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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
eVOCResource, ontology, data or information resource, controlled vocabularyTHIS RESOURCE IS NO LONGER SUPPORTED, documented September 6, 2016. Set of orthogonal controlled vocabularies that unifies gene expression data by facilitating a link between the genome sequence and expression phenotype information. The system associates labelled target cDNAs for microarray experiments, or cDNA libraries and their associated transcripts with controlled terms in a set of hierarchical vocabularies. eVOC consists of four orthogonal controlled vocabularies suitable for describing the domains of human gene expression data including Anatomical System, Cell Type, Pathology and Developmental Stage. The four core eVOC ontologies provide an appropriate set of detailed human terms that describe the sample source of human experimental material such as cDNA and SAGE libraries. These expression terms are linked to libraries and transcripts allowing the assessment of tissue expression profiles, differential gene expression levels and the physical distribution of expression across the genome. Analysis is currently possible using EST and SAGE data, with microarray data being incorporated. The eVOC data is increasingly being accepted as a standard for describing gene expression and eVOC ontologies are integrated with the Ensembl EnsMart database, the Alternate Transcript Diversity Project and the UniProt Knowledgebase. Several groups are currently working to provide shared development of this resource such that it is of maximum use in unifying transcript expression information.mouse, mapping, cdna, development, microarray, expression, expressed sequence, anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation, treatment, gene expression, genome sequence, expression phenotype, genome, sequence, phenotype, anatomical system, cell type, pathology, anatomySCR_010704(eVOC, RRID:SCR_010704)University of the Western Cape; Bellville; South Africa European Union, South African Department of Arts Culture Science and Technology, South African National Research Foundation, Wellcome Trustrelated to: OBO, Bgee: a dataBase for Gene Expression EvolutionPMID:12799354Last checked downnlx_84448
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 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_154134
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-0000-02864
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
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 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_24389
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_91504
VectorBaseResource, service resource, data or information resource, data repository, storage service resource, databaseBioinformatics Resource Center for invertebrate vectors. Provides web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of biowarfare or bioterrorism or causing emerging or re-emerging diseases.blast, clustalw, hmmer, vector, genomics, genome, sequence, population, insecticide resistance, annotation, microarray, gene expression, anatomy, pathogen, human, transcript, transcriptome, protein, proteome, mitochondria sequence, bioinformatics resource center, pathogen, arthropoda, vector control, ontology, software, source code, mitochondrial sequence, data analysis service, image collectionSCR_005917(VectorBase, RRID:SCR_005917)European Bioinformatics Institute , University of Notre Dame; Indiana; USA European Union, Evimalar network of excellence, INFRAVEC, NIAIDrelated to: ClustalW2, AnoBase: An Anopheles database, Hmmer, recommended by: National Library of Medicine, BRAIN Initiative, listed by: re3data.orgReferences (5)Last checked downnif-0000-03624
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 (, 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_151387
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-0000-00538
Chernobyl Tissue BankResource, biomaterial supply resource, material resourceThe CTB (Chernobyl Tissue Bank) is an international cooperation that collects, stores and disseminates biological samples from tumors and normal tissues from patients for whom the aetiology of their disease is known - exposure to radioiodine in childhood following the accident at the Chernobyl power plant. The main objective of this project is to provide a research resource for both ongoing and future studies of the health consequences of the Chernobyl accident. It seeks to maximize the amount of information obtained from small pieces of tumor by providing multiple aliquots of RNA and DNA extracted from well documented pathological specimens to a number of researchers