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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)

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222 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
GOannaResource, analysis service resource, data analysis service, service resource, production service resourceGOanna is used to find annotations for proteins using a similarity search. The input can be a list of IDs or it can be a list of sequences in FASTA format. GOanna will retrieve the sequences if necessary and conduct the specified BLAST search against a user-specified database of GO annotated proteins. The resulting file contains GO annotations of the top BLAST hits. The sequence alignments are also provided so the user can use these to access the quality of the match. Platform: Online toolagriculture, annotation, protein, ontology or annotation search engine, ontology or annotation editorSCR_005684(GOanna, RRID:SCR_005684)AgBase Mississippi State University; Mississippi; USA, MSU Bagley College of Engineering, MSU College of College of Veterinary Medicine, MSU Life Science and Biotechnology Institute, MSU Office of Research, USDArelated to: Gene Ontology, listed by: Gene Ontology ToolsReferences (2)Last checked upnlx_149139
GOSlimViewerResource, analysis service resource, data analysis service, service resource, production service resourceService to summarize the GO function associated with a data set using prepared GO Slim sets. The input is a tab separated list of gene product IDs and GO IDs.agriculture, browser, slimmer-type tool, gene ontology, gene, ontology, ontology or annotation browserSCR_005665(GOSlimViewer, RRID:SCR_005665)AgBase Mississippi State University; Mississippi; USA, MSU Bagley College of Engineering, MSU College of College of Veterinary Medicine, MSU Life Science and Biotechnology Institute, MSU Office of Research, USDArelated to: Gene Ontology, listed by: Gene Ontology Tools, OMICtoolsReferences (2)Last checked upnlx_149103, OMICS_02270
GraphWebResource, analysis service resource, data analysis service, service resource, production service resourceGraphWeb allows the detection of modules from biological, heterogeneous and multi-species networks, and the interpretation of detected modules using Gene Ontology, cis-regulatory motifs and biological pathways. GraphWeb is a public web server for graph-based analysis of biological networks that: * analyses directed and undirected, weighted and unweighted heterogeneous networks of genes, proteins and microarray probesets for many eukaryotic genomes; * integrates multiple diverse datasets into global networks; * incorporates multispecies data using gene orthology mapping; * filters nodes and edges based on dataset support, edge weight and node annotation; * detects gene modules from networks using a collection of algorithms; * interprets discovered modules using Gene Ontology, pathways, and cis-regulatory motifs. Platform: Online toolanalysis, biological network, ontology or annotation visualization, protein interaction, gene id conversion, orthology mapping, network visualization, graph clustering, gene ontology, cis-regulatory motif, module, network, pathway, biological pathway, motif, visualization, protein interaction, orthology mapping, network visualization, graph clustering, analysis, statistical analysis, term enrichmentSCR_005746(GraphWeb, RRID:SCR_005746)BIIT - Bioinformatics Algorithmics and Data Mining Group Estonian Science Foundation, European Union FP6related to: Gene Ontology, listed by: Gene Ontology ToolsPMID:18460544Last checked upnlx_149205
SpotfireResource, software resourceThe Spotfire Gene Ontology Advantage Application integrates GO annotations with gene expression analysis in Spotfire DecisionSite for Functional Genomics. Researchers can select a subset of genes in DecisionSite visualizations and display their distribution in the Gene Ontology hierarchy. Similarly, selection of any process, function or cellular location in the Gene Ontology hierarchy automatically marks the corresponding genes in DecisionSite visualizations. Platform: Windows compatibleanalysis, predictive analytics, big data, visualization, gene ontology, annotation, gene expression, functional genomics, gene, function, cellular location, statistical analysis, genomicsSCR_008858(Spotfire, RRID:SCR_008858)related to: Gene Ontology, listed by: Gene Ontology Tools, Metabolomics WorkbenchLast checked upnlx_149169
