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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: Sep 14, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
Glyco-CDResource, data set, data or information resourceManually curated, comprehensive repository of clusters of differentiation (CDs) which are a) defined as distinct oligosaccharide sequences as part of either glycoproteins and/or glycosphingolipids and b) defined as proteins which have carbohydrate recognition sites (CRDs) or as carbohydrate binding lectins. The data base is generated by exhaustive search of literature and other online data banks related to carbohydrates and proteins. This data bank is the beginning of an effort to provide concise, relevant information of carbohydrate-related CDs in a user- friendly manner. For users convenience the data bank under menu browse of GlycoCD is arranged in two section namely carbohydrate recognition CDs (CRD CD) and glycan CD. The carbohydrate recognition CD part is the collection of proteins which recognize glycan structures by means of the CRDs. Glycan CD is the part in which CDs are summarized which characterize specific oligosaccharide structures. The GlycoCD databank has been developed with the aim to assist the immunologist, cell biologist as well as the clinician who wants to keep up with the present knowledge in this field of glycobiology.carbohydrate, glycobiology, glycan, lectin, antigen, interaction, protein, cell surface molecule, microarray, carbohydrate recognition, cluster of differentiation, oligosaccharide sequence, glycoprotein, glycosphingolipid, carbohydrate recognition site, leukocyte, antibody, endothelial cell, epithelial cellSCR_001574(Glyco-CD, RRID:SCR_001574)glycosciences.de European UnionPMID:22847935Last checked downnlx_152887http://www.glycosciences.de//Glyco-CD/
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
Genes to Cognition - Biological ResourcesResource, biomaterial supply resource, material resource, organism supplierBiological resources, including gene-targeting vectors, ES cell lines, antibodies, and transgenic mice, generated for its phenotyping pipeline as part of the Genes to Cognition research program are freely-available to interested researchers. Available Transgenic Mouse Lines: *Hras1 (H-ras) knockout,C57BL/6J *Dlg4 (PSD-95) knockout,129S5 *Dlg4 (PSD-95) knockout,C57BL/6J *Dlg3 (SAP102) knockout with hprt mutation,129S5 *Dlg3 (SAP102) knockout (wild-type for hprt,C57BL/6J *Syngap1 (SynGAP) knockout (from 8.24 clone), C57BL/6J *Dlg4 (PSD-95) guanylate kinase domain deletion, C57BL/6J *Ptk2 (FAK) knockout,C57BL/6Jtransgenic, mutant mouse strain, c57bl/6j, 129s5, transgenic mouse line, vector, es cell line, transgenic mouseSCR_001675(Genes to Cognition - Biological Resources, RRID:SCR_001675)University of Edinburgh; Scotland; United Kingdom BBSRC, EPSRC, European Union, Framework Programme, Gatsby Charitable Foundation, Human Frontiers Science Programme, MRC, NSF, Wellcome Trustlisted by: One Mind Biospecimen Bank ListingLast checked downnif-0000-10163http://www.genes2cognition.org/mice_resources/http://www.genes2cognition.org/resources.html
Kidney and Urinary Pathway Knowledge BaseResource, data analysis service, production service resource, analysis service resource, data set, service resource, storage service resource, data repository, data or information resourceA collection of omics datasets (mRNA, proteins and miRNA) that have been extracted from PubMed and other related renal databases, all related to kidney physiology and pathology giving KUP biologists the means to ask queries across many resources in order to aggregate knowledge that is necessary for answering biological questions. Some microarray raw datasets have also been downloaded from the Gene Expression Omnibus and analyzed by the open-source software GeneArmada. The Semantic Web technologies, together with the background knowledge from the domain's ontologies, allows both rapid conversion and integration of this knowledge base. SPARQL endpoint http://sparql.kupkb.org/sparql The KUPKB Network Explorer will help you visualize the relationships among molecules stored in the KUPKB. A simple spreadsheet template is available for users to submit data to the KUPKB. It aims to capture a minimal amount of information about the experiment and the observations made.kidney, urinary, urine, pathway, molecule, visualizer, gene, protein, mirna, metabolite, mrna, microarray, ortholog, rdf, renal cell, anatomy, animal model, disease, sparql, proteomics, ontology, biomarker, gene expression, physiology, pathologySCR_001746(Kidney and Urinary Pathway Knowledge Base, RRID:SCR_001746)University of Manchester; Manchester; United Kingdom , National Institute of Health and Medical Research; Rennes; France Kidney diseaseEuropean Union, FP7, ICT-2007.4.4 e-LICO projectrelated to: NIDDK Information Network, Gene Expression Omnibus, Gene Ontology, KEGG, submitted by: NIDDK Information NetworkPMID:21624162Last checked downnlx_154134http://www.e-lico.eu/kupkb
