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on page 1 showing 20 out of 38 results

Cite this (1000 Fungal Genome Project, RRID:SCR_016463)

URL: https://genome.jgi.doe.gov/programs/fungi/1000fungalgenomes.jsf

Resource Type: Resource, topical portal, data access protocol, database, web service, organism-related portal, portal, software resource, project portal, data or information resource

Web application to provide genomic information for fungi. Includes sequenced fungal genomes, those in progress, and selected nominations. Nomination of new species for genome sequencing in the families or only one reference genome possible after providing DNA/RNA samples for their sequencing. Used to explore the diversity of fungi important for energy and the environment.

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    AFTOL

Cite this (AFTOL, RRID:SCR_004650)

URL: http://www.aftol.org/

Resource Type: Resource, data repository, biospecimen repository, data set, service resource, storage service resource, data or information resource, material storage repository

To enhance the understanding of the evolution of the Kingdom Fungi, 1500+ species were sampled for eight gene loci across all major fungal clades, plus a subset of taxa for a suite of morphological and ultrastructural characters with resulting data: AFTOL Molecular Database (generated by WASABI - Web Accessible Sequence Analysis for Biological Inference), Blast search the AFTOL Database (generated by WASABI), AFTOL primers (generated by WASABI), AFTOL primers by species (generated by WASABI), AFTOL alignments, and the AFTOL Structural and Biochemical Database. Users may submit samples to the AFTOL project. AFTOL is a collaboration centered around four universities in the United States: Duke University (Francois Lutzoni and Rytas Vilgalys), Clark University (David Hibbett), Oregon State University (Joey Spatafora), and University of Minnesota (David McLaughlin). Participants throughout the world have donated vouchers, taxon samples, and gene sequences. The aim of the project is to reconstruct the fungal tree of life using all available data for eight loci (nuclear ribosomal DNA: LSU, SSU, ITS (including 5.8s, ITS1 and ITS2); RNA polymerase II: RPB1, RPB2; elongation factor 1-alpha; mitochondrial SSU rDNA, and mitochondrial ATP synthase protein subunit 6). A further objective of this study is to summarize and integrate current knowledge regarding fungal subcellular features within this new phylogenetic framework. The name of the bioinformatic package developed for AFTOL is WASABI which provides an efficient communication platform to facilitate the collection and dissemination of molecular data to (and from) the laboratories and participants. All molecular data can be viewed, downloaded, verified, and corrected by the participants of AFTOL. A central goal of the WASABI interface is to establish an automated analysis framework that includes basecalling of newly generated chromatograms, contig assembly, quality verification of sequences (including a local BLAST), sequence alignment, and congruence test. Gene sequences that pass all tests and are finally verified by their authors will undergo automated phylogenetic analysis on a regular schedule. Although all steps are initially carried out noninteractively, the users can verify and correct the results at any step and thus initiate the reanalysis of dependent data.

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    APD

Cite this (APD, RRID:SCR_006606)

URL: http://aps.unmc.edu/AP/main.php

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Database and data analysis system dedicated to glossary, nomenclature, classification, information search, prediction, design, and statistics of Antimicrobial peptides and beyond. The peptide data stored in the APD were gleaned from the literature (PubMed, PDB, Google, and Swiss-Prot) manually in the past several years. Peptides will be registered into this database if: # they are from natural sources (bacteria, protozoa, fungi, plants, and animals); # their antimicrobial activities are demonstrated (MIC

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    ATCC

Cite this (ATCC, RRID:SCR_001672)

URL: http://www.atcc.org/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, biomaterial supply resource, standard specification, narrative resource, international standard specification, service resource, storage service resource, reagent supplier, data or information resource, material resource, material storage repository

Global nonprofit biological resource center (BRC) and research organization that provides biological products, technical services and educational programs to private industry, government and academic organizations. Its mission is to acquire, authenticate, preserve, develop and distribute biological materials, information, technology, intellectual property and standards for the advancement and application of scientific knowledge. The primary purpose of ATCC is to use its resources and experience as a BRC to become the world leader in standard biological reference materials management, intellectual property resource management and translational research as applied to biomaterial development, standardization and certification. ATCC characterizes cell lines, bacteria, viruses, fungi and protozoa, as well as develops and evaluates assays and techniques for validating research resources and preserving and distributing biological materials to the public and private sector research communities.

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Cite this (Atlas of Living Australia, RRID:SCR_006467)

URL: http://www.ala.org.au/

Resource Type: Resource, database, service resource, storage service resource, software resource, image repository, data repository, data or information resource

Repository of scientifically collected data on all the known species in Australia aggregated from a wide range of data providers: museums, herbaria, community groups, government departments, individuals and universities. Data records consist of images, literature, molecular DNA data, identification keys, species interaction data, species profile data, nomenclature, source data, conservation indicators, and spatial data. Several standards are preferred for data provided to the Atlas. Use this site to: * access information pages for each species containing photos, descriptions, maps and observations * access scientific and common names * explore the flora and fauna reported around your neighborhood * learn about Australia's biodiversity collections at museums, herbaria and other institutions * learn about citizen science projects * map, analyze and visualize biodiversity and environmental data and trends * access tools to help track changes in biodiversity and the environment * download and use open source tools * download biodiversity data * access images, literature and genetic information through Australian nodes of international data repositories * volunteer for digitization projects. The Atlas of Living Australia (Atlas) and its associated information systems provides web services for accessing information over the internet.