UBERONResource, ontology, data or information resource, controlled vocabularyAn integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. Uberon consists of over 10000 classes (March 2014) representing structures that are shared across a variety of metazoans. The majority of these classes are chordate specific, and there is large bias towards model organisms and human.anatomy, comparative, evolution, organ system, anatomical structure, body part, organ, tissue, body, vertebrate, function, phenotype, expression, model organism, oboSCR_010668(UBERON, RRID:SCR_010668)OBO ARRA, DOE, NCRR, NHGRI, NSFrelated to: Gene Ontology, used by: Monarch Initiative, Neuroscience Information Framework, listed by: BioPortalPMID:22293552Last checked upnlx_74404
Onto-TranslateResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceIn the annotation world, the same piece of information can be stored and viewed differently across different databases. For instance, more than one Affymetrix probe ID can refer to the same GenBank sequence (accession number) and more than one nucleotide sequence from GenBank can be grouped in a single UniGene cluster. The result of Onto-Express depends on whether the input list contains Affymetrix probe IDs, GenBank accession numbers or UniGene cluster IDs. The user has to be aware of relations between the different forms of the data in order to interpret correctly the results. Even if the user is aware of the relationships and knows how to convert them, most existing tools allow conversions of individual genes. Onto-Translate is a tool that allows the user to perform easily such translations. Affymetrix probe IDs, etc., translate GO terms into other identifiers like GenBank accession number, Uniprot IDs. User account required. Platform: Online toolannotation, gene, analysis, database or data warehouse, other analysis, affymetrix probe id, affymetrix, probe id, translate go terms into other identifiers like genbank accession number, genbank accession number, uniprot id, gene ontology, translateSCR_005725(Onto-Translate, RRID:SCR_005725)Wayne State University; Michigan; USA related to: Gene Ontology, listed by: Gene Ontology ToolsPMID:15215428Last checked downnlx_149182
Gene Ontology Browsing Utility (GOBU)Resource, software resource, source codeGene Ontology Browsing Utility (GOBU) (GOBU) is a Java-based software program for integrating biological annotation catalogs under an extendable software architecture. Users may interact with the Gene Ontology and user-defined hierarchy data of genes, and then use its plugins to (and not limited to) (1) browse the GO hierarchy with user defined data, (2) browse GO-oriented expression levels in the user data, (3) compute GO enrichment, and/or (4) customize data reporting. A set of classes and utility functions has been established so that a customized program can be made as a plugin or a command-line tool that programmically manipulate the Gene Ontology and specified user data. See the source code repository for examples. Reference Lin WD, Chen YC, Ho JM, Hsiao CD. GOBU: Toward an Integration Interface for Biological Objects. Journal of Information Science and Engineering. 2006 22(1):19-29. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatibleannotation, gene, browser, computation, visualization, software library, statistical analysis, term enrichment, ontology or annotation browser, ontology or annotation visualizationSCR_005662(Gene Ontology Browsing Utility (GOBU), RRID:SCR_005662)Academia Sinica; Taipei; Taiwan related to: Gene Ontology, listed by: Gene Ontology ToolsLast checked downnlx_149098
categoryCompareResource, software resource, software application, data analysis software, data processing softwareA software package for meta-analysis of high-throughput experiments using feature annotations. It calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).annotation, go, gene expression, multiple comparison, pathway, geneSCR_001223(categoryCompare, RRID:SCR_001223)Bioconductor related to: Gene Ontology, CRAN, uses: Cytoscape, listed by: OMICtoolsLast checked upOMICS_02122
GFINDer: Genome Function INtegrated DiscovererResource, analysis service resource, data analysis service, service resource, production service resourceMulti-database system providing large-scale lists of user-classified sequence identifiers with genome-scale biological information and functional profiles biologically characterizing the different gene classes in the list. GFINDer automatically retrieves updated annotations of several functional categories from different sources, identifies the categories enriched in each class of a user-classified gene list, and calculates statistical significance values for each category. Moreover, GFINDer enables to functionally classify genes according to mined functional categories and to statistically analyze the obtained classifications, aiding in better interpreting microarray experiment results. \\nTHIS SERVICE IS NO LONGER AVAILABLE. Documented on August 16,2019annotation, statistical analysis, mining, genome, function, sequence, functional profile, gene, microarraySCR_008868(GFINDer: Genome Function INtegrated Discoverer, RRID:SCR_008868)Polytechnic University of Milan; Milan; Italy related to: Gene Ontology, listed by: Gene Ontology ToolsReferences (2)Last checked downnlx_149256https://www.hsls.pitt.edu/obrc/index.php?page=URL1098209538
