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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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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
GenePaintResource, atlas, expression atlas, data or information resource, reference atlas, databaseDigital atlas of gene expression patterns in developing and adult mouse. Several reference atlases are also available through this site. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections. Sections are available from several developmental ages: E10.5, E14.5 (whole embryos), E15.5, P7 and P56 (brains only). To retrieve expression patterns, search by gene name, site of expression, GenBank accession number or sequence homology. For viewing expression patterns, GenePaint.org features virtual microscope tool that enables zooming into images down to cellular resolution.gene expression, adult mouse, annotated, c57bl6, mouse, mouse embryo, mrna, non radioactive in situ hybridization, light microscopy, molecular neuroanatomy resource, in situ hybridization, embryonic, postnatal, adult, brain, head, annotation, rna probe, sequence, anatomical structureSCR_003015(GenePaint, RRID:SCR_003015)Max Planck Institute for Biophysical Chemistry; Gottingen; Germany BMBF, Burroughs Wellcome Fund, European Union, Max Planck Society, Merck Genome Research Institute, NINDS, Romansky EndowmentReferences (2)Last checked upnif-0000-00009, SCR_017526
Ligand-Gated Ion Channel DatabaseResource, data or information resource, databaseDatabase providing access to information about transmembrane proteins that exist under different conformations, with three primary subfamilies: the cys-loop superfamily, the ATP gated channels superfamily, and the glutamate activated cationic channels superfamily. Due to the lack of evolutionary relationship, these three superfamilies are treated separately. It currently contains 554 entries of ligand-activated ion channel subunits. In this database one may find: the nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Additionally, the atomic coordinates of subunits, or portion of subunits, are provided when available. Redundancy is kept to a minimum, i.e. one entry per gene. Each entry in the database has been manually constructed and checked by a researcher of the field in order to reduce the inaccuracies to a minimum. NOTE: This database is not actively maintained anymore. People should not consider it as an up-to-date trustable resource. For any new work, they should consider using alternative sources, such as UniProt, Ensembl, Protein Databank etc.equilibrium, extracellular, gabaa, gated, gene, genetics, 3d model, alignment, anionic, atomic, atp, cationic, cellular, molecular, channel, compartment, computation, conformation, coordinate, cys-loop, glutamate, glycine, histamine, homologous, ion, ion channel, ligand, membrane, nicotinic, nucleic acid, phylogenetic, pore, portion, proteic, nucleic acid, protein, phylogeny, receptor, segment, sequence, sequence data, serotonin, subunit, superfamily, transmembraneSCR_002418(Ligand-Gated Ion Channel Database, RRID:SCR_002418)European Bioinformatics Institute Biotech and Biomed contracts, Centre National de la Recherche Scientifique, College of France; Paris; France, European Union, French Ministry of Higher Education and Research, Institut Pasteurlisted by: re3data.orgReferences (2)Last checked upnif-0000-00037
Brede DatabaseResource, data or information resource, databaseA database of human data from functional neuroimaging scientific articles containing Talairach coordinates that provides data for novel information retrieval techniques and automated meta-analyses. Each article in this database is identified by a unique number: A WOBIB. Some of the structure of the Brede database is similar to the structure of the BrainMap database (Research Imaging Center, San Antonio). The database is inspired by the hierarchical structure of BrainMap with scientific articles (bib structures) on the highest level containing one or more experiments (exp structure, corresponding to a contrast in general linear model analyses), these in turn comprising one or more locations (loc structures). The information on the bib level (author, title, ...) is setup automatically from PubMed while the rest of the information is entered manually in a Matlab graphical user interface. On the loc level this includes the 3D stereotactic coordinates in either Talairach or MNI space, the brain area (functional, anatomical or cytoarchitectonic area) and magnitude values such as Z-score and P-value. On the exp level information such as modality, scanner and behavioral domain are recorded with external components (such as face recognition or kinetic boundaries) organized in a directed graph and marked up with Medical Subject