Introduction

LaminDB is an open-source data management tool that makes it easy to query, trace and govern datasets across diverse storage formats and locations. Like git, LaminDB runs anywhere and captures relevant context about your work. This includes the data flow through models and analyses, the entities and notes defining your work, and the features & schemas of datasets. It takes about a minute to install LaminDB and create a database on your laptop or in the cloud.

Why?

1. Untraceable results cannot be trusted, especially when non-verifiable tasks are delegated to agents.

2. Without effective access to multimodal data, models burn tokens or fail entirely.

3. Without governing changes to data akin to governing changes to software with git, it’s hard to evaluate agents, debug their mistakes, and safely merge their contributions.

Especially in life sciences, hard-to-verify tasks are abundant, data formats are heterogeneous, and teams need end-to-end traceability for GxP compliance (21 CFR Part 11 and EU Annex 11).

Existing data lakehouses aren’t a comprehensive solution. They only address the 2nd and 3rd of these problems for a single table or array format, such as parquet or zarr.

How?

• lineage → trace results across agent sessions, notebooks, scripts & workflows

• lakehouse → manage datasets in any format (parquet, zarr, …) with time travel, schema evolution & ACID guarantees; load/query with your favorite engine (Polars, DuckDB, annbatch, …)

• LIMS & ELN → unified schema-based records management with support for ontologies & notes

• FAIR datasets → validate & annotate files, DataFrame, AnnData, SpatialData, …

• governance → manage changes via branching & versioning

Architecture? → docs

• zero lock-in → open source, using open standards (metadata in SQLite/Postgres, data in parquet, zarr, etc.)

• scalable → hit storage & database directly through your pydata or R stack, no REST API involved

• simple → pip install lamindb or install.packages('laminr') · no Docker required, no separate backend

• unified access → local, S3, GCP, etc. · Postgres, SQLite · ontologies

• distributed → zero-copy data sharing across databases & storage

• reproducible → track agent traces, source code & compute environments

• ACID → snapshot isolation & time travel via transactional metadata records across datasets in any format (parquet, zarr, etc.)

• idempotent → re-run logic without worries about duplications or overwrites

• decoupled compute → run your favorite engine (Polars, DuckDB, data loaders, …) with all its benefits

• integrations → bio ontologies, git, nextflow, vitessce, redun, and more

• extensible → create custom plug-ins based on the Django ORM, the basis for LaminDB’s registries

Who?

Scientists and engineers at leading research institutions and biotech companies, including:

• Industry → Pfizer, Altos Labs, RefinedScience, Ensocell Therapeutics, …

• Academia & Research → scverse, DZNE (National Research Center for Neuro-Degenerative Diseases), Helmholtz Munich (National Research Center for Environmental Health), …

• Research Hospitals → Global Immunological Swarm Learning Network: Harvard, MIT, Stanford, ETH Zürich, Charité, U Bonn, Mount Sinai, …

From personal research projects to pharma-scale deployments managing petabytes of data across:

entities	OOMs
observations & datasets	10¹² & 10⁶
runs & transforms	10⁹ & 10⁵
proteins & genes	10⁹ & 10⁶
biosamples & species	10⁵ & 10²
…	…

UI, permissions, audit logs, hosting? → LaminHub

LaminHub is a collaboration hub built on LaminDB similar to how GitHub is built on git:

• permissions → role-based, fine-grained access management for humans, bots & teams

• audit logs → full traceability for compliance

• single sign-on → social logins, Okta, Ping, and other providers

• secure → SOC2 certified, monitoring ISO27001 & HIPAA compliance

• scale → transparently manage many databases and storage locations

Architecture:

• zero lock-in → LaminDB ensures data remains accessible even if you cancel LaminHub

• permissions on the Postgres & storage layer → no need for an intermediate web service

• TRE (Trusted Research Environment) → manage sensitive data from e.g. the UK Biobank

• auto-generated REST API → optional REST interface for JavaScript-based web applications

UI:

• lineage → interactive graphs for records, datasets, notebooks & pipelines

• catalog → browse, search & query records and datasets

• notebooks, workflows, runs → visualize & launch executions

• versioning → manage data & code revisions

• LIMS & ELN → records & notes integrated with ontologies

• schemas, features, labels → manage data models

Give it a try by exploring public databases at lamin.ai/explore. It’s free and no account is required.