Blast2GOResource, software resource, software applicationAn ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. Blast2GO (B2G) joins in one universal application similarity search based GO annotation and functional analysis. B2G offers the possibility of direct statistical analysis on gene function information and visualization of relevant functional features on a highlighted GO direct acyclic graph (DAG). Furthermore B2G includes various statistics charts summarizing the results obtained at BLASTing, GO-mapping, annotation and enrichment analysis (Fisher''''s Exact Test). All analysis process steps are configurable and data import and export are supported at any stage. The application also accepts pre-existing BLAST or annotation files and takes them to subsequent steps. The tool offers a very suitable platform for high throughput functional genomics research in non-model species. B2G is a species-independent, intuitive and interactive desktop application which allows monitoring and comprehending the whole annotation and analysis process supported by additional features like GO Slim integration, evidence code (EC) consideration, a Batch-Mode or GO-Multilevel-Pies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatibleannotation, visualization, analysis, functional genomics, editor, statistical analysis, slimmer-type tool, ontology or annotation editor, functional analysis, direct acyclic graph, analysis, high throughput, functional genomicsSCR_005828(Blast2GO, RRID:SCR_005828)Principe Felipe Research Centre; Valencia; Spain eTumour Project, MCyTrelated to: Gene Ontology, listed by: Gene Ontology Tools, OMICtoolsPMID:16081474Last checked downnlx_149335, OMICS_01475
FlyMineResource, data analysis service, data access protocol, production service resource, analysis service resource, database, web service, service resource, software resource, data or information resourceAn integrated database of genomic, expression and protein data for Drosophila, Anopheles, C. elegans and other organisms. You can run flexible queries, export results and analyze lists of data. FlyMine presents data in categories, with each providing information on a particular type of data (for example Gene Expression or Protein Interactions). Template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category. Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries. Access our FlyMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby and & Java APIanopheles, genome, c. elegans, drosophila, gene, chromosomal location, genomics, proteomics, gene expression, interaction, homology, function, regulation, protein, phenotype, pathway, disease, publicationSCR_002694(FlyMine, RRID:SCR_002694)University of Cambridge; Cambridge; United Kingdom NHGRI, Wellcome Trustrelated to: FlyBase, Universal Protein Resource, Ensembl, InterPro, BioGRID, Research Collaboratory for Structural Bioinformatics Protein Data Bank, Tree families database, IntAct, Gene Ontology, GOA, ArrayExpress, REDfly Regulatory Element Database for Drosophilia, KEGG, ReactomePMID:17615057Last checked upnif-0000-02845
ONTO-PERLResource, software resource, source codeONTO-PERL is a collection of Perl modules to handle OBO-formatted ontologies (like the Gene Ontology). This code distribution gathers object-oriented modules (for dealing with ontology elements such as Term, Relationship and so forth), scripts (for typical tasks such as format conversions: obo2owl, owl2obo; besides, there are also many examples that can be easily adapted for specific applications), and a set of test files to ensure the suite''''s implementation quality. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatibleapplication programming interface, software library, ontology, analysis, development, biomedicalSCR_005731(ONTO-PERL, RRID:SCR_005731)Comprehensive Perl Archive Network , Norwegian University of Science and Technology; Trondheim; Norway European Union FP6related to: Gene Ontology, OBO, listed by: Gene Ontology ToolsPMID:18245124Last checked upnlx_149191
