gh-k-dense-ai-claude-scientific-skills-scientific-skills/skills/lamindb/references/core-concepts.md

LaminDB Core Concepts

This document covers the fundamental concepts and building blocks of LaminDB: Artifacts, Records, Runs, Transforms, Features, and data lineage tracking.

Artifacts

Artifacts represent datasets in various formats (DataFrames, AnnData, SpatialData, Parquet, Zarr, etc.). They serve as the primary data objects in LaminDB.

Creating and Saving Artifacts

From file:

import lamindb as ln

# Save a file as artifact
ln.Artifact("sample.fasta", key="sample.fasta").save()

# With description
artifact = ln.Artifact(
    "data/analysis.h5ad",
    key="experiments/scrna_batch1.h5ad",
    description="Single-cell RNA-seq batch 1"
).save()

From DataFrame:

import pandas as pd

df = pd.read_csv("data.csv")
artifact = ln.Artifact.from_dataframe(
    df,
    key="datasets/processed_data.parquet",
    description="Processed experimental data"
).save()

From AnnData:

import anndata as ad

adata = ad.read_h5ad("data.h5ad")
artifact = ln.Artifact.from_anndata(
    adata,
    key="scrna/experiment1.h5ad",
    description="scRNA-seq data with QC"
).save()

Retrieving Artifacts

# By key
artifact = ln.Artifact.get(key="sample.fasta")

# By UID
artifact = ln.Artifact.get("aRt1Fact0uid000")

# By filter
artifact = ln.Artifact.filter(suffix=".h5ad").first()

Accessing Artifact Content

# Get cached local path
local_path = artifact.cache()

# Load into memory
data = artifact.load()  # Returns DataFrame, AnnData, etc.

# Streaming access (for large files)
with artifact.open() as f:
    # Read incrementally
    chunk = f.read(1000)

Artifact Metadata

# View all metadata
artifact.describe()

# Access specific metadata
artifact.size          # File size in bytes
artifact.suffix        # File extension
artifact.created_at    # Timestamp
artifact.created_by    # User who created it
artifact.run          # Associated run
artifact.transform    # Associated transform
artifact.version      # Version string

Records

Records represent experimental entities: samples, perturbations, instruments, cell lines, and any other metadata entities. They support hierarchical relationships through type definitions.

Creating Records

# Define a type
sample_type = ln.Record(name="Sample", is_type=True).save()

# Create instances of that type
ln.Record(name="P53mutant1", type=sample_type).save()
ln.Record(name="P53mutant2", type=sample_type).save()
ln.Record(name="WT-control", type=sample_type).save()

Searching Records

# Text search
ln.Record.search("p53").to_dataframe()

# Filter by fields
ln.Record.filter(type=sample_type).to_dataframe()

# Get specific record
record = ln.Record.get(name="P53mutant1")

Hierarchical Relationships

# Establish parent-child relationships
parent_record = ln.Record.get(name="P53mutant1")
child_record = ln.Record(name="P53mutant1-replicate1", type=sample_type).save()
child_record.parents.add(parent_record)

# Query relationships
parent_record.children.to_dataframe()
child_record.parents.to_dataframe()

Runs & Transforms

These capture computational lineage. A Transform represents a reusable analysis step (notebook, script, or function), while a Run documents a specific execution instance.

Basic Tracking Workflow

import lamindb as ln

# Start tracking (beginning of notebook/script)
ln.track()

# Your analysis code
data = ln.Artifact.get(key="input.csv").load()
# ... perform analysis ...
result.to_csv("output.csv")
artifact = ln.Artifact("output.csv", key="output.csv").save()

# Finish tracking (end of notebook/script)
ln.finish()

Tracking with Parameters

ln.track(params={
    "learning_rate": 0.01,
    "batch_size": 32,
    "epochs": 100,
    "downsample": True
})

# Query runs by parameters
ln.Run.filter(params__learning_rate=0.01).to_dataframe()
ln.Run.filter(params__downsample=True).to_dataframe()

Tracking with Projects

# Associate with project
ln.track(project="Cancer Drug Screen 2025")

# Query by project
project = ln.Project.get(name="Cancer Drug Screen 2025")
ln.Artifact.filter(projects=project).to_dataframe()
ln.Run.filter(project=project).to_dataframe()

Function-Level Tracking

Use the @ln.tracked() decorator for fine-grained lineage:

@ln.tracked()
def preprocess_data(input_key: str, output_key: str, normalize: bool = True) -> None:
    """Preprocess raw data and save result."""
    # Load input (automatically tracked)
    artifact = ln.Artifact.get(key=input_key)
    data = artifact.load()

