc4cbdfa6 | https://www.ebi.ac.uk/ols/ontologies/pw |
Tissue
| created_at | created_by_id | run_id | updated_at | uid | name | ontology_id | abbr | synonyms | description | public_source_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||
| 17 | 2024-05-19 23:25:32.858701+00:00 | 1 | None | 2024-05-19 23:25:32.858744+00:00 | 7SvOepT5 | buccal salivary gland | UBERON:0012102 | None | None | A Salivary Gland That Is Part Of A Cheek. | 25 |
| 16 | 2024-05-19 23:25:32.858512+00:00 | 1 | None | 2024-05-19 23:25:32.858592+00:00 | 6TiLnvMv | serous gland | UBERON:0000409 | None | None | A Gland In Which The Principal Secretory Cells... | 25 |
| 15 | 2024-05-19 23:25:32.165451+00:00 | 1 | None | 2024-05-19 23:25:32.165527+00:00 | 4o2HviGe | multicellular anatomical structure | UBERON:0010000 | None | multicellular structure | An Anatomical Structure That Has More Than One... | 25 |
| 14 | 2024-05-19 23:25:31.655854+00:00 | 1 | None | 2024-05-19 23:25:31.655931+00:00 | 7HJIkVT2 | organ | UBERON:0000062 | None | None | Anatomical Structure That Performs A Specific ... | 25 |
| 13 | 2024-05-19 23:25:31.004720+00:00 | 1 | None | 2024-05-19 23:25:31.004790+00:00 | 1piRkddj | digestive system element | UBERON:0013765 | None | digestive organ|digestive system organ | Any Of The Organs Or Elements That Are Part Of... | 25 |
| 12 | 2024-05-19 23:25:31.004530+00:00 | 1 | None | 2024-05-19 23:25:31.004611+00:00 | 2PA5WYod | gland | UBERON:0002530 | None | glandular organ | An Organ That Functions As A Secretory Or Excr... | 25 |
| 11 | 2024-05-19 23:25:30.497369+00:00 | 1 | None | 2024-05-19 23:25:30.497411+00:00 | 6dBB06kF | exocrine gland | UBERON:0002365 | None | glandula exocrina|ducted gland | A Gland That Secretes Products (Excluding Horm... | 25 |
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