Arabidopsis Hormone DatabaseResource, data repository, ontology, database, service resource, storage service resource, controlled vocabulary, data or information resourceDatabase providing a systematic and comprehensive view of morphological phenotypes regulated by plant hormones, as well as regulatory genes participating in numerous plant hormone responses. By integrating the data from mutant studies, transgenic analysis and gene ontology annotation, genes related to the stimulus of eight plant hormones were identified, including abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonic acid and salicylic acid. Another pronounced characteristics of this database is that a phenotype ontology was developed to precisely describe all kinds of morphological processes regulated by plant hormones with standardized vocabularies. To increase the coverage of phytohormone related genes, the database has been updated from AHD to AHD2.0 adding and integrating several pronounced features: (1) added 291 newly published Arabidopsis hormone related genes as well as corrected information (e.g. the arguable ABA receptors) based on the recent 2-year literature; (2) integrated orthologues of sequenced plants in OrthoMCLDB into each gene in the database; (3) integrated predicted miRNA splicing site in each gene in the database; (4) provided genetic relationship of these phytohormone related genes mining from literature, which represents the first effort to construct a relatively comprehensive and complex network of hormone related genes as shown in the home page of our database; (5) In convenience to in-time bioinformatics analysis, they also provided links to a powerful online analysis platform Weblab that they have recently developed, which will allow users to readily perform various sequence analysis with these phytohormone related genes retrieved from AHD2.0; (6) provided links to other protein databases as well as more expression profiling information that would facilitate users for a more systematic analysis related to phytohormone research. Please help to improve the database with your contributions.arabidopsis thaliana, hormone, hormone function, hormone gene, phytohormone, abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonic acid, salicylic acid, microarray, phenotype, gene, mirna prediction, expression, mutant, blast, orthologue, mirna splicing site, root, cotyledon, leaf, hypocotyl, stem, flower, silique, seed, embryo, stress, morphology, plant, hormone, regulatory gene, mutant, transgenic, annotation, data analysis serviceSCR_001792(Arabidopsis Hormone Database, RRID:SCR_001792)Peking University; Beijing; China Ministry of Education of China, Ministry of Science and Technology of China, National Natural Science Foundation of Chinarelated to: Gene OntologyReferences (2)Last checked upnif-0000-02559
ProbeExplorerResource, analysis service resource, data analysis service, service resource, production service resourceProbe Explorer is an open access web-based bioinformatics application designed to show the association between microarray oligonucleotide probes and transcripts in the genomic context, but flexible enough to serve as a simplified genome and transcriptome browser. Coordinates and sequences of the genomic entities (loci, exons, transcripts), including vector graphics outputs, are provided for fifteen metazoa organisms and two yeasts. Alignment tools are used to built the associations between Affymetrix microarrays probe sequences and the transcriptomes (for human, mouse, rat and yeasts). Search by keywords is available and user searches and alignments on the genomes can also be done using any DNA or protein sequence query. Platform: Online toolbioinformatics, microarray, oligonucleotide probe, transcript, genomic, genome, transcriptome, alignment, affymetrix, probe sequence, dna, protein, sequence, statistical analysisSCR_007116(ProbeExplorer, RRID:SCR_007116)University of Salamanca; Salamanca; Spain related to: Gene Ontology, listed by: Gene Ontology ToolsLast checked upnlx_149275
Blip: Biomedical Logic ProgrammingResource, software resourceBiomedical Logical Programming (Blip) is a research-oriented deductive database and prolog application library for handling biological and biomedical data. It includes packages for advanced querying of ontologies and annotations. Blip underpins the Obol tool. Here are some distinguishing characteristics of Blip * Lightweight. Bloat-free: Blip only has as many modules as it needs to do its job. * Fast. * Declarative. Say what you want to do, not how you want to do it * Blip can be Query-oriented: specify your data sources and ask your query * Blip can be Application-oriented: it is designed to be used as an application library used by other bioinformatics tools * Mature and fully functional ontology module for handling both OBO-style ontologies and OWL ontologies. * Modules for handling biological sequences and sequence features. (currently limited functionality, added as needed) * A systems biology module for querying pathway and interaction data. (currently limited functionality, added as needed) * Relational database integration. SQL can be viewed as a highly restricted dialect of Prolog. Although the