For private data & commercial usage, see: lamin.ai/pricing.

Quickstart

To install the Python package with recommended dependencies, use:

pip install lamindb

Install with minimal dependencies.

The lamindb package adds data-science related dependencies through the [full] extra, see here.

For a minimal install of the lamindb namespace, use:

pip install lamindb-core

Agent? See .agents/, docs/ and llms.txt.

Query databases

You can browse public databases at lamin.ai/explore. To access laminlabs/cellxgene, run:

Py

import lamindb as ln

db = ln.DB("laminlabs/cellxgene")  # a database object for queries
df = db.Artifact.to_dataframe()    # a dataframe listing datasets & models

R

library(laminr)
ln <- import_module("lamindb")

db <- ln$DB("laminlabs/cellxgene")  # a database object for queries
df <- db$Artifact$to_dataframe()    # a dataframe listing datasets & models

To get a specific dataset, run:

Py

artifact = db.Artifact.get("BnMwC3KZz0BuKftR")  # a metadata object for a dataset
artifact.describe()                             # describe the context of the dataset

R

artifact <- db$Artifact$get("BnMwC3KZz0BuKftR")  # a metadata object for a dataset
artifact$describe()                             # describe the context of the dataset

See the output.

Access the content of the dataset via:

Py

local_path = artifact.cache()  # return a local path from a cache
adata = artifact.load()        # load object into memory
accessor = artifact.open()     # return a streaming accessor

R

local_path <- artifact$cache()  # return a local path from a cache
adata <- artifact$load()        # load object into memory
accessor <- artifact$open()     # return a streaming accessor

For broader queries of cellxgene, see docs.lamin.ai/cellxgene.

Create artifacts

To initialize a new database in a development directory, run:

lamin init --modules bionty  # mount module bionty

To connect to an existing database - you can create one at lamin.ai - run:

lamin login
lamin connect account/name  # tip: add flag `--here` to scope to current directory

To save a file or folder via the API:

Py

import lamindb as ln
# → connected lamindb: account/instance

open("sample.fasta", "w").write(">seq1\nACGT\n")        # create dataset
ln.Artifact("sample.fasta", key="sample.fasta").save()  # save dataset

R

library(laminr)
ln <- import_module("lamindb")
# → connected lamindb: account/instance

writeLines(">seq1\nACGT\n", "sample.fasta")        # create dataset
ln$Artifact("sample.fasta", key = "sample.fasta")$save()  # save dataset

To save a file or folder via the CLI, run:

lamin save sample.fasta --key sample.fasta

To load an artifact via the CLI into a local cache, run:

lamin load --key sample.fasta

Read more about the CLI: docs.lamin.ai/cli.

Trace data, code & agents

To track agent sessions, install the library skill: uvx library-skills --skill lamindb.

To track source code, inputs, outputs, logs, and environment of a script or notebook, use ln.track() and ln.finish():

Py

import lamindb as ln
# → connected lamindb: account/instance

ln.track()                                              # track code execution
open("sample.fasta", "w").write(">seq1\nACGT\n")        # create dataset
ln.Artifact("sample.fasta", key="sample.fasta").save()  # save dataset
ln.finish()                                             # mark run as finished

R

library(laminr)
ln <- import_module("lamindb")
# → connected lamindb: account/instance

ln$track()                                              # track code execution
writeLines(">seq1\nACGT\n", "sample.fasta")        # create dataset
ln$Artifact("sample.fasta", key = "sample.fasta")$save()  # save dataset
ln$finish()                                             # mark run as finished

If running this snippet as a script (python create_fasta.py), you’ll get the following data lineage:

Py

artifact = ln.Artifact.get(key="sample.fasta")  # get artifact by key
artifact.describe()      # context of the artifact
artifact.view_lineage()  # fine-grained lineage

R

artifact <- ln$Artifact$get(key = "sample.fasta")  # get artifact by key
artifact$describe()      # context of the artifact
artifact$view_lineage()  # fine-grained lineage

Watch a mini video: youtu.be/yK3ODFZLL1A

Access run & transform.

