Open falexwolf opened 1 month ago
Artifact(uid='kOUejI4cVj3rHcOG0000', is_latest=True, description='mock AnnData', suffix='.h5ad', type='dataset', size=20336, hash='8z6kAdTVBaDIDuA6aivzNg', n_observations=3, _hash_type='md5', _accessor='AnnData', visibility=1, _key_is_virtual=True, created_at=2024-10-22 19:44:26 UTC)
Provenance
.storage: Storage = 's3://lamin-us-west-2/6uvjeXbzpPH2'
.transform: Transform = 'Curate datasets'
.run: Run = '2024-10-22 19:37:01 UTC'
.created_by: User = 'sunnyosun'
Labels
.cell_types: CellType
Simple fields
.uid: CharField
.name: CharField
.ontology_id: CharField
.abbr: CharField
.synonyms: TextField
.description: TextField
.created_at: DateTimeField
.updated_at: DateTimeField
Relational fields
.created_by: User
.run: Run
.source: bionty.Source
.parents: bionty.CellType
.artifacts: Artifact
Bionty fields
.children: bionty.CellType = 'astrocyte', 'cerebral cortex pyramidal neuron', 'oligodendrocyte'
.experimental_factors: ExperimentalFactor
Simple fields
.uid: CharField
.name: CharField
.ontology_id: CharField
.abbr: CharField
.synonyms: TextField
.description: TextField
.molecule: TextField
.instrument: TextField
.measurement: TextField
.created_at: DateTimeField
.updated_at: DateTimeField
Relational fields
.created_by: User
.run: Run
.source: bionty.Source
.parents: bionty.ExperimentalFactor
.artifacts: Artifact
Bionty fields
.children: bionty.ExperimentalFactor = 'single-cell RNA sequencing'
.ulabels: ULabel
Simple fields
.uid: CharField
.name: CharField
.description: TextField
.reference: CharField
.reference_type: CharField
.created_at: DateTimeField
.updated_at: DateTimeField
Relational fields
.created_by: User
.run: Run
.parents: ULabel
.transforms: Transform
.children: ULabel
.artifacts: Artifact
.collections: Collection = 'D0001', 'D0002', 'D0003'
Features
'assay_ontology_id': cat[bionty.ExperimentalFactor] = 'single-cell RNA sequencing'
'cell_type': cat[bionty.CellType] = 'astrocyte', 'cerebral cortex pyramidal neuron', 'oligodendrocyte'
'donor': cat[ULabel] = 'D0001', 'D0002', 'D0003'
Feature sets
'var' = 'CD4', 'TCF7', 'CD8A', 'CD3E', 'PDCD1'
'obs' = 'cell_type', 'assay_ontology_id', 'donor'
It's OK In prod (e.g. here https://docs.lamin.ai/scrna#populate-metadata-registries-based-on-an-artifact)
I just saw it in a notebook from @sunnyosun