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  • Guide
  • API
  • Changelog

How to

  • Query & search
    • Query & search registries
    • Slice arrays
  • Track notebooks, scripts & functions
  • Curate datasets
  • Manage biological registries
  • Transfer data

Other topics

  • FAQ
    • Pydantic & Pandera vs. LaminDB
    • Will data get duplicated upon re-running code?
    • Will data & metadata stay in sync?
    • Can I disable tracking run inputs?
    • What happens when importing lamindb and the instance is not yet setup?
    • How do I validate & annotate arbitrary data structures?
    • What happens if I import a schema module without lamindb?
    • Where to store external links and IDs?
    • When does visibility of artifacts and collections change?
    • How to delete records?
    • Keep artifacts local in a cloud instance
    • Django field validation
    • Why should I not index datasets with gene symbols?
    • How does search work?
  • Storage
    • Track artifacts, in-memory objects & folders [S3 storage]
    • Add, replace, cache and delete artifacts
    • Test AnnDataAccessor
    • Prepare transfer artifacts from a local instance to a cloud instance
    • Transfer artifacts from a local instance to a cloud instance
    • Vitessce integration

Where to store external links and IDs?¶

When registering data in LaminDB, you might want to store a reference link or ID to indicate the source of the collection.

We have reference and reference_type fields for this purpose, they are available for Collection, Transform, Run and ULabel.

# !pip install lamindb
!lamin init --storage testreference
→ initialized lamindb: testuser1/testreference
import lamindb as ln
→ connected lamindb: testuser1/testreference

Let’s say we have a few donor samples that came form Vendor X, in order to chase back the orders, I’d like to keep track the donor ids provided by the vendor:

ln.ULabel(
    name="donor 001", reference="VX984545", reference_type="Donor ID from Vendor X"
)
ULabel(uid='sEFqSLFO', name='donor 001', is_type=False, reference='VX984545', reference_type='Donor ID from Vendor X', branch_id=1, space_id=1, created_by_id=1, created_at=<django.db.models.expressions.DatabaseDefault object at 0x7f4deb744980>)
!lamin delete --force testreference
• deleting instance testuser1/testreference

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What happens if I import a schema module without lamindb?

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When does visibility of artifacts and collections change?

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