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    BaCelLo

Cite this (BaCelLo, RRID:SCR_011965)

URL: http://gpcr.biocomp.unibo.it/bacello/

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable.

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    BOLD

Cite this (BOLD, RRID:SCR_004278)

URL: http://www.barcodinglife.com/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, storage service resource, data repository, data or information resource

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.

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Cite this (Catalogue of Life, RRID:SCR_006701)

URL: http://www.catalogueoflife.org/

Resource Type: Resource, data or information resource, database

Comprehensive and authoritative global index of species of animals, plants, fungi and micro-organisms. It consists of a single integrated species checklist and taxonomic hierarchy. The Catalogue holds essential information on the names, relationships and distributions of over 1.3 million species. This figure continues to rise as information is compiled from diverse sources around the world. There are two distinct versions of the Catalogue of Life: the Dynamic Checklist and the Annual Checklist. Choose the version most suited to your needs. If you have a taxonomic database and would like to join the Species 2000 federation of databases in the Catalogue of Life please contact the Species 2000 Secretariat: all candidate databases go through a peer review process. The Annual Checklist Exchange Format defines the format for exchanging data.

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Cite this (Cell Type Ontology, RRID:SCR_004251)

URL: http://cellontology.org

Resource Type: Resource, ontology, data or information resource, controlled vocabulary

Ontology designed as a structured controlled vocabulary for cell types. It was constructed for use by the model organism and other bioinformatics databases. It includes cell types from prokaryotes, mammals, and fungi. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases.

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Cite this (Ensembl Genomes, RRID:SCR_006773)

URL: http://www.ensemblgenomes.org/

Resource Type: Resource, web service, software resource, data or information resource, data access protocol, database

Database portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualization platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Many of the databases supporting the portal have been built in close collaboration with the scientific community - essential for maintaining the accuracy and usefulness of the resource. A common set of user interfaces (which include a graphical genome browser, FTP, BLAST search, a query optimized data warehouse, programmatic access, and a Perl API) is provided for all domains. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualized in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site.

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Cite this (EOL - Encyclopedia of Life, RRID:SCR_005905)

URL: http://eol.org/

Resource Type: Resource, database, portal, data or information resource

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.

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Cite this (Fungal Genome Initiative, RRID:SCR_003169)

URL: http://www.broad.mit.edu/annotation/fungi/fgi/

Resource Type: Resource, data set, data or information resource

Produces and analyzes sequence data from fungal organisms that are important to medicine, agriculture and industry. The FGI is a partnership between the Broad Institute and the wider fungal research community, with the selection of target genomes governed by a steering committee of fungal scientists. Organisms are selected for sequencing as part of a cohesive strategy that considers the value of data from each organism, given their role in basic research, health, agriculture and industry, as well as their value in comparative genomics.

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Cite this (Fungal Gross Anatomy Ontology, RRID:SCR_010322)

URL: http://purl.bioontology.org/ontology/FAO

Resource Type: Resource, ontology, data or information resource, controlled vocabulary

A structured controlled vocabulary for the anatomy of fungi.

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    FungiDB

Cite this (FungiDB, RRID:SCR_006013)

URL: http://fungidb.org/fungidb/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

FungiDB is a database for functional and evolutionary comparison of fungal genomes. FungiDB is a functional genomic resource for pan-fungal genomes that was developed in partnership with the Eukaryotic Pathogen Bioinformatic resource center (http://EuPathDB.org). FungiDB uses the same infrastructure and user interface as EuPathDB, which allows for sophisticated and integrated searches to be performed using an intuitive graphical system. The current release of FungiDB contains genome sequence and annotation from 18 species spanning several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal "Zygomycete" lineage Mucormycotina. Additionally, FungiDB contains cell cycle microarray data, hyphal growth RNA-sequence data and yeast two hybrid interaction data. The underlying genomic sequence and annotation combined with functional data, additional data from the FungiDB standard analysis pipeline and the ability to leverage orthology provides a powerful resource for in silico experimentation.

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    GBrowse

Cite this (GBrowse, RRID:SCR_006829)

URL: http://gbrowse.org/

Resource Type: Resource, data or information resource, database

A database and interactive web site for manipulating and displaying annotations on genomes. Features include: detailed views of the genome; use of a variety of premade or personally made glyphs ; customizable order and appearance of tracks by administrators and end-users; search by annotation ID, name, or comment; support of third party annotation using GFF formats; DNA and GFF dumps; connectivity to different databases, including BioSQL and Chado; and a customizable plug-in architecture (e.g. run BLAST, find oligonucleotides, design primers, etc.). GBrowse is distributed as source code for Macintosh OS X, UNIX and Linux platforms, and as pre-packaged binaries for Windows machines. It can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. The wiki portion accepts data submissions.