Py

run = artifact.run                     # get the run object
transform = artifact.run.transform     # get the transform object
run.describe()                  # context of the run

R

run <- artifact$run                     # get the run object
transform <- artifact$run$transform     # get the transform object
run$describe()                  # context of the run

Py

transform.describe()  # context of the transform

R

transform$describe()  # context of the transform

To track a workflow, decorate a function:

import lamindb as ln

@ln.flow()
def create_fasta(fasta_file: str = "sample.fasta"):
    open(fasta_file, "w").write(">seq1\nACGT\n")    # create dataset
    ln.Artifact(fasta_file, key=fasta_file).save()  # save dataset

if __name__ == "__main__":
    create_fasta()

Beyond what you get for scripts & notebooks, this automatically tracks function & CLI params and integrates well with established Python workflow managers: docs.lamin.ai/track. To integrate advanced bioinformatics pipeline managers like Nextflow, see docs.lamin.ai/pipelines.

A richer example.

Here is a re-construction of the project of Schmidt et al. (Science, 2022):

A phenotypic CRISPRa screening result is integrated with scRNA-seq data. Here is the result of the screen input:

You can explore it here.

Annotate & query artifacts

To annotate and query by entities:

Py

# create entities
my_label = ln.ULabel(name="My universal label").save()
my_project = ln.Project(name="My project label").save()

# annotate
artifact.ulabels.add(my_label)
artifact.projects.add(my_project)

# query
ln.Artifact.filter(ulabels=my_label, projects=my_project).to_dataframe()

R

# create entities
my_label <- ln$ULabel(name = "My universal label")$save()
my_project <- ln$Project(name = "My project label")$save()

# annotate
artifact$ulabels$add(my_label)
artifact$projects$add(my_project)

# query
ln$Artifact$filter(ulabels = my_label, projects = my_project)$to_dataframe()

This also works for custom entities, for example, ontology terms:

Py

import bionty as bt

# import an entity from a public ontology source, e.g., by name or an ontology ID
hek293 = bt.CellLine.from_source(name="HEK293").save()
hras = bt.Gene.from_source(ensembl_gene_id="ENSG00000174775").save()

# annotate
artifact.cell_lines.add(hek293)
artifact.genes.add(hras)

# query
ln.Artifact.filter(cell_lines=hek293, genes=hras).to_dataframe(
    include=["cell_lines__name", "genes__symbol"]
)

R

bt <- import_module("bionty")

# import an entity from a public ontology source, e$g., by name or an ontology ID
hek293 <- bt$CellLine$from_source(name = "HEK293")$save()
hras <- bt$Gene$from_source(ensembl_gene_id = "ENSG00000174775")$save()

# annotate
artifact$cell_lines$add(hek293)
artifact$genes$add(hras)

# query
ln$Artifact$filter(cell_lines = hek293, genes = hras)$to_dataframe(
    include = list("cell_lines__name", "genes__symbol")
)

To annotate & query by features:

Py

from datetime import date

# define features
gc_content = ln.Feature(name="gc_content", dtype=float).save()
seq_date = ln.Feature(name="seq_date", dtype=date).save()

# annotate
artifact.features.set_values({
    gc_content: 0.55,
    seq_date: date.today(),
})

# query
ln.Artifact.filter(seq_date == date.today()).to_dataframe(include="features")

R

datetime <- import_module("datetime")
date <- datetime$date

# define features
gc_content <- ln$Feature(name = "gc_content", dtype = "float")$save()
seq_date <- ln$Feature(name = "seq_date", dtype = date)$save()

# annotate
artifact$features$set_values(list(
    gc_content = 0.55,
    seq_date = date$today()
))

# query
ln$Artifact$filter(seq_date == date$today())$to_dataframe(include = "features")

To query by auto-tracked metadata:

Py

# by storage location and size
ln.Artifact.filter(storage__root=ln.settings.storage.root)
ln.Artifact.filter(size__gt=1e6).to_dataframe()

# by data lineage
ln.Artifact.filter(run=run).to_dataframe()
ln.Artifact.filter(run__transform=transform).to_dataframe()

# include more information in resulting dataframe
ln.Artifact.to_dataframe(include=["run__transform__key", "storage__root"])

R

# by storage location and size
ln$Artifact$filter(storage__root = ln$settings$storage$root)
ln$Artifact$filter(size__gt = 1e6)$to_dataframe()

# by data lineage
ln$Artifact$filter(run = run)$to_dataframe()
ln$Artifact$filter(run__transform = transform)$to_dataframe()