Headings (MeSH) where possible. The database is distributed as part of the Brede neuroinformatics toolbox (hendrix.imm.dtu.dk/software/brede/) which also provides the functions to manipulate and analyze the data. The Brede Toolbox is a program package primarily written in Matlab. As of 2006/11, 186 papers with 586 experiments.neuroinformatics, functional neuroimaging, talairach, mni, brain, fmri, neuroimaging, matlab, pet, positron emission tomography, functional magnetic resonance imaging, multichannel electroencephalography, eeg, magnetoencephalography, near infrared spectroscopic imaging, single photon emission computed tomography, mri, coordinate, brain function, brain region, ontologySCR_003327(Brede Database, RRID:SCR_003327)Technical University of Denmark; Lyngby; Denmark European Union, Project MAPAWAMOrelated to: Brede Wiki, Brede Toolbox, Brede Toolbox, Brede Wiki, brainmap.org, Integrated Manually Extracted Annotation, used by: NIF Data FederationReferences (2)Last checked upnif-0000-00064
Information Hyperlinked Over ProteinsResource, service resource, data or information resource, databaseInformation system that provides a network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. It provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research. Moreover, this literature network can be superimposed on experimental interaction data (e.g., yeast-two hybrid data from Drosophila melanogaster and Caenorhabditis elegans) to make possible a simultaneous analysis of new and existing knowledge. The network contains half a million sentences and 30,000 different genes from humans, mice, D. melanogaster, C. elegans, zebrafish, Arabidopsis thaliana, yeast and Escherichia coli.phenotype, gene, protein, interaction, pathology, physiology, gene network, network, literature, gene function, text-miningSCR_004829(Information Hyperlinked Over Proteins, RRID:SCR_004829)Autonomous University of Madrid; Madrid; Spain European Unionrelated to: PubMed, listed by: OMICtoolsPMID:15226743Last checked upnif-0000-00232, OMICS_01185
EurexpressResource, atlas, expression atlas, data or information resource, image collection, databaseGenome transcriptome atlas by RNA in situ hybridization on sagittal sections of developing mouse at embryonic day 14.5. Consists of searchable database of annotated images that can be interactively viewed. Anatomy based expression profiles for coding genes and microRNAs, tissue specific genes. Expression data generated by using human and murine tissue arrays.Genome, transcriptome, atlas, RNA, in situ, hybrydization, sagittal, section, developing, mouse, embryo, expression, geneSCR_005093(Eurexpress, RRID:SCR_005093)Telethon Institute of Genetics and Medicine; Naples; Italy Association pour la Recherche sur le Cancer, European Union, Ingenio 2010 MEuropean Union, Max Planck Society, MRC, Swiss National Science Foundation, Telethon Foundation, VI Frameworkrelated to: EMAGE Gene Expression Database, aGEM, listed by: GUDMAP Ontology , NIDDK Information NetworkPMID:21267068Last checked upnif-0000-00243http://www.eurexpress.org/ee/databases/anatomy/treeFrames.jsp
LyngbyResource, software resource, software application, data analysis software, data processing softwareMatlab toolbox for the analysis of functional neuroimages (PET, fMRI). The toolbox contains a number of models: FIR-filter, Lange-Zeger, K-means clustering among others, visualizations and reading of neuroimaging files.functional, statistical, fmri, pet, matlab, neuroimagingSCR_007143(Lyngby, RRID:SCR_007143)THOR Center for Neuroinformatics BIOMED2, Danish Research Council, DOE, European Union, Human Brain Project, MAPAWAMO, NASA, NIDA, NIMH, NSFlisted by: BiositemapsLast checked upnif-0000-00324
IMEx - The International Molecular Exchange ConsortiumResource, organization portal, database, consortium, service resource, portal, storage service resource, data repository, community building portal, data or information resourceInteraction database from international collaboration between major public interaction data providers who share curation effort and develop set of curation rules when capturing data from both directly deposited interaction data or from publications in peer reviewed journals. Performs complete curation of all protein-protein interactions experimentally demonstrated within publication and makes them available in single search interface on common website. Provides data in standards compliant download formats. IMEx partners produce their own separate resources, which range from all encompassing molecular interaction databases, such as are maintained by IntAct, MINT and DIP, organism-centric resources such as BioGrid or MPIDB or biological domain centric, such as MatrixDB. They have committed to making records available, via PSICQUIC webservice, which have been