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on page 1 showing 20 out of 73 results from 1 sources

Cite this (Acromine Disambiguator, RRID:SCR_006923)

URL: http://www.nactem.ac.uk/software/acromine_disambiguation/

Resource Type: Resource, web service, software resource, service resource, data access protocol

Service that disambiguates acronyms from Medline in text through your browsers; or use the RESTful Service for integrating it with your applications. Reference: Okazaki, N., Ananiadou, S. and Tsujii, J. (2010). Building a High Quality Sense Inventory for Improved Abbreviation Disambiguation.Bioinformatics, Oxford University Press.

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Cite this (AcroMine, RRID:SCR_013196)

URL: http://www.nactem.ac.uk/software/acromine/

Resource Type: Resource, web service, software resource, service resource, data access protocol

An acronym dictionary which can be used to find distinct expanded forms of acronyms from MEDLINE. This freely available service can be used through your browser or by integrating it with your applications using the ReSTful service. Acromine identifies abbreviation definitions by assuming a word sequence co-occurring frequently with a parenthetical expression to be a potential expanded form. Applied to the whole MEDLINE (9,635,599 abstracts), the implemented system extracted 68,007 abbreviation candidates and recognized 467,402 expanded forms. The current Acromine achieves 99% precision and 82-95% recall on our evaluation corpus that roughly emulates the whole MEDLINE.

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Cite this (AntiJen, RRID:SCR_001750)

URL: http://www.ddg-pharmfac.net/antijen/AntiJen/antijenhomepage.htm

Resource Type: Resource, data or information resource, database

Database with quantitative binding data for peptides binding to various cells including MHC Ligand, TCR-MHC complexes, T-cell epitopes, TAP, B-cell, and immunological protein-protein interactions. Information in each entry includes peptide libraries, copy numbers, and diffusion coefficient data.

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Cite this (Arabidopsis Nucleolar Protein Database, RRID:SCR_001793)

URL: http://bioinf.scri.sari.ac.uk/cgi-bin/atnopdb/home

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

Database of proteins found in the nucleoli of Arabidopsis, identified through proteomic analysis. The Arabidopsis Nucleolar Protein database (AtNoPDB) provides information on the plant proteins in comparison to human and yeast proteins, and images of cellular localizations for over a third of the proteins. A proteomic analysis was carried out of nucleoli purified from Arabidopsis cell cultures and to date 217 proteins have been identified. Many proteins were known nucleolar proteins or proteins involved in ribosome biogenesis. Some proteins, such as spliceosomal and snRNP proteins, and translation factors, were unexpected. In addition, proteins of unknown function which were either plant-specific or conserved between human and plant, and proteins with differential localizations were identified.

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Cite this (ARK-Genomics: Centre for Functional Genomics, RRID:SCR_002214)

URL: http://www.ark-genomics.org/

Resource Type: Resource, organization portal, database, core facility, service resource, portal, access service resource, data or information resource

A high-throughput technology laboratory focused on studies of genome structure and genetic variation, gene expression and gene function, it provides an extensive range of services including: * DNA sequencing of model and non-model genomes using both Next Generation and Sanger sequencing * Gene expression analysis using both microarrays and Next Generation Sequencing * High throughput genotyping of SNP and copy number variants * Data collection and analysis supported in-house high performance computing facilities and expertise * Extensive EST clone collections for a number of animal species * All of the commercially available microarray tools from Affymetrix, Illumina, Agilent and Nimblegen * Parentage testing using microsatellites and smaller SNP panels ARK-Genomics has developed a network of researchers whom they support through each stage of their genomics research, from grant application, experimental design and technology selection, performing wet laboratory protocols, through to the analysis of the data often in conjunction with commercial partners. An important part of the ARK-Genomics service is the opportunity to engage with other scientists and to raise awareness through their training courses, networking events such as their successful conference series.

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Cite this (BioJS, RRID:SCR_003119)

URL: https://github.com/biojs

Resource Type: Resource, data processing software, software library, software application, data visualization software, software resource, software toolkit

An open source JavaScript library of components for visualisation of biological data on the web.

