Versioned tabular datasets with provenance tracking and citation indexing
The Parkinson's Progression Markers Initiative (PPMI) is a landmark observational study of 400+ newly diagnosed PD patients followed longitudinally with clinical, imaging, and biomarker data. CSF alph
Cryo-EM structural data of tau filament polymorphs from human brain tissue, including AD paired helical filaments (PHF), PSP 4R-tau strains, CBD 4R-tau strains (astrocytic plaques), and CTE strains. F
Aggregated wearable sensor, smartphone, and clinical digital biomarker datasets for neurodegeneration prediction, including the UPDRS/MDS-UPDRS sensor substudy, the FDA MyStudies digital PD data, and
Single-cell RNA-seq atlas profiling p16/p21-positive senescent cells in aging human brain, including senescent astrocytes, microglia, and oligodendrocyte precursors. Includes data from Musi et al. 201
Aggregated polysomnography (PSG) and sleep EEG studies examining sleep disruption as biomarker and driver of neurodegeneration, including the Wisconsin Sleep Cohort, the SHHS (Sleep Heart Health Study
Curated collection of 16S rRNA amplicon sequencing studies comparing gut microbiome composition in Parkinson's disease patients vs. controls, including the landmark Sampson et al. 2016 Cell study (GEO
Reference neuropathological staging data for tau (Braak 0-VI) and alpha-synuclein (Braak PD stages 1-6) pathology progression, derived from the original Braak et al. studies (2003 Neurobiology of Agin
Multi-study atlas of gene expression changes in the aging mouse brain, spanning 3 to 24 months of age across multiple brain regions. Combines bulk RNA-seq from the Tabula Muris Senis (Allen Institute
Genome-wide CRISPR screen datasets in neuronal cell lines and iPSC-derived neurons identifying genes modifying neurodegeneration. Includes Hart et al. 2015 Science (essential gene screen), Tian et al.
Proteomic characterization of blood-brain barrier surface receptors including transferrin receptor (TfR1), LRP1, TMEM30A, and related antibody transcytosis targets. Aggregated from BBB proteomics stud
The Human Connectome Project (HCP) provides high-resolution structural and functional MRI data from 1,200+ healthy young adults plus the Lifespan HCP for aging cohorts. Provides normative connectome d
Open-access neural dynamics recordings from Allen Institute. Includes electrophysiology datasets spanning hippocampal circuits, cortical dynamics, and sensory processing in mouse models. Provides circ
ENCODE Project data for neuronal and brain cell types including H3K27ac, H3K4me3, H3K27me3 ChIP-seq and ATAC-seq profiling of neurons, astrocytes, and microglia. Provides reference chromatin state map
UK Biobank Alzheimer's disease by proxy GWAS (Marioni et al. 2018; PMID 30315176). IEU OpenGWAS accession ieu-b-2. Phenotype: one or both parents with self-reported AD (UKB Fields 20107/20110). N=314,
Registered via Biomni parity pipeline. URL: https://www.niagads.org/node/42221 | Version: 2024-06 | Institution: NIAGADS
Registered via Biomni parity pipeline. URL: https://github.com/sqjin/CellChat | Version: 2024-06 | Institution: CUHK
Structured registry of Alzheimer's Disease clinical trials with NCT identifiers, source URLs, update timestamps, phase, status, mechanism, intervention, enrollment, and evidence tiers. Covers active r
Registered via Biomni parity pipeline. URL: https://clinicaltrials.gov/api/query/study_fields | Version: 2026-04 | Institution: NIH/NLM
Wisconsin Registry for Alzheimer's Prevention (WRAP) — longitudinal AD-risk cohort with cognitive assessments, A/T/N CSF biomarkers (Aβ42/40, p-tau181, t-tau, NfL, neurogranin), neuroimaging (AV45/PiB
Registered via Biomni parity pipeline. URL: http://adni.loni.usc.edu/data-samples/adni-data/ | Version: 2024-12 | Institution: UCSF/Loni UCLA
Registered via Biomni parity pipeline. URL: https://naccdata.org/data-access/uniform-data-set | Version: 2024-06 | Institution: NACC/UW
Registered via Biomni parity pipeline. URL: http://adni.loni.usc.edu/data-samples/adni-data/ | Version: 2024-12 | Institution: UCSF/Loni UCLA
Registered via Biomni parity pipeline. URL: https://platform.opentargets.org/disease/MONDO_0004975/associations | Version: 2026-04 | Institution: OpenTargets
Registered via Biomni parity pipeline. URL: https://www.ebi.ac.uk/gwas/efotraits/EFO_0000249 | Version: 2026-04 | Institution: NHGRI-EBI
Registered via Biomni parity pipeline. URL: https://www.synapse.org/#!Synapse:syn3606086 | Version: 2024-06 | Institution: Rush University
Registered via Biomni parity pipeline. URL: https://www.synapse.org/#!Synapse:syn21587433 | Version: 2024-03 | Institution: Banner/Army MRT
Registered via Biomni parity pipeline. URL: https://www.synapse.org/#!Synapse:syn3157744 | Version: 2024-03 | Institution: Mayo Clinic
Registered via Biomni parity pipeline. URL: https://www.synapse.org/#!Synapse:syn3157743 | Version: 2024-03 | Institution: Mount Sinai
Registered via Biomni parity pipeline. URL: https://cellxgene.cziscience.com/ | Version: 2025-01 | Institution: CZIS
Registered via Biomni parity pipeline. URL: https://knowledge.brain-map.org/spatialdata | Version: 2025-01 | Institution: Allen Institute
Registered via Biomni parity pipeline. URL: https://cellxgene.cziscience.com/collections/1ca90a40-d852-4f62-8ed2-68886a6a33d4 | Version: 2024-12 | Institution: University of Washington
Registered via Biomni parity pipeline. URL: https://www.ncbi.nlm.nih.gov/gene/4137 | Version: 2024-06 | Institution: NCBI
Registered via Biomni parity pipeline. URL: https://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000186868 | Version: 112 | Institution: EBI/Sanger
Registered via Biomni parity pipeline. URL: https://gmrepo.humangut.info/ | Version: 2024-01 | Institution: HKUST
Registered via Biomni parity pipeline. URL: https://www.ebi.ac.uk/ena/browser/view/PRJNA385613 | Version: 2024-06 | Institution: Various
Registered via Biomni parity pipeline. URL: https://www.synapse.org/#!Synapse:syn3388564 | Version: 2024-06 | Institution: Rush University
Registered via Biomni parity pipeline. URL: https://cellxgene.cziscience.com/collections/1ca90a40-d852-4f62-8ed2-68886a6a33d4 | Version: 2024-12 | Institution: University of Washington
Registered via Biomni parity pipeline. URL: https://www.rcsb.org/structure/6CU7 | Version: 2024-06 | Institution: RCSB
Registered via Biomni parity pipeline. URL: https://alphafold.ebi.ac.uk/entry/P37840 | Version: 2024-01 | Institution: DeepMind/EMBL-EBI
Registered via Biomni parity pipeline. URL: https://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/release/20130502/ | Version: Phase 3 | Institution: NCBI/IGSR
Registered via Biomni parity pipeline. URL: https://www.niagads.org/node/42221 | Version: 2024-06 | Institution: NIAGADS
Ground-truth answer key for the OT-AD Target Ranking benchmark (bench_ot_ad_target_ranking_v1). Each row is a gene symbol; is_top10pct indicates whether the gene falls in the top 10% of Open Targets P