curated to IMEx rules and are available to users as single, non-redundant set of curated publications which can be searched at the IMEx website. Data is made available in standards-compliant tab-deliminated and XML formats, enabling to visualize data using wide range of tools. Consortium is open to participation of additional partners and encourages deposition of data, prior to publication, and will supply unique accession numbers which may be referenced within final article. Submitters may send their data directly to any of member databases using variety of formats, but should conform to guidelines as to minimum information required to describe data.protein-protein interaction, nonredundant, protein interaction, interaction, proteomics, metadata standard, short course, molecular interactionSCR_002805(IMEx - The International Molecular Exchange Consortium, RRID:SCR_002805)European Bioinformatics Institute European Unionrelated to: MatrixDB, MPIDB, Database of Interacting Proteins, Database of Interacting Proteins, InnateDB, IntAct, Interaction Reference Index, MPIDB, Universal Protein Resource, InnateDB, MatrixDB, BioGRID, I2D, Molecular Connections NetPro, SIB Swiss Institute of Bioinformatics, IntAct, PSI-MI, PSICQUIC, mentha, Bioconductor, listed by: OMICtools, affiliated with: MINT, works_with: CellPhoneDB, Cytoscape, IntAct, MINT, MPact: Representation of Interaction Data at MIPS, Molecular Connections NetPro, BioGRID, InnateDB, BINDReferences (2)Last checked upnif-0000-00447, OMICS_01545http://imex.sourceforge.net/
aneurISTResource, topical portal, production service resource, analysis service resource, data analysis service, standard specification, narrative resource, service resource, portal, knowledge environment, data or information resourceAn IT infrastructure for the management, integration and processing of data associated with the diagnosis and treatment of cerebral aneurysm and subarachnoid hemorrhage. This new paradigm to understand and manage cerebral aneurysms, provides an integrated decision support system to assess the risk of aneurysm rupture in patients and to optimize their treatments. aneurIST benefits patients with better diagnostics, prevention and treatment because it combines efforts of clinicians and industry. Through research clinicians gain a greater insight in aneurysm understanding, while industry will be dragged by these achievements to develop more suitable medical devices to treat the disease. This infrastructure : * Facilitate clinicians the diagnosis and study of the disease, as a result of providing a seamless access to patient data using data fusion and processing of complex information spanning from the molecular to the personal level. * Provide a better planning and personalization of minimally invasive interventional procedures for patients, after linking modern diagnostic imaging to computational tools. * Collaborate in the development, extension and exploitation of standards and protocols at all project stages. * Share biomedical knowledge providing access to a set of software tools and platforms such as aneuLink, aneuFuse, aneuRisk, aneuEndo, aneuCompute and aneuInfo. * Create awareness through scientific dissemination and collaboration. * Explore the business opportunities directly arising from aneurIST. It intends to provide an integrated decision support system to assess the risk of aneurysm rupture in patients and to optimize their treatments. Software: * aneuLink will create an IT environment with the goal of establishing a link between genomics and disease. * aneuFuse will fuse diagnostic, modelling and simulation data into a coherent representation of the patient''s condition. * aneuRisk will provide clinicians with a tool to facilitate the personalized risk assessment and guidelines establishment to treat patients. * aneuEndo will develop computational tools to optimize and customize the design of endovascular devices. * aneuInfo will enable access to clinical and epidemiological data distributed in public and project-specific protected databases. * aneuCompute will provide aneurIST with distributed computing capabilities ensuring secure data transport.gene, genetic, adult, cerebral aneurysm, cerebral brain hemorrhage, cerebral hemorrhage, cerebral parenchymal hemorrhage, cerebral hemorrhage, clinical, genomic, human, intracerebral hemorrhage, intracranial aneurysm, subarachnoid hemorrhage, risk, aneurysm rupture, patient, treatment, infrastructure, platform, genomics, disease, personalized risk assessment, bioinformatics, clinical, data management, data integration, data processing, software tool, cerebrumSCR_007427(aneurIST, RRID:SCR_007427)Pompeu Fabra University; Barcelona; Spain Cerebral aneurysm, Subarachnoid hemorrhage, AgingEuropean Union, Sixth FPPriority 2 of the Information Society Technologies ISTLast checked downnif-0000-00538http://www.cilab.upf.edu/aneurist1/