Arabidopsis ReactomeResource, data or information resource, databaseCurated database of core pathways and reactions in plant biology that covers biological pathways ranging from the basic processes of metabolism to high-level processes such as cell cycle regulation. While it is targeted at Arabidopsis pathways, it also includes many biological events from other plant species. This makes the database relevant to the large number of researchers who work on other plants. Arabidopsis Reactome currently contains both in-house curated pathways as well as imported pathways from AraCyc and KEGG databases. All the curated information is backed up by its provenance: either a literature citation or an electronic inference based on sequence similarity. Their ontology ensures that the various events are linked in an appropriate spatial and temporal context.pathway, reaction, biological processSCR_002063(Arabidopsis Reactome, RRID:SCR_002063)John Innes Centre; Norwich; United Kingdom European Unionuses: AraCyc, KEGG, listed by: 3DVCLast checked downnif-0000-20812
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
GenomEUtwinResource, disease-related portal, topical portal, database, biomaterial supply resource, research forum portal, portal, material resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Study of genetic and life-style risk factors associated with common diseases based on analysis of European twins. The population cohorts used in the Genomeutwin study consist of Danish, Finnish, Italian, Dutch, English, Australian and Swedish twins and the MORGAM population cohort. This project will apply and develop new molecular and statistical strategies to analyze unique European twin and other population cohorts to define and characterize the genetic, environmental and life-style components in the background of health problems like obesity, migraine, coronary heart disease and stroke, representing major health care problems worldwide. The participating 8 twin cohorts form a collection of over 0.6 million pairs of twins. Tens of thousands of DNA samples with informed consents for genetic studies of common diseases have already been stored from these population-based twin cohorts. Studies targeted to cardiovascular traits are now being undertaken in MORGAM, a prospective case-cohort study. MORGAM cohorts include approximately 6000 individuals, drawn from population-based cohorts consisting of more than 80 000 participants who have donated DNA samples.genetic, environment, lifestyle, gene, diseaseSCR_002843(GenomEUtwin, RRID:SCR_002843)University of Helsinki; Helsinki; Finland TwinEuropean Unionrelated to: KI Biobank - TwinGene, listed by: One Mind Biospecimen Bank ListingLast checked downnif-0000-25218
MicroArray and Gene Expression Markup LanguageResource, narrative resource, interchange format, markup language, standard specification, data or information resourceA language / data exchange format designed to describe and communicate information about microarray based experiments that is based on XML and can describe microarray designs, microarray manufacturing information, microarray experiment setup and execution information, gene expression data and data analysis results. MAGE-ML has been automatically derived from Microarray Gene Expression Object Model (MAGE-OM), which is developed and described using the Unified Modelling Language (UML) -- a standard language for describing object models. Descriptions using UML have an advantage over direct XML document type definitions (DTDs), in many respects. First they use graphical representation depicting the relationships between different entities in a way which is much easier to follow than DTDs. Second, the UML diagrams are primarily meant for humans, while DTDs are meant for computers. Therefore MAGE-OM should be considered as the primary model, and MAGE-ML will be explained by providing simplified fragments of MAGE-OM, rather then XML DTD or XML Schema. (from the description by Ugis Sarkans) The field of gene expression experiments has several distinct technologies that a standard must include. These include single vs. dual channel experiments, cDNA vs. oligonucleotides. Because of these different technologies and different types of gene expression experiments, it is not expected that all aspects of the standard will be used by all organizations. Given the massive amount of data associated with a single set of experiments, it is felt that Extensible Markup Language (XML) is the best way to describe the data. The use of a Document Type Definition (DTD) allows a well-defined tag set, a vocabulary, to describe the domain of gene expression experiments. It also has the virtue of compressing very well so that files in an XML format compress to ten percent of their original size. XML is now widely accepted as a data exchange format across multiple platforms.microarray, gene expression, bioinformaticsSCR_003023(MicroArray and Gene Expression Markup Language, RRID:SCR_003023) MAGE , European Bioinformatics Institute European Union, TEMBLOR projectrelated to: MADAM, MIAME, RNA Abundance Database, listed by: 3DVCLast checked downnif-0000-30390
JASPARResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceDatabase of a curated, non-redundant set of profiles derived from published collections of experimentally defined transcription factor binding sites for multicellular eukaryotes. It is useful to scientists seeking models for specific factors or structural classes, or if experimental evidence is paramount. The prime difference to similar resources (TRANSFAC, TESS etc) consist of the open data access, non-redundancy and quality: JASPAR CORE is a smaller set that is non-redundant and curated. JASPAR is a collection of transcription factor DNA-binding preferences, modeled as matrices. These can be converted into Position Weight Matrices (PWMs or PSSMs), used for scanning genomic sequences. JASPAR is the only database with this scope where the data can be used with no restrictions (open-source). The database is complemented by a web interface for browsing, searching and subset selection, an online sequence analysis utility and a suite of programming tools for genome-wide and comparative genomic analysis of regulatory regions. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval.structural class, transcription factor binding site, profile, regulatory region, genome, genomic, matrix, transcription factor, binding site, dnaSCR_003030(JASPAR, RRID:SCR_003030) Karolinska Institutet; Stockholm; Sweden , University of Copenhagen; Copenhagen; Denmark Carlsberg Foundation, EMBRACEa Sixth Framework Network of Excellence, European Union, Novo Nordisk Foundation, Research Council of Norway, Sars Centrerelated to: Babelomics, listed by: OMICtools, re3data.orgReferences (3)Last checked downnif-0000-03061, OMICS_00538http://129.177.120.189/cgi-bin/jaspar2010/jaspar_db.pl, http://jaspar.cgb.ki.se
Biobanking and Biomolecular Resources Research Infrastructure (BBMRI)Resource, topical portal, database, biomaterial supply resource, portal, material resource, data or information resourceBBMRI is a pan-European and internationally broadly accessible research infrastructure and a network of existing and de novo biobanks and biomolecular resources. The infrastructure will include samples from patients and healthy persons, representing different European populations (with links to epidemiological and health care information), molecular genomic resources and biocomputational tools to optimally exploit this resource for global biomedical research. During the past 3 years BBMRI has grown into a 53-member consortium with over 280 associated organizations (largely biobanks) from over 30 countries, making it the largest research infrastructure project in Europe. During the preparatory phase the concept of a functional pan-European biobank was formulated and has now been presented to Member States of the European Union and for associated states for approval and funding. BBMRI will form an interface between specimens and data (from patients and European populations) and top-level biological and medical research. This can only be achieved through a distributed research infrastructure with operational units in all participating Member States. BBMRI will be implemented under the ERIC (European Research Infrastructure Consortium) legal entity. BBMRI-ERIC foresees headquarters (central coordination) in Graz, Austria, responsible for coordination of the activities of National Nodes established in participating countries. BBMRI is in the process of submitting its application to the European Commission for a legal status under the ERIC regulation, with an expected start date at the end of 2011. Major synergism, gain of statistical power and economy of scale will be achieved by interlinking, standardizing and harmonizing - sometimes even just cross-referencing - a large variety of well-qualified, up-to date, existing and de novo national resources. The network should cover (1) major European biobanks with blood, serum, tissue or other biological samples, (2) molecular methods resource centers for human and model organisms of biomedical relevance, (3) and biocomputing centers to ensure that databases of samples in the repositories are dynamically linked to existing databases and to scientific literature as well as to statistical expertise. Catalog of European Biobanks www.bbmriportal.eu Username: guest / Password: catalogue The catalogue is intended to be used as a reference for scientists seeking information about biological samples and data suitable for their research. The BBMRI catalogue of European Biobanks provides a high-level description of Europe''s biobanks characteristics using a portal solution managing metadata and aggregate data of biobanks. The catalogue can be queried by country, by biobank, by ICD-groups, by specimen types, by specific strengths, by funding and more. A search function is available for all data.blood, serum, tissue, dna, cdna, rna, plasma, cell line, bodily fluid, urine, blood cell isolate, buffy coat, patient, healthy, normal, cryopreserved, paraffin embedded, clinical dataSCR_004226(Biobanking and Biomolecular Resources Research Infrastructure (BBMRI), RRID:SCR_004226)Medical University of Graz; Graz; Austria All, Patient, Healthy, NormalEuropean Unionrelated to: BioResource Impact Factor, German Biobank Registry, BioMedBridges, Biological Resource Centre - National Institute for Cancer Research, listed by: One Mind Biospecimen Bank ListingLast checked downnlx_24389http://www.bbmri.eu/index.php
