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

Automated system for constructing putative homology groups from complete gene sets of wide range of eukaryotic species. Databse that provides system for automatic detection of homologs, including paralogs and orthologs, among annotated genes of sequenced eukaryotic genomes. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences. Reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man, Mouse Genome Informatics, Zebrafish Information Network, Saccharomyces Genome Database and FlyBase.

Proper citation: HomoloGene (RRID:SCR_002924) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Web tool for an organized view of the transcriptome. Collection of the computationally identified transcripts from the same locus. Information on protein similarities, gene expression, cDNA clones, and genomic location. System for automatically partitioning GenBank sequences into a non redundant set of gene oriented clusters.

Proper citation: UniGene (RRID:SCR_004405) Copy   

•   Source: SciCrunch Registry

http://www.data-archive.ac.uk

Organization which acquires, curates, and provides access to a collection of digital data in the social sciences and humanities in the United Kingdom.

Proper citation: UK Data Archive (RRID:SCR_014708) Copy   

•   Source: SciCrunch Registry

https://www.inptdat.de

Interdisciplinary data platform provides access to research data and information from all fields of applied plasma physics and plasma medicine. Aims at distributing, publishing and archiving of data and information, supporting findability, accessibility, interoperability and re-use of data, for low temperature plasma physics community.Most of data are freely available and can be used under terms of license listed on dataset description page. Each dataset can be identified, cited and shared by using Digital Object Identifier.

Proper citation: INPTDAT (RRID:SCR_022167) Copy   

•   Source: SciCrunch Registry

http://beetlebase.org/

A centralized sequence database and community resource for Tribolium genetics, genomics and developmental biology containing genomic sequence scaffolds mapped to 10 linkage groups, genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The current version of Beetlebase is built on the Tribolium castaneum 3.0 Assembly (Tcas 3.0) released by the Human Genome Sequencing Center at the Baylor College of Medicine. The database is constructed using the upgraded Generic Model Organism Database (GMOD) modules. The genomic data is stored in a PostgreSQL relational database using the Chado schema and visualized as tracks in GBrowse. The genetic map is visualized using the comparative genetic map viewer CMAP. To enhance search capabilities, the BLAST search tool has been integrated with the GMOD tools. Tribolium castaneum is a very sophisticated genetic model organism among higher eukaryotes. As the member of a primitive order of holometabolous insects, Coleoptera, Tribolium is in a key phylogenetic position to understand the genetic innovations that accompanied the evolution of higher forms with more complex development. Coleoptera is also the largest and most species diverse of all eukaryotic orders and Tribolium offers the only genetic model for the profusion of medically and economically important species therein. The genome sequences may be downloaded.

Proper citation: BeetleBase (RRID:SCR_001955) Copy   

•   Source: SciCrunch Registry

http://www.barcodinglife.com/

DNA barcode data with an online workbench that supports data validation, annotation, and publication for specimen, distributional, and molecular data. The data platform consists of three main modules, a data portal, a database of barcode clusters, and data collection workbench. The Public Data Portal provides access to all public barcode data which consists of data generated using the Workbench module as well as data mined from other sources. The Barcode Index Number (BIN) system assigns a unique identifier to each sequence cluster of COI, providing an interim taxonomic system for species in the animal kingdom. The workbench module integrates secure databases with analytical tools to provide a private collaborative environment for researchers to collect, analyze, and publish barcode data and ancillary DNA sequences. This platform also provides an annotation framework that supports tagging and commenting on records and their components (i.e. taxonomy, images, and sequences), allowing for community-based validation of barcode data. By providing specialized services, it aids in the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. Public data records include record identifiers, taxonomy, specimen details, collection information and sequence data. Data that has been publicly released through BOLD can be retrieved manually through the BOLD public interface or automatically through BOLD web services. BOLD analytical tools are available for any data set that exists in BOLD (including publicly available data). Analytical tools can be accessed through the BOLD Project Console under the headings Sequences Analysis or Specimen Aggregates. Some examples include Taxon ID Tree, Alignment Viewer, Distribution Maps, and Image Library.

