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http://dbptm.mbc.nctu.edu.tw/

dbPTM is a database that compiles information on protein post-translational modifications (PTM) such as the modified sites, solvent accessibility of surrounding amino acids, protein secondary and tertiary structures, protein domains, and protein variations. The version 2.0 of dbPTM integrates the experimentally validated PTM sites with referable literatures from Swiss-Prot, Phospho.ELM, O-GLYCBASE, and UbiProt. In all of the collected PTM information, about 25 types of PTM with enough experimentally validated sites are trained the profile hidden Markov models (HMMs) to detect the potential PTM sites with 100% specificity against Swiss-Prot proteins. To help users investigating more detail in each type of PTM, the substrate peptide specificity such as positional amino acid frequency, solvent accessibility and secondary structure surrounding the modified sites are also provided. Moreover, the information of orthologous protein clusters is provided to users for analyzing whether the PTM sites located in the evolutionary conserved regions or not., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: dbPTM: An informational repository of proteins and post-translational modifications (RRID:SCR_007619) Copy   

•   Source: SciCrunch Registry
  

http://swissmodel.expasy.org/repository

Database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.

Proper citation: SWISS-MODEL Repository (RRID:SCR_013032) Copy   

•   Source: SciCrunch Registry
  

https://cccells.org/

Repository stores tissue samples and uses them to create cell lines. The cell lines and xenografts can be used as model to understand cancers and to test new treatments. Researchers all over the world can request cell lines and models to use in their research.

Proper citation: Alex's Lemonade Stand Foundation for Childhood Cancer Childhood Cancer Repository (RRID:SCR_025812) Copy   

•   Source: SciCrunch Registry
  

https://www.ctrnet.ca/

The Canadian Tumour Repository Network (CTRNet) is a not-for-profit consortium of leading provincial tumor banks and programs that furthers Canadian health research. CTRNet provides interested researchers with a streamlined process to obtain quality human tissue and human tissue products from member tumor banks. The benefits of working with CTRNet.ca include: * The ability for researchers to search for quality controlled tissue samples from Canada''''s leading tumor banks in one central location and for biobanks to display and make their biospecimens available for research users. * Learning opportunities in tissue handling, research design and relevant technology training and innovations. * Invitation to CTRNet workshops and conferences. * A resource for current news links and discussion forums about cancer research and tumor banking. The vision of CTRNet is to create new opportunities for translational cancer research that will improve cancer outcomes in Canada and beyond. Through the creation and maintenance of an online pan-Canadian network, researchers will gain unprecedented access to a new and comprehensive source of tissue and clinical data. The network is a sustainable resource and operates according to the highest scientific and ethical standards for research to benefit all Canadians. Currently CTRNet has the following member banks: * CBCF Tumor Bank Alberta * Manitoba Tumour Bank * Ontario Tumour Bank * British Columbia Cancer Agency Tumour Tissue Repository (BCCA-TTR) * Le r��seau de recherche en cancer du FRSQ * NCIC Clinical Trials Group

Proper citation: Canadian Tumour Repository Network (RRID:SCR_004192) Copy   

•   Source: SciCrunch Registry
  

http://www.ninds.nih.gov/research/parkinsonsweb/amr/amr_mice_ucla_repository.htm

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 26, 2011. Information for depositors Investigators who are willing to share mice with the PD research community through this resource should send an email to PDMice_at_ninds.nih.gov describing the mouse. The submission will be reviewed by the PD Models Repository Oversight Committee and, if accepted, a copy of the MTA will be sent by return email. NINDS is most interested in distributing mice that have been characterized in a peer-reviewed publication, but other models will certainly be considered. The email should describe the following: The protocol for identification from tail DNA. The health report of the mice to be shipped (the report has to be less than 2 months old). Information about the strain and any special needs for care and breeding. Information about any publications involving the mice Certification that mice are not encumbered by continuing intellectual property or other rights to any research, data or discovery utilizing the animals. Information for consumers Investigators desiring to study the mice available through the repository should send a request via email to PDMice_at_ninds.nih.gov. Requests will be reviewed by the PD Models Repository Oversight Committee and priority will be determined on a first come, first served basis; two breeding pairs will typically be shipped to any single requester. As detailed in the MTA, mice are not available for commercial research, including but not limited to drug screening. Neither the creator nor UCLA have a role in the governance of the Repository, and specifically, cannot impose conditions upon availability or distribution. It is anticipated that until the Repository is in a mode of steady state production, requests will be collected and mice distributed as supply allows. The email requesting mice should include: A brief description of the protocol Either a copy of the IACUC approval letter or numberNINDS/UCLA Repository for Parkinson's Disease Mouse Models: One of the most immediate and important benefits of discoveries regarding the genetic or environmental causes of Parkinson's disease (PD) is the subsequent development of animal models wherein therapeutic and/or preventative interventions may be studied. The widespread availability of such models is critically important to making progress against a disorder that affects more than 500,000 Americans at any given time. The National Institute of Neurological Disorders and Stroke (NINDS) fully recognizes the burden placed on investigators by the financial and logistical realities of distributing high demand research resources. Some investigators have deposited their mice with national distribution facilities but many mouse models are not available through such resources. Developing means to facilitate greater sharing of mouse models of PD is one of the goals developed by the PD research community at the July 2002 summit meeting convened by the NIH Director. Accordingly, as part of the effort to accelerate PD research, NINDS and the University of California at Los Angeles (UCLA) created a resource that will distribute transgenic mouse models of human PD that are not yet available through national commercial resources. Investigators who are willing to share mice with the PD research community can simply arrange with NINDS to have the mice deposited at UCLA and investigators desiring to study the mice may arrange with NINDS to obtain two breeding pairs. The process will use Material Transfer Agreements created specifically for this arrangement.