# include more information in resulting dataframe
ln$Artifact$to_dataframe(include = list("run__transform__key", "storage__root"))

Read more: docs.lamin.ai/organize or docs.lamin.ai/query-search

Create records & notes

You can create record types to model metadata for any entity:

Py

# create record types
experiment_type = ln.Record(name="Experiments", is_type=True).save()
sample_type = ln.Record(name="Samples", is_type=True).save()

# create an experiment
experiment1 = ln.Record(
    name="Experiment 1",
    features={seq_date: date.today()},
    type=experiment_type
).save()

# create a sample that links to "Experiment 1" via a feature
experiment = ln.Feature(name="experiment", dtype=experiment_type).save()
sample1 = ln.Record(
    features={gc_content: 0.5, experiment: experiment1},
    type=sample_type
).save()

# export all experiments and all samples
experiment_type.to_dataframe()
sample_type.to_dataframe()

R

# create record types
experiment_type <- ln$Record(name = "Experiments", is_type = TRUE)$save()
sample_type <- ln$Record(name = "Samples", is_type = TRUE)$save()

# create an experiment
experiment1 <- ln$Record(
    name = "Experiment 1",
    features = list(seq_date = date$today()),
    type = experiment_type
)$save()

# create a sample that links to "Experiment 1" via a feature
experiment <- ln$Feature(name = "experiment", dtype = experiment_type)$save()
sample1 <- ln$Record(
    features = list(gc_content = 0.5, experiment = experiment1),
    type = sample_type
)$save()

# export all experiments and all samples
experiment_type$to_dataframe()
sample_type$to_dataframe()

You can save markdown notes as records:

lamin save <topic>/<my-note.md>

To load a record back as a markdown file, run:

lamin load https://lamin.ai/laminlabs/lamindata/record/mNDJgWFrkWQVW3ox

Watch a mini video: youtu.be/NRzVQXJaRH8

Read more: docs.lamin.ai/manage-records.

Validate datasets

Here is how you ingest a DataFrame:

Py

import pandas as pd

df = pd.DataFrame({
    "seq_str": ["ACGT", "TGCA"],
    "gc_content": [0.55, 0.54],
    "experiment_note": ["Looks great", "Ok"],
    "seq_date": [date(2025, 10, 24), date(2025, 10, 25)],
})
ln.Artifact.from_dataframe(df, key="my_datasets/sequences.parquet").save()  # no validation

R

pd <- import_module("pandas")

df <- pd$DataFrame(list(
    seq_str = list("ACGT", "TGCA"),
    gc_content = list(0.55, 0.54),
    experiment_note = list("Looks great", "Ok"),
    seq_date = list(date(2025L, 10L, 24L), date(2025L, 10L, 25L))
))
ln$Artifact$from_dataframe(df, key = "my_datasets/sequences.parquet")$save()  # no validation

The simplest way to validate & annotate the content of the dataframe is the built-in schema valid_features:

Py

ln.Feature(name="seq_str", dtype=str).save()  # define remaining features
ln.Feature(name="experiment_note", dtype=str).save()
artifact = ln.Artifact.from_dataframe(
    df,
    key="my_datasets/sequences.parquet",
    schema="valid_features"  # validate columns against features
).save()
artifact.describe()

R

ln$Feature(name = "seq_str", dtype = "str")$save()  # define remaining features
ln$Feature(name = "experiment_note", dtype = "str")$save()
artifact <- ln$Artifact$from_dataframe(
    df,
    key = "my_datasets/sequences.parquet",
    schema = "valid_features"  # validate columns against features
)$save()
artifact$describe()

You can filter for datasets by schema and then launch distributed queries or batch load distributed datasets. For tables, see: docs.lamin.ai/tables. For arrays, see: docs.lamin.ai/arrays.