Proper citation: BOLD (RRID:SCR_004278) Copy   

•   Source: SciCrunch Registry

http://www.emouseatlas.org/emage

A database of in situ gene expression data in the developing mouse embryo and an accompanying suite of tools to search and analyze the data. mRNA in situ hybridization, protein immunohistochemistry and transgenic reporter data is included. The data held is spatially annotated to a framework of 3D mouse embryo models produced by EMAP (e-Mouse Atlas Project). These spatial annotations allow users to query EMAGE by spatial pattern as well as by gene name, anatomy term or Gene Ontology (GO) term. The conceptual framework which houses the descriptions of the gene expression patterns in EMAGE is the EMAP Mouse Embryo Anatomy Atlas. This consists of a set of 3D virtual embryos at different stages of development, as well as an accompanying ontology of anatomical terms found at each stage. The raw data images can be conventional 2D photographs (of sections or wholemount specimens) or 3D images of wholemount specimens derived from Optical Projection Tomography (OPT) or confocal microscopy. Users may submit data using a Data submission tool or without.

Proper citation: EMAGE Gene Expression Database (RRID:SCR_005391) Copy   

•   Source: SciCrunch Registry

https://www.dataone.org/

A distributed framework and cyberinfrastructure for open, persistent, and secure access to Earth observational data. It ensures the preservation, access, use and reuse of multi-scale, multi-discipline, and multi-national science data via three primary cyberinfrastucture elements and a broad education and outreach program. The DataONE Investigator Toolkit is a collection of software tools for finding, using, and contributing data in DataONE. DataONE currently hosts three Coordinating Nodes that provide network-wide services to enhance interoperability of the Member Nodes and support indexing and replication services. Coordinating Nodes provide a replicated catalog of Member Node holdings and make it easy for scientists to discover data wherever they reside, also enabling data repositories to make their data and services more broadly available to the international community. DataONE Coordinating Nodes are located at the University of New Mexico, the University of California Santa Barbara and at the University of Tennessee (in collaboration with Oak Ridge National Laboratory). DataONE comprises a distributed network of data centers, science networks or organizations. These organizations can expose their data within the DataONE network through the implementation of the DataONE Member Node service interface. In addition to scientific data, Member Nodes can provide computing resources, or services such as data replication, to the DataONE community.

Proper citation: DataONE (RRID:SCR_003999) Copy   

•   Source: SciCrunch Registry

https://www.synapse.org/

A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data.

Proper citation: Synapse (RRID:SCR_006307) 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

https://b2share.eudat.eu/

Used to store, publish and share research data in FAIR way. Facilitates research data storage, guarantees long-term persistence of data and allows data, results or ideas to be shared worldwide.Supports community domains with metadata extensions, access rules and publishing workflows.

Proper citation: B2SHARE Eudat (RRID:SCR_023135) Copy   

•   Source: SciCrunch Registry

http://www.polardata.ca

Repository of metadata and data that describes and provides access to diverse data sets generated by Arctic and Antarctic researchers. The metadata records follow ISO 19115 and Federal Geographic Data Committee (FGDC) standard formats to provide exchange with other data centres. The records cover a wide range of disciplines from natural sciences and policy, to health and social sciences. The PDC Geospatial Search tool is available to the public and researchers alike and allows searching data using a mapping interface and other parameters.

Proper citation: Polar Data Catalogue (RRID:SCR_023131) Copy   

•   Source: SciCrunch Registry

https://aperta.ulakbim.gov.tr

Aperta is the name of the Turkish Open Archive.You can upload your scientific studies within the scope of Aperta to this portal or you can easily access the uploaded studies.

Proper citation: Aperta Turkey Open Archive (RRID:SCR_023128) Copy   

•   Source: SciCrunch Registry

https://repository.library.brown.edu/studio/

Collection contains open and publicly funded data sets created by Brown University faculty and student researchers. Increasingly, publishers, and funders are requiring that protocols, data sets, metadata, and code underlying published research be retained and preserved, their locations cited within publications, and shared with other researchers and the public. The deposits here endeavor to be in line with FAIR Principles (Findable, Accessible, Interoperable, Reusable). If you would like to deposit data set into this collection for the purposes of citation/linking within publication and public dissemination, then please log in, zip up and upload your file, and request digital object identifier (DOI) for your data citation.

Proper citation: Brown Digital Repository (RRID:SCR_023144) Copy   

•   Source: SciCrunch Registry

https://data.bioheritage.nz/

Data catalogue and repository for New Zealand's Biological Heritage National Science Challenge.

Proper citation: BioHeritage National Science Challenge Data Repository (RRID:SCR_023141) Copy   

•   Source: SciCrunch Registry

http://matrixdb.univ-lyon1.fr/

Freely available database focused on interactions established by extracellular proteins and polysaccharides, taking into account the multimeric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data. It includes interaction data extracted from the literature by manual curation, and offers access to relevant data involving extracellular proteins provided by the IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database. The database reports mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. Interactions with lipids and cations are also reported. MatrixDB is focused on mammalian interactions, but aims to integrate interaction datasets of model organisms when available. MatrixDB provides direct links to databases recapitulating mutations in genes encoding extracellular proteins, to UniGene and to the Human Protein Atlas that shows expression and localization of proteins in a large variety of normal human tissues and cells. MatrixDB allows researchers to perform customized queries and to build tissue- and disease-specific interaction networks that can be visualized and analyzed with Cytoscape or Medusa. Statistics (2013): 2283 extracellular matrix interactions including 2095 protein-protein and 169 protein-glycosaminoglycan interactions.

