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Data Repositories

Data Repositories

These tools are organized by a description of their functionality, their RRID (Research Resource Identification), data modality, and which Allen Institute resource's data was utilized for this tool. The authors of the tool are listed first by computational contributors then by academic authors when the tool has a relevant publication.

BIL (Brain Image Library)

Link 

The Brain Image Library (BIL) is a searchable public data repository for large brain image datasets. Each sample is labeled with modality, technique, related organization, organism, method, and structure.

RRID

SCR_017272

Modality

morphology

Allen Resource Utilized

Allen Mouse Brain Atlas, Allen Human Brain Atlas 

Author

Biomedical Applications Group at the Pittsburgh Supercomputing Center and the Center for Biological Imaging at the University of Pittsburgh

Blue Brain Cell Atlas

Link 

The Blue Brain Cell Atlas describes the number, types, and positions of cells in all areas of the mouse brain. It provides densities and positions of all excitatory, inhibitory, and neuromodulatory neurons, as well as astrocytes, oligodendrocytes, and microglia in each of the brain regions defined in Allen Mouse Brain Atlas. Users can download cell numbers for statistical analysis, as well as cell positions and types for modeling and visualizing brain areas. The foundational workflow uses imaging data from Allen Institute Common Coordinate Framework to generate cell positions and assign their type using API for data access. 

RRID

SCR_019266

Modality

morphology, electrophysiology, gene expression

Allen Resource Utilized

Allen Mouse Brain  Atlas, Allen Institute Common Coordinate Framework

Author

Csaba Erö

Year Released

2018

Brain Architecture Project

Link 

The Brain Architecture Project collects research resources from various databases to form one homogenous portal of interactive tools and resources. The focus of the portal is creating the first brain-wide mesoscopic connectivity diagram. 

RRID

SCR_004283

Modality

gene expression, morphology

Allen Resource Utilized

Allen Mouse Brain Atlas

Author

Partha Mitra

Year Released

2008

BrainStars

Link 

BrainStars (or B*) is a quantitative expression database of the adult mouse brain. The database has a genome-wide expression profile at 51 adult mouse CNS regions. 

RRID

SCR_005810

Modality

gene expression

Allen Resource Utilized

Allen Mouse Brain Reference Atlas

Author

RIKEN Center for Developmental Biology

Year Released

2009

Cellxgene 

Link Relevant Publication 

The cellxgene tool is a web browser for single-cell transcriptomics data. This browser allows the user to visualize over 1 million cells, cross-filter and compare data of interest, and utilize existing analysis software to interact with the data.

RRID

SCR_021059

Software Type

data repository, visualization tool, data analysis

Modality

gene expression

Allen Resource Utilized

Allen Cell Types Database

Author

Chan Zuckerberg Initiative

Year Released

2021

DANDI: Distributed Archives for Neurophysiology Data Integration

Link 

DANDI is a platform for publishing, sharing, and processing neurophysiology data. The archive is a living repository that enables collaboration within and across labs, and contains neurophysiology data including electrophysiology, optophysiology, and behavioral time-series, as well as images from immunostaining experiments.

RRID

SCR_017571

Modality

electrophysiology, gene expression

Allen Resource Utilized

Allen Institute Cell Types Database

Year Released

2019

DBGap

Link 

DBGap, the database of Genotypes and Phenotypes, was developed to store and share the data and results from studies that have investigated the interaction of genotypes and phenotypes in humans. 

RRID

SCR_002709

Modality

human genotype and phenotype

Allen Resource Utilized

Allen Human Brain Atlas, Cell Types Database

Year Released

2006

Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas

Link Relevant Publication

This website visualizes and shares Franklin and Paxinos (FP) based anatomical labels in Allen Common Coordinate Framework (CCF). The anatomical labels were digitized based on Allen ontology, and this web interface was created for easy visualization. These labels isolate and identify mouse brain anatomical structures and the open source data sharing feature facilitates the refinement of anatomical labels and data integration within a single anatomical platform.

RRID

SCR_019267

Modality

neuroanatomy

Allen Resource Utilized

Allen Institute Common Coordinate Framework, Allen ontology

Author

Yongsoo Kim

Year Released

2019

Gene Expression Omnibus (Geo) 

Link 

GEO is a public functional genomics data repository with array- and sequence-based data. This data repository also includes tools to help users query as well as download experiments and curated gene expression profiles. 

RRID

SCR_005012

Modality

gene expression

Allen Resource Utilized

Allen Mouse Brain Atlas

Year Released

2000

Integrated Brain Gene Expression

Link 

Virtual database indexing brain region gene expression data in mice from Gene Expression Nervous System Atlas (GENSAT), Allen Mouse Brain Atlas, and Mouse Genome Institute (MGI). 

RRID

SCR_004197

Modality

gene expression

Allen Resource Utilized

Allen Mouse Brain Atlas

Author

FAIR Data Informatics Lab

Year Released

2017

Linked Neuron Data

Link 

Linked Neuron Data provides multiple interactive resources for extracting, integrating, linking, and analyzing brain data and knowledge from multiple scales and multiple data sources. This web tool includes a brain structure visualization tool, a brain association graph, a morphology data repository, as well as a brain knowledge and semantic search engine.

