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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Oct 12, 2019)

Physical Resource or Software Tool Software

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
SuperPred: Drug classification and target predictionResource, data analysis service, database, analysis service resource, production service resource, service resource, data or information resourcePublicly available web-server to predict medical indication areas based on properties and similarity of chemical compounds. The web-server translates a user-defined molecule into a structural fingerprint that is compared to about 6300 drugs, which are enriched by 7300 links to molecular targets of the drugs, derived through text mining followed by manual curation. Links to the affected pathways are provided. The similarity to the medical compounds is expressed by the Tanimoto coefficient that gives the structural similarity of two compounds. A similarity score higher than 0.85 results in correct ATC prediction for 81% of all cases. As the biological effect is well predictable, if the structural similarity is sufficient, the web-server allows prognoses about the medical indication area of novel compounds and to find new leads for known targets. The combination of physicochemical property and similarity searching provides the possibility to detect new biologically active compounds and novel targets for drug-like compounds. SuperPred can be applied for drug repositioning purposes, too. A further intention of SuperPred is to find side effects elicited by drugs caused through off-target hits.drug, drug class, drug target, addiction, anatomical therapeutic chemical, application area, biological activity, chemical, chemical classification, chemical property, classification, compound, molecular target, molecule, nervous system, pathway, pharmacological property, physicochemical property, prediction, activity spectra, substance, structural similarity, structure, tanimoto coefficient, tanimoto score, target prediction, target-prediction server, therapeutic approach, therapeutic property, drug classification, target prediction, similarity score, targetSCR_002691(SuperPred: Drug classification and target prediction, RRID:SCR_002691)Charite - Universitatsmedizin Berlin; Berlin; Germany DFG, IRTG Berlin-Boston-Kyoto and Deutsche Krebshilfe., SFB 449PMID:18499712Last checked upnif-0000-00415
Annotation OntologyResource, ontology, data or information resource, controlled vocabularyA vocabulary for performing several types of annotation - comment, entities annotation (or semantic tags), textual annotation (classic tags), notes, examples, erratum... - on any kind of electronic document (text, images, audio, tables...) and document parts. AO is not providing any domain ontology but it is fostering the reuse of the existing ones for not breaking the principle of scalability of the Semantic Web.annotation, semantic tag, text mining, semantic web, standardSCR_002862(Annotation Ontology, RRID:SCR_002862)Harvard Medical School; Massachusetts; USA Eli Lilly and Company, EMD Serono, Inc.related to: Annotea, W3C Open Annotation Community Group, DOMEO, listed by: FORCE11PMID:21624159Last checked upnif-0000-02943https://www.force11.org/node/4718
LaunchpadResource, software resource, software application, software repository, software development toolA 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.sharing, software, tracking, translation, computer science, web service, source codeSCR_006853(Launchpad, RRID:SCR_006853)listed by: re3data.orgLast checked upnif-0000-10278
VideoLectures.NETResource, narrative resource, training material, video resource, data or information resourceAward-winning free and open access educational video lectures repository. The lectures are given by distinguished scholars and scientists at the most important and prominent events like conferences, summer schools, workshops and science promotional events from many fields of Science. The portal is aimed at promoting science, exchanging ideas and fostering knowledge sharing by providing high quality didactic contents not only to the scientific community but also to the general public. All lectures, accompanying documents, information and links are systematically selected and classified through the editorial process taking into account also users' comments.artificial science, machine learning, network, science, semantic, lecture, biology, chemistry, computers, computer science. environment, health sciences, life science, mathematics, medicine, physics, thechnologySCR_001972(VideoLectures.NET, RRID:SCR_001972)Jozef Stefan Institute; Ljubljana; Slovenia European UnionLast checked upnif-0000-10544