Erasmus MC Tissue BankResource, biomaterial supply resource, service resource, material resource, tissue bankThe Erasmus MC Virtual Tissue Bank is embedded in the department of Pathology. The collection is meant for medical research purposes only. This concerns a typical clinical based pathology biobank. Tissue samples left over from surgical resection specimen are stored under liquid nitrogen and can be requested by Erasmus MC scientists for medical scientific experiments. An application has been developed to enable scientists to search the collection on-line and request tissue samples over the Erasmus MC Intranet. Every request shall be judged according to procedures determined by the Erasmus MC Tissue Bank. A growing need is anticipated for large collections of well-diagnosed fresh frozen tumor tissue and, if available, corresponding pre-malignant and normal tissue samples. Scientific research on patient residual material has to comply with strict rules and regulations. Equipment The Erasmus MC Tissue bank manages the PALM microdissection laser for the center for Biomics, which is available through the center for Biomics ONLY after having followed an introduction course. Additionally, a complete TMA (Tissue Micro Array) platform, fully funded by the Josephine Nefkens Stichting, consisting of a Beecher Automated Tissue Arrayer ATA 27 and a Virtual Microscope or Nanozoomer from Hamamatsu and Medical Solutions with TMA analyses software strongly supports translational research on tissue samples. Complete histologic Images from the Virtual Microscope are available within the Erasmus MC Intranet or available on the Internet either by overview or a direct example.clinical, tumor tissue, tissue, pre-malignant tissue, normal tissue, liquid nitrogen, fresh frozen, frozen, tumorSCR_004945(Erasmus MC Tissue Bank, RRID:SCR_004945)TumorEuropean Unionlisted by: One Mind Biospecimen Bank ListingLast checked downnlx_91504http://www.erasmusmc.nl/pathologie/clinicalpathology/tissuebank/161390/
FIVA - Functional Information Viewer and AnalyzerResource, software resource, software application, data processing softwareFunctional Information Viewer and Analyzer (FIVA) aids researchers in the prokaryotic community to quickly identify relevant biological processes following transcriptome analysis. Our software is able to assist in functional profiling of large sets of genes and generates a comprehensive overview of affected biological processes. Currently, seven different modules containing functional information have been implemented: (i) gene regulatory interactions, (ii) cluster of orthologous groups (COG) of proteins, (iii) gene ontologies (GO), (iv) metabolic pathways (v) Swiss Prot keywords, (vi) InterPro domains - and (vii) generic functional categories. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatiblegene, gene expression, gene expression pattern, functional profile, statistical analysis, metabolic pathway, gene ontology, function, ortholog, gene regulatory interaction, biological process, transcriptome, visualization, analysisSCR_005776(FIVA - Functional Information Viewer and Analyzer, RRID:SCR_005776)MolGen Center IOP Genomics, European Union, industrial partners in the NWO-BMI project number 050.50.206 on Computational Genomics of Prokaryotes, Netherlands Organization for Scientific Researchrelated to: Gene Ontology, listed by: Gene Ontology ToolsPMID:17237043Last checked downnlx_149245
GoAnnotatorResource, analysis service resource, data analysis service, service resource, production service resourceA tool for assisting the GO annotation of UniProt entries by linking the GO terms present in the uncurated annotations with evidence text automatically extracted from the documents linked to UniProt entries. Platform: Online tooltext mining, protein, gene ontology, annotationSCR_005792(GoAnnotator, RRID:SCR_005792)University of Lisbon; Lisbon; Portugal European Unionrelated to: Gene Ontology, Universal Protein Resource, listed by: Gene Ontology ToolsPMID:17181854Last checked downnlx_149303