Functional Anatomy of the Cerebro-Cerebellar System (FACCS)Resource, data analysis service, production service resource, analysis service resource, database, service resource, storage service resource, data repository, data or information resourcePublic neuroscience database providing a collection of published data describing structure and structure-function relationships in one of the largest projection systems of the brain: the cerebro-cerebellar system. It also gives access to a suite of tools that allow the user to visualize and analyze any selected combination of data sets. Contact them if you are interested in contributing data. The overall goal is to improve communication of results and permit re-use of previously published data in new contexts. FACCS is a part of the Rat Brain WorkBench, a new research and development project funded by The Research Council of Norway, the Centre for Molecular Biology and Neuroscience, and the European Union. The project is directed by Jan G. Bjaalie, Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.axonal tracer, axon tracing, brain, cerebellum, cerebral cortex, cerebro-cerebellar function, cerebro-cerebellar structure, cerebro-cerebellar system, injection, injection site, labeled cells, labeled fibers, pontine nuclear complex, pontine nuclei, video, cerebellar cortexSCR_001661(Functional Anatomy of the Cerebro-Cerebellar System (FACCS), RRID:SCR_001661)University of Oslo; Oslo; Norway Centre for Molecular Biology and Neuroscience, European Union, Research Council of NorwayReferences (2)Last checked downnif-0000-02317
Proteome 2D-PAGE DatabaseResource, database, service resource, storage service resource, software resource, data repository, data or information resourceThe Proteome 2D-PAGE Database system for microbial research is a curated database for storing and investigating proteomics data. Software tools are available and for data submission, please contact the Database Curator. Established at the Max Plank Institution for Infection Biology, this system contains four interconnected databases: i.) 2D-PAGE Database: Two dimensional electrophoresis (2-DE) and mass spectrometry of diverse microorganisms and other organisms. This database currently contains 4971 identified spots and 1228 mass peaklists in 44 reference maps representing experiments from 24 different organisms and strains. The data were submitted by 84 Submitters from 24 Institutes and 12 nations. It also contains various software tools that are important in formatting and analyzing gels and mass peaks; software include: *TopSpot: Scanning the gel, editing the spots and saving the information *Fragmentation: Fragmentation of the gel image into sections *MS-Screener: Perl script to compare the similarity of MALDI-PMF peaklists *MS-Screener update: MS-Screener can be used to compare mass spectra (MALDI-MS(/MS) as well as ESI-MS/MS spectra) on the basis of their peak lists (.dta, .pkm, .pkt, or .txt files), to recalibrate mass spectra, to determine and eliminate exogenous contaminant peaks, and to create matrices for cluster analyses. *GelCali: Online calibration of the Mr- and pI-axis of 2-DE gels with mathematical regression methods ii.)Isotope Coded Affinity Tag (ICAT)-LC/MS database: Isotope Coded Affinity Tag (ICAT)-LC/MS data for Mycobacterium tuberculosis strain BCG versus H37Rv. iii.) FUNC_CLASS database: Functional classification of diverse microorganism. This database also integrates genomic, proteomic, and metabolic data. iv.) DIFF database: Presentation of differently regulated proteins obtained by comparative proteomic experiments using computerized gel image analysis.microbial research, electrophoresis, mass spectrometry, mycobacterium tuberculosis, protein regulationSCR_001678(Proteome 2D-PAGE Database, RRID:SCR_001678)Max Planck Institute for Infection Biology; Berlin; Germany BMBF, European UnionLast checked upnif-0000-02523
ConsensusPathDBResource, data or information resource, databaseAn integrative interaction database that integrates different types of functional interactions from heterogeneous interaction data resources. Physical protein interactions, metabolic and signaling reactions and gene regulatory interactions are integrated in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. With human, yeast and mouse complex functional interactions, it currently constitutes the most comprehensive publicly available interaction repository for these species. Different ways of utilizing these integrated interaction data, in particular with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways is offered.gene regulatory network, pathway, gene regulatory network, molecular interaction, interaction, gene regulation, protein interaction, genetic