datasets
Training and evaluation data, with the modality, task and licence stated up front. Listed live from the Hugging Face Hub.
bio-mcp-data
Bio-MCP-Data
A repository containing biological datasets that will be used by BIO-MCP MCP (Model Context Protocol) standard.
About
This repository hosts biological data assets formatted to be compatible with the Model Context Protocol, enabling AI models to efficiently access and process biological information. The data is managed using Git Large File Storage (LFS) to handle large biological datasets.
Purpose
Provide standardized biological datasets for AI… See the full description on the dataset page: https://huggingface.co/datasets/longevity-genie/bio-mcp-data.aging-gene-expression-single-cell-mouse
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
https://www.nature.com/articles/s41586-020-2496-1#Sec2
Code to download and process this dataset is available in: https://github.com/seanome/2025-longevity-x-ai-hackathon
Dataset structure is originally from AnnData.
Descriptions of each data file is below.
Data Files
This dataset contains multiple parquet files, one for each sheet in the original Excel file:… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/aging-gene-expression-single-cell-mouse.tabula-muris-senis-bladder-smartseq2
Bladder Tissue from Tabula Muris Senis
Tabula Muris Senis is a mammalian aging single-cell gene expression dataset, downloaded from https://cellxgene.cziscience.com/collections/0b9d8a04-bb9d-44da-aa27-705bb65b54eb. This dataset represents the Bladder tissue, using the SmartSeq2 full-length mRNA library preparation method for single cells.
Code to download and process this dataset is available in: https://github.com/seanome/2025-longevity-x-ai-hackathon
Ageing is characterized by a… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/tabula-muris-senis-bladder-smartseq2.cell2sentence4longevity-data
Dataset Card: longevity-genie/cell2sentence4longevity-data
Summary
This repository contains preprocessed single-cell RNA-seq (scRNA‑seq) datasets prepared as “cell sentences” for training and evaluation of cells2sentence-style models. Each cell is represented as a space‑separated sequence of top expressed gene symbols, enabling language‑model style training for tasks such as biological age prediction and other downstream applications.
This dataset targets fine‑tuning and… See the full description on the dataset page: https://huggingface.co/datasets/longevity-genie/cell2sentence4longevity-data.my_datasetcleaned_data
Cleaned Tabula Muris Senis Single-Cell Data and other aging datasets
This dataset contains LLM-cleaned single-cell transcriptomic annotations from the Tabula Muris Senis project, specifically for mouse tissues processed with SmartSeq2, and ALL OTHER DATASETS WITH AGING IN THE FILENAME :-) . The cleaning and annotation were performed using large language models (OpenAI and Claude), enabling enriched metadata and corrected cell type labels.
🧬 Over 1.3 million rows and 78.17 GB… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/cleaned_data.transcriptomic-atlas-mouse
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Code to download and process this dataset is available in: https://github.com/seanome/2025-longevity-x-ai-hackathon
Dataset structure is originally from AnnData.
Descriptions of each data file is below.
transcriptomic-atlas-mouse_expression.parquet
The main expression matrix containing gene expression data.
transcriptomic-atlas-mouse_sample_metadata.parquet
Metadata for each… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/transcriptomic-atlas-mouse.cell2sentence4longevity-opengenes-datapan-cancer-nuclei-seg
Nuclear Aging Morphometry Dataset: TCGA Bladder Cancer Nuclei Features for Longevity Research
Dataset Description
This dataset provides nuclear morphometric features extracted from TCGA bladder cancer histopathology slides, specifically designed for aging and longevity research. The dataset contains quantitative shape measurements of >1M individual nuclei across multiple fields of view, enabling machine learning approaches to study cellular aging, senescence biomarkers… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/pan-cancer-nuclei-seg.mouse-muscle-aging-atlas-snRNAseq
Mouse Skeletal Muscle Aging Atlas (sn/scRNA-seq) Dataset
Dataset Overview
This dataset comprises single-nucleus and single-cell RNA sequencing (sn/scRNA-seq) data specifically focusing on the mouse skeletal muscle across different age groups. It serves as a valuable resource for investigating cell-type-specific gene expression changes and cellular composition shifts that occur during the aging process in a crucial mammalian model system.