Proper citation: MatrixDB (RRID:SCR_001727) Copy   

•   Source: SciCrunch Registry

http://www.archive.org/

An Internet library offering the general public access to historical collections that exist in digital format including texts, audio, moving images, and software. Additionally it provides archived web pages in their collections, and specialized services for adaptive reading and information access for the blind and other persons with disabilities. Founded in 1996 and located in San Francisco, the Archive has been receiving data donations from Alexa Internet and others. In late 1999, the organization started to grow to include more well-rounded collections.

Proper citation: Internet Archive (RRID:SCR_001682) Copy   

•   Source: SciCrunch Registry

http://www.myexperiment.org/

Community repository and virtual research environment where scientists can safely publish their workflows and experiment plans, share them with groups and find and use those of others. Workflows, other digital objects and collections (called Packs) can be swapped, sorted and searched. It supports Linked data, has a SPARQL Endpoint and REST API and is based on an open source Ruby on Rails codebase. Scientific workflows in various formats can be uploaded. Specific support is provided for Taverna workflows for which the system displays relevant metadata, components and visual previews, that are retrieved directly from workflow files. Version history for workflows is collected. This feature allows the contributor to keep previous versions of the workflow available, when the latest one is uploaded. This brings additional benefit for the users by allowing them to view the development stages of the workflow towards its latest implementation.

Proper citation: myExperiment (RRID:SCR_001795) Copy   

•   Source: SciCrunch Registry

http://neuromorpho.org/index.jsp

Centrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications that contains some of the most complete axonal arborizations digitally available in the community. Each neuron is represented by a unique identifier, general information (metadata), the original and standardized ASCII files of the digital morphological reconstruction, and a set of morphometric features. It contains contributions from over 100 laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared. Users may browse by species, brain region, cell type or lab name. Users can also download morphological reconstructions for research and analysis. Deposition and distribution of reconstruction files ultimately prevents data loss. Centralized curation and annotation aims at minimizing the effort required by data owners while ensuring a unified format. It also provides a one-stop entry point for all available reconstructions, thus maximizing data visibility and impact.

Proper citation: NeuroMorpho.Org (RRID:SCR_002145) Copy   

•   Source: SciCrunch Registry

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

Repository providing free access to marine geophysical data (e.g. bathymetry, seismic data, magnetics, gravity, images) and related land-based data from NSF-funded research conducted throughout the global oceans. Data Portals include GeoPRISMS, MARGINS, Ridge 2000, Antarctic and Southern Ocean Data Synthesis, the Global Multi-Resolution Topography Synthesis, and Seismic Reflection Field Data Portal. Primary data types served are multibeam bathymetric data from the ocean floor, seismic reflection data imaging below the seafloor, and multi-disciplinary ship based data from the Southern Ocean. Other holdings include deep-sea photographic transects, and ultra-high resolution bathymetry, temperature probe data, biological species compilations, MAPR and CTD data. Derived data products and sets include microseismicity catalogs, images, visualization scenes, magnetic and gravity compilations, grids of seismic layer thickness, velocity models, GIS project files, and 3D visualizations. Tools to discover, explore, and visualize data are available. They deliver catalogs, maps, and data through standard programmatic interfaces. GeoMapApp, a standalone data visualization and analysis tool, permits dynamic data exploration from a map interface and the capability to generate and download custom grids and maps and other data. Through GeoMapApp, users can access data hosted at the MGDS, at other data repositories, and import their own data sets. Global Multi-Resolution Topography (GMRT) is a continuously-updated compilation of seafloor bathymetry integrated with global land topography. It can be used to create maps and grids and it can be accessed through several standard programmatic interfaces including GeoMapApp and Google Earth. The GMRT compilation can also be explored in 3D using Virtual Ocean. The MGDS MediaBank contains high quality images, illustrations, animations and video clips that are organized into galleries. Media can be sorted by category, and keyword and map-based search options are provided. Each item in the MediaBank is accompanied by metadata that provides access to a cruise catalog and data repository.

Proper citation: Marine Geoscience Data System (RRID:SCR_002164) Copy   

•   Source: SciCrunch Registry