interaction, biochemical reaction, drug-target interaction, molecule, visualization, gene, protein, complex, metaboliteSCR_002231(ConsensusPathDB, RRID:SCR_002231)Max Planck Institute for Molecular Genetics; Berlin; Germany European Unionrelated to: BIND, BioCarta Pathways, BioGRID, CORUM, Database of Interacting Proteins, DrugBank, HPRD - Human Protein Reference Database, HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism, Integrating Network Objects with Hierarchies, InnateDB, IntAct, KEGG, MINT, MIPS Mammalian Protein-Protein Interaction Database, MatrixDB, NetPath, Research Collaboratory for Structural Bioinformatics Protein Data Bank, PDZBase, Pathway Interaction Database, PIG - Pathogen Interaction Gateway, PINdb, PharmGKB, PhosphoPOINT, PhosphoSitePlus: Protein Modification Site, Reactome, Small Molecule Pathway Database, SignaLink, SPIKE, Therapeutic Target Database, WikiPathways, listed by: OMICtoolsReferences (4)Last checked upnif-0000-02684, OMICS_01903
CYGD - Comprehensive Yeast Genome DatabaseResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceThe MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition, the data of various projects on related yeasts are used for comparative analysis.saccharomyces cerevisiae, yeast, yeast genome, genomeSCR_002289(CYGD - Comprehensive Yeast Genome Database, RRID:SCR_002289)DFG, European Union, Federal Ministry of Education Science Research and Technology, Government of the Brussels Region - Belgiumrelated to: FunSpecPMID:15608217Last checked upnif-0000-02713
Mammalian Degradome DatabaseResource, data or information resource, databaseA database of human, chimpanzee, mouse, and rat proteases and protease inhibitors, as well as as the growing number of hereditary diseases caused by mutations in protease genes. Analysis of the human and mouse genomes has allowed us to annotate 581 human, 580 chimpanzee, 667 mouse, and 655 rat protease genes. Proteases are classified in five different classes according to their mechanism of catalysis. Proteases are a diverse and important group of enzymes representing >2% of the human, chimpanzee, mouse and rat genomes. This group of enzymes is implicated in numerous physiological processes. The importance of proteases is illustrated by the existence of 99 different hereditary diseases due to mutations in protease genes. Furthermore, proteases have been implicated in multiple human pathologies, including vascular diseases, rheumatoid arthritis, neurodegenerative processes, and cancer. During the last ten years, our laboratory has identified and characterized more than 60 human protease genes. Due to the importance of proteolytic enzymes in human physiology and pathology, we have recently introduced the concept of Degradome, as the complete repertoire of proteases expressed by a tissue or organism. Thanks to the recent completion of the human, chimpanzee, mouse, and rat genome sequencing projects, we were able to analyze and compare for the first time the complete protease repertoire in those mammalian organisms, as well as the complement of protease inhibitor genes. This webpage also contains the Supplementary Material of Human and mouse proteases: a comparative genomic approach Nat Rev Genet (2003) 4: 544-558, Genome sequence of the brown Norway rat yields insights into mammalian evolution Nature (2004) 428: 493-521, A genomic analysis of rat proteases and protease inhibitors Genome Res. (2004) 14: 609-622, and Comparative genomic analysis of human and chimpanzee proteases Genomics (2005) 86: 638-647.degradome, mammalian, protease inhibitor, protease, gene, protease gene, genetic disease, proteolysis, protease structure, ancillary domain, genomic, genomeSCR_007624(Mammalian Degradome Database, RRID:SCR_007624)University of Oviedo; Oviedo; Spain Disease of proteolysisCancerDegradome-FP6 and FP7, European Union, Fundacion Lilly, Fundacion M Botin, Obra Social Cajastur, Spanish Ministry of Science and Innovationrelated to: Ancillary Domains Associated With Human and Mouse ProteasesPMID:18776217Last checked upnif-0000-02746
FunSimMatResource, data analysis service, data access protocol, production service resource, analysis service resource, database, web service, service resource, software resource, data or information resourceFunSimMat is a comprehensive resource of semantic and functional similarity values. It allows ranking disease candidate proteins for OMIM diseases and searching for functional similarity values for proteins (extracted from UniProt), and protein families (Pfam, SMART). FunSimMat provides several different semantic and functional similarity measures for each protein pair using the Gene Ontology annotation from UniProtKB and the Gene Ontology Annotation project at EBI (GOA). There are several search options available: Disease candidate