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Cite this (BioModels Database, RRID:SCR_001993)

URL: http://www.ebi.ac.uk/biomodels-main/

Resource Type: Resource, topical portal, database, international standard specification, standard specification, narrative resource, service resource, portal, storage service resource, data repository, data or information resource

Repository of peer-reviewed, published, computational models that allows biologists to store, search and retrieve published mathematical models from the field of systems biology, but also more generally those of biological interest. Models in the database can be used to generate sub-models, can be simulated online, and can be converted between different representational formats. This resource also features programmatic access via Web Services. Each model is curated to verify that it corresponds to the reference publication and gives the proper numerical results. Curators also annotate the components of the models with terms from controlled vocabularies and links to other relevant data resources allowing users to search accurately for the models they need. The models can be retrieved in the SBML format and import/export facilities are being developed to extend the spectrum of formats supported by the resource.

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Cite this (bioNerDS, RRID:SCR_006784)

URL: http://bionerds.sourceforge.net/

Resource Type: Resource, source code, software application, text-mining software, data set, software resource, data or information resource

A named entity recognizer for the recovery of bioinformatics databases and software from primary literature. The entity recognizer achieved an F-measure of between 63% and 91% on different datasets (63%78% at the document level). Results from full-text literature analysis for both Genome Biology and BMC Bioinformatics journals are available as well as a full list of references and links for the various major resources mentioned. Data generated data can be used for exploration of bioinformatics database and software usage. This tool makes heavy use of GATE (version 6.1). It can be run in sandbox mode, which means a installation of GATE is not a prerequisite, but you will instead need to point the config to a unzipped gate_plugins directory instead (located in the bin/BMC_Files directory).

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Cite this (BrainTrap: Fly Brain Protein Trap Database, RRID:SCR_003398)

URL: http://braintrap.inf.ed.ac.uk/braintrap/

Resource Type: Resource, data or information resource, d spatial image, database

This database contains information on protein expression in the Drosophila melanogaster brain. It consists of a collection of 3D confocal datasets taken from EYFP expressing protein trap Drosophila lines from the Cambridge Protein Trap project. Currently there are 884 brain scans from 535 protein trap lines in the database. Drosophila protein trap strains were generated by the St Johnston Lab and the Russell Lab at the University of Cambridge, UK. The piggyBac insertion method was used to insert constructs containing splice acceptor and donor sites, StrepII and FLAG affinity purification tags, and an EYFP exon (Venus). Brain images were acquired by Seymour Knowles-Barley, in the Armstrong Lab at the University of Edinburgh. Whole brain mounts were imaged by confocal microscopy, with a background immunohistochemical label added to aid the identification of brain structures. Additional immunohistochemical labeling of the EYFP protein using an anti-GFP antibody was also used in most cases. The trapped protein signal (EYFP / anti-GFP), background signal (NC82 label), and the merged signal can be viewed on the website by using the corresponding channel buttons. In all images the trapped protein / EYFP signal appears green and the background / NC82 channel appears magenta. Original .lsm image files are also available for download.

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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 (CGDB, RRID:SCR_011959)

URL: http://sbcb.bioch.ox.ac.uk/cgdb/

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

A database of membrane protein/lipid interactions by coarse-grained molecular dynamics simulations.

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Cite this (CHEBI, RRID:SCR_002088)

URL: http://www.ebi.ac.uk/chebi/

Resource Type: Resource, data or information resource, database

A database of chemical compounds and other small molecular entities that incorporates an ontological classification of chemical compounds of biological relevance, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms. ChEBI uses nomenclature, symbolism and terminology endorsed by the International Union of Pure and Applied Chemistry (IUPAC) and the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB). Molecules directly encoded by the genome (e.g. nucleic acids, proteins and peptides derived from proteins by cleavage) are not as a rule included in ChEBI.

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Cite this (CHiCAGO, RRID:SCR_014941)

URL: http://regulatorygenomicsgroup.org/chicago

Resource Type: Resource, software resource, software application, data analysis software, data processing software, software toolkit

Statistical pipeline for detecting significant chromosomal interactions in Capture Hi-C data. CHiCAGO uses a convolution background model accounting for both random Brownian collisions between chromatin fragments and technical noise. CHiCAGO then performs a p-value weighting procedure based on the expected true positive rates at different distance ranges, with scores representing soft-thresholded -log weighted p-values.

