Curated resources related to Neuroscience and Mental health for open data science
- The Stanley Brain Collection is a large collection of tissue specimens that include five cohorts including Neuropathology Consortium, Array Collection, New Collection, Depression Collection and the Parietal Collection. http://www.stanleyresearch.org/brain-research/
- The Maryland Brain Collection (MBC) is another collection of brain tissue from post-mortem individuals with SCZ and controls http://www.stanleyresearch.org/brain-research/maryland-brain-bank/.
- Genomic Psychiatry Cohort (GPC), a data repository managed by NIMH for the investigation of SCZ, BD, OCD and controls and includes over 30,000 participants https://www.downstate.edu/psychiatry/research/index.html
- The ProteomeXchange Consortium is a repository for proteomics datasets and includes data on CSF among others could be studied for association with MH disorders http://proteomecentral.proteomexchange.org/cgi/GetDataset
- Boersema et al describe the activities of the Biology/Disease-driven (B/D) working groups of the HPP focused on protein aggregation diseases including AD and Parkinson’s
- The Psychiatric Genomics Consortium unites investigators to perform genome-wide genomic data for psychiatric disorders and contains more than 900,000 samples covering ASD, ADHD, BP, MDD, SCZ and many more https://www.med.unc.edu/pgc/.
- Logue et al describe the activities Psychiatric Genomics Consortium Posttraumatic Stress Disorder Workgroup and describe their first large scale GWAS that includes over 10000 cases and 30000 controls
- Gene expression omnibus is a NCBI data repository for high throughput molecular data including gene expression, micoRNA expression, RNA-seq data on numerous diseases and disorders including mental health disorders. https://www.ncbi.nlm.nih.gov/geo/.
- Religious Orders Study (ROS) and the Rush Memory and Aging Project (MAP) are large datasets in AD that includes data whole genome sequencing (WGS, DNA methylation, chromatin immunoprecipitation with sequencing (Chip-seq), RNA-seq and microRNA expression profiling. These rich datasets are shared with the research community through the DREAM challenge and the National Institute of Aging AMP-AD research program. https://dss.niagads.org/cohorts/religious-orders-study-memory-and-aging-project-rosmap/
- Another large multi-omics dataset with AD data is The Mount Sinai Brain Bank (MSBB) study made available through the AMP-AD Knowledge Portal in Synapse. https://adknowledgeportal.synapse.org/
- OpenNeuro: https://openneuro.org/ is a resource for sharing of neuroscience data
- Neuroimaging Informatics Tools and Resources Clearinghouse Image Repository (NITRC): https://www.nitrc.org/. Has comprehensive information on an ever expanding scope of neuroinformatics software and data.
- The Functional Connectomes Project is also available through NITRC. It comprises data from >1400 healthy subjects who underwent fMRI scans that assessed their brain activity when their minds were at rest.
- The Cancer Imaging Archive (TCIA) , focused on cancer but includes brain cancer datasets TCGA-GBM (Glioblastoma), TCGA-LGG (Lower Grade Glioma), Rembrandt: https://www.cancerimagingarchive.net/
- Imaging data commons (IDC), focused on cancer but incluces brain cancer datasets. Have option to connect tools to the data via a google cloud platform. https://datacommons.cancer.gov/repository/imaging-data-commons
- Genomics
- phs000979.v1.p1 (PRJNA293910) Gene Expression in Postmortem DLPFC and Hippocampus from Schizophrenia and Mood Disorders
- phs000473.v2.p2 (PRJNA157243, PRJNA94281) Sweden-Schizophrenia Population-Based Case-Control Exome Sequencing
- phs000687.v1.p1 Bulgarian Schizophrenia Trio Sequencing Study
- phs000738.v1.p1 Exome Sequencing in Schizophrenia Families
- phs000608.v1.p1 Whole-Genome Profiling to Detect Schizophrenia Methylation Markers
- phs000448.v1.p1 Genetics of Schizophrenia in an Ashkenazi Jewish Case-Control Cohort
- phs000021.v3.p2 Genome-Wide Association Study of Schizophrenia
- phs000167.v1.p1 Molecular Genetics of Schizophrenia-nonGAIN Sample (MGS nonGAIN)
- Proteomics
- PRIDE (PRoteomics IDEntifications), the leading proteomics data repository, has only three SCZ-related data sets: two in rat models and one in a mouse model.