prioritization: * Rank candidate proteins using any OMIM disease entry * Compare a list of proteins to any OMIM disease entry * Compare all human proteins to any OMIM disease entry Functional similarity: * Compare one protein / protein family to a list of proteins / protein families * Compare a list of GO terms to a list of proteins / protein families Semantic similarity: * For a list of GO terms, FunSimMat performs an all-against-all comparison and displays the semantic similarity values. FunSimMat provides an XML-RPC interface for performing automatic queries and processing of the results as well as a RestLike Interface. Platform: Online toolfunctional similarity value, protein family, protein similarity, semantic similarity value, similarity value, functional similarity, disease gene candidate prioritization, disease, protein, protein family, disease candidate prioritization, semantic similarity, gene ontology, visualization, annotation, database or data warehouseSCR_002729(FunSimMat, RRID:SCR_002729)Max-Planck-Institute for Informatics; Saarbrucken; Germany European Union, German National Genome Research Network, Klinische Forschergrupperelated to: Gene Ontology, listed by: Gene Ontology ToolsReferences (2)Last checked upnif-0000-02860
Genes to Cognition DatabaseResource, data or information resource, databaseDatabase of protein complexes, protocols, mouse lines, and other research products generated from the Genes to Cognition project, a project focused on understanding molecular complexes involved in synaptic transmission in the brain.allele, gene list, mouse line, human disease, phenotyping, plasticity, behavior, proteonomics, brain, cognition, cognition disorder, learning, memory, neuroscience, experimental protocol, synapse proteomics, synapseSCR_002735(Genes to Cognition Database, RRID:SCR_002735)BBSRC, EPSRC, European Union, Framework Programme, Gatsby Charitable Foundation, Human Frontiers Science Programme, MRC, NSF, Wellcome TrustLast checked downnif-0000-02864http://www.genes2cognition.org/cgi-bin/SearchView
Gene OntologyResource, organization portal, consortium, portal, project portal, knowledge environment resource, data or information resourceComputable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases.gene, product, annotation, molecular, function, cellular, biological, role, database, query, obo, gold standardSCR_002811(Gene Ontology, RRID:SCR_002811)European Union, NHGRIrelated to: GenNav, SynaptomeDB, High-Throughput GoMiner, Onto-Design, OnEx - Ontology Evolution Explorer, Avadis, GONUTS, PiNGO, Automated Microarray Pipeline, categoryCompare, globaltest, Semantic Measures Library, WegoLoc, AnimalTFDB, MEME Suite - Motif-based sequence analysis tools, Arabidopsis Hormone Database, DAVID, Arabidopsis thaliana Protein Interactome Database, TM4 Microarray Software Suite - TIGR MultiExperiment Viewer, pSTIING, GoMiner, FunSimMat, GeneSpeed- A Database of Unigene Domain Organization , Centre for Modeling Human Disease Gene Trap Resource, Patterns of Gene Expression in Drosophila Embryogenesis, Babelomics, BioPerl, GeneCruiser, GOLEM An interactive, graphical gene-ontology visualization, navigation, and analysis tool, GOToolBox Functional Investigation of Gene Datasets, Cotton EST Database, MouseNET, PLANTTFDB, T-profiler, Physico-Chemical Process, Integrated Molecular Interaction Database, SEGS, GOCat, Quantitative Enrichment of Sequence Tags, Neural-Immune Gene Ontology, INMEX, StRAnGER, QuickGO, Repository of molecular brain neoplasia data, Cardiovascular Gene Ontology Annotation Initiative, PANTHER, Short Time-series Expression Miner (STEM), DATFAP, GORetriever, Gene Ontology Browsing Utility (GOBU), GeneTools, GOSlimViewer, go-moose, Network Ontology Analysis, Onto-Compare, Onto-Express, OntoVisT, STRAP, CGAP GO Browser, COBrA, Gene Class Expression, GeneInfoViz, GOfetcher, GoFish, GOProfiler, GOanna, Manatee, Pandora - Protein ANnotation Diagram ORiented Analysis, TAIR Keyword Browser, Wandora, GOTaxExplorer, Onto-Miner, Onto-Translate, ToppGene Suite , DBD - Slim Gene Ontology, ONTO-PERL, Blip: Biomedical Logic Programming, OWL API, CLENCH, BiNGO: A Biological Networks Gene Ontology tool, CateGOrizer, FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products, ProteInOn, GeneMerge, GraphWeb, ClueGO, CLASSIFI - Cluster Assignment for Biological Inference, GOHyperGAll, FuncAssociate: The Gene Set Functionator, GOdist, FuncExpression, FunCluster, FIVA - Functional Information Viewer and Analyzer, GARBAN, GOEx - Gene Ontology Explorer, SGD Gene Ontology Slim Mapper, GOArray, SNPsandGO, GoSurfer, GOtcha, MAPPFinder, GoAnnotator, MetaGeneProfiler, OntoGate, ProfCom - Profiling of complex functionality, SerbGO, SOURCE, Ontologizer, THEA - Tools for High-throughput Experiments Analysis, Generic GO Term Mapper, GREAT: Genomic