QGeneResource, source code, data analysis software, data processing software, software application, software resource, simulation softwareA free, open-source, computationally efficient Java program for comparative analyses of QTL mapping data and population simulation that runs on any computer operating system. (entry from Genetic Analysis Software) It is written with a plug-in architecture for ready extensibility. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Source code is available on request.gene, genetic, genomic, java, qtl mapping, trait analysis, trait, population, simulation, map, quantitative trait locus, comparisonSCR_003209(QGene, RRID:SCR_003209)Kansas State University; Kansas; USA NSF, USDA-NRI Applied Plant Genomics Programlisted by: Genetic Analysis SoftwarePMID:18940826Last checked upnif-0000-31383http://coding.plantpath.ksu.edu/qgene
signalml.orgResource, software resource, software application, programming languageAn XML-based language designed for metadescription of formats, used for digital storage of biomedical time series. Using SignalML, information on the structure of binary data files can be simply and efficiently coded. Once written, this information can be used by any software, which - owing to this metadescription - can read data files in the original format. This eliminates the need for conversions and duplication of data. signalml.org provides the following resources for interchange of relevant information and ideas: * SignalML wiki * Newsgroup / mailing list The main current software project is Svarog - a SignalML-compliant signal viewer, annotator, analyzer and (future) recorder. Svarog is written in Java and is currently best fitted for display of EEG and MEG signals. Also open platform for implementing advanced signal processing methods in user-friendly environment, at the moment interfacs for Java code, standalone executables and Matlab code via Matlab Builder for Java.analyzer, annotator, binary data, digital storage, metadescription, recorder, eeg, meg, electrocorticography, eeg modeling, forward - inverse, meg modeling, modelingSCR_003383(signalml.org, RRID:SCR_003383)University of Warsaw; Warsaw; Poland Committee for Scientific Research Polandlisted by: NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked upnif-0000-32899http://www.nitrc.org/projects/incf_signalml
Ontology Development and Information ExtractionResource, software resource, software toolkit, source codeA software toolkit to code document sets with ontologies or to enrich existing ontologies with new concepts from the document set. It contains algorithms for Named Entity Recognition, Co-reference resolution, concept discovery, discourse reasoning and attribute value extraction. The project aimed to develop a toolkit that will provide the following functionality: * Build text processing pipelines that use ontologies to annotate documents. * Enrich ontologies with new concepts that are automatically discovered in documents. * Populate an information model automatically from information extracted from documents. ODIE is open source software released under the LGPL v3.0 License. ODIE is written in Java and uses the Eclipse RCP Framework for the UI. The source code is organized into Eclipse projects.ontology, annotation, named entity recognition, java, ontology enrichment, information extraction, natural language processingSCR_003405(Ontology Development and Information Extraction, RRID:SCR_003405)Stanford University; Stanford; California listed by: 3DVC, FORCE11, BiositemapsLast checked downnif-0000-33009
PythonxyResource, software resource, software application, source codePython(x,y) is a free scientific and engineering development software for numerical computations, data analysis and data visualization based on Python programming language, Qt graphical user interfaces and Spyder interactive scientific development environment. Its purpose is to help scientific programmers used to interpreted languages (such as MATLAB or IDL) or compiled languages (C/C++ or Fortran) to switch to Python. C/C++ or Fortran programmers should appreciate to reuse their code as is by wrapping it so it can be called directly from Python scripts. With Python(x,y), one can do: * interactive calculations including for example 2D and 3D plotting or symbolic maths, * simple functionnal programming (with MATLAB-like syntax) as well as powerful object-oriented programming, * scientific projects development from the simplest script to the most sophisticated application thanks to Qt development framework and Spyder development environment, * parallel computing on multicore/processors computers or even clusters (with Parallel Python), ...and a lot more! Python(x,y) has five main features: * collecting scientific-oriented Python libraries and development environment tools ; * collecting almost all free related documentation ; * providing a quick guide to get started in Python / Qt / Spyder ; * providing an all-in-one setup program, so the user can install or uninstall all these packages and features by clicking on one button only.program, language, python, computation, data analysis, data visualization, pluginSCR_006903(Pythonxy, RRID:SCR_006903)Last checked upnlx_149232http://www.pythonxy.com
