Table 1.
Key data repositories useful for systems immunology.
| Data Type | Repository | Key Features | Number of datasets as of May 2024 |
Date of establishment |
|---|---|---|---|---|
| Mass spectrometry (MS)-based Proteomics | PRIDE: PRoteomics IDEntifications Database (46) (https://www.ebi.ac.uk/pride/) | Direct submission allowed, data visualization and annotation tools. | 26847 | 2005 |
| MassIVE (47) (https://massive.ucsd.edu/) | Direct submission allowed, data analysis tools. | 15,231 | N/A | |
| PeptideAtlas (48) (https://peptideatlas.org/) | Curated database, no data analysis tools. | N/A | 2006 | |
| Panorma (49) (https://panoramaweb.org/) | Data from targeted proteomics experiments, direct submissions allowed, tools for designing and analyzing targeted proteomics experiments. | 596 | 2014 | |
| iProX (50) (https://www.iprox.cn/) | Direct submission allowed, no data analysis tools. | 4792 Projects (3602 Public Projects) | 2019 | |
| JPOST (51) (https://repository.jpostdb.org/) | Direct submission allowed, no data analysis tools. | 2671 projects | 2017 | |
| MS-based Metabolomics | MetaboLights (52) (https://www.ebi.ac.uk/metabolights) |
Direct submission allowed, no data analysis tools | 1496 | 2012 |
| National Metabolomics Data Repository (NMDR; https://www.metabolomicsworkbench.org/data/DRCCDataDeposit.php) | Direct submission allowed, no data analysis tools. | 2788 | 2020 | |
| ELISA, ELISPOT, Luminex | ImmPort (53) (https://www.immport.org/) | Immunology-focused, direct submission allowed, rich metadata in relational database, no data analysis tools. | 262, 54, 61 | 2018 |
| Flow Cytometry | ImmPort (53) (https://www.immport.org/) | Immunology-focused, direct submission allowed, rich metadata in relational database, no data analysis tools. | 257 | 2018 |
| FlowRepository (54) (https://flowrepository.org/) | Direct submission allowed, follows MIFlowCyt standard, endorsed by International Society for Advancement of Cytometry (ISAC), no data analysis tools. | ~2125 | 2012 | |
| Imaging | Image Data Resource (55) (IDR; https://idr.openmicroscopy.org/) | Direct submission allowed, handles variety of image types, no data analysis tools. | 127 Studies | 2017 |
| The Cell (CIL-CCDB) (56): (http://www.cellimagelibrary.org/) | Curated database, no data analysis. | 57 | 2012 | |
| Cancer Imaging Archive (TCIA) (57): (https://www.cancerimagingarchive.net/) | Data de-identified, allows direct submissions, no analysis tools. | N/A | 2013 | |
| NGS and array data | Sequence Read Archive (58) (SRA; https://www.ncbi.nlm.nih.gov/sra) | Allows direct submissions of sequencing data, no analysis tools. | N/A | 2007 |
| Database of Genotypes and Phenotypes (59) (dbGAP; https://www.ncbi.nlm.nih.gov/gap/) | Allows direct submissions of sequencing data, controlled access repository for human genotype/phenotype data. | 309 general use studies ie: sharable according to these (60) terms and nothing else. | 2006 | |
| The Bioinformation and DNA Data Bank of Japan (61) (DDBJ; https://www.ddbj.nig.ac.jp/) | Allows direct submissions of sequencing and array data, provides advanced search functionalities and built-in analysis tools. | 4,250,864,039 Sequences | 1987 | |
| European Nucleotide Archive (62) (ENA; (https://www.ebi.ac.uk/ena) | Allows direct submission of sequencing and data, no data analysis tools. | 4.6 billion Sequences | 1982 | |
| Gene Expression Omnibus (63) (GEO; https://www.ncbi.nlm.nih.gov/geo/) | Allow direct submissions of sequencing and MIAME-compliant array data as well as processed data, some data analysis tools. | 4348 | 2000 | |
| Single Cell Sequencing | Single Cell Portal: (https://singlecell.broadinstitute.org/) | Allows submission of sequencing and processed single cell data files, data visualization and analysis tools. | 670 total studies found | 2018 |
| Single Cell Expression Atlas (64) (https://www.ebi.ac.uk/gxa/sc/home) | Curated database, data visualization and analysis. | 355 | 2018 | |
| Spatial Transcriptomics | CROST (65) (https://ngdc.cncb.ac.cn/crost/home) | Curated database, supports different technologies, rich suite of data analysis and visualization tools. | 182 | 2024 |
| Spatial DB (66) (http://www.spatialomics.org/SpatialDB/) |
Curated database, supports different technologies, some data analysis tools. | 24 | ||
| STOmicsDB (67) (https://db.cngb.org/stomics/) |
Curated database, allows direct submission, some data visualization and analysis tools. | 228 | ||
| Spatial Omics DataBase (68) (SODB; https://gene.ai.tencent.com/SpatialOmics/) | Curated database, supports different technologies, some data visualization and analysis tools. | 3145 | 2023 | |
| Aquila (69) (https://aquila.cheunglab.org) | Curated database, allows direct submission, some data visualization and analysis tools. | 110 | 2023 | |
| Single Cell Sequencing | Single Cell Portal (70) (https://singlecell.broadinstitute.org/) | Allows submission of sequencing-based spatial transcriptomic data, data visualization and analysis tools. | 670 total studies found | 2018 |
| Multi-modal OMICs | Single Cell Atlas (71) (https://www.singlecellatlas.org/) | Curated database, multiple data types, data visualization and analysis. | NA | 2024 |
| Generalist | Zenodo – commercial (https://zenodo.org/) | 50GB dataset limit, any file type, GitHub integration, DOI creation, version control, immediate release, usage statistics. | 1,609 Projects | 2013 |
| Figshare -commercial: (https://figshare.com/) | 20 GB per user, any file type, DOI creation, version control, private and public release, usage statistics. | N/A | 2012 | |
| BioStudies (72) (https://www.ebi.ac.uk/biostudies/) | Allows the integration of metadata, orphan data, and data found in other EBI databases and link to a paper. | 2,398,047 | 2015 | |
| FAIRDOMHub (33) (https://fairdomhub.org) | Allows the integration of metadata, orphan data, and data found in other databases and link to a paper. | 402 projects | 2017 |