Tools   Select Another Resource Report Type

http://zfin.org

Model organism database that serves as central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. Data represented are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. Data formats include text, images and graphical representations.Serves as primary community database resource for laboratory use of zebrafish. Developed and supports integrated zebrafish genetic, genomic, developmental and physiological information and link this information extensively to corresponding data in other model organism and human databases.

Proper citation: Zebrafish Information Network (ZFIN) (RRID:SCR_002560) Copy   

•   Source: SciCrunch Registry

http://ecogene.org/

Database that contains updated information about the Escherichia coli K-12 genome and proteome sequences, including extensive gene bibliographies. Users are able to download customized tables, perform Boolean query comparisons, generate sets of paired DNA sequences, and download any E. coli K-12 genomic DNA sub-sequence. BLAST functions, microarray data, an alphabetical index of genes, and gene overlap queries are also available. The Database Table Downloads Page provides a full list of EG numbers cross-referenced to the new cross-database ECK numbers and other common accession numbers, as well as gene names and synonyms. Monthly release archival downloads are available, but the live, daily updated version of EcoGene is the default mysql database for download queries.

Proper citation: EcoGene (RRID:SCR_002437) Copy   

•   Source: SciCrunch Registry

http://www.drugbank.ca/

Bioinformatics and cheminformatics database that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.

Proper citation: DrugBank (RRID:SCR_002700) Copy   

•   Source: SciCrunch Registry

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

Database for genomes that have been completely sequenced, have active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. Includes nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases. All entries follow NCBI's format for data collections. Content of Entrez Gene represents result of curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases, and from many other databases available from NCBI. Records are assigned unique, stable and tracked integers as identifiers. Content is updated as new information becomes available.

Proper citation: Entrez Gene (RRID:SCR_002473) Copy   

•   Source: SciCrunch Registry

http://factfinder2.census.gov/

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 2, 2025. Database that provides access to population, housing, economic, and geographic data from several censuses and surveys about the United States, Puerto Rico and the Island Areas. Census data may be compiled into tables, maps and downloadable files, which can be viewed or printed. A large selection of pre-made tables and maps satisfies many information requests. By law, no one is permitted to reveal information from these censuses and surveys that could identify any person, household, or business. The following data are available: * American Community Survey * ACS Content Review * American Housing Survey * Annual Economic Surveys * Annual Surveys of Governments * Census of Governments * Decennial Census * Economic Census * Equal Employment Opportunity (EEO) Tabulation * Population Estimates Program * Puerto Rico Community Survey

Proper citation: American FactFinder (RRID:SCR_002932) Copy   

•   Source: SciCrunch Registry

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

Database of related protein sequences (clusters) consisting of proteins derived from the annotations of whole genomes, organelles and plasmids. It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses. It contains annotation information, publications, domains, structures, and external links and analysis tools including multiple alignments, phylogenetic trees, and genomic neighborhoods (ProtMap). Data is available for download via Protein Clusters FTP

Proper citation: Protein Clusters (RRID:SCR_003459) Copy   

•   Source: SciCrunch Registry

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

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

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://eol.org/

Database that gathers, generates, and shares taxa, images, videos, and sounds to freely provide knowledge about life on earth to increase awareness and understanding of living nature. Free EOL memberships are ranked so members have greater authority and editorial abilities based on their level of expertise.

Proper citation: EOL - Encyclopedia of Life (RRID:SCR_005905) 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://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

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

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.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

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