PiNGOResource, software resourceA Java-based tool to easily find unknown genes in a network that are significantly associated with user-defined target Gene Ontology (GO) categories. PiNGO is implemented as a plugin for Cytoscape, a popular open source software platform for visualizing and integrating molecular interaction networks. PiNGO predicts the categorization of a gene based on the annotations of its neighbors, using the enrichment statistics of its sister tool BiNGO. Networks can either be selected from the Cytoscape interface or uploaded from file. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatiblegene, annotation, network, candidate gene, biological network, ontology or annotation search engine, statistical analysis, term enrichment, functional similarity, functional prediction, search engine, windows, mac os x, linux, unixSCR_000692(PiNGO, RRID:SCR_000692)Ghent University; Ghent; Belgium related to: Gene Ontology, Cytoscape, listed by: Gene Ontology Tools, OMICtoolsPMID:21278188Last checked upnlx_149330, OMICS_02281
PIDO - Primary Immunodeficiency Disease OntologyResource, ontology, data or information resource, controlled vocabularyThe Primary Immunodeficiency Disease Ontology Project is developing an ontology for the phenotypic description of Primary Immunodeficiency Diseases. The ontology can be used for integrative research in both biomedical and clinical research. Primary Immunodeficiency Diseases (PIDs) are Mendelian diseases, caused by defects or deletions of genes involved in the development, regulation and maintenance of the immune system. They usually affect newborns and toddlers, but can also manifest much later in life. Information about PIDs is often widely scattered across the research literature and a number of databases. PIDO is an attempt to develop both a machine- as well as a human-comprehensible representation of these diseases, starting with a phenotypic descriptions of disease.phenotype, disease, young human, childSCR_005834(PIDO - Primary Immunodeficiency Disease Ontology, RRID:SCR_005834)Google Project Hosting , Hannover Medical School; Lower Saxony; Germany Primary Immunodeficiency DiseaseBBSRC, DFG, European Union FP7, Hannover Medical School; Lower Saxony; Germanyrelated to: PIDFinderPMID:21949270Last checked upnlx_149345
SNPediaResource, wiki, narrative resource, data or information resourceWiki investigating human genetics including information about the effects of variations in DNA, citing peer-reviewed scientific publications. It is used by Promethease to analyze and help explain your DNA. It is based on a wiki model in order to foster communication about genetic variation and to allow interested community members to help it evolve to become ever more relevant. As the cost of genotyping (and especially of fully determining your own genomic sequence) continues to drop, we''''ll all want to know more - a lot more - about the meaning of these DNA variations and SNPedia will be here to help. SNPedia has been launched to help realize the potential of the Human Genome Project to connect to our daily lives and well-being. For more information see the Wikipedia page, http://en.wikipedia.org/wiki/SNPedia * Download URL: http://www.SNPedia.com/index.php/Bulk * Web Service URL: http://bots.SNPedia.com/api.phpdna, genetics, gene, genome, genoset, genotype, medicine, medical condition, genetic variation, dna, genetic variation, genomics, single nucleotide polymorphism, medical association, phenotypic association, genealogical association, variation, genome annotation, phenotype, web serviceSCR_006125(SNPedia, RRID:SCR_006125)related to: Monarch InitiativePMID:22140107Last checked upnlx_151604
lapdftextResource, software resource, software application, text extraction softwareSoftware that facilitates accurate extraction of text from PDF files of research articles for use in text mining applications. It is intended for both scientists and natural language processing (NLP) engineers interested in getting access to text within specific sections of research articles. The system extracts text blocks from PDF-formatted full-text research articles and classifies them into logical units based on rules that characterize specific sections. The LA-PDFText system focuses only on the textual content of the research articles. The current version of LA-PDFText is a baseline system that extracts text using a three-stage process: * identification of blocks of contiguous text * classification of these blocks into rhetorical categories * extraction of the text from blocks grouped section-wise.text mining, pdf, text extraction, natural language processingSCR_006167(lapdftext, RRID:SCR_006167)University of Southern California; Los Angeles; USA NCRR, NIGMS, NIMH, NSFlisted by: FORCE11PMID:22640904Last checked upnlx_151668
Biodiversity Heritage LibraryResource, data or information resource, bibliography, databaseCollection 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.literature, taxonomy, scientific illustration, botany, biology, natural history, biodiversity, extinct animal, herbaria, ecology, botanical library, extinctSCR_008969(Biodiversity Heritage Library, RRID:SCR_008969)Atherton Seidell Endowment Fund, Gordon and Betty Moore Foundation, Institute of Museum and Library Services, MacArthur Foundation via the Encyclopedia of Life, Richard Lounsbery Foundation, Smithsonian Institutionrelated to: EOL - Encyclopedia of Life, listed by: re3data.orgLast checked upnlx_152035
