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http://force11.org/

A collaboration which works to transform scholarly communications through advanced use of computers and the Web. FORCE11 advocates the digital publishing of papers in order to enable more effective scholarly communication. The virtual community also advocates the publication of software tools and research communication by means of social media channels. As such, FORCE11 provides access to information and tools for the wider scientific community.

Proper citation: FORCE11 (RRID:SCR_005334) Copy   

•   Source: SciCrunch Registry

http://www.crystallography.net/

Database of crystal structures of organic, inorganic, metal-organic compounds and minerals, excluding biopolymers. It currently contains ~291204 entries (July 2014) in crystallographic information file format, with nearly full coverage of the International Union of Crystallography publications, and is growing in size and quality. Deposit your data: An interface allows you to upload, validate and edit CIF files before submitting them for deposition.

Proper citation: Crystallography Open Database (COD) (RRID:SCR_005874) Copy   

•   Source: SciCrunch Registry

http://www.icpsr.umich.edu/icpsrweb/NACDA/

Archive of data relevant to gerontological and aging research. Used to advance research on aging. Subjects include demographic, social, economic, and psychological characteristics of older adults, physical health and functioning of older adults, and health care needs of older adults. NACDA staff represents team of professional researchers, archivists and technicians who work together to obtain, process, distribute, and promote data relevant to aging research.

Proper citation: National Archive of Computerized Data on Aging (NACDA) (RRID:SCR_005876) Copy   

•   Source: SciCrunch Registry

https://datadryad.org

International, curated, digital repository that makes the data underlying scientific publications discoverable, freely reusable, and citable. Particularly data for which no specialized repository exists. Provides the infrastructure for, and promotes the re-use of, data underlying the scholarly literature. Governed by a nonprofit membership organization. Membership is open to any stakeholder organization, including but not limited to journals, scientific societies, publishers, research institutions, libraries, and funding organizations. Most data are associated with peer-reviewed articles, although data associated with non-peer reviewed publications from reputable academic sources, such as dissertations, are also accepted. Used to validate published findings, explore new analysis methodologies, repurpose data for research questions unanticipated by the original authors, and perform synthetic studies.UC system is member organization of Dryad general subject data repository.

Proper citation: Dryad Digital Repository (RRID:SCR_005910) 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://phenome.jax.org/centers/QTLA

Raw data from various QTL (quantitative trait loci) studies using rodent inbred line crosses. Data are available in the .csv format used by R/qtl and pseudomarker programs. In some cases analysis scripts and/or results are posted to accompany the data. These data are provided as a courtesy to the genetic mapping community and may be used for purposes of developing or testing new analysis methods or software and for meta-analysis of quantitative traits. The authors of the datasets retain individual ownership of the data. As a courtesy to the authors, please alert them in advance of any publications that result from reanalysis of these data or obtain permission prior to redistribution of data or results. In all data sets and files, the marker locations have been translated to Cox build 37 coordinates unless otherwise stated. Please consider contributing your data to the QTL Archive.

Proper citation: QTL Archive (RRID:SCR_006213) Copy   

•   Source: SciCrunch Registry

http://www.gwascentral.org/

Publicly available database of summary level findings from genetic association studies in humans, including genome wide association studies (GWAS). Previously named HGBASE, HGVbase and HGVbaseG2P.

Proper citation: GWAS Central (RRID:SCR_006170) Copy   

•   Source: SciCrunch Registry

https://data.caltech.edu/

Data and software repository from CalTech.

Proper citation: CaltechDATA (RRID:SCR_017602) Copy   

•   Source: SciCrunch Registry

http://researchdata.4tu.nl/en/home/

Multidisciplinary data repository for a consortium of universities in the Netherlands housing over datasets with a focus on scientific and technical data. Most data were produced by Dutch researchers including datasets from doctoral research. Users can deposit up to 1G by completing an upload form. Collection development foci include applied sciences, biomedical technology, earth sciences, and technology and construction. 4TU.Datacentrum is a collaboration of the libraries of the three leading technical universities - Delft University of Technology, Eindhoven University of Technology and the University of Twente.

