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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://scienceofbehaviorchange.org/about/
Repository for behavioral science measures that have been validated or are in process of being validated in accordance with SOBC Experimental Medicine Approach.
Proper citation: Science of Behavior Change Research Network (RRID:SCR_017385) Copy
Open platform for analyzing and sharing neuroimaging data from human brain imaging research studies. Brain Imaging Data Structure ( BIDS) compliant database. Formerly known as OpenfMRI. Data archives to hold magnetic resonance imaging data. Platform for sharing MRI, MEG, EEG, iEEG, and ECoG data.
Proper citation: OpenNeuro (RRID:SCR_005031) Copy
An infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org).
Proper citation: iTools (RRID:SCR_009626) Copy
Project aims to promote data sharing, archiving, and reuse among researchers who study human development. Focuses on creating tools for scientists to store, manage, preserve, analyze and share video and related data.
Proper citation: Databrary (RRID:SCR_010471) Copy
Digital repository software written in C# / ASP.net for powering digital libraries in a Windows server environment. Standards-based repository keeps all files in METS/MODS packages. Several related applications are available as well and the libraries can work independently as great digital library resources. SobekCM allows users to discover online resources via semantic and full-text searches, as well as a variety of different browse mechanisms. For each digital resource in the repository there are a plethora of display options, which may be selected by an appropriately authenticated use. This repository includes online metadata editing and online submissions in support of institutional repositories.
Proper citation: SobekCM (RRID:SCR_003225) Copy
https://www.coretrustseal.org/
International, community based, nongovernmental, and nonprofit organization promoting sustainable and trustworthy data infrastructures governed by Standards and Certification Board. Offers to any data repository core level certification based on tDSA–WDS Core Trustworthy Data Repositories Requirements catalogue and procedures. CoreTrustSeal Data Repository certification replaces the DSA certification and WDS Regular Members certification.
Proper citation: Core Trust Seal (RRID:SCR_021679) Copy
Non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids. Facilitates archiving and distributing DNA-based research reagents and associated data to scientists worldwide. Repository contains over 65,000 plasmids, including special collections on CRISPR, fluorescent proteins, and ready-to-use viral preparations. There is no cost for scientists to deposit plasmids, which saves time and money associated with shipping plasmids themselves. All plasmids are fully sequenced for validation and sequencing data is openly available. We handle the appropriate Material Transfer Agreements (MTA) with institutions, facilitating open exchange and offering intellectual property and liability protection for depositing scientists. Furthermore, we curate free educational resources for the scientific community including a blog, eBooks, video protocols, and detailed molecular biology resources.
Proper citation: Addgene (RRID:SCR_002037) Copy
https://www.metabolome-express.org
A metabolomics database which contains GC/MS metabolomics datasets. General users can search a curated annotated metabolite database, a metabolite response statistics database, experimental datasets, and uncurated repositories. Registered users can use Metabolome Express for data processing and management.
Proper citation: MetabolomeExpress (RRID:SCR_014670) Copy
https://metagenote.niaid.nih.gov/
Quick and intuitive way to annotate data from genomics studies including microbiome. Project to aid researchers in applying standardized metadata describing what, where, how, and when of samples collected in genomics study. Collection of METAdata of GEnomics studies on web based NOTEbook. Metadata are stored in centralized repository and validated according to guidelines from Genomics Standard Consortium, which are also supported by repositories and large microbiome initiatives such as NCBI, European Bioinformatics Institute (EBI), and Earth Microbiome Project. Upon request from researchers, data will also be submitted for publication via NCBI Sequence Read Archive (SRA) repository.
Proper citation: METAGENOTE (RRID:SCR_018494) Copy
https://ismrmrd.github.io/apidocs/1.5.0/
Prerequisite for sharing magnetic resonance imaging reconstruction algorithms and code is a common raw data format. This repository describes such common raw data format, which attempts to capture the data fields that are required to describe the magnetic resonance experiment with enough detail to reconstruct images. The repository also contains a C/C++ library for working with the format.
Proper citation: ISMRMRD (RRID:SCR_024043) Copy
https://github.com/ABCD-STUDY/Minimally-Processed-Image-Sharing
Software to share ABCD minimally processed data. It uploads minimally-processed MRI data to the NDA ( Non-Disclosure Agreement) ABCD (Adolescent Brain Cognitive Development) repository.
Proper citation: Minimally-Processed-Image-Sharing (RRID:SCR_016016) Copy
https://www.ncbi.nlm.nih.gov/labs/virus/vssi
Community portal for viral sequence data from RefSeq, GenBank and other NCBI repositories. Integrative, value added resource designed to support retrieval, display and analysis of curated collection of virus sequences and large sequence datasets. Used to increase usability of data archived in GenBank and other NCBI repositories.
Proper citation: NCBI Virus (RRID:SCR_018253) Copy
https://ngdc.cncb.ac.cn/gsa-human/
Data repository for archiving raw sequence data, which provides data storage and sharing services for worldwide scientific communities. Data repository specialized for human genetic related data derived from biomedical researches.
Proper citation: China National Center for Bioinformation Genome Sequence Archive for Human database (RRID:SCR_027207) Copy
Project to facilitate the construction of a Data Discovery Index. The data discovery index (DDI) is to do for data what PubMed (and PubMed Central) did for the literature. Biomedical researchers and healthcare institutions should be enabled to share their data in a way that advances science and protects privacy. They will find ways to facilitate structuring, discovery, and accessing of data without requiring people to understand complex standards that only a few specialized groups can decipher. bioCADDIE will pursue the following aims: # Provide ease in finding accessible data of interest according to disease, data modality (e.g., imaging, molecular measurements), and/or demographics through simple and intuitive computer interfaces that allow quick ranking, visualization, and summarization of data resources - this requires methods for automated indexing (i.e., creation of metadata), tools that allow free text searches, accessibility tools that decode consent requirements, etc. # Assist data producers on how to publish data for maximal discoverability and assessment of impact of disseminated data through data citation networks; and # Train data producers and data users in relevant tools related to biomedical data sharing. This will be done through online resources, workshops, and dissemination of best practices through publication of articles about data discovery in different venues (a) scholarly publications, and (b) lay press news articles.