SWI-Prolog in-memory database is fast and scalable, sometimes it is nice to be able to fetch data from an external database. Blip contains a generic SQL utility module and predicate mappings for the GO database, Ensembl and Chado * Integration with a variety of bioinformatics file formats. SWI-Prolog has a variety of fast libraries for dealing with XML, RDF and tabular data files. Blip provides bridges from bio file formats encoded using these syntaxes into its native models. For other syntaxes, Blip seamlessly integrates other packages such as BioPerl and go-perl. Although these dependencies require extra installation, there is no point reinventing the wheel * Rapid development of web applications. Blip extends SWI-Prolog''''s excellent http support with a simple and powerful logical-functional-programming style application server, serval. This has been used to prototype a fully-featured next-generation replacement for the GO project amigo browser. * Scalable. Blip is not intended to be a toy system on toy data (although it is happy to be used as a toy if you like!). It is intended to be used as an application component and a tool operating on real-world biological and biomedical data Blip is written in SWI-Prolog, a fast, robust and scalable implementation of ISO Prolog. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatiblebiology, biomedical, ontology, annotation, software library, bioinformatics, moduleSCR_005733(Blip: Biomedical Logic Programming, RRID:SCR_005733)Berkeley Bioinformatics Open-Source Projects related to: Gene Ontology, listed by: Gene Ontology ToolsLast checked upnlx_149193
Integrated Manually Extracted AnnotationResource, data set, data or information resourceA virtual database of annotations made by 50 database providers (April 2014) - and growing (see below), that map data to publication information. All NIF Data Federation sources can be part of this virtual database as long as they indicate the publications that correspond to data records. The format that NIF accepts is the PubMed Identifier, category or type of data that is being linked to, and a data record identifier. A subset of this data is passed to NCBI, as LinkOuts (links at the bottom of PubMed abstracts), however due to NCBI policies the full data records are not currently associated with PubMed records. Database providers can use this mechanism to link to other NCBI databases including gene and protein, however these are not included in the current data set at this time. (To view databases available for linking see, http://www.ncbi.nlm.nih.gov/books/NBK3807/#files.Databases_Available_for_Linking ) The categories that NIF uses have been standardized to the following types: * Resource: Registry * Resource: Software * Reagent: Plasmid * Reagent: Antibodies * Data: Clinical Trials * Data: Gene Expression * Data: Drugs * Data: Taxonomy * Data: Images * Data: Animal Model * Data: Microarray * Data: Brain connectivity * Data: Volumetric observation * Data: Value observation * Data: Activation Foci * Data: Neuronal properties * Data: Neuronal reconstruction * Data: Chemosensory receptor * Data: Electrophysiology * Data: Computational model * Data: Brain anatomy * Data: Gene annotation * Data: Disease annotation * Data: Cell Model * Data: Chemical * Data: Pathways For more information refer to Create a LinkOut file, http://neuinfo.org/nif_components/disco/interoperation.shtm Participating resources ( http://disco.neuinfo.org/webportal/discoLinkoutServiceSummary.do?id=4 ): * Addgene http://www.addgene.org/pgvec1 * Animal Imaging Database http://aidb.crbs.ucsd.edu * Antibody Registry http://www.neuinfo.org/products/antibodyregistry/ * Avian Brain Circuitry Database http://www.behav.org/abcd/abcd.php * BAMS Connectivity http://brancusi.usc.edu/ * Beta Cell Biology Consortium http://www.betacell.org/ * bioDBcore http://biodbcore.org/ * BioGRID http://thebiogrid.org/ * BioNumbers http://bionumbers.hms.harvard.edu/ * Brain Architecture Management System http://brancusi.usc.edu/bkms/ * Brede Database http://hendrix.imm.dtu.dk/services/jerne/brede/ * Cell Centered Database http://ccdb.ucsd.edu * CellML Model Repository http://www.cellml.org/models * CHEBI http://www.ebi.ac.uk/chebi/ * Clinical Trials Network (CTN) Data Share http://www.ctndatashare.org/ * Comparative Toxicogenomics Database http://ctdbase.org/ * Coriell Cell Repositories http://ccr.coriell.org/ * CRCNS - Collaborative Research in Computational Neuroscience - Data sharing http://crcns.org * Drug Related Gene Database https://confluence.crbs.ucsd.edu/display/NIF/DRG * DrugBank http://www.drugbank.ca/ * FLYBASE http://flybase.org/ * Gene Expression Omnibus http://www.ncbi.nlm.nih.gov/geo/ * Gene Ontology Tools http://www.geneontology.org/GO.tools.shtml * Gene Weaver