Can I use LaminDB with cloud storage providers?

Yes, LaminDB supports local filesystems, AWS S3, Google Cloud Storage, and S3-compatible systems like MinIO or Cloudflare R2.

Which biological ontologies does LaminDB support?

Through its Bionty integration, it supports ontologies for genes, proteins, cell types, tissues, diseases, phenotypes, pathways, and organisms.

Is LaminDB compatible with single-cell analysis tools?

Absolutely. It features deep integration with AnnData, MuData, and scVI-tools, including specialized curators for validating single-cell metadata.

What is the primary purpose of the LaminDB skill?

LaminDB is used to make biological data queryable, traceable, and reproducible by providing a framework for managing datasets, tracking lineage, and validating metadata against ontologies.

Does this skill help with workflow automation?

Yes, it provides specific guidance for integrating LaminDB with workflow managers like Nextflow, Snakemake, and Redun to track pipeline execution.

LaminDB Biological Data Framework

Name: LaminDB Biological Data Framework
Author: Zehong-Wang

byZehong-Wang

0•

Ciencia de Datos y ML

Manages biological datasets with automated lineage tracking, ontology-based validation, and FAIR data principles through a unified Python API.

LaminDB is an open-source data framework designed specifically for biological research, enabling scientists and engineers to create queryable, traceable, and reproducible data lakehouses. It bridges the gap between raw data and analysis by providing built-in support for biological ontologies, automated computational lineage, and seamless integration with workflow managers like Nextflow and Snakemake. Whether managing single-cell genomics, spatial transcriptomics, or clinical datasets, LaminDB ensures data remains findable and interoperable across the entire research lifecycle while maintaining strict version control and environment tracking.

Características Principales

01Unified querying across diverse formats including AnnData, Parquet, Zarr, and TileDB-SOMA

02Robust schema validation and curation workflows for FAIR compliance

03Standardized biological annotation using integrated ontologies like Ensembl and Mondo

04Cloud-native storage integration with AWS S3, Google Cloud, and PostgreSQL support

050 GitHub stars

06Automated lineage tracking for data, code, and computational environments

Casos de Uso

01Tracking provenance and reproducibility in complex ML pipelines integrated with W&B or MLflow

02Building a centralized, searchable data lakehouse for cross-study biological meta-analysis

03Validating and annotating single-cell RNA-seq datasets with canonical cell type ontologies

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add zehong-wang/kosmos lamindb

For use in Claude.ai and ChatGPT

Download Skill