Proper citation: 4TU.Datacentrum (RRID:SCR_006295) Copy   

•   Source: SciCrunch Registry

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

Public archive providing a comprehensive record of the world''''s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. All submitted data, once public, will be exchanged with the NCBI and DDBJ as part of the INSDC data exchange agreement. The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources including submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centers and routine and comprehensive exchange with their partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature. ENA is made up of a number of distinct databases that includes the EMBL Nucleotide Sequence Database (Embl-Bank), the newly established Sequence Read Archive (SRA) and the Trace Archive. The main tool for downloading ENA data is the ENA Browser, which is available through REST URLs for easy programmatic use. All ENA data are available through the ENA Browser. Note: EMBL Nucleotide Sequence Database (EMBL-Bank) is entirely included within this resource.

Proper citation: European Nucleotide Archive (ENA) (RRID:SCR_006515) Copy   

•   Source: SciCrunch Registry

http://datastar.mannlib.cornell.edu/

A single library software prototype transitioning to a to an open-source platform ready for adoption and extension at other institutions wishing to provide research data sharing and discovery services. Datastar''''s ability to expose metadata about research datasets in a standard semantic format called Linked Data will be enhanced to support selective interchange of related information with VIVO, an open-source semantic researcher networking tool gaining prominence through adoption at multiple U.S. universities, in the federal government, and internationally.

Proper citation: DataStaR (RRID:SCR_006381) Copy   

•   Source: SciCrunch Registry

http://rgd.mcw.edu

Database for genetic, genomic, phenotype, and disease data generated from rat research. Centralized database that collects, manages, and distributes data generated from rat genetic and genomic research and makes these data available to scientific community. Curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data is provided. Facilitates investigators research efforts by providing tools to search, mine, and analyze this data. Strain reports include description of strain origin, disease, phenotype, genetics, immunology, behavior with links to related genes, QTLs, sub-strains, and strain sources.

Proper citation: Rat Genome Database (RGD) (RRID:SCR_006444) 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://antibodyregistry.org/

Public registry of antibodies with unique identifiers for commercial and non-commercial antibody reagents to give researchers a way to universally identify antibodies used in publications. The registry contains antibody product information organized according to genes, species, reagent types (antibodies, recombinant proteins, ELISA, siRNA, cDNA clones). Data is provided in many formats so that authors of biological papers, text mining tools and funding agencies can quickly and accurately identify the antibody reagents they and their colleagues used. The Antibody Registry allows any user to submit a new antibody or set of antibodies to the registry via a web form, or via a spreadsheet upload.

Proper citation: Antibody Registry (RRID:SCR_006397) Copy   

•   Source: SciCrunch Registry

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

Service providing functional analysis of proteins by classifying them into families and predicting domains and important sites. They combine protein signatures from a number of member databases into a single searchable resource, capitalizing on their individual strengths to produce a powerful integrated database and diagnostic tool. This integrated database of predictive protein signatures is used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites. InterPro adds in-depth annotation, including GO terms, to the protein signatures. You can access the data programmatically, via Web Services. The member databases use a number of approaches: # ProDom: provider of sequence-clusters built from UniProtKB using PSI-BLAST. # PROSITE patterns: provider of simple regular expressions. # PROSITE and HAMAP profiles: provide sequence matrices. # PRINTS provider of fingerprints, which are groups of aligned, un-weighted Position Specific Sequence Matrices (PSSMs). # PANTHER, PIRSF, Pfam, SMART, TIGRFAMs, Gene3D and SUPERFAMILY: are providers of hidden Markov models (HMMs). Your contributions are welcome. You are encouraged to use the ''''Add your annotation'''' button on InterPro entry pages to suggest updated or improved annotation for individual InterPro entries.