HUBzeroResource, software resource, software application, data management software, software library, software toolkitOpen source software platform for building powerful Web portals that support scientific discovery, learning, and collaboration. Some refer to such web sites as collaboratories supporting team science. They call them hubs because each site becomes a focal point for its user community. HUBzero includes a powerful content management system built to support scientific activities. Users of a HUB can work together in projects, publish datasets and computational tools with Digital Object Identifiers (DOIs), and make these publications available for others to use--not as dusty downloads, but as live, interactive digital resources. Simulation/modeling tools published on a hub can be accessed with the click of a button. They run on cloud computing resources, campus clusters, and other national high-performance computing (HPC) facilities and serve up compelling visualizations. Projects can create public or private groups for collaboration and take advantage of over 10,000 Joomla! software extensions that provide additional functionality.platform, dissemination, collaboration, computational science, engineering, cyberinfrastructure, digital object identifierSCR_006384(HUBzero, RRID:SCR_006384)Indiana University School of Medicine; Indiana; USA related to: Clinical and Translational Science Awards ConsortiumPMID:21476852Last checked upnlx_152165
CERMINEResource, data analysis service, software library, production service resource, analysis service resource, software application, service resource, software resource, software toolkit, text extraction softwareJava library and a web service for extracting metadata and content from scientific articles in born-digital form. The system analyses the entire content of a PDF file containing a publication and attempts to extract information such as: the title of the article, journal information (title, etc.), bibliographic information (volume, issue, page numbers, etc.), authors and affiliations, keywords, abstract, bibliographic references and structured sections hierarchy.java library, java, metadata extraction, page segmentation, content classification, bibliographic reference parsing, parse, extraction system, pdfSCR_008993(CERMINE, RRID:SCR_008993)University of Warsaw; Warsaw; Poland National Centre for Research and Development Polandused by: Paperity, listed by: FORCE11Last checked upnlx_152512
Drosophila anatomy and development ontologiesResource, ontology, data or information resource, controlled vocabularyA structured controlled vocabulary of the anatomy of Drosophila melanogaster. These ontologies are query-able reference sources for information on Drosophila anatomy and developmental stages. They also provide controlled vocabularies for use in annotation and classification of data related to Drosophila anatomy, such as gene expression, phenotype and images. They were originally developed by FlyBase, who continue to maintain them and have used them for over 200,000 annotations of phenotypes and expression. Extensive use of synonyms means that, given a suitably sophisticated autocomplete, users can find relevant content by searching with almost any anatomical term they find in the literature. These ontologies are developed in the web ontology language OWL2. Their extensive formalization in OWL can be used to drive sophisticated query systems.anatomy, development, developmental stage, gene expression, phenotype, owlSCR_001607(Drosophila anatomy and development ontologies, RRID:SCR_001607) SourceForge , FlyBase NHGRIrelated to: OBO, Flannotator, REDfly Regulatory Element Database for Drosophilia, Bgee: a dataBase for Gene Expression EvolutionLast checked downnlx_153871
NIF Web ServicesResource, web service, software resource, data access protocolRepresentational State Transfer (REST) model based service for accessing a set of Neuroscience Information Framework (NIF) data through a fixed set of operations. They are defined by a WADL file which allows clients to automatically generate code for these services. The services (AnnotateService, FederationService, LdaService, LexicalService, LiteratureService, QueryService, SummaryService, VocabularyService) include the ability to: * Retrieve a federation summary, e.g., http://nif-services.neuinfo.org/servicesv1/v1/summary?q=* * Retrieve data records from a NIF federation source for a search, e.g., http://nif-services.neuinfo.org/servicesv1/v1/federation/data/nif-0000-00007-1?q=purkinje * Retrieve registry data records from NIF, e.g., http://nif-services.neuinfo.org/servicesv1/v1/federation/data/nlx_144509-1?q=miame * Retrieve a complete search summary, e.g., http://nif-services.neuinfo.org/servicesv1/v1/federation/search?q=cortex * Retrieve NIF auto-complete suggestions, e.g., http://nif-services.neuinfo.org/servicesv1/v1/vocabulary?prefix=hippo * Use the NIF annotator for arbitrary text, e.g., http://nif-services.neuinfo.org/servicesv1/v1/annotate?content=The%20cerebellum%20is%20a%20wonderful%20thing These services are documented for developers in the WADL file (and client stubs should have the comments embedded in them). Visit, http://nif-services.neuinfo.org/servicesv1/ for more informationrest, data sharing, wadlSCR_001631(NIF Web Services, RRID:SCR_001631)Neuroscience Information Framework related to: SciCrunch Registry, NIF Literature, OntoQuest, used by: NIF Data FederationLast checked downnlx_153899
