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http://neurodatabase.org

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 09, 2015. A repository of neurophysiology data conforming to BrainML data models and protocols: BrainML-formatted experimental data submissions are published in searchable, browsable form. Registered users may submit new experiments. The site contains spike trains, voltage time series, and some derived histograms from single cell and multi-unit activity. The database focuses on in vivo somatosensory and visual activity during task performance. This resource contains only a few datasets, but they are of high quality and have been used for reanalysis by several parties. There are three primary interfaces for querying data from this repository: a web-based browse interface, a web-based HTML query form, and a Java web start desktop application. In addition, there is an XML interface useful for direct access by software clients. To download the source code, please read and acknowledge the license agreement.

Proper citation: Neurodatabase.org (RRID:SCR_007091) Copy   

•   Source: SciCrunch Registry
  

http://smd.princeton.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 17, 2021. Database to store, annotate, view, analyze and share microarray data. It provides registered users access to their own data, provides users access to public data, and tools with which to analyze those data, to any public user anywhere in the world. The GenePattern software package has been incorporated directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability. SMD search options allow the user to Search By Experiments, Search By Datasets, or Search By Gene Names. Web services are provided using common standards, such as Simple Object Access Protocol (SOAP). This enables both local and remote researchers to connect to an installation of the database and retrieve data using pre-defined methods, without needing to resort to use of a web browser.

Proper citation: SMD (RRID:SCR_004987) Copy   

•   Source: SciCrunch Registry
  

https://senselab.med.yale.edu/OrModelDB/

A repository of the results of the efforts of the scientific community in computationally elucidating the structure of the olfactory receptor with a view to establishing a mechanistic basis for OR-odorant binding.

Proper citation: ORModelDB (RRID:SCR_014578) Copy   

•   Source: SciCrunch Registry
  

http://www.pazar.info/

Database that unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein-DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data ''boutiques'' within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PAZAR (RRID:SCR_005410) Copy   

•   Source: SciCrunch Registry
  

http://www.opentopography.org/

Accepts and provides access to high-resolution (meter to sub-meter scale) Earth science-oriented topography data (e.g. LiDAR) and bathymetric data, and related tools and resources. The OpenTopography Tool Registry provides a community populated clearinghouse of software, utilities, and tools oriented towards high-resolution topography data (e.g. collected with LiDAR technology) handling, processing, and analysis. Tools registered range from source code to full-featured software applications. Contributions to the registry via the Contribute a Tool page are welcome. OpenTopography also hosts a dataset catalog to which users can register datasets hosted elsewhere; these entries are discoverable by users alongside OpenTopography hosted datasets. Lidar point cloud data are available in LAS, LAZ and ASCII formats. Raster datasets and derived products can be downloaded in Arc ASCII, IMG, and GeoTIFF formats. Derived products and visualizations are available in Google Earth KML format. The OpenTopography user community and advisory committee provides feedback to define the scope of collaborations on data hosting and cyberinfrastructure development

Proper citation: OpenTopography (RRID:SCR_002204) Copy   

•   Source: SciCrunch Registry
  

http://www.informatics.jax.org/expression.shtml

Community database that collects and integrates the gene expression information in MGI with a primary emphasis on endogenous gene expression during mouse development. The data in GXD are obtained from the literature, from individual laboratories, and from large-scale data providers. All data are annotated and reviewed by GXD curators. GXD stores and integrates different types of expression data (RNA in situ hybridization; Immunohistochemistry; in situ reporter (knock in); RT-PCR; Northern and Western blots; and RNase and Nuclease s1 protection assays) and makes these data freely available in formats appropriate for comprehensive analysis. There is particular emphasis on endogenous gene expression during mouse development. GXD also maintains an index of the literature examining gene expression in the embryonic mouse. It is comprehensive and up-to-date, containing all pertinent journal articles from 1993 to the present and articles from major developmental journals from 1990 to the present. GXD stores primary data from different types of expression assays and by integrating these data, as data accumulate, GXD provides increasingly complete information about the expression profiles of transcripts and proteins in different mouse strains and mutants. GXD describes expression patterns using an extensive, hierarchically-structured dictionary of anatomical terms. In this way, expression results from assays with differing spatial resolution are recorded in a standardized and integrated manner and expression patterns can be queried at different levels of detail. The records are complemented with digitized images of the original expression data. The Anatomical Dictionary for Mouse Development has been developed by our Edinburgh colleagues, as part of the joint Mouse Gene Expression Information Resource project. GXD places the gene expression data in the larger biological context by establishing and maintaining interconnections with many other resources. Integration with MGD enables a combined analysis of genotype, sequence, expression, and phenotype data. Links to PubMed, Online Mendelian Inheritance in Man (OMIM), sequence databases, and databases from other species further enhance the utility of GXD. GXD accepts both published and unpublished data.