Watch a mini video: youtu.be/Ji6E7hTnReQ

To validate an AnnData, call:

Py

import anndata as ad
import numpy as np
import pandas as pd

adata = ad.AnnData(
    X=np.ones((21, 10)),
    obs=pd.DataFrame({'cell_type_by_model': ['T cell', 'B cell', 'NK cell'] * 7}),
    var=pd.DataFrame(index=[f'ENSG{i:011d}' for i in range(10)])
)
artifact = ln.Artifact.from_anndata(
    adata,
    key="my_datasets/scrna.h5ad",
    schema="ensembl_gene_ids_and_valid_features_in_obs"
).save()
artifact.describe()

R

ad <- import_module("anndata")
np <- import_module("numpy")
pd <- import_module("pandas")

adata <- anndata::AnnData(
    X = np$ones((21, 10)),
    obs = pd$DataFrame(list(cell_type_by_model = rep(list('T cell', 'B cell', 'NK cell'), 7))),
    var = pd$DataFrame(index = sprintf("ENSG%010d", 1:10))
)
artifact <- ln$Artifact$from_anndata(
    adata,
    key = "my_datasets/scrna.h5ad",
    schema = "ensembl_gene_ids_and_valid_features_in_obs"
)$save()
artifact$describe()

To validate a SpatialData or any other array-like dataset, you need to construct a Schema. You can do this by composing simple pandera-style schemas: docs.lamin.ai/curate.

Use branching & versioning

LaminDB co-versions code and datasets for you. If you edit and run the create_fasta.py script, you’ll automatically create a new version of the transform and the sample.fasta artifact.

The edited script

Py

# create_fasta.py
import lamindb as ln

ln.track()
open("sample.fasta", "w").write(">seq1\nTGCA\n")  # a new sequence
ln.Artifact("sample.fasta", key="sample.fasta", features={"experiment": "Experiment 1"}).save()  # annotate with the new experiment
ln.finish()

R

# create_fasta$py
library(laminr)
ln <- import_module("lamindb")

ln$track()
writeLines(">seq1\nTGCA\n", "sample.fasta")  # a new sequence
ln$Artifact("sample.fasta", key = "sample.fasta", features = list(experiment = "Experiment 1"))$save()  # annotate with the new experiment
ln$finish()

Py

artifact_latest = ln.Artifact.get(key="sample.fasta")  # pass version for a previous version: ln.Artifact.get(key="sample.fasta", version="1.0")
artifact_latest.versions.to_dataframe()                # all versions of that artifact
artifact_latest.run.transform.versions.to_dataframe()  # all versions of the transform that created the artifact

R

artifact_latest <- ln$Artifact$get(key = "sample.fasta")  # pass version for a previous version: ln$Artifact$get(key = "sample.fasta", version = "1.0")
artifact_latest$versions$to_dataframe()                # all versions of that artifact
artifact_latest$run$transform$versions$to_dataframe()  # all versions of the transform that created the artifact

To isolate changes, create a contribution branch and switch to it as in git:

lamin switch -c my_branch

To merge a contribution branch into main, run:

lamin switch main  # switch to the main branch
lamin merge my_branch  # merge contribution branch into main

Read more: docs.lamin.ai/manage-changes.

Watch a mini video: youtu.be/rzRwcMj6-fc

Share datasets

To share data in a lineage-aware way, transfer objects from a source database to your default database:

Py

db = ln.DB("laminlabs/lamindata")
artifact = db.Artifact.get(key="example_datasets/mini_immuno/dataset1.h5ad")
artifact.save()

R

db <- ln$DB("laminlabs/lamindata")
artifact <- db$Artifact$get(key = "example_datasets/mini_immuno/dataset1.h5ad")
artifact$save()

This is zero-copy for the artifact’s data in storage. Read more: docs.lamin.ai/transfer.

Manage ontologies

bionty gives you >20 public ontologies so that you don’t have build ontologies for basic biological entities from scratch. The Gene registry was used to validate the ENSG ids in the adata just before. Here is how you import a public ontology source into the CellType registry:

Py

import bionty as bt

bt.CellType.import_source()  # import the default ontology
bt.CellType.to_dataframe()   # your extensible cell type ontology in a simple registry

R

bt <- import_module("bionty")

bt$CellType$import_source()  # import the default ontology
bt$CellType$to_dataframe()   # your extensible cell type ontology in a simple registry

You can then create objects, e.g. for labeling, analogous to ULabel or Project:

Py

t_cell = bt.CellType.get(name="T cell")
artifact.cell_types.add(t_cell)

R

t_cell <- bt$CellType$get(name = "T cell")
artifact$cell_types$add(t_cell)

Read more: docs.lamin.ai/manage-ontologies.

Watch a mini video: youtu.be/3vpWjHj3Kw8