Regions Enrichment of Annotations Tool, GoBean - a Java application for Gene Ontology enrichment analysis, TXTGate, GO-Module, IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures, G-SESAME - Gene Semantic Similarity Analysis and Measurement Tools, MalaCards, FSST - Functional Similarity Search Tool, Expression Profiler, GOChase, GoPubMed, Whatizit, REViGO, WEGO - Web Gene Ontology Annotation Plot, Blast2GO, InterProScan, PubSearch, TrED, CharProtDB: Characterized Protein Database, VirHostNet: Virus-Host Network, Pathbase, GO Online SQL Environment (GOOSE), Neurobehavior Ontology, InterSpecies Analysing Application using Containers, KOBAS, ConceptWiki, GeneTerm Linker, Bioconductor, ErmineJ, Gene Ontology For Functional Analysis (GOFFA), MGI GO Browser, Comparative Toxicogenomics Database, GOEAST - Gene Ontology Enrichment Analysis Software Toolkit, Ontology Lookup Service, LexGrid, WebGestalt: WEB-based GEne SeT AnaLysis Toolkit, G:Profiler, OwlSim, GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool, YeTFaSCo, FastSemSim, RamiGO, AutismKB, GeneCodis, FunSpec, FunNet - Transcriptional Networks Analysis, PhenoM - Phenomics of yeast Mutants, agriGO, GOblet, DynGO, SeqExpress, ProbeExplorer, ECgene: Gene Modeling with Alternative Splicing, Organelle DB, Gemma, Candidate Genes to Inherited Diseases, Proteome Analyst PA-GOSUB, Network Analysis, Visualization and Graphing TORonto, GOstat, Onto-Express To Go (OE2GO), Tk-GO, EGAN: Exploratory Gene Association Networks, Spotfire, GOMO - Gene Ontology for Motifs, GFINDer: Genome Function INtegrated Discoverer, Generic GO Term Finder, Agile Protein Interactomes DataServer, AgingDB, UBERON, Algal Functional Annotation Tool, gsGator, Flash Gviewer, Cerebellar Development Transcriptome Database, PlantNATsDB - Plant Natural Antisense Transcripts DataBase, EASE: the Expression Analysis Systematic Explorer, PiGenome, L2L Microarray Analysis Tool, MeGO, CELDA Ontology, Diabetes Disease Portal, MatrixDB, Kidney and Urinary Pathway Knowledge Base, MouseCyc, Candida Genome Database, Honey Bee Brain EST Project, ECO, FlyMine, Gramene, 3D-Interologs, Biomine, UniProtKB, NCBI BioSystems Database, EBIMed, Coremine Medical, EMAGE Gene Expression Database, GeneMANIA, Yeast Search for Transcriptional Regulators And Consensus Tracking, GeneTrail, Magic, Mouse Genome Informatics (MGI), FlyBase, InterPro, InnateDB, canSAR, HPRD - Human Protein Reference Database, CRCView, Integrated Manually Extracted Annotation, LegumeIP, Renal Disease Portal, PhenoGO, DOAF, OBO, used by: NIF Data Federation, GreenPhylDB, LIPID MAPS Proteome Database, Aging Portal, Monarch Initiative, ChannelPedia, Open PHACTS, CoPub, PhenoGO, Database for Annotation Visualization and Integrated Discovery, MitoMiner, dcGO, Pathway Analysis Tool for Integration and Knowledge Acquisition, barleyGO, SynGO, Functional Annotation, listed by: BioPortal, OBO, OMICtools, affiliated with: Mouse Genome Informatics: The Gene Ontology Project, works_with: topGO, DIANA-mirPathReferences (2)Last checked upnif-0000-02915, OMICS_02278http://bioportal.bioontology.org/ontologies/GO
IMGT/GENE-DBResource, international standard specification, narrative resource, data or information resource, standard specification, databaseIMGT/GENE-DB is the comprehensive IMGT genome database for immunoglobulin (IG) and T cell receptor (TR) genes from human and mouse, and, in development, from other vertebrates. IMGT/GENE-DB is the international reference for the IG and TR gene nomenclature and works in close collaboration with the HUGO Nomenclature Committee, Mouse Genome Database and genome committees for other species. IMGT/GENE-DB allows a search of IG and TR genes by locus, group and subgroup, which are CLASSIFICATION concepts of IMGT-ONTOLOGY. Short cuts allow the retrieval gene information by gene name or clone name. Direct links with configurable URL give access to information usable by humans or programs. An IMGT/GENE-DB entry displays accurate gene data related to genome (gene localization), allelic polymorphisms (number of alleles, IMGT reference sequences, functionality, etc.) gene expression (known cDNAs), proteins and structures (Protein displays, IMGT Colliers de Perles). It provides internal links to the IMGT sequence databases and to the IMGT Repertoire Web resources, and external links to genome and generalist sequence databases. IMGT/GENE-DB manages the IMGT reference directory used by the IMGT tools for IG and TR gene and allele comparison and assignment, and by the IMGT databases for gene data annotation.SCR_006964(IMGT/GENE-DB, RRID:SCR_006964)IMGT - the international ImMunoGeneTics information system Centre National de la Recherche Scientifique, European Union, Ministere de l'Education Nationale de l'Enseignement Superieur et de la RecherchePMID:15608191Last checked downnif-0000-03012http://imgt.cines.fr, http://imgt.cines.fr/cgi-bin/GENElect.jv