world-wide and to conserve this valuable material for future generations of scientists. It exists to promote collaborative, rather than competitive, research on a limited biological resource. Tissue is collected to an approved standard operating procedure (SOP) and is snap frozen; the presence or absence of tumor is verified by frozen section. A representative paraffin block is also obtained for each case. Where appropriate, we also collect fresh and paraffin-embedded tissue from loco-regional metastases. Currently we do not issue tissue but provide extracted nucleic acid, paraffin sections and sections from tissue microarrays from this material. The project is coordinated from Imperial College, London and works with Institutes in the Russian Federation (the Medical Radiological Research Centre in Obninsk) and Ukraine (the Institute of Endocrinology and Metabolism in Kiev) to support local scientists and clinicians to manage and run a tissue bank for those patients who have developed thyroid tumors following exposure to radiation from the Chernobyl accident. Belarus was also initially included in the project, but is currently suspended for political reasons.SCR_010662(Chernobyl Tissue Bank, RRID:SCR_010662)Imperial College London; London; United Kingdom Tumor, Normal, Exposure to radioiodine in childhood following the accident at the Chernobyl power plantEuropean Union, NCI, Sasakawa Memorial Health Foundationlisted by: One Mind Biospecimen Bank ListingLast checked upnlx_70828
MINTResource, data or information resource, databaseA database that focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The curated data can be analyzed in the context of the high throughput data and viewed graphically with the MINT Viewer. This collection of molecular interaction databases can be used to search for, analyze and graphically display molecular interaction networks and pathways from a wide variety of species. MINT is comprised of separate database components. HomoMINT, is an inferred human protein interatction database. Domino, is database of domain peptide interactions. VirusMINT explores the interactions of viral proteins with human proteins. The MINT connect viewer allows you to enter a list of proteins (e.g. proteins in a pathway) to retrieve, display and download a network with all the interactions connecting them.protein-protein interaction, protein, interaction, virus, peptide, organelle co-localization, pathway, molecular interaction, papillomavirus, epstein-barr virus, hepatitis b virus, hepatitis c virus, human adenovirus, human herpesvirus, human immunodeficiency virus, influenza a virus, vaccinia virus, simian virus 40, virus strains, virus protein, orthologous protein, network, proteomics, orthologSCR_001523(MINT, RRID:SCR_001523)University of Rome Tor Vergata; Rome; Italy AIRC Associazione Italiana per la Ricerca sul Cancro, ENFIN, European Union, HUPO Proteomics Standards Initiative, IMEx - The International Molecular Exchange Consortium, Interaction Proteome Projectrelated to: MPIDB, TissueNet - The Database of Human Tissue Protein-Protein Interactions, InteroPorc, Interaction Reference Index, Pathway Commons, ConsensusPathDB, VirusMINT, PSICQUIC Registry, Agile Protein Interactomes DataServer, uses: IntAct, PSI-MI, listed by:, affiliated with: IMEx - The International Molecular Exchange Consortium, works_with: IMEx - The International Molecular Exchange ConsortiumReferences (8)Last checked upnlx_152821
MatrixDBResource, service resource, data or information resource, production service resource, databaseFreely available database focused on interactions established by extracellular proteins and polysaccharides, taking into account the multimeric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data. It includes interaction data extracted from the literature by manual curation, and offers access to relevant data involving extracellular proteins provided by the IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database. The database reports mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. Interactions with lipids and cations are also reported. MatrixDB is focused on mammalian interactions, but aims to integrate interaction datasets of model organisms when available. MatrixDB provides direct links to databases recapitulating mutations in genes encoding extracellular proteins, to UniGene and to the Human Protein Atlas that shows expression and localization of proteins in a large variety of normal human tissues and cells. MatrixDB allows researchers to perform customized queries and to build tissue- and disease-specific interaction networks that can be visualized and analyzed with Cytoscape or Medusa. Statistics (2013): 2283 