The data was sourced from the… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/mouse-muscle-aging-atlas-snRNAseq.bio-faiss-longevity-v1
bio-faiss-longevity-v1
A FAISS index + metadata for scientific retrieval
Contents
index.faiss: FAISS index (cosine w/ inner product).
meta.jsonl: one JSON per chunk; fields include chunk_id, paper_id, title, section, subsection, paragraph_index, keywords, boost.
index.info.json: (optional) dimensions, index type, faiss version.
Build provenance
Chunking: hierarchical (section→paragraph→~480-token chunks, ~15% overlap)
Embedder:… See the full description on the dataset page: https://huggingface.co/datasets/bio-protocol/bio-faiss-longevity-v1.human-muscle-aging-atlas-snRNAseq
Human Skeletal Muscle Aging Atlas (sn/scRNA-seq) Dataset
1. Data Overview
This dataset provides single-nucleus and single-cell RNA sequencing (sn/scRNA-seq) data specifically focusing on the human skeletal muscle across different age groups. It serves as a rich resource for investigating cell-type specific gene expression changes and cellular composition shifts that occur during the aging process in a critical human tissue.
The original data was sourced from the Human… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/human-muscle-aging-atlas-snRNAseq.human-cornea-snRNAseq
Human Cornea Atlas (snRNA-seq) Dataset
Dataset Overview
This dataset comprises single-nucleus RNA sequencing (snRNA-seq) data specifically focusing on the cellular heterogeneity of the human cornea. It provides a high-resolution view of various cell populations and their gene expression profiles across different layers of this critical ocular tissue.
The data was sourced from a research paper providing a comprehensive single-cell transcriptome atlas of the human cornea.… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/human-cornea-snRNAseq.ainciburu2023
Dataset Card for ainciburu_processed
Dataset Summary
This dataset comprises ~115,000 CD34+ hematopoietic stem and progenitor cells (HSPCs) profiled via 10x Genomics single-cell RNA-seq from healthy young, elderly, and myelodysplastic syndrome (MDS) patients. The data originates from:
Uncovering perturbations in human hematopoiesis associated with healthy aging and myeloid malignancies at single-cell resolution— Ainciburu et al., eLife (2023)PMCID: PMC9904760DOI:… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/ainciburu2023.sc-human-blood-aging-atlas
sc-human-blood-aging-atlas
Study Description
This dataset accompanies the study “Single-cell atlas of healthy human blood unveils age-related loss of NKG2C+GZMB− CD8+ memory T cells and accumulation of type 2 memory CD4+/CD8+ T cells”, which provides a comprehensive single-cell transcriptomic and proteomic landscape of peripheral blood from healthy individuals across the adult lifespan.
Using single-cell RNA sequencing (scRNA-seq) integrated with TCR/BCR profiling and… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/sc-human-blood-aging-atlas.sc-ImmuAging
🧬 sc-ImmuAging – Human PBMC Single-Cell Aging Clock Dataset
This dataset includes curated feature selections from peripheral blood mononuclear cells (PBMCs) used to train aging clock models across five major immune cell types. It was derived from the sc-ImmuAging project to understand how aging affects the immune system at the single-cell level using machine learning models.
📦 Dataset Contents
sc-ImmuAging.parquet — Long-format data containing gene features per immune… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/sc-ImmuAging.Human_Ageing_Genomic_Resources
🧬 Human Ageing Genomic Resources (HAGR)
This dataset collection is derived from the Human Ageing Genomic Resources (HAGR), a curated set of databases focusing on the genetics of human aging, longevity, and cellular senescence. It includes several valuable resources formatted as .parquet files for easy use in data science and machine learning pipelines.
📦 Files Included
drugage.parquet: Database of drugs that affect lifespan in model organisms.
genage_human.parquet:… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/Human_Ageing_Genomic_Resources.cultured_meat_paragraphscivil-engineering-longevity
Civil Engineering Longevity
Infrastructure durability data for civil engineering.