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    GOblet

Cite this (GOblet, RRID:SCR_006998)

URL: http://goblet.molgen.mpg.de/cgi-bin/goblet2008/goblet.cgi

Resource Type: Resource, data analysis service, production service resource, analysis service resource, software application, service resource, software resource

Tool that performs annotation based on GO and pathway terms for anonymous cDNA or protein sequences. It uses the species independent GO structure and vocabulary together with a series of protein databases collected from various sites, to perform a detailed GO annotation by sequence similarity searches. The sensitivity and the reference protein sets can be selected by the user. GOblet runs automatically and is available as a public service on our web server. GOblet expects query sequences to be in FASTA-Format (with header-lines). Protein and nucleotide sequences are accepted. Total size of all sequences submitted per request should not be larger than 50kb currently. For security reasons: Larger post's will be rejected. Due to limited capacities the queries may be processed in batches depending on the server load. The output of the BLAST job is filtered automatically and the relevant hits are displayed. In addition, the respective GO-terms are shown together with the complete GO-hierarchy of parent terms.

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Cite this (G:Profiler, RRID:SCR_006809)

URL: http://biit.cs.ut.ee/gprofiler/

Resource Type: Resource, analysis service resource, software resource, data analysis service, service resource, production service resource

A web-based toolset for functional profiling of gene lists from large-scale experiments. It has a simple web interface with powerful visualization. It currently supports 85 species, including mammals, fungi, plants, insects, etc, from the Ensembl and Ensembl Genomes databases. g:Profiler consists of the following tools: * g:GOSt retrieves most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs to a user-specified group of genes, proteins or microarray probes. g:GOSt also allows analysis of ranked or ordered lists of genes, visual browsing of GO graph structure, interactive visualization of retrieved results, and many other features. Multiple testing corrections are applied to extract only statistically important results. * g:Convert allows conversion between gene or protein names, database IDs and microarray probes of more than 100 types. A mix of various IDs may be presented as input; output options include HTML, text and XLS spreadsheet. * g:Orth retrieves orthologs for a given set of genes, proteins or probes in a selected organism. Graphical representation also shows orthologs present in all g:Profiler organisms. * g:Sorter searches for similar expression profiles to a given gene, protein or probe in a large set of public microarray datasets from the Gene Expression Omnibus (GEO) database. * g:Cocoa provides a compact interface for comparing enrichments of multiple gene lists. Platform: Online tool

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    GRBio

Cite this (GRBio, RRID:SCR_002228)

URL: http://grbio.org/

Resource Type: Resource, data access protocol, database, web service, people resource, software resource, data or information resource

Database of biological collections in natural history museums, herbaria, and other biorepositories resulting from a merger of Index Herbariorum (IH), Biodiversity Collections Index (BCI) and biorepositories.org. It contains more than 14,000 records for biorepository institutions, their collections, and staff members. Their two main goals are to improve access to information about biorepositories, the collections and specimens they house, and the researchers and collection managers who work there; and to facilitate electronic linkages to this information through web services that will rely on unique identifiers assigned to biorepositories and collections. The Consortium for the Barcode of Life (CBOL) has developed and will manage GRBio in collaboration with IH and BCI and in consultation with GBIF and NCBI. GRBio includes four categories of data records that provide information on: * Institutional repositories such as museums, herbaria, botanical gardens, zoos, biomedical research institutes and culture centers; * Institutional collection records such as the bird, algal or insect collections within an institutional repository; * Personal collections such as field samples held by a researcher before they have been accessioned into an institutional collection, or privately owned specimens held by non-researchers; and * Staff members at institutional repositories GRBio operates as a moderated community-curated resource. The community is invited to check and update their records and to register institutions, collections and staff members that have not already been registered. GRBio offers registration of institutional collections, "personal" research collections that have not yet been accessioned into an institutional repository, and privately owned collections.

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Cite this (Human Epigenome Browser, RRID:SCR_006208)

URL: http://epigenomegateway.wustl.edu/

Resource Type: Resource, source code, data analysis software, data processing software, software application, data set, software resource, data or information resource

Software tool for visualizing and interacting with whole-genome datasets. The browser currently hosts Human Epigenome Atlas data produced by the Roadmap Epigenomics project, but its use of advanced, multi-resolution data formats and its user-friendly interface make it possible for investigators to upload and visualize their own data as custom tracks. The Human Epigenome Browser is developed and maintained by the Epigenome Informatics Group at Washington University in St. Louis.

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Cite this (Index Fungorum, RRID:SCR_008975)

URL: http://www.indexfungorum.org/names/names.asp

Resource Type: Resource, data access protocol, database, web service, service resource, storage service resource, software resource, data repository, data or information resource

International project database indexing all formal names (scientific names) in the Fungi Kingdom. Index Fungorum provides Life Science Identifiers (LSIDs) for records in its database and indicates the status of a name. In the returns from the search page a currently correct name is indicated in green, while others are in blue (a few, aberrant usages of names are indicated in red). All names are linked to pages giving the correct name, with lists of synonyms. Index Fungorum provides a SOAP protocol web service for searching its database and retrieving records. A WSDL file describing the services is available. (adapted from Wikipedia)

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