MH Open data resources

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).
National Institute of Mental Health (NIMH) O https://www.nimh.nih.gov/index.shtml The institute within the National Institutes of Health (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 (HHS).
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 (CT) 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, schizophrenia and bipolar disorder.
Mental Health Research Network 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 is 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 (electroencephalograph-EEG and magneto-encephalography- MEG).
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 schizophrenia, 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 non-coding 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 schizophrenia, 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 schizophrenia. More recently, the scope has expanded to other conditions and other types of genetic variation beyond single nucleotide variants.
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 more than 4,500 curated resources and access to more than 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 magnetic resonance imaging (MRI), diffusion tensor imaging (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 6 human brains. In situ hybridization 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 over 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 dataset consists of a traveling subject study of 5 healthy subjects, each scanned on 10 different 1.5 to 4 T scanners. The FBIRN Phase 2 and Phase 3 datasets consist of subjects with schizophrenia or schizoaffective disorder along with healthy comparison subjects scanned at multiple sites. The BIRN Data Repository (BDR) includes imaging, clinical, cognitive, and physiological data.
OpenfMRI P https://openfmri.org/about/ A repository of human brain imaging data collected using MRI and EEG. Started in 2010, it initially focused only on task-based MRI, but is now open to all forms of neuroimaging data. 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 schizophrenia subjects. Data sources include Functional Biomedical Informatics Research Network (FBIRN), Northwestern University Schizophrenia Data and Software Tool (NUSDAST), Collaborative Informatics and Neuroimaging Suite (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.
SNC Integrative Database (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 Stanley Neuropathology Consortium (SNC) within the Stanley Medical Research Institute (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 functional MRI brain scans from people with schizophrenia and healthy non-psychiatric controls. Currently has data on approximately 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.
database of Genotypes and Phenotypes (dbGap) P https://www.ncbi.nlm.nih.gov/gap Developed by the NIH’s National Center for Biotechnology Information (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 lab values.
European Genome-phenome Archive (EGA) P https://www.ega-archive.org/ Developed in partnership between the European Bioinformatics Institute (UK) and the Centre for Genomic Regulation (Spain), the EGA is a platform for archiving and sharing of all types of consented, personally identifiable genetic and phenotypic data resulting from biomedical research projects. Authorization to the data is managed in partnership with the data providing organizations.
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 Metabolomics Workbench 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 Data Discovery Index (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 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, post-translational modifications and supporting spectral evidence. Most of the datasets 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.
ArrayExpress 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 are imported from GEO, while others are submitted directly.
GEMMA P http://www.chibi.ubc.ca/Gemma/ Gemma is a web site, 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 dataset discovery across omics data resources spanning eight international repositories, including both open and controlled access data resources. The resource provides key metadata for each dataset and uses this metadata to enable search capabilities and identification of related datasets. OmicsDI helps researchers to idenitfy groups of related, multi-omics datasets across repositories.
Repositive P https://repositive.io/ Federated access to human genomic data from 52 data sources. This resource also offers grouped “collections” of data and the ability for researchers to post what datasets they are looking for and to be notified by other users about relevant resources.