Expression ProfilerResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice.other analysis, cluster, analysis, visualization, gene expression, genomic, gene ontology, gene association, microarray, protein-protein interaction, geneSCR_005821(Expression Profiler, RRID:SCR_005821)European Bioinformatics Institute Estonian Science Foundation, European Union, Wellcome Trustrelated to: Gene Ontology, listed by: Gene Ontology ToolsPMID:15215431Last checked downnlx_149323
KI Biobank - TwinGeneResource, disease-related portal, topical portal, research forum portal, biomaterial supply resource, portal, material resource, data or information resourceIn collaboration with GenomeEUtwin, the TwinGene project investigates the importance of quantitative trait loci and environmental factors for cardiovascular disease. It is well known that genetic factors are of considerable importance for some familial lipid syndromes and that Type A Behavior pattern and increased lipid levels infer increased risk for cardiovascular disease. It is furthermore known that genetic factors are of importance levels of blood lipid biomarkers. The interplay of genetic and environmental effects for these risk factors in a normal population is less well understood and virtually unknown for the elderly. In the TwinGene project twins born before 1958 are contacted to participate. Health and medication data are collected from self-reported questionnaires, and blood sampling material is mailed to the subject who then contacts a local health care center for blood sampling and a health check-up. In the simple health check-up, height, weight, circumference of waist and hip, and blood pressure are measured. Blood is sampled for DNA extraction, serum collection and clinical chemistry tests of C-reactive protein, total cholesterol, triglycerides, HDL and LDL cholesterol, apolipo??protein A1 and B, glucose and HbA1C. The TwinGene cohort contains more than 10000 of the expected final number of 16000 individuals. Molecular genetic techniques are being used to identify Quantitative Trait Loci (QTLs) for cardiovascular disease and biomarkers in the TwinGene participants. Genome-wide linkage and association studies are ongoing. DZ twins have been genome-scanned with 1000 STS markers and a subset of 300 MZ twins have been genome-scanned with Illumina 317K SNP platform. Association of positional candidate SNPs arising from these genomscans are planned. The TwinGene project is associated with the large European collaboration denoted GenomEUtwin (www.genomeutwin.org, see below) which since 2002 has aimed at gathering genetic data on twins in Europe and setting up the infrastructure needed to enable pooling of data and joint analyses. It has been the funding source for obtaining the genome scan data. Types of samples: * EDTA whole blood * DNA * Serum Number of sample donors: 12 044 (sample collection completed)quantitative trait loci, environmental factor, cardiovascular disease, environment, genetic, gene, lipid syndrome, lipid, health, medication, questionnaire, c-reactive protein, total cholesterol, triglyceride, hdl, ldl, cholesterol, apolipo-protein a1, apolipo-protein b, glucose, hba1c, genome-wide linkage study, genome-wide association study, genomeSCR_006006(KI Biobank - TwinGene, RRID:SCR_006006)Karolisnka Biobank TwinEuropean Union, NIH, SSF, VRrelated to: GenomEUtwin, Swedish Twin Registry, listed by: One Mind Biospecimen Bank ListingLast checked downnlx_151387http://ki.se/ki/jsp/polopoly.jsp?d=29354&a=31600&l=en
Sanger Mouse Resources PortalResource, database, biomaterial supply resource, production service resource, material service resource, service resource, cell repository, material resource, biomaterial manufacture, data or information resourceDatabase of mouse research resources at Sanger: BACs, targeting vectors, targeted ES cells, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen. The Wellcome Trust Sanger Institute generates, characterizes, and uses a variety of reagents for mouse genetics research. It also aims to facilitate the distribution of these resources to the external scientific community. Here, you will find unified access to the different resources available from the Institute or its collaborators. The resources include: 129S7 and C57BL6/J bacterial artificial chromosomes (BACs), MICER gene targeting vectors, knock-out first conditional-ready gene targeting vectors, embryonic stem (ES) cells with gene targeted mutations or with retroviral gene trap insertions, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen.bacterial artificial chromosome, vector, embryonic stem cell, mutant mouse line, phenotype, 129s7, c57bl6/j, gene, knockout, gene expression, genetics, chromosome, mutant, mouse line, mammal, marker symbolSCR_006239(Sanger Mouse Resources Portal, RRID:SCR_006239)Wellcome Trust Sanger Institute; Hinxton; United Kingdom European Union, NCRR, NHGRI, Wellcome Trustrelated to: Ensembl, Monarch Initiative, listed by: One Mind Biospecimen Bank ListingLast checked downnlx_151819
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