Proper citation: bioCADDIE (RRID:SCR_004018) Copy
Centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. Originally it was developed to provide a common data exchange format and repository to support proteomics literature publications. This remit has grown with PRIDE, with the hope that PRIDE will provide a reference set of tissue-based identifications for use by the community. The future development of PRIDE has become closely linked to HUPO PSI. PRIDE encourages and welcomes direct user submissions of protein and peptide identification data to be published in peer-reviewed publications. Users may Browse public datasets, use PRIDE BioMart for custom queries, or download the data directly from the FTP site. PRIDE has been developed through a collaboration of the EMBL-EBI, Ghent University in Belgium, and the University of Manchester.
Proper citation: Proteomics Identifications (PRIDE) (RRID:SCR_003411) Copy
https://portal.dbmi.hms.harvard.edu/projects/GRDR/
Data repository of de-identified patient data, aggregated in a standardized manner, to enable analyses across many rare diseases and to facilitate various research projects, clinical studies, and clinical trials. The aim is to facilitate drug and therapeutics development, and to improve the quality of life for the many millions of people who are suffering from rare diseases. The goal of GRDR is to enable analyses of data across many rare diseases and to facilitate clinical trials and other studies. During the two-year pilot program, a web-based template will be developed to allow any patient organization to establish a rare disease patient registry. At the conclusion of the program, guidance will be available to patient groups to establish a registry and to contribute de-identified patient data to the GRDR repository. A Request for Information (RFI) was released on February 10, 2012 requesting information from patient groups about their interest in participating in a GRDR pilot project. ORDR selected 30 patient organizations to participate in this pilot program to test the different functionalities of the GRDR. Fifteen (15) organizations with established registries and 15 organizations that do not have patient registry. The 15 patient groups, each without a registry, were selected to assist in testing the implementation of the ORDR Common Data Elements (CDEs) in the newly developed registry infrastructure. These organizations will participate in the development and promotion of a new patient registry for their rare disease. The GRDR program will fund the development and hosting of the registry during the pilot program. Thereafter, the patient registry is expected to be self-sustaining.The 15 established patient registries were selected to integrate their de-identified data into the GRDR to evaluate the data mapping and data import/export processes. The GRDR team will assist these organizations in mapping their existing registry data to the CDEs. Participating registries must have a means to export their de-identified registry data into a specified data format that will facilitate loading the data into the GRDR repository on a regular basis. The GRDR will also develop the capability to link patients'''' data and medical information to donated biospecimens by using a Voluntary Global Unique Patient Identifier (GUID). The identifier will enable the creation of an interface between the patient registries that are linked to biorepositories and the Rare Disease Human Biospecimens/Biorepositories (RD-HUB) http://biospecimens.ordr.info.nih.gov/.
Proper citation: GRDR (RRID:SCR_008978) Copy
NIH funded collaboration between researchers and librarians to build behavioral project oriented data repository containing decades of knowledge from educational and developmental sciences on individuals across the full range of abilities.
Proper citation: LDbase (RRID:SCR_025052) Copy
http://platform.visiome.neuroinf.jp/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023.Analytical tools. Archive files may be written in any format and may include explanatory figures, program sources, readme files, and other related files. The readme file describes the purpose and usage of the archive file. This data sharing framework allows users to improve the reproducibility of simulations. Users can browse the platform contents via branch sites (A catalogue of illusions, Visitope), which introduce user friendly view of items such as basic images and original artworks of visual illusions with high resolution. The items in Visiome Platform are useful not only for reproducing the published results, but also for advancing and expanding the research in Vision Science.
Proper citation: Visiome Platform (RRID:SCR_003049) Copy
http://www.biobankcentral.org/resource/wwibb.php
THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 27, 2013. Web-based portal to connect all the constituencies in the global biobank community. The project seeks to increase the transparency and accessibility of the scientific research process by connecting researchers with an additional source of funding - microinvestments received from the broader online community. In exchange for these public investments, researchers will maintain research logs detailing the play-by-play progress made in their project, as well as publishing all of their data in a public database under a science commons license. These research projects, in turn, will serve to continually update a research-based neuroscience-based human brain & body curriculum. Biobanks are the meeting point of two major information trends in biomedical research: the generation of huge amounts of genomic and other laboratory data, and the electronic capture and integration of patient clinical records. They are comprised of large numbers of human biospecimens supplemented with clinical data. Biobanks when implemented effectively can harness the power of both genomic and clinical data and serve as a critical bridge between basic and applied research, linking laboratory to patient and getting to cures faster. As science and technology leaders work to address the many challenges facing U.S. biobanks logistical, technical, ethical, financial, intellectual property, and IT BioBank Central will serve as an accurate and timely source of knowledge and news about biorepositories and their role in research and drug development. The Web site also provides a working group venue, patient and public education programs, and a forum for international collaboration and harmonization of best practices.
Proper citation: BioBank Central (RRID:SCR_008645) Copy
Commercial collaborative research platform for hosting and analyzing datasets.Data platform for academic research. Redivis provides organizations with central hub where researchers can easily discover, access, and analyze their data.
Proper citation: Redivis (RRID:SCR_023111) Copy
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