Proper citation: InterPro (RRID:SCR_006695) Copy   

•   Source: SciCrunch Registry

http://www.maizegdb.org

Collection of data related to crop plant and model organism Zea mays. Used to synthesize, display, and provide access to maize genomics and genetics data, prioritizing mutant and phenotype data and tools, structural and genetic map sets, and gene models and to provide support services to the community of maize researchers. Data stored at MaizeGDB was inherited from the MaizeDB and ZmDB projects. Sequence data are from GenBank. Data are searchable by phenotype, traits, Pests, Gel Pattern, and Mutant Images.

Proper citation: MaizeGDB (RRID:SCR_006600) Copy   

•   Source: SciCrunch Registry

http://www.gigasciencejournal.com/

An online open-access open-data journal, publishing ''big-data'' studies from the entire spectrum of life and biomedical sciences whose publication format links standard manuscript publication with its affiliated database, GigaDB, that hosts all associated data, provides data analysis tools, cloud-computing resources, and a DOI assignment to every dataset. GigaScience covers not just ''omic'' type data and the fields of high-throughput biology currently serviced by large public repositories, but also the growing range of more difficult-to-access data, such as imaging, neuroscience, ecology, cohort data, systems biology and other new types of large-scale sharable data. Supporting the open-data movement, they require that all supporting data and source code be publicly available in a suitable public repository and/or under a public domain CC0 license in the BGI GigaScience database. Using the BGI cloud as a test environment, they also consider open-source software tools / methods for the analysis or handling of large-scale data. When submitting a manuscript, please contact them if you have datasets or cloud applications you would like them to host. To maximize data usability submitters are encouraged to follow best practice for metadata reporting and are given the opportunity to submit in ISA-Tab format.

Proper citation: GigaScience (RRID:SCR_006565) Copy   

•   Source: SciCrunch Registry

http://flybase.org/

Database of Drosophila genetic and genomic information with information about stock collections and fly genetic tools. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. Additionally, FlyBase accepts data submissions. FlyBase can be searched for genes, alleles, aberrations and other genetic objects, phenotypes, sequences, stocks, images and movies, controlled terms, and Drosophila researchers using the tools available from the "Tools" drop-down menu in the Navigation bar.

Proper citation: FlyBase (RRID:SCR_006549) Copy   

•   Source: SciCrunch Registry

http://www.unavco.org/

A non-profit university-governed consortium that facilitates geoscience research and education using geodesy. It rovides access to and submission of Geodetic GPS / GNSS Data, Geodetic Imaging Data, Strain and Seismic Borehole Data, and Meteorological Data. Data access web services/API provides the ability to use a command line interface to query metadata and obtain URLs to data and products. UNAVCO also provides a variety of software, including web applications, and desktop utilities for scientists, instructors, students, and others. Web-based data visualization and mapping tools provide users with the ability to view postprocessed data while web-based geodetic utilities provide ancillary information. Downloadable stand-alone software utilities include applications for configuring instruments, managing data collection, download and transfer, and performing computations on the raw data, e.g., data pre-processing or processing. The UNAVCO Facility in Boulder, Colorado is the primary operational activity of UNAVCO and exists to support university and other research investigators in their use of geophysical sensor technology for Earth sciences research. The Facility performs this task in part by archiving GNSS/GPS data and data products for current and future applications. Other data types that scientists use for Earth deformation studies are also held in the UNAVCO Archive collections. UNAVCO operates a community Archive, which provides long-term secure storage and easy retrieval of GNSS data, strain data, various derived products and related metadata. The Archive primarily stores high-precision geodetic data used for research purposes, collected under National Science Foundation and NASA sponsored projects. UNAVCO provides many learning opportunities including: Short Courses and Workshops, Educational Resources, RESESS Research Student Internships, and Technical Training.

Proper citation: UNAVCO (RRID:SCR_006706) 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