Proper citation: NINDS/UCLA Repository for Parkinson's Disease Mouse Models (RRID:SCR_007319) Copy   

•   Source: SciCrunch Registry
  

http://odc-sci.org

Portal for sharing spinal cord injury data from basic and clinical research to promote transparency, rigor and reproducibility. Community based repository for spinal cord injury research.

Proper citation: Open Data Commons for Spinal Cord Injury (RRID:SCR_016673) Copy   

•   Source: SciCrunch Registry
  

https://gdex.ucar.edu/

Provides data for atmospheric and ocean sciences research. Contains collection of meteorological, atmospheric composition, and oceanographic observations, and operational and reanalysis model outputs, integrated with NSF NCAR High Performance Compute services to support atmospheric and geosciences research. The RDA is managed by the Data Engineering and Curation Services group of the Computational and Information Systems Laboratory at the NSF National Center for Atmospheric Research.

Proper citation: The Geoscience Data Exchange (RRID:SCR_026989) Copy   

•   Source: SciCrunch Registry
  

https://dash.nichd.nih.gov/

Repository to store and access de-identified data from NICHD funded research studies for purposes of secondary research use. It serves as mechanism for NICHD-funded extramural and intramural investigators to share research data from studies in accordance with NIH Data Sharing Policy and NIH Genomic Data Sharing Policy.

Proper citation: Data and Specimen Hub (NICHD DASH) (RRID:SCR_016314) Copy   

•   Source: SciCrunch Registry
  

http://www.hmpdacc.org/

Common repository for diverse human microbiome datsets and minimum reporting standards for Common Fund Human Microbiome Project.

Proper citation: HMP Data Analysis and Coordination Center (RRID:SCR_004919) Copy   

•   Source: SciCrunch Registry
  

http://idr.openmicroscopy.org/about/

Public repository of reference image datasets from published scientific studies. Platform for publishing, mining and integrating bioimaging data, following FAIR principles and Euro-BioImaging/ELIXIR imaging strategy using OMERO and Bio-Formats open source software built by Open Microscopy Environment. Deployed on OpenStack cloud running on EMBL-EBI’s Embassy resource, it includes image data linked to independent studies from genetic, RNAi, chemical, localisation and geographic high content screens, super resolution microscopy, and digital pathology.

Proper citation: Image Data Resource (IDR) (RRID:SCR_017421) Copy   

•   Source: SciCrunch Registry
  

https://www.antibodysociety.org/the-airr-community/airr-data-commons/

Network of distributed repositories that adhere to standards set out by AIRR Community. This collection contains standards and repositories either created by the AIRR community or approved for use within AIRR community.

Proper citation: AIRR Data Commons (RRID:SCR_022597) Copy   

•   Source: SciCrunch Registry
  

http://www.ebi.ac.uk/pdbe/emdb/

Repository for electron microscopy density maps of macromolecular complexes and subcellular structures at Protein Data Bank in Europe. Covers techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography.

Proper citation: Electron Microscopy Data Bank at PDBe (MSD-EBI) (RRID:SCR_006506) Copy   

•   Source: SciCrunch Registry
  

https://www.niagads.org/

National genetics data repository facilitating access to genotypic and phenotypic data for Alzheimer's disease (AD). Data include GWAS, whole genome (WGS) and whole exome (WES), expression, RNA Seq, and CHIP Seq analyses. Data for the Alzheimer’s Disease Sequencing Project (ADSP) are available through a partnership with dbGaP (ADSP at dbGaP). Repository for many types of data generated from NIA supported grants and/or NIA funded biological samples. Data are deposited at NIAGADS or NIA-approved sites. Genetic Data and associated Phenotypic Data are available to qualified investigators in scientific community for secondary analysis.