http://www.GeneWeaver.org * GeneDB http://www.genedb.org/Homepage * Glomerular Activity Response Archive http://gara.bio.uci.edu * GO http://www.geneontology.org/ * Internet Brain Volume Database http://www.cma.mgh.harvard.edu/ibvd/ * ModelDB http://senselab.med.yale.edu/modeldb/ * Mouse Genome Informatics Transgenes ftp://ftp.informatics.jax.org/pub/reports/MGI_PhenotypicAllele.rpt * NCBI Taxonomy Browser http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html * NeuroMorpho.Org http://neuromorpho.org/neuroMorpho * NeuronDB http://senselab.med.yale.edu/neurondb * SciCrunch Registry http://neuinfo.org/nif/nifgwt.html?tab=registry * NIF Registry Automated Crawl Data http://lucene1.neuinfo.org/nif_resource/current/ * NITRC http://www.nitrc.org/ * Nuclear Receptor Signaling Atlas http://www.nursa.org * Olfactory Receptor DataBase http://senselab.med.yale.edu/ordb/ * OMIM http://omim.org * OpenfMRI http://openfmri.org * PeptideAtlas http://www.peptideatlas.org * RGD http://rgd.mcw.edu * SFARI Gene: AutDB https://gene.sfari.org/autdb/Welcome.do * SumsDB http://sumsdb.wustl.edu/sums/ * Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat http://www.temporal-lobe.com/ * The Cell: An Image Library http://www.cellimagelibrary.org/ * Visiome Platform http://platform.visiome.neuroinf.jp/ * WormBase http://www.wormbase.org * YPED http://medicine.yale.edu/keck/nida/yped.aspx * ZFIN http://zfin.orgbiomedical, bibliographic, linkout, literatureSCR_008876(Integrated Manually Extracted Annotation, RRID:SCR_008876)Integrated related to: BAMS Connectivity, BioGRID, BioNumbers, PubMed, Brain Architecture Management System, CellML Model Repository, CHEBI, Comparative Toxicogenomics Database, Coriell Cell Repositories, Drug Related Gene Database, DrugBank, Gene Weaver, Internet Brain Volume Database, Cell Centered Database, Brede Database, ModelDB, NeuronDB, NeuroMorpho.Org, Nuclear Receptor Signaling Atlas , Cell Image Library (CIL), Animal Imaging Database, Olfactory Receptor DataBase, Glomerular Activity Response Archive, CRCNS, OMIM, Rat Genome Database (RGD), Visiome Platform, NIDA Data Share, bioDBcore, Addgene, Antibody Registry, Beta Cell Biology Consortium , FlyBase, SumsDB, SciCrunch Registry, Mouse Genome Informatics Transgenes, NCBI Taxonomy, OpenNeuro, PeptideAtlas, Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat, NIF Registry Automated Crawl Data, AutDB, Gene Expression Omnibus, Gene Ontology, Avian Brain Circuitry Database, Zebrafish Information Network, GeneDB, WormBase, YPED, used by: NIF Data Federation, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC), Gene Ontology ToolsReferences (2)Last checked downnlx_149407http://neuinfo.org/nif/nifgwt.html?query=nlx_149407, https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_149407-1
OBOResource, data or information resource, standard specification, narrative resource, knowledge environment, ontology, controlled vocabularyA collaboration involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain. In addition to a listing of OBO ontologies, this site provides a statement of the OBO Foundry principles, discussion fora, technical infrastructure, and other services to facilitate ontology development. Feedback is welcome and participation encouraged.biomedical, metadata standard, gold standardSCR_007083(OBO, RRID:SCR_007083)Berkeley Bioinformatics Open-Source Projects related to: MeGO, Drosophila anatomy and development ontologies, Cell Type Ontology, OBO-Edit, go-perl, OWLTools, Zebrafish Anatomical Ontology, OBO Tracker: Plant Ontology (PO) TERM requests, eVOC, OnEx - Ontology Evolution Explorer, BioPerl, dkCOIN , Standards-based Infrastructure with Distributed Resources, OntoVisT, COBrA, Wandora, ONTO-PERL, Genomic Standards Consortium, Ontology Lookup Service, LexGrid, SBO, RIKEN integrated database of mammals, DOAF, Gene Ontology, listed by: FORCE11, lists: CHEBI, NCI Thesaurus, Porifera Ontology, Gazetteer, Human Disease Ontology, Information Artifact Ontology, Teleost Anatomy Ontology, Gene Ontology, Spider Ontology, Mental Functioning Ontology, Ascomycete Phenotype Ontology, Beta Cell Genomics Ontology, Biological Collections Ontology, Emotion Ontology, Chemical Methods Ontology, Chemical Information Ontology, Clinical Measurement Ontology, Common Anatomy Reference Ontology, Experimental Conditions Ontology, Dictyostelium Discoideum Anatomy Ontology, Fission Yeast Phenotype Ontology, Fly Taxonomy, FlyBase Controlled Vocabulary, Hymenoptera Anatomy Ontology, Influenza Ontology, Lipid Ontology, Kinetic Simulation Algorithm Ontology, Malaria Ontology, Measurement Method Ontology, Minimal Anatomical Terminology, Ontology for Genetic Interval, Ontology for Parasite LifeCycle, Ontology of Adverse Events, Ontology of Medically Related Social Entities, Ontology of Vaccine Adverse Events, Pathway Ontology, Plant Environmental Conditions, Plant Trait Ontology, Population and Community Ontology, RNA Ontology, Rat Strain Ontology, Subcellular Anatomy Ontology, Software Ontology, Suggested Ontology for Pharmacogenomics, Vertebrate Taxonomy Ontology, Physico-Chemical Process, Adverse Event Reporting Ontology, Xenopus Anatomy Ontology, Cell Line Ontology, HPO - Human Phenotype Ontology, Neurobehavior Ontology, Ontology for Biomedical Investigations, Comparative Data Analysis Ontology, Ontology for General Medical Science, Physico-Chemical Methods and Properties, Gene Regulation OntologyPMID:17989687Last checked upnlx_22892