INFEVERSResource, data set, service resource, data repository, storage service resource, data or information resourceRegistry for Familial Mediterranean Fever (FMF) and hereditary inflammatory disorders mutations. As of 2014, it includes twenty genes including: MEFV, MVK, TNFRSF1A, NLRP3, NOD2, PSTPIP1, LPIN2 and NLRP7, and contains over 1338 sequence variants. Confidential data, simple and complex alleles are accepted. For each gene, a menu offers: 1) a tabular list of the variants that can be sorted by several parameters; 2) a gene graph providing a schematic representation of the variants along the gene; 3) statistical analysis of the data according to the phenotype, alteration type, and location of the mutation in the gene; 4) the cDNA and gDNA sequences of each gene, showing the nucleotide changes along the sequence, with a color-based code highlighting the gene domains, the first ATG, and the termination codon; and 5) a download menu making all tables and figures available for the users, which, except for the gene graphs, are all automatically generated and updated upon submission of the variants. The entire database was curated to comply with the HUGO Gene Nomenclature Committee (HGNC) and HGVS nomenclature guidelines, and wherever necessary, an informative note was provided.sequence variant, mutation, allele, genetics, dna, rna, protein, disease, heredity, inflammation, gene, function, phenotype, complex allele, simple allele, exon, intron, cdna sequence, genomic sequence, gdnaSCR_007738(INFEVERS, RRID:SCR_007738)Familial Mediterranean Fever, Auto-inflammatory Disorder, Hereditary Auto-inflammatory DisorderEuropean Unionrelated to: Human Genome Variation Society, HGNC, listed by: re3data.orgReferences (3)Last checked upnif-0000-03022http://fmf.igh.cnrs.fr/infevers
IntActResource, service resource, data or information resource, data repository, storage service resource, databaseOpen source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions. Direct user submissions of molecular interaction data are encouraged, which may be deposited prior to publication in a peer-reviewed journal. The IntAct Database contains (Jun. 2014): * 447368 Interactions * 33021 experiments * 12698 publications * 82745 Interactors IntAct provides a two-tiered view of the interaction data. The search interface allows the user to iteratively develop complex queries, exploiting the detailed annotation with hierarchical controlled vocabularies. Results are provided at any stage in a simplified, tabular view. Specialized views then allows "zooming in" on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available.protein domain, motif, protein interaction, molecular interaction, interaction, protein, binary interaction, complex, data set, protein-protein interaction, pathway, small molecule-protein, nucleic acid-protein, small molecule, nucleic acid, protein binding, chromatin, cancer, apoptosis, molecular biology, virus, source code, isoform, gold standardSCR_006944(IntAct, RRID:SCR_006944)European Bioinformatics Institute European Unionrelated to: 3D-Interologs, IMEx - The International Molecular Exchange Consortium, MPIDB, TissueNet - The Database of Human Tissue Protein-Protein Interactions, InteroPorc, Interaction Reference Index, Pathway Commons, ConsensusPathDB, FlyMine, IMEx - The International Molecular Exchange Consortium, Integrated Molecular Interaction Database, VirHostNet: Virus-Host Network, PSICQUIC Registry, Universal Protein Resource, SIB Swiss Institute of Bioinformatics, I2D, InnateDB, MatrixDB, MBInfo, AgBase, Cardiovascular Gene Ontology Annotation Initiative, PSI-MI, Monarch Initiative, Agile Protein Interactomes DataServer, used by: ChannelPedia, MINT, Pathway Analysis Tool for Integration and Knowledge Acquisition, listed by: 3DVC, re3data.org, OMICtools, works_with: IMEx - The International Molecular Exchange ConsortiumReferences (5)Last checked upnif-0000-03026, OMICS_01918
IntEnz- Integrated relational Enzyme databaseResource, data or information resource, databaseIntEnz (Integrated relational Enzyme database) is a freely available resource focused on enzyme nomenclature. IntEnz is created in collaboration with the Swiss Institute of Bioinformatics (SIB). This collaboration is responsible for the production of the ENZYME resource. IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions.enzyme categories, enzyme classification, enzyme nomenclature, enzyme reaction categories, enzyme, gold standardSCR_002992(IntEnz- Integrated relational Enzyme database, RRID:SCR_002992)European Bioinformatics Institute , SIB Swiss Institute of Bioinformatics European Unionrelated to: ENZYMELast checked upnif-0000-03028
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