    # Process
    if normalize:
        data = (data - data.mean()) / data.std()

    # Save output (automatically tracked)
    ln.Artifact.from_dataframe(data, key=output_key).save()

# Each call creates a separate Transform and Run
preprocess_data("raw/batch1.csv", "processed/batch1.csv", normalize=True)
preprocess_data("raw/batch2.csv", "processed/batch2.csv", normalize=False)

Accessing Lineage Information

# From artifact to run
artifact = ln.Artifact.get(key="output.csv")
run = artifact.run
transform = run.transform

# View details
run.describe()          # Run metadata
transform.describe()    # Transform metadata

# Access inputs
run.inputs.to_dataframe()

# Visualize lineage graph
artifact.view_lineage()

Features

Features define typed metadata fields for validation and querying. They enable structured annotation and searching.

Defining Features

from datetime import date

# Numeric feature
ln.Feature(name="gc_content", dtype=float).save()
ln.Feature(name="read_count", dtype=int).save()

# Date feature
ln.Feature(name="experiment_date", dtype=date).save()

# Categorical feature
ln.Feature(name="cell_type", dtype=str).save()
ln.Feature(name="treatment", dtype=str).save()

Annotating Artifacts with Features

# Single values
artifact.features.add_values({
    "gc_content": 0.55,
    "experiment_date": "2025-10-31"
})

# Using feature registry records
gc_content_feature = ln.Feature.get(name="gc_content")
artifact.features.add(gc_content_feature)

Querying by Features

# Filter by feature value
ln.Artifact.filter(gc_content=0.55).to_dataframe()
ln.Artifact.filter(experiment_date="2025-10-31").to_dataframe()

# Comparison operators
ln.Artifact.filter(read_count__gt=1000000).to_dataframe()
ln.Artifact.filter(gc_content__gte=0.5, gc_content__lte=0.6).to_dataframe()

# Check for presence of annotation
ln.Artifact.filter(cell_type__isnull=False).to_dataframe()

# Include features in output
ln.Artifact.filter(treatment="DMSO").to_dataframe(include="features")

Nested Dictionary Features

For complex metadata stored as dictionaries:

# Access nested values
ln.Artifact.filter(study_metadata__detail1="123").to_dataframe()
ln.Artifact.filter(study_metadata__assay__type="RNA-seq").to_dataframe()

Data Lineage Tracking

LaminDB automatically captures execution context and relationships between data, code, and runs.

What Gets Tracked

• Source code: Script/notebook content and git commit
• Environment: Python packages and versions
• Input artifacts: Data loaded during execution
• Output artifacts: Data created during execution
• Execution metadata: Timestamps, user, parameters
• Computational dependencies: Transform relationships

Viewing Lineage

# Visualize full lineage graph
artifact.view_lineage()

# View captured metadata
artifact.describe()

# Access related entities
artifact.run              # The run that created it
artifact.run.transform    # The transform (code) used
artifact.run.inputs       # Input artifacts
artifact.run.report       # Execution report

Querying Lineage

# Find all outputs from a transform
transform = ln.Transform.get(name="preprocessing.py")
ln.Artifact.filter(transform=transform).to_dataframe()

# Find all artifacts from a specific user
user = ln.User.get(handle="researcher123")
ln.Artifact.filter(created_by=user).to_dataframe()

# Find artifacts using specific inputs
input_artifact = ln.Artifact.get(key="raw/data.csv")
runs = ln.Run.filter(inputs=input_artifact)
ln.Artifact.filter(run__in=runs).to_dataframe()

Versioning

LaminDB manages artifact versioning automatically when source data or code changes.

Automatic Versioning

# First version
artifact_v1 = ln.Artifact("data.csv", key="experiment/data.csv").save()

# Modify and save again - creates new version
# (modify data.csv)
artifact_v2 = ln.Artifact("data.csv", key="experiment/data.csv").save()

Working with Versions

# Get latest version (default)
artifact = ln.Artifact.get(key="experiment/data.csv")

# View all versions
artifact.versions.to_dataframe()

# Get specific version
artifact_v1 = artifact.versions.filter(version="1").first()

# Compare versions
v1_data = artifact_v1.load()
v2_data = artifact.load()

Best Practices

1. Use meaningful keys: Structure keys hierarchically (e.g., project/experiment/sample.h5ad)
2. Add descriptions: Help future users understand artifact contents
3. Track consistently: Call ln.track() at the start of every analysis
4. Define features upfront: Create feature registry before annotation
5. Use typed features: Specify dtypes for better validation
6. Leverage versioning: Don't create new keys for minor changes
7. Document transforms: Add docstrings to tracked functions
8. Set projects: Group related work for easier organization and access control
9. Query efficiently: Use filters before loading large datasets
10. Visualize lineage: Use view_lineage() to understand data provenance