openSNPResource, source code, database, service resource, storage service resource, software resource, data repository, data or information resourceDatabase of raw data from people who have shared their direct-to-customer (DTC) genetic results from 23andMe, deCODEme or FamilyTreeDNA. Logged-In users can search the database for users with specific phenotypes and mass-download all corresponding SNP-datasets. This allows you to get datasets like All genotyping files of openSNP-users that have Alzheimer and the corresponding control group. They are currently working on providing API-access. You can also use JSON to get access to openSNP-data and some other ways: If you want to automate the file-downloads for a given phenotype the RSS-feeds could help you. Inside the RSS-XML there are 2 flags you could use to automatically create correct genotype-groups: gives you the variation of this user at the phenotype you are looking at and gives you the download link. If you were genotyped by 23andMe, deCODEme or FamilyTreeDNA (contact them regarding others) you can upload the raw genotype data which you can download from your DTC test provider. The data will then be openly available for the world to see and download. They also parse these SNPs and annotate them. For annotation they include the manually curated SNPedia and find Open Access primary publications which appear in the journals of The Public Library of Science (PLoS), an Open Access publishing group. Additionally they screen Mendeley, a crowd-sourced repository of scientific publications. You can also publish some of your phenotypes so some day it might get possible to associate some SNPs with phenotypes. You can also share your knowledge about SNPs and phenotypes with other users and can socialize.SNP, genotype, phenotype, snp, genetic variation, disease, trait, genetics, genome wide association study, crowdsourcing, data setSCR_001636(openSNP, RRID:SCR_001636)related to: Monarch InitiativeLast checked upnlx_153904
Antarctic and Southern Ocean Data PortalResource, data access protocol, database, web service, service resource, storage service resource, software resource, data repository, data or information resourceAccepts and provides access to geoscience data, primarily marine, collected from oceanographic expeditions in the Antarctic region. The synthesis began in 2003 as the Antarctic Multibeam Bathymetry and Geophysical Data Synthesis (AMBS) with a focus on multibeam bathymetry field data and other geophysical data from the Southern Ocean collected with the R/V N. B. Palmer. In 2005, the effort was expanded to include all routine underway geophysical and oceanographic data collected with both the R/V N. B. Palmer and R/V L. Gould, the two primary research vessels serving the US Antarctic Program. Data available include seafloor bathymetry, subbottom profiling, trackline gravity and magnetics, meteorological, and water column data as well as basic cruise information for all Palmer and Gould expeditions. Seafloor bathymetry data are provided both as raw swath data as well as in gridded form through the Global Multi-Resolution Topography (GMRT) synthesis. This gridded compilation of seafloor bathymetry data can be accessed through GeoMapApp, Create Maps and Grids and through an OGC-compliant Web Map Service. GeoMapApp is an integrated mapping application that provides access to many additional regional bathymetric grids, seismic, radar, gravity and magnetics profiles as well as other map and grid compilations for the Antarctic continent including LIMA.oceanography, ocean, marine, antarctic, southern ocean, geoscience, polar, seafloor, bathymetry, subbottom profiling, trackline gravity, magnetics, meteorological, water column, map, gridSCR_002193(Antarctic and Southern Ocean Data Portal, RRID:SCR_002193)Marine Geoscience Data System NSFlisted by: CINERGI, re3data.orgLast checked upnlx_154703
Academic Seismic Portal at LDEOResource, data or information resource, databaseSeismic Reflection Field Data from the academic research community. Their partner Academic Seismic Portal at UTIG offers additional seismic resources, http://www.ig.utexas.edu/sdc/seismicSCR_002194(Academic Seismic Portal at LDEO, RRID:SCR_002194)Marine Geoscience Data System NSFrelated to: Academic Seismic Portal at UTIG, listed by: CINERGILast checked upnlx_154704
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