Proper citation: National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS) (RRID:SCR_007314) Copy   

•   Source: SciCrunch Registry
  

https://data.niaid.nih.gov/

Unified search engine for infectious and immune-mediated disease datasets. Enables users to find datasets from biomedical research repositories. It indexes metadata from multiple NIH-funded and generalist repositories. Provides filters, prebuilt queries, and dataset collections to simplify the discovery process for users. The Portal additionally provides documentation and an API for programmatic access to harmonized metadata.

Proper citation: NIAID Data Ecosystem Discovery Portal (RRID:SCR_027614) Copy   

•   Source: SciCrunch Registry
  

http://media.marine-geo.org/

A collection of high-quality images and videos for education and outreach from the Integrated Earth Data Applications Facility. Albums include: Ridge2000, MARGINS, GeoMapApp, GeoPRISMS, Antarctic and Southern Ocean, Global Multi-Resolution Topography. To contribute your media to Media Bank, you are asked to supply metadata with each image/video supplied.

Proper citation: Marine Geosciences Data System MediaBank (RRID:SCR_006875) Copy   

•   Source: SciCrunch Registry
  

http://www.ndriresource.org/NDRI_Initiatives/HBDI/36/

Database of medical history and genealogical data on over 6700 families who are affected by type 1 diabetes and a repository of DNA and immortalized cell lines collected from 500 families. This database and repository was originally created to help researchers uncover the genetic causes of type 1 diabetes but today, it is also used by researchers who study type 2 diabetes, diabetic complications, autoimmune diseases, kidney disease, and other disorders. The following resources and services are available to researchers through HBDI: * International Type 1 Diabetes Database: This database includes more than 6700 families with diabetes, related complications and other genetic diseases. There are extensive genealogical and medical histories for more than 90,000 individuals. NDRI conducts searches of the database for approved research requests. * HBDI Catalog: The catalog contains 503 family pedigrees with associated cell lines, DNA, and serum for research. Also available are HLA-typing and auto-antibody test results for diabetes families in the catalog. * HBDI Repository: The HBDI repository contains cell lines, DNA, and HLA typing information from 480 families, and frozen buffy coats from 23 families, all with Type 1 diabetes. They have recently expanded the repository to include specimens from individuals with rare diseases. * Customized Collections: NDRI will collect data from patients and physicians, conduct phone interviews and collect blood and other specimens for research on request., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Human Biological Data Interchange (RRID:SCR_004591) Copy   

•   Source: SciCrunch Registry
  

https://arcticdata.io/

Data and software repository for Arctic section of National Science Foundation’s Office of Polar Programs. Repository has CoreTrustSeal certification so that the data can be used, shared, and preserved over long timespan. Helps research community reproducibly preserve and discover all products of NSF funded science in Arctic, including data, metadata, software, documents, and provenance that link these in coherent knowledge model. Initiative is the partnership between National Center for Ecological Analysis and Synthesis at UC Santa Barbara, DataONE, and National Centers for Environmental Information.

Proper citation: Arctic Data Center (RRID:SCR_024599) Copy   

•   Source: SciCrunch Registry
  

https://docs.airr-community.org/en/stable/api/adc_api.html

Provides programmatic access to query and download AIRR-seq data. ADC API uses JSON as its communication format, and standard HTTP methods like GET and POST. ADC API is read only and mechanism of inclusion of AIRR-seq studies into data repository is left up to repository. ADC API Specification explains how to construct and execute API requests and interpret API responses.

Proper citation: Adaptive Immune Receptor Repertoire Data Commons API Specification (RRID:SCR_022591) Copy   

•   Source: SciCrunch Registry
  

https://researchdata.bbk.ac.uk

Repository allows all researchers at Birkbeck to upload data, and get DOI.Data in the Birkbeck Data Repository is stored on Arkivum server.This is a very secure storage space, which will allow our data to remain unchanged and accessible for many years after it is deposited.

Proper citation: Birkbeck Research Data (RRID:SCR_023139) Copy   

•   Source: SciCrunch Registry
  

https://github.com/obophenotype/brain_data_standards_ontologies

Repository for co-ordinating work on ontologies for Brain Data Standards Project. Automate data driven cell type ontology development for Brain Data Standards initiative.

Proper citation: Brain Data Standards Ontology (RRID:SCR_022822) Copy   

•   Source: SciCrunch Registry