Proper citation: Gene Expression Database (RRID:SCR_006539) Copy   

•   Source: SciCrunch Registry
  

http://protchem.hunnu.edu.cn/toxin/

Database of animal toxins, this most recent release (2009) focused on constructing a global-scale animal toxin-channel interaction network based on literature and database annotations through the integration of an ion channel database into ATDB 2.0. Most ion channel sequences were categorized and annotated with a hierarchic controlled term system (Ion Channel Ontology). More than 55,022 possible T-C interactions were extracted by text mining which link the toxin and ion channel database. These interaction data were classified carefully based on evidence type, in which 9,193 high confidence interactions were annotated in active site level. A web-based T-C interaction network view was build to visualize and make data access easy. The features and updates of ATDB 2.0 are summarized as follows: # AN interaction dataset including 55,022 toxin-channel interactions # Ion channel database (5,097 entries) # Ontology for ion channel classification (Ion Channel Ontology) # 3000 maps for toxins and ion channels interaction # More than 600 additional toxin entries # PDB view to visualize 3-D structure of molecule # More flexible option for data downloads. You may submit new toxins to the database.

Proper citation: Animal Toxin Database (RRID:SCR_007035) Copy   

•   Source: SciCrunch Registry
  

http://www.eyemoviepedia.com/

Archive and access films from the field of Ophthalmology for free on highly secure servers for permanent access and citeability. A citeable identification number (specific addressing using DOI), allows for citation of individual films in journal publications. Films may be commented by the author either in speech, or in text. Key wording provided by the authors at the time of submission, make each film recognizable to internet search machines.

Proper citation: eyeMoviePedia (RRID:SCR_003541) Copy   

•   Source: SciCrunch Registry
  

http://www.ncbi.nlm.nih.gov/nucest

Nucleotide database as collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.

Proper citation: Nucleotide database (RRID:SCR_004630) Copy   

•   Source: SciCrunch Registry
  

http://www.metabolomicsworkbench.org/data/metabolitedatabase.php

A database which contains structures and annotations of biologically relevant metabolites from public repositories such as LIPID MAPS, ChEBI, HMDB, PubChem, and KEGG. Users can search for molecular structure based on substructure, text, or mass.

Proper citation: Metabolomics Workbench Metabolite Database (RRID:SCR_014633) Copy   

•   Source: SciCrunch Registry
  

http://dgv.tcag.ca/dgv/app/home

Public repository that accepts direct submissions and provides archiving, accessioning and distribution of publicly available genomic structural variants, in all species. Variants are accessioned at the study and sample level, granting stable identifiers that can be used in publications. DGVa data is integrated with other EBI resources, including comprehensive EBI search and Ensembl genome browser. Exchanges data with companion database, dbVar, at National Center for Biotechnology Information.NOTE: since 2019 DGVa doesn't accept submissions. Please send the data for submission to European Variation Archive (EVA).

Proper citation: Database of Genomic Variants Archive (DGVa) (RRID:SCR_004896) Copy   

•   Source: SciCrunch Registry
  

https://np-mrd.org/

Database and respository for NMR data associated with natural products and specialized metabolites.

Proper citation: Natural Products Magnetic Resonance Database (RRID:SCR_026534) Copy   

•   Source: SciCrunch Registry
  

http://conp.ca/

Web interface that facilitates open science for neuroscience community by simplifying global access to and sharing of datasets and tools. Portal internalizes typical data cycle of research project, beginning with data acquisition, followed by data processing with published tools, and ultimately publication of results with link to original dataset. Platform to form interactive network of collaborations in brain research, interdisciplinary student training, international partnerships, clinical translation and open publishing. Provides unified interface to Canadian neuroscience research community. Open neuroscience research with sharing of both data and methods, to create large-scale databases, development of standards for sharing, facilitation of advanced analytic strategies, open dissemination to global community of neuroscience data and methods, and establishment of training programs for next generation of computational neuroscience researchers.

Proper citation: Canadian Open Neuroscience Platform (RRID:SCR_016433) Copy   

•   Source: SciCrunch Registry
  

http://www.physionet.org/

Collection of dissemination and exchange recorded biomedical signals and open-source software for analyzing them. Provides facilities for cooperative analysis of data and evaluation of proposed new algorithm. Providies free electronic access to PhysioBank data and PhysioToolkit software. Offers service and training via on-line tutorials to assist users at entry and more advanced levels. In cooperation with annual Computing in Cardiology conference, PhysioNet hosts series of challenges, in which researchers and students address unsolved problems of clinical or basic scientific interest using data and software provided by PhysioNet. All data included in PhysioBank, and all software included in PhysioToolkit, are carefully reviewed. Researchers are further invited to contribute data and software for review and possible inclusion in PhysioBank and PhysioToolkit. Please review guidelines before submitting material.