Usage
from datasets import load_dataset
dataset = load_dataset("infra-durability-proj/civil-engineering-longevity")
df = dataset["train"].to_pandas()
Or use the provided loader:
from loader import load_data
df = load_data()
Schema
Metrics
Column
Type
Description
redundancy_factor
float
Normalized metric
load_distribution
float
Normalized metric… See the full description on the dataset page: https://huggingface.co/datasets/infra-durability-proj/civil-engineering-longevity.GSE120180
🧬 GSE120180 – Single-Cell Transcriptomics of Aging Human Skin
This dataset contains single-cell RNA-seq profiles from aging human skin, originally published as part of the GEO Series GSE120180. The dataset has been converted to .parquet format for faster I/O and compatibility with machine learning pipelines.
📂 Dataset Overview
Original Source: GEO: GSE120180
Species: Homo sapiens
Tissue: Human skin
Technique: 10x Genomics scRNA-seq
Format: .parquet (converted… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/GSE120180.mouse-glioblastoma-snRNAseq
Mouse Glioblastoma Atlas (snRNA-seq) Dataset
Dataset Overview
This dataset comprises single-nucleus RNA sequencing (snRNA-seq) data from the brain (glioblastoma tumors and their microenvironment) of both young and aged mice. It provides a high-resolution cellular and molecular census of glioblastoma, a highly aggressive brain tumor, with crucial insights into its age-related characteristics.
The original data was sourced from a CELLxGENE Discover collection titled… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/mouse-glioblastoma-snRNAseq.huberman_lab_Dr__Sara_Gottfried_How_to_Optimize_Female_Hormone_Health_for_Vitality__Longevityriken2018
Dataset Card for riken2018_processed
Dataset Summary
This dataset is derived from single-cell RNA-seq of peripheral blood mononuclear cells (PBMCs) from supercentenarians (ages 110+) and younger controls, processed from the study:
Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians— Hashimoto et al., PNAS (2019)DOI:10.1073/pnas.1907883116
The final object includes cells from three experimental batches (firstrun, SC1, SC2) and… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/riken2018.huberman_lab_Dr._Sara_Gottfried_How_to_Optimize_Female_Hormone_Health_for_Vitality__Longevityhuberman_lab_AMA_12_Thoughts_on_Longevity_Supplements__Resveratrol_NR_NMN_Etc____How_to_Improve_huberman_lab_Dr__Rhonda_Patrick_Micronutrients_for_Health__LongevityImmune-Aging-transcriptomic
🧬 Single-Cell Transcriptomic Insights into Immune Aging in Human PBMCs
This dataset was extracted from the supplementary tables of the publication:
Title: Single-cell transcriptomic landscape of human immune agingJournal: Cell Research (Nature Publishing Group), 2021DOI: 10.1038/s41422-020-00412-6
📂 Dataset Description
The data was extracted using OCR techniques from PDF tables and saved in .parquet format for easy use in data science pipelines. Each row… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/Immune-Aging-transcriptomic.smulders_longevity_extracted
🧬 Smulders Longevity Extracted Dataset
This dataset was extracted from the publication:
Genetics of human longevity: From variants to genes to pathwaysJournal of Internal Medicine, 2023 — Smulders et al.DOI: 10.1111/joim.13690
It contains structured gene names and SNP identifiers mentioned throughout the paper.
📄 Dataset Description
Column
Description
type
Entry type: Gene or SNP
id
The gene name or SNP ID
The gene names are uppercase… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/smulders_longevity_extracted.huberman_lab_Dr__Satchin_Panda_Intermittent_Fasting_to_Improve_Health_Cognition__Longevitymoskalev_papersAll Alexey Moskalev paper found inside semantic-scholar that have pubmed ids.
The parquet file schema is:
root
|-- corpusid: long (nullable = true)
|-- updated: string (nullable = true)
|-- content_source_oainfo_license: string (nullable = true)
|-- content_source_oainfo_openaccessurl: string (nullable = true)
|-- content_source_oainfo_status: string (nullable = true)
|-- content_source_pdfsha: string (nullable = true)
|-- content_source_pdfurls: array (nullable = true)
| |--… See the full description on the dataset page: https://huggingface.co/datasets/longevity-genie/moskalev_papers.