- Metabolomics
- EBI’s Metabolights and NCBI’s Metabolomics Workbench (MW) are two major metabolomics data repositories
- Imaging repositories
- SchizConnect is a federated portal that integrates data from three neuroimaging consortia on SCZ: FBIRN's Human Imaging Database (HID), MRN's Collaborative Imaging and Neuroinformatics System (COINS) and the Northwestern University Schizophrenia Data and Software Tool (NUSDAST) project
Open data resources for biomarker discovery in mental health, particularly in schizophrenia (Taken from PMC6585382)
Note: Type: O, organizational entity; I, initiative; P, platform
| Resource | Type | URL | Notes |
|---|---|---|---|
| Enhancing Neuro Imaging Genetics Through Meta Analysis (ENIGMA) | O | http://enigma.ini.usc.edu/ongoing/enigma-schizophrenia-working-group/ | The ENIGMA Network brings together researchers in imaging genomics to understand brain structure, function and disease, based on brain imaging and genetic data. Includes Schizophrenia Working Group (ENIGMA-SCZ) |
| NIMH | O | https://www.nimh.nih.gov/index.shtml | The institute within the NIH that focuses on mental health and disease. The NIMH is one of 27 institutes and centers within NIH, which is part of the US Department of Health and Human Services |
| Open Translational Science In Schizophrenia (OPTICS) | O | https://sites.google.com/site/opticsschizophrenia/home | A time-limited proof of concept pilot project designed to provide a forum for translational science based on Janssen clinical trial data made available to qualified investigators |
| Stanley Medical Research Institute (SMRI) | O | http://www.stanleyresearch.org/ | A nonprofit organization supporting research on the causes of, and treatments for, SCZ and bipolar disorder |
| Mental Health Research Network (MHRN) | O | http://hcsrn.org/mhrn | Consortium of 13 health system research centers dedicated to improving patient mental health through research, practice and policy. Supported by a cooperative agreement from the NIMH. The MHRN conducts pragmatic research in health systems serving over 12 million patients |
| Common Mind Consortium | I | http://commonmind.org | Public–private partnership to generate and analyze large-scale genomic data across several brain regions from human subjects with neuropsychiatric disease and to make these data and the associated analytical results broadly available to qualified investigators |
| Human Connectome Project (HCP) | I | http://www.humanconnectome.org/ | Large NIH-funded project for integrating genomics, behavior and brain imaging. Currently, high-resolution imaging data are available on 1200 individuals. Primary modalities measure brain activity (resting state fMRI and task-evoked fMRI), white matter integrity (diffusion imaging and T2 FLAIR) and oscillatory brain activity (EEG and) |
| NIMH Human Genetics Initiative | I | https://www.nimhgenetics.org/nimh_human_genetics_initiative/ | Intended to establish a national resource of clinical and diagnostic information and immortalized cell lines from individuals with SCZ, bipolar disorder or Alzheimer's disease and their relatives, available to qualified investigators for research on the genetic basis of these disorders |
| PsychENCODE | I | https://www.synapse.org//#! Synapse: syn4921369/wiki/235539 | Funded by the NIMH with the goal of accelerating discovery of noncoding functional genomic elements in the human brain and elucidating their role in the molecular pathophysiology of psychiatric disorders |
| Stanley Neuropathology Consortium (SNC) | I | http://www.stanleyresearch.org/brain-research/neuropathology-consortium/ | A collection of 60 brains, consisting of 15 each diagnosed with SCZ, bipolar disorder or major depression, and unaffected controls. Samples may be requested for research purposed. Associated data are available in the SNC Integrative Database (SNCID)—see below |
| Psychiatrics Genomics Consortium (PGC) | I | http://www.med.unc.edu/pgc | Founded in 2007, the PGC includes over 800 investigators from 38 countries with the goal of conducting meta- and mega-analyses of genomic data for psychiatric disorders. The initial focus was on autism, attention-deficit hyperactivity disorder, bipolar disorder, major depressive disorder and SCZ. More recently, the scope has expanded to other conditions and other types of genetic variation beyond SNVs |
| Neuroscience Information Framework (NIF) | I/P | https://neuinfo.org/ | An NIH-funded framework for identifying, locating, relating, accessing, integrating and analyzing information from the neuroscience research enterprise. NIF has come to refer to both this initiative and the set of tools and platforms that make up that framework including the registry of electronic resources and the discovery portal for searching those resources. NIF includes >4500 curated resources and access to > 100 databases |
| Allen Brain Atlas/Data Portal | I/P | http://human.brain-map.org/ | The Allen Institute for Brain Science is dedicated to understanding how the human brain works in health and disease. The Allen Human Brain Atlas integrates anatomic and genomic information across the brain. Data modalities include MRI, DTI, histology and gene expression data derived from both microarray and in situ hybridization (ISH) approaches. Microarray data are spatially mapped to the MRI. Complete microarray and RNA-seq data are available for six human brains. ISH data are available for ∼50 SCZ brains |
| NIMH Repository and Genomics Resource (RGR) | P | https://www.nimhgenetics.org/available_data/schizophrenia/ | Includes 100+ studies, including CommonMind, PsychENCODE. Formerly the Center for Collaborative Genomic Studies on Mental Disorders, the RGR was established in 1998 through the NIMH Human Genetics Initiative to leverage and increase the value of human genetic samples and data produced through NIMH-funded research. It contains a collection of > 150 000 well-characterized, high-quality patient and control samples from patients with a range of mental disorders. The RGR’s Biologic Core and a Data Management Core are external to NIH |