Proper citation: PhysioNet (RRID:SCR_007345) Copy   

•   Source: SciCrunch Registry
  

https://bolin.su.se/data/

Provides open access to Climate and Earth System Data from scientists at the centre and their collaborators. Helps to make your data open, FAIR and visually appealing. Each dataset and source code in the Bolin Centre Database is assigned a unique DOI. This makes it easy to cite and find your data. If dataset has more than one version, each version will have its own DOI.

Proper citation: Bolin Centre Database (RRID:SCR_023142) Copy   

•   Source: SciCrunch Registry
  

http://www.tcdb.org/

Curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from variety of living organisms based on IUBMB-approved transporter classification (TC) system. Descriptions, TC numbers, and examples of over 600 families of transport proteins are provided. TC system is analogous to Enzyme Commission (EC) system for classification of enzymes, except that it incorporates both functional and phylogenetic information. TCDB users may submit their own sequenced proteins and descriptions for inclusion into database. The software tools used are all freely available for download. These programs are used for analysis of Protein and DNA sequences. Programs require UNIX server to run.

Proper citation: Transporter Classification Database (RRID:SCR_004490) Copy   

•   Source: SciCrunch Registry
  

http://www.massbank.jp/?lang=en

Public repository of mass spectral data which allows users to search similar spectra on a peak-to-peak basis, on a neutral loss-to-neutral loss basis, or by the m/z value and molecular formula, search chemical compounds by substructures, and keyword search chemical compounds

Proper citation: MassBank (RRID:SCR_015535) Copy   

•   Source: SciCrunch Registry
  

http://www.biodiversity.aq/

International effort that seeks to increase our knowledge and understanding of Antarctic and Southern Ocean biodiversity.It is a community of researchers, data custodians and developers from around the world that supports the mobilisation publication, retrieval and analysis of Antarctic and Southern Ocean biodiversity data in a free and open manner in line with the Antarctic treaty and the FAIR data Principles (Finable, Accessible, Interoperable, Reusable). The SCAR Antarctic biodiversity Portal has a number of portals dedicated to specific types of data and information on Antarctic and Southern Ocean Biodiversity.We aim to create an information ecosystem of various data bases, data systems, web services tools etc that can be used by anyone with an interest in Antarctic and Southern Ocean biodiversity.Biodiversity.aq is an international initiative of the Scientific Committee on Antarctic Research (SCAR). It finds it roots in the Census of Antarctic Marine Life and started in 2005. The central facilities are hosted by the Royal Belgian Institute for Natural sciences (RBINS, www.naturalsciences.be) and the Belgian Biodiversity Platform (BBPf, www.biodiversity.be).The SCAR Antarctic Biodiversity Portal is the regional thematic node of the Ocean Biodiversity Information System (OBIS, www.obis.org), the Global Biodiversity Information Facility (GBIF, www.gbif.org) and works closely together with the Southern Ocean Observation System (SOOS, www.soos.aq).

Proper citation: SCAR Antarctic Biodiversity Portal (RRID:SCR_023136) Copy   

•   Source: SciCrunch Registry
  

http://treebase.org/treebase-web/

Repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all kinds of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or in review can be submitted to TreeBASE but will not be available to the public until they have passed peer review.

Proper citation: TreeBASE (RRID:SCR_005688) Copy   

•   Source: SciCrunch Registry
  

https://www.med.unc.edu/pgc/

Consortium conducting meta-analyses of genome-wide genetic data for psychiatric disease. Focused on autism, attention-deficit hyperactivity disorder, bipolar disorder, major depressive disorder, schizophrenia, anorexia nervosa (AN), Tourette syndrome (TS), and obsessive-compulsive disorder (OCD). Used to investigate common single nucleotide polymorphisms (SNPs) genotyped on commercial arrays, structural variation (copy number variation) and uncommon or rare genetic variation. To participate you are asked to upload data from your study to central computer used by this consortium. Genetic Cluster Computer serves as data warehouse and analytical platform for this study . When data from your study have been incorporated, account will be provided on central server and access to all GWAS genotypes, phenotypes, and meta-analytic results relevant to deposited data and participation aims. NHGRI GWAS Catalog contains updated information about all GWAS in biomedicine, and is usually excellent starting point to find comprehensive list of studies. Files can be obtained by any PGC member for any disease to which they contributed data. These files can also be obtained by application to NIMH Genetics Repository. Individual-level genotype and phenotype data requires application, material transfer agreement, and informed consent consideration. Some datasets are also in controlled-access dbGaP and Wellcome Trust Case-Control Consortium repositories. PGC members can also receive back cleaned and imputed data and results for samples they contributed to PGC analyses.

Proper citation: Psychiatric Genomics Consortium (RRID:SCR_004495) Copy   

•   Source: SciCrunch Registry