RRID

SCR_003658

Software Type

data repository, data analysis 

Modality

gene expression, morphology, neuroanatomy

Allen Resource Utilized

Allen Mouse Brain Atlas, Allen Human Brain Atlas, Allen Developing Mouse Brain Atlas, Allen Developing Human Brain Atlas, Allen Non-Human Primate Atlas

Author

Yi Zeng, Hunagfu Cunqing, Dongsheng Wang, Hongyin Zhu, Tielin Zhang

Year Released

2013

ModelDB

Link 

ModelDB is a curated database of published computational neuroscience models to be openly accessed, downloaded, and tested. Models can be coded in any language and can be viewed before downloading. 

RRID

SCR_007271

Modality

neural systems

Allen Resource Utilized

Allen Institute Cell Types Database

Author

SenseLab Project

Year Released

1998

National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site (NIAGADS)

Link Relevant Publication

NIAGADS is a data repository of genotypic data related to Alzheimer’s disease and related dementias (ADRD) and aging. 

RRID

SCR_007314

Modality

gene expression

Allen Resource Utilized

Allen Mouse Brain Atlas

Author

Li-San Wang, Gerard Schellenberg, Christian J. Stoeckert, Jr., Adam Naj, Yuk Yee (Fanny) Leung, University of Pennsylvania School of Medicine

Year Released

2018

NeMO: Neuroscience Multi-omic Data Archive

Link Relevant Publication

The NeMO data repository houses omic data from several large-scale brain research projects. NeMO data includes genomic region data, transcription factor data, as well as cytosine and histone modification data.

RRID

SCR_016152

Modality

gene expression

Allen Resource Utilized

Allen Cell Types Database

Author

Owen White, Institute for Genome Sciences, University of Maryland School of Medicine

Year Released

2017

NeuroMorpho

Link 

NeuroMorpho is a curated inventory of digitally reconstructed neurons along with peer-reviewed publications. The format of the neuronal data includes a unique identifier, general information, the original and standardized ASCII files of the digital morphological reconstruction, and a set of morphometric features. The data is searchable by species, brain region, cell type, or lab name. 

RRID

SCR_002145

Modality

morphology

Allen Resource Utilized

Allen Institute Cell Types Database, Allen Institute Brain Explorer

Author

Giorgio Ascoli

Year Released

2006

Open Source Brain

Link 

Open Source Brain is a data resource for collaboratively developing and sharing computational models of neural systems. To foster open processing of this data, ModelDB includes facilities to analyze, visualize and transform models into standardized formats (NeuroML and PyNN). 

RRID

SCR_001393

Modality

neural systems

Allen Resource Utilized

Allen Institute Cell Types Database

Author

Nicholas Cain, Padraig Gleeson, Shreejoy Tripathy 

Year Released

2022

Recombinase (cre) Activity

Link 

Recombinase (cre) Activity is a curated data platform with all recombinase-containing transgenes and knock-ins developed in mice, creating a comprehensive resource for delineating known activity patterns and searching for relevant mouse resources.

RRID

SCR_006585

Modality

genetics, epigenetics

Allen Resource Utilized

Allen Mouse Brain Reference Atlas

SageBionetworks Portals 

Link 

The SageBionetworks Portals provide web interfaces for research institutions to exchange, share, and publish curated data or other digital resources. 

RRID

SCR_023844

Modality

Alzheimer's Disease, cell types

Allen Resource Utilized

Seattle Alzheimer's Disease Brain Cell Atlas, Cell Types Database

Year Released

2019

Single Cell Portal

Link

The Single Cell Portal (SCP) is both a data hub and a cell visualization tool. The user can search by study or by gene and visualize the data through plots showing cell clusters, gene expression within and across studies, three-dimensional trajectories, and chromosomal rearrangements.

RRID

SCR_014816

Software Type

data repository, visualization tool, data analysis

Modality

gene expression

Allen Resource Utilized

Allen Cell Types Database

Author

Jon Bistline, Eric Weitz, Jean Chang, Vicky Horst, Timothy Tickle

VisiGene Image Browser 

Link 

VisiGene Image Browser is a virtual microscope for viewing in situ images that show where a gene is used in an organism, often down to cellular resolution. The user can examine cell-by-cell as well as tissue-by-tissue expression patterns, retrieve images that meet specific search criteria, then interactively zoom and scroll across the collection.

RRID

SCR_003341

Software Type

data repository, visualization tool

Modality

gene expression

Allen Resource Utilized

Allen Mouse Brain Reference Atlas

Author

Jim Kent, Galt Barber

 

 

Disclaimer

This list of third-party tools utilizing Allen Brain Map resources is for informational purposes only and do not constitute an endorsement or approval by Allen Institute of any of the tools or other products, services, or opinions of the associated organizations. Allen Institute bears no responsibility for the accuracy, legality, or content of the external tools or for that of subsequent links. The descriptions of these tools were adapted from their individual websites.