| Function Biomedical Informatics Research Network Data Repository (FBIRN DR) | P | fbirnbdr.nbirn.net: 8080 (BROKEN) | FBIRN was initially focused on assessing major sources of variation of fMRI data generated across different scanners. The FBIRN Phase 1 data set consists of a traveling subject study of five healthy subjects, each scanned on 10 different 1.5 to 4 T scanners. The FBIRN Phase 2 and Phase 3 data sets consist of subjects with SCZ or schizoaffective disorder along with healthy comparison subjects scanned at multiple sites. The BIRN Data Repository (BDR) includes imaging, clinical, cognitive and physiological data |
| OpenNeuro (previously OpenfMRI) | P | https://openneuro.org/(https://openfmri.org/) | A neuroimaging repository to enable reproducible analysis and data sharing. Started in 2010, it initially focused only on task-based MRI, but is now open to all forms of neuroimaging data, reflected in the name transition from OpenfMRI to OpenNeuro. Data are anonymized before distribution to protect the confidentiality of participants and distributed using a Public Domain license |
| Research Domain Criteria Database (RDoC DB) | P | https://data-archive.nimh.nih.gov/rdocdb/ | A data repository for the harmonization and sharing of research data related to the RDoC initiative and mental health research more generally. The actual platform uses software designed to host the NIH’s National Database for Autism Research (NDAR) |
| SchizConnect | P | http://schizconnect.org/ | Federated access to several neuroimaging databases with images acquired on SCZ subjects. Data sources include FBIRN, NUSDAST, COINS and MCIC (maintained by the Mental Illness and Neuroscience Discovery Institute, now the Mind Research Network). More than 1100 subjects with >1000 have imaging data, including resting state fMRI, task-related fMRI, structural and diffusion imaging |
| SNCID | P | http://sncid.stanleyresearch.org/ | Web-based tool for exploring neuropathological traits, gene expression and associated biological processes in psychiatric disorders generated by the SNC within the SMRI |
| Australian Schizophrenia Research Bank | P | http://www.schizophreniaresearch.org.au/bank/ | A research database and storage facility that links clinical and neuropsychological information, blood samples and structural and fMRI brain scans from people with SCZ and healthy nonpsychiatric controls, and currently has data on ∼900 cases and 900 controls |
| Internet Brain Volume Database (IBVD) | P | http://ibvd.virtualbrain.org/ | Centered around publications as the central data structure, IBVD is a Web-based searchable database of brain neuroanatomic volumetric observations that enables electronic access to the results in the published literature |
| dbGap | P | https://www.ncbi.nlm.nih.gov/gap | Developed by the NIH’s NCBI to archive and distribute the data and results from studies that have investigated the interaction of genotype and phenotype. While the focus is on genomic data, other data types are included as well, for example metabolomic data and laboratory values |
| Metabolights | P | http://www.ebi.ac.uk/metabolights/ | A database for Metabolomics experiments and derived information. Metabolights is the slightly more established European counterpart to the NIH’s MW and the recommended metabolomics repository for a number of top journals |
| DataMed | P | http://datamed.org/ | Data search engine portal to enable users to search for data across different repositories developed for the NIH BD2K DDI by the bioCADDIE project team. The initial prototype release (v2.0) features a set of data repositories selected by the bioCADDIE team, with a form to suggest additional repositories for inclusion |
| Metabolomics Workbench (MW) | P | http://www.metabolomicsworkbench.org/ | A repository for metabolomics data and metadata, MW provides analysis tools and access to metabolite standards, protocols, tutorials and training |
| PRIDE | P | https://www.ebi.ac.uk/pride/archive/ | A centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, posttranslational modifications and supporting spectral evidence. Most of the data sets related to mental health disorders in PRIDE are derived from animal models |
| Synapse | P | https://www.synapse.org/ | Sage Bionetworks’ software platform for data sharing and provenance tracking. Synapse enables researchers to carry out, track and communicate research in real time and enables co-location of scientific content (data, code, results) and narrative descriptions of that work. The platform is agnostic regarding biomedical domain or data type and hosts a number of different file types and projects funded by a number of different sources |
| GEO | P | https://www.ncbi.nlm.nih.gov/geo/ | An international public repository developed by the NIH NCBI that archives and freely distributes microarray, next-generation sequencing and other high-throughput functional genomics data submitted by the research community |
| AE | P | https://www.ebi.ac.uk/arrayexpress/ | The European counterpart to GEO. AE is an archive of functional genomics data from high-throughput functional genomics experiments. A subset of experiments is imported from GEO, while others are submitted directly |
| GEMMA | P | http://www.chibi.ubc.ca/Gemma/ | Gemma is a website, database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles |
| OmicsDI | P | http://www.omicsdi.org | Enables data set discovery across omics data resources spanning eight international repositories, including both open and controlled access data resources. The resource provides key metadata for each data set and uses this metadata to enable search capabilities and identification of related data sets. OmicsDI helps researchers to idenitfy groups of related, multi-omics data sets across repositories |