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

Databases of protein sequences and 3D structures of proteins. Collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

Proper citation: NCBI Protein Database (RRID:SCR_003257) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/genomes/FLU/

Database of data obtained from the NIAID Influenza Genome Sequencing Project as well as from GenBank, combined with tools for flu sequence analysis and annotation. In addition, it provides links to other resources that contain flu sequences, publications and general information about flu viruses. Users can search the Flu database, build queries, retrieve sequences, and apply analysis tools. This includes selecting influenza sequences by virus, subtype, host, and other criteria, finding complete genome sets, aligning sequence and others in the database (up to 1000 sequences), viewing clustering and phylogenetic trees, BLAST searching a flu sequence against the database, and more.

Proper citation: Influenza Virus Resource (RRID:SCR_002984) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/genbank/tpa/

Database designed to capture experimental or inferential results that support submitter-provided annotation for sequence data that the submitter did not directly determine but derived from GenBank primary data. Records are divided into two categories: * TPA:experimental: Annotation of sequence data is supported by peer-reviewed wet-lab experimental evidence. * TPA:inferential: Annotation of sequence data by inference (where the source molecule or its product(s) have not been the subject of direct experimentation) TPA records are retrieved through the Nucleotide Database and feature information on the sequence, how it was cataloged, and proper way to cite the sequence information.

Proper citation: TPA (RRID:SCR_003593) Copy   

•   Source: SciCrunch Registry

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

Database of three-dimensional structures of macromolecules that allows the user to retrieve structures for specific molecule types as well as structures for genes and proteins of interest. Three main databases comprise Structure-The Molecular Modeling Database; Conserved Domains and Protein Classification; and the BioSystems Database. Structure also links to the PubChem databases to connect biological activity data to the macromolecular structures. Users can locate structural templates for proteins and interactively view structures and sequence data to closely examine sequence-structure relationships. * Macromolecular structures: The three-dimensional structures of biomolecules provide a wealth of information on their biological function and evolutionary relationships. The Molecular Modeling Database (MMDB), as part of the Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more. It is possible, for example, to find 3D structures for homologs of a protein of interest by following the Related Structure link in an Entrez Protein sequence record. * Conserved domains and protein classification: Conserved domains are functional units within a protein that act as building blocks in molecular evolution and recombine in various arrangements to make proteins with different functions. The Conserved Domain Database (CDD) brings together several collections of multiple sequence alignments representing conserved domains, in addition to NCBI-curated domains that use 3D-structure information explicitly to define domain boundaries and provide insights into sequence/structure/function relationships. * Small molecules and their biological activity: The PubChem project provides information on the biological activities of small molecules and is a component of NIH''''s Molecular Libraries Roadmap Initiative. PubChem includes three databases: PCSubstance, PCBioAssay, and PCCompound. The PubChem data are linked to other data types (illustrated example) in the Entrez system, making it possible, for example, to retrieve information about a compound and then Link to its biological activity data, retrieve 3D protein structures bound to the compound and interactively view their active sites, and find biosystems that include the compound as a component. * Biological Systems: A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. The NCBI BioSystems Database provides centralized access to biological pathways from several source databases and connects the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system. BioSystem records list and categorize components (illustrated example), such as the genes, proteins, and small molecules involved in a biological system. The companion FLink icon FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems.

Proper citation: NCBI Structure (RRID:SCR_004218) Copy   

•   Source: SciCrunch Registry

https://fairsharing.org/collections/

Web-based, searchable portal of three interlinked registries, containing both in-house and crowdsourced manually curated descriptions of standards, databases and data policies, combined with integrated view across all three types of resource. By registering your resource on FAIRsharing, you gain credit for your work, increase its visibility outside of your direct domain, reduce potential for unnecessary reinvention and proliferation of standards and databases.

Proper citation: FAIRsharing (RRID:SCR_004177) Copy   

•   Source: SciCrunch Registry

https://mps.csb.pitt.edu/

Open source database used for analyzing and modeling compound interactions with human and animal organ models.Platform for experimental design, data management, and analysis, and to combine experimental data with reference data, to enable computational modeling. Resource for relating in vitro organ model data to multiple biochemical, preclinical, and clinical data sources on in vivo drug effects.

Proper citation: Microphysiology Systems Database (RRID:SCR_021126) 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

https://launchpad.net/

A software collaboration platform that provides: Bug tracking, Code hosting using Bazaar, Code reviews, Ubuntu package building and hosting, Translations, Mailing lists, Answer tracking and FAQs, and Specification tracking. Launchpad can host your project''s source code using the Bazaar version control system.

Proper citation: Launchpad (RRID:SCR_006853) Copy   

•   Source: SciCrunch Registry

http://www.accdc.com/

Comprehensive lists of plant and animal species, with a rarity rank and legal status for each. It has has over 635,000 geo-located records of species occurrences and over 40,000 records of extremely rare to uncommon species in the Atlantic region, including New Brunswick, Nova Scotia, Prince Edward Island, Newfoundland, and Labrador. The Atlantic CDC also maintains biological and other types of data in a variety of linked databases. The CDC welcomes inquiries from those who would like to contribute data about plant or animal species at risk or rare communities in Atlantic Canada. Its mission is to assemble and provide objective and understandable data and expertise about species and ecological communities of conservation concern, including those at risk, and undertake field biological inventories to support decision-making, research, and education in Atlantic Canada. The Atlantic CDC develops species location data, known as element occurrence records. Occurrence precision (accuracy) ranges from quite precise (within meters) to less precise (within counties) but most commonly it is within 1 5 km. Element occurrence (EO) refers to one or more locations considered important to the continued existence of a species or ecological community. For species, over 30 types of data: taxonomy, biology, etc. are typically examined when identifying EOs. An EO is generally the habitat occupied by a local population. However, occurrence varies among species and some species have more than one type of occurrence (e.g., breeding and winter occurrences). Breeding colonies, breeding ponds, denning sites, and hibernacula are general examples of different types of animal EOs. For an ecological community, an EO may be the area containing a patch of that community type.