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Cite this (COBrA, RRID:SCR_005677)

URL: http://www.xspan.org/

Resource Type: Resource, software resource

COBrA is a Java-based ontology editor for bio-ontologies that distinguishes itself from other editors by supporting the linking of concepts between two ontologies, and providing sophisticated analysis and verification functions. In addition to the Gene Ontology and Open Biology Ontologies formats, COBrA can import and export ontologies in the Semantic Web formats RDF, RDFS and OWL. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

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Cite this (Complex Portal, RRID:SCR_015038)

URL: https://www.ebi.ac.uk/intact/complex/#annotations:fIzBXhJPEeej78Pl6R0ScA

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

Database and encyclopaedic resource of macromolecular complexes found in key model organisms from scientific literature. Data includes protein-only complexes, protein-small molecules, and protein-nucleic acid complexes. The information within the portal is manually curated and available for download.

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Cite this (EchoBASE, RRID:SCR_002430)

URL: http://www.ecoli-york.org/

Resource Type: Resource, data or information resource, database

A database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655. It has been created to integrate information from post-genomic experiments into a single resource with the aim of providing functional predictions for the 1500 or so gene products for which we have no knowledge of their physiological function. While EchoBASE provides a basic annotation of the genome, taken from other databases, its novelty is in the curation of post-genomic experiments and their linkage to genes of unknown function. Experiments published on E. coli are curated to one of two levels. Papers dealing with the determination of function of a single gene are briefly described, while larger dataset are actually included in the database and can be searched and manipulated. This includes data for proteomics studies, protein-protein interaction studies, microarray data, functional genomic approaches (looking at multiple deletion strains for novel phenotypes) and a wide range of predictions that come out of in silico bioinformatic approaches. The aim of the database is to provide hypothesis for the functions of uncharacterized gene products that may be used by the E. coli research community to further our knowledge of this model bacterium.

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Cite this (EMDataBank.org: Unified Data Resource for Cryo Electron Microscopy, RRID:SCR_003207)

URL: http://www.emdatabank.org

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

A unified global portal for deposition and retrieval of cryo electron microscopy (3DEM) density maps, atomic models, and associated metadata, as well as a resource for news, events, software tools, data standards, validation methods for the 3DEM community. It is a joint effort among investigators of the Protein Databank in Europe (PDBe) at the European Bioinformatics Institute, the Research Collaboratory for Structural Bioinformatics (RCSB) at Rutgers, and the National Center for Macromolecular Imaging (NCMI) at Baylor College of Medicine. A major goal of the EMDataBank project in their current funding period is to work with the 3DEM community to (1) establish data-validation methods that can be used in the process of structure determination, (2) define the key indicators of a well-determined structure that should accompany every deposition, and (3) implement appropriate validation procedures for maps and map-derived models into a 3DEM validation pipeline. The EM Validation Task Force (EM VTF) has made initial recommendations to guide development of 3DEM validation criteria. Their aim is to facilitate the many processes needed to assess, establish, and disseminate validation methods and standards. The Web Service allows other applications to obtain data regarding maps/structures in the EMDB. The data is returned in XML format.

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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 (Ensembl, RRID:SCR_002344)

URL: http://www.ensembl.org/

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

A collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. The goal of Ensembl is to automatically annotate the genome, integrate this annotation with other available biological data and make the data publicly available via the web. The range of available data has also expanded to include comparative genomics, variation and regulatory data. Ensembl allows users to: upload and analyze data and save it to an Ensembl account; search for a DNA or protein sequence using BLAST or BLAT; fetch desired data from the public database, using the Perl API; download the databases via FTP in FASTA, MySQL and other formats; and mine Ensembl with BioMart and export sequences or tables in text, HTML, or Excel format. The DNA sequences and assemblies used in the Ensembl genebuild are provided by various projects around the world. Ensembl has entered into an agreement with UCSC and NCBI with regard to sequence identifiers in order to improve consistency between the data provided by different genome browsers. The site also links to the Ensembl blog with updates on new species and sequences as they are added to the database.

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Cite this (Eukaryotic Linear Motif, RRID:SCR_003085)

URL: http://elm.eu.org

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

Computational biology resource for investigating candidate functional sites in eukarytic proteins. Functional sites which fit to the description linear motif are currently specified as patterns using Regular Expression rules. To improve the predictive power, context-based rules and logical filters are being developed and applied to reduce the amount of false positives. The current version of the ELM server provides core functionality including filtering by cell compartment, phylogeny, globular domain clash (using the SMART/Pfam databases) and structure. In addition, both the known ELM instances and any positionally conserved matches in sequences similar to ELM instance sequences are identified and displayed (see ELM instance mapper). Although the ELM resource contains a large collection of functional site motifs, the current set of motifs is not exhaustive.

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