agriGOResource, data analysis service, database, analysis service resource, production service resource, service resource, data or information resourceA web-based tool and database for the gene ontology analysis. Its focus is on agricultural species and is user-friendly. The agriGO is designed to provide deep support to agricultural community in the realm of ontology analysis. Compared to other available GO analysis tools, unique advantages and features of agriGO are: # The agriGO especially focuses on agricultural species. It supports 45 species and 292 datatypes currently. And agriGO is designed as an user-friendly web server. # New tools including PAGE (Parametric Analysis of Gene set Enrichment), BLAST4ID (Transfer IDs by BLAST) and SEACOMPARE (Cross comparison of SEA) were developed. The arrival of these tools provides users with possibilities for data mining and systematic result exploration and will allow better data analysis and interpretation. # The exploratory capability and result visualization are enhanced. Results are provided in different formats: HTML tables, tabulated text files, hierarchical tree graphs, and flash bar graphs. # In agriGO, PAGE and SEACOMPARE can be used to carry out cross-comparisons of results derived from different data sets, which is very important when studying multiple groups of experiments, such as in time-course research. Platform: Online toolbrowser, gene, online tool, visualization, statistical analysis, term enrichment, text mining, ontology or annotation browser, ontology or annotation visualization, database or data warehouseSCR_006989(agriGO, RRID:SCR_006989)China Agricultural University; Beijing; China Ministry of Science and Technology of Chinarelated to: Gene Ontology, listed by: Gene Ontology Tools, OMICtoolsPMID:20435677Last checked upnlx_149099, OMICS_02265
Tk-GOResource, software resourceTk-GO is a GUI wrapping the basic functions of the GO AppHandle library from BDGP. GO terms are presented in an explorer-like browser, and behavior can be configured by altering Perl scripts. All available documentation is included in the download. Tk-GO uses the GO database (connects directly to the BDGP database by default) but is user-configurable. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatiblebrowser, gene, ontology or annotation browserSCR_008855(Tk-GO, RRID:SCR_008855)Illumina related to: Gene Ontology, listed by: Gene Ontology ToolsLast checked upnlx_149133
Cardiovascular Gene Ontology Annotation InitiativeResource, data set, data or information resourceFull Gene Ontology annotation to genes associated with cardiovascular processes. Every GO annotation made, is attributed to an identified source, such as a publication identifier (PMID), and an indication of the type of evidence which supports the association between the gene product and the GO term. Over 4,000 cardiovascular associated genes have been identified. A variety of tools have been provided to enable cardiovascular scientists to review the annotation of their ''''favorite'''' gene and suggest information that may be missing, inaccurate or incomplete in these annotations. Annotation suggestions can be sent through the feedback form or by email. The Gene Ontology (GO) vocabulary is the established standard for the functional annotation of gene products. By using GO to curate scientific literature and by integrating results from high-quality high-throughput experiments they will create an information-rich resource for the cardiovascular-research community, enabling researchers to rapidly evaluate and interpret existing data and generate hypotheses to guide future research.cardiovascular process, heart disease, cardiovascular, heart, cardiovascular system, annotation, gene, functional annotation, gene product, gold standardSCR_004795(Cardiovascular Gene Ontology Annotation Initiative, RRID:SCR_004795)University College London; London; United Kingdom British Heart Foundationrelated to: Gene Ontology, IntActReferences (2)Last checked upnlx_79058http://www.ebi.ac.uk/GOA/CVI/
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