Proper citation: Atlantic Canada Conservation Data Centre (RRID:SCR_006061) Copy   

•   Source: SciCrunch Registry

https://borealisdata.ca/dataverse/dv/?q=*

Data repository to preserve and provide access to agricultural and environmental data produced during research projects undertaken at the University of Guelph including datasets on topics such as crop yield, soil moisture, weather and agroforestry. A special emphasis is placed on research funded by Ontario Ministry of Agriculture and Food (OMAF) and MRA.

Proper citation: Agri-environmental Research Data Repository (RRID:SCR_006317) Copy   

•   Source: SciCrunch Registry

http://biodiversitylibrary.org/

Collection of legacy literature in biodiversity assembled by an international consortium of natural history and botanical libraries. It also serves as the foundational literature component of the Encyclopedia of Life. Browse by author, title, subject, collection, map, year, language, and contributor. Taxonomic search using UBio. Also supports data export and a variety of machine interfaces.

Proper citation: Biodiversity Heritage Library (RRID:SCR_008969) 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://pubchem.ncbi.nlm.nih.gov/

Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI).

Proper citation: PubChem (RRID:SCR_004284) Copy   

•   Source: SciCrunch Registry

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

The European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - they work to collate, maintain and provide access to the global repository of macromolecular structure data. The main objectives of the work at PDBe are: * to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces. * to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data). * to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites. Several sophisticated tools are also available for the structural analysis of macromolecules.

Proper citation: PDBe - Protein Data Bank in Europe (RRID:SCR_004312) Copy   

•   Source: SciCrunch Registry

https://nda.nih.gov/

The National Institute of Mental Health Data Archive (NDA) makes available human subjects data collected from hundreds of research projects across many scientific domains. Research data repository for data sharing and collaboration among investigators. Used to accelerate scientific discovery through data sharing across all of mental health and other research communities, data harmonization and reporting of research results. Infrastructure created by National Database for Autism Research (NDAR), Research Domain Criteria Database (RDoCdb), National Database for Clinical Trials related to Mental Illness (NDCT), and NIH Pediatric MRI Repository (PedsMRI).

Proper citation: NIMH Data Archive (RRID:SCR_004434) Copy   

•   Source: SciCrunch Registry

http://figshare.com/

Repository for all data, figures, theses, publications, posters, presentations, filesets, videos, datasets, negative data in a citable, shareable and discoverable manner with Digital Object Identifiers. Allows to upload any file format to be made visualisable in the browser so that figures, datasets, media, papers, posters, presentations and filesets can be disseminated in a way that the current scholarly publishing model does not allow. Features integration with ORCID, Symplectic Elements, can import items from Github and is a source tracked by Altmetric.com. Figshare gives users unlimited public space and 1GB of private storage space for free. Data are digitally preserved by CLOCKSS. Supported by Digital Science, a division of Macmillan Publishers Limited, as a community-based, open science project that retains its autonomy.

Proper citation: FigShare (RRID:SCR_004328) Copy   

•   Source: SciCrunch Registry

http://www.data.gov/

Catalog of data sets that are generated and held by the Federal Government, including data, tools and resources to conduct research, develop web and mobile applications, design data visualizations, etc. Data.gov provides descriptions of the Federal datasets (metadata), information about how to access the datasets, and tools that leverage government datasets. The data catalogs will continue to grow as datasets are added. Federal, Executive Branch data are included in the first version of Data.gov.

Proper citation: Data.gov (RRID:SCR_004712) Copy   

•   Source: SciCrunch Registry

http://www.rhea-db.org/

Manually annotated reaction database where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest) which provides detailed information about structure, formula and charge. Rhea provides built-in validations that ensure both elemental and charge balance of the reactions. The database has been populated with the reactions found in the Enzyme Commission (EC) list (and in the IntEnz and ENZYME databases), extending it with additional known reactions of biological interest. While the main focus of Rhea is enzyme-catalyzed reactions, other biochemical reactions are also included. Rhea is a manually annotated resource and it provides: stable reaction identifiers for each of its reactions; directionality information if the physiological direction of the reaction is known; the possibility to link several reactions together to form overall reactions; extensive cross-references to other resources including enzyme-catalyzed and other metabolic reactions, such as the EC list (in IntEnz), KEGG, MetaCyc and UniPathway; and chemical substructure and similarity searches on compounds in Rhea.

Proper citation: RHEA (RRID:SCR_004713) 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.ebi.ac.uk/intact

Open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions. Direct user submissions of molecular interaction data are encouraged, which may be deposited prior to publication in a peer-reviewed journal. The IntAct Database contains (Jun. 2014): * 447368 Interactions * 33021 experiments * 12698 publications * 82745 Interactors IntAct provides a two-tiered view of the interaction data. The search interface allows the user to iteratively develop complex queries, exploiting the detailed annotation with hierarchical controlled vocabularies. Results are provided at any stage in a simplified, tabular view. Specialized views then allows "zooming in" on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available.

Proper citation: IntAct (RRID:SCR_006944) Copy   

•   Source: SciCrunch Registry