Genes to Cognition: Neuroscience Research ProgrammeResource, blog, topical portal, software application, narrative resource, portal, software resource, training material, data or information resourceA neuroscience research program that studies genes, the brain and behavior in an integrated manner, established to elucidate the molecular mechanisms of learning and memory, and shed light on the pathogenesis of disorders of cognition. Central to G2C investigations is the NMDA receptor complex (NRC/MASC), that is found at the synapses in the central nervous system which constitute the functional connections between neurons. Changes in the receptor and associated components are thought to be in a large part responsible for the phenomenon of synaptic plasticity, that may underlie learning and memory. G2C is addressing the function of synapse proteins using large scale approaches combining genomics, proteomics and genetic methods with electrophysiological and behavioral studies. This is incorporated with computational models of the organization of molecular networks at the synapse. These combined approaches provide a powerful and unique opportunity to understand the mechanisms of disease genes in behavior and brain pathology as well as provide fundamental insights into the complexity of the human brain. Additionally, Genes to Cognition makes available its biological resources, including gene-targeting vectors, ES cell lines, antibodies, and transgenic mice, generated for its phenotyping pipeline. The resources are freely-available to interested researchers.electrophysiological, es cell, functional, gene, gene-target vector, genetic, 1295s, allele, antibody, behavior, behavioral, brain, c57bl/6j, central nervous system, clone, cognition, computation, connection, deletion, disease, disorder, dlg3, dlg4, domain, genomic, guanylate kinase, hprt gene, hras1, human, knockout, learning, mechanism, memory, model, molecular, mouse, mutation, network, neuron, neuroscience, nmda receptor complex, pathogenesis, phenotyping, protein, proteomics, ptk2, strain, synapse, synaptic plasticity, syngap1, transgenic, modelSCR_007121(Genes to Cognition: Neuroscience Research Programme, RRID:SCR_007121)Wellcome Trust Sanger Institute; Hinxton; United Kingdom BBSRC, EPSRC, European Union, Framework Programme, Gatsby Charitable Foundation, Human Frontiers Science Programme, MRC, NSF, Wellcome Trustlisted by: 3DVCLast checked downnif-0000-10235
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/
BovMap DatabaseResource, service resource, data or information resource, data repository, storage service resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Database containing information on the cattle genome comprising loci list, phenes list, homology query, cattle maps, gene list, and chromosome homology. The objective of BovMap is to develop a set of anchored loci for the cattle genome map. In total, 58 clones were hybridized with chromosomes and identified loci on 22 of the 31 different bovine chromosomes. Three clones contained satellite DNA. Two or more markers were placed on 12 chromosomes. Sequencing of the microsatellites and flanking regions was performed directly from 43 cosmids, as previously reported. Primers were developed for 39 markers and used to describe the polymorphism associated with the corresponding loci. Users are also allowed to summit their own data for Bovmap. An integrated cytogenetic and meiotic map of the bovine genome has also been developed around the Bovmap database. One objective that Bovmap uses as the mapping strategy for the bovine genome uses large insert clones as a tool for physical mapping and as a source of highly polymorphic microsatellites for genetic typing.genetic, bovine, cattle, chromosome, clone, cosmid, cow, cytogenetic, dna, genome, homology, locus, meiotic, phene, polymorphism, sequence, map, geneSCR_008145(BovMap Database, RRID:SCR_008145)INRA - French National Institute for Agricultural Research; Paris; France European UnionLast checked downnif-0000-20968
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  1. RRID Portal Resources

    Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.

  2. Navigation

    You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.

  3. Logging in and Registering

    If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.

  4. Searching

    Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:

    1. Use quotes around phrases you want to match exactly
    2. You can manually AND and OR terms to change how we search between words
    3. You can add "-" to terms to make sure no results return with that term in them (ex. Cerebellum -CA1)
    4. You can add "+" to terms to require they be in the data
    5. Using autocomplete specifies which branch of our semantics you with to search and can help refine your search
  5. Collections

    If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.

  6. Facets

    Here are the facets that you can filter the data by.

  7. Further Questions

    If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.