Quickstart

!lamin init --storage ./test-clinicore --schema bionty,clinicore

import clinicore as cl

cl.Project

→ connected lamindb: testuser1/test-clinicore

Project
  Simple fields
    .uid: CharField
    .name: CharField
    .description: TextField
    .created_at: DateTimeField
    .updated_at: DateTimeField
  Relational fields
    .created_by: User
    .run: Run
    .artifacts: Artifact
    .collections: Collection
  Clinicore fields
    .biosamples: clinicore.Biosample

project = cl.Project(name="Project 001", description="This is a test project").save()

project

Project(uid='eDiEX4fe', name='Project 001', description='This is a test project', created_by_id=1, updated_at='2024-09-02 15:00:14 UTC')

import bionty as bt

medication_source = bt.Source.get(name="chebi")
cl.Medication.add_source(medication_source)

→ due to lack of write access, LaminDB won't manage storage location: s3://bionty-assets/

→ source added!

Source(uid='2Wsn', entity='clinicore.Medication', organism='all', name='chebi', version='2024-07-27', in_db=False, currently_used=True, description='Chemical Entities of Biological Interest', url='s3://bionty-assets/df_all__chebi__2024-07-27__Drug.parquet', source_website='https://www.ebi.ac.uk/chebi/', created_by_id=1, dataframe_artifact_id=1, updated_at='2024-09-02 15:00:17 UTC')

medication = cl.Medication.from_source(name="Vismione D").save()

medication

Medication(uid='13okFM0p', name='Vismione D', ontology_id='CHEBI:10000', chembl_id='CHEMBL487795', synonyms='Vismione D', created_by_id=1, source_id=97, updated_at='2024-09-02 15:00:19 UTC')