extracellular matrix interactions including 2095 protein-protein and 169 protein-glycosaminoglycan interactions.extracellular, protein fragment, biomolecule, cation, cleavage, collagen, glycosaminoglycan, human, interaction, laminin, lipid, mammalian, matricryptin, matrikin, matrix, molecule, monomer, mulimerization, multimer, polysaccharide, protein, protein-carbohydrate interaction, protein-protein interaction, recognition, thrombospondin, interactome, extracellular protein, protein-polysaccharide interaction, extracellular interaction, molecular interaction, model organism, inorganic, small molecule-protein, small molecule, extracellular matrix protein, protein-glycosaminoglycan interactionSCR_001727(MatrixDB, RRID:SCR_001727)Claude Bernard University Lyon 1; Lyon; France European Unionrelated to: IMEx - The International Molecular Exchange Consortium, Gene Ontology, PSI-MI, HPRD - Human Protein Reference Database, Interaction Reference Index, ConsensusPathDB, IMEx - The International Molecular Exchange Consortium, PSICQUIC Registry, IntAct, listed by: re3data.orgReferences (2)Last checked upnif-0000-10226
InteroPorcResource, source code, data analysis service, data analysis software, data processing software, database, analysis service resource, software application, production service resource, service resource, software resource, data or information resourceAutomatic prediction tool to infer protein-protein interaction networks, it is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8. Users can use this page to ask InteroPorc for all species present in Integr8. Some results are already computed and users can run InteroPorc to investigate any other species. Currently, the following databases are processed and merged (with datetime of the last available public release for each database used): IntAct, MINT, DIP, and Integr8.orthology, prediction, protein interaction, tool, sequenced genome, proteinprotein interaction, inferred interaction, molecular interaction, interaction, proteinSCR_002067(InteroPorc, RRID:SCR_002067)CEA; Gif sur Yvette; France European Union, French Atomic Energy Commission, French National Agency of Research, Marie Curie Fellowshiprelated to: Integr8 : Access to complete genomes and proteomes, IntAct, MINT, Database of Interacting Proteins, PSICQUIC RegistryPMID:18508856Last checked upnif-0000-20816
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
Current Controlled TrialsResource, service resource, data or information resource, data repository, storage service resource, databaseFree-to-view clinical trials register of clinical trials worldwide, it allows users to search, register and share information about randomized controlled trials. Publication services are also available via the range of open access peer-reviewed journals published by BioMed Central. Current Controlled Trials is run by an editorial and technical in-house team. It receives advice from an international Advisory Group, including academics, doctors and health care specialists of international renown. The Advisory Group provides valuable guidance on the current activities and possible new directions of Current Controlled Trials' two databases, the metaRegister of Controlled Trials (mRCT) and the International Standard Randomised Controlled Trial Number (ISRCTN) scheme.controlled trial, health, public health, science, trial, randomized controlled trial, clinical trialSCR_002325(Current Controlled Trials, RRID:SCR_002325)administrative fee, European Union, Science Navigation Grouprelated to: ISRCTN Registry, uses: ISRCTN RegistryLast checked upnif-0000-21104
EnsemblResource, data analysis service, data access protocol, database, web service, production service resource, analysis service resource, catalog, service resource, software resource, data or information resourceCollection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.collection, genome, dataset, database, vertebrate, eukaryotic, DNA, protein, sequence, search, automaticly, annotate, dataSCR_002344(Ensembl, RRID:SCR_002344)European Bioinformatics Institute , Wellcome Trust Sanger Institute; Hinxton; United Kingdom BBSRC, EMBL, European Union, FP6, FP7, MRC, NHGRI, Wellcome Trustrelated to: Ensembl Genomes, GermOnline, CandiSNPer, Human Splicing Finder, NGS-SNP, Sanger Mouse Resources Portal, DECIPHER, Ensembl Genomes, PeptideAtlas, AnimalTFDB, Bgee: a dataBase for Gene Expression Evolution, FlyMine, Rat Gene Symbol Tracker, UniParc at the EBI, go-db-perl, UniParc, G:Profiler, RIKEN integrated database of mammals, VBASE2, p300db, used by: NIF Data Federation, Animal QTLdb, Monarch Initiative, ChannelPedia, Blueprint Epigenome, HmtPhenome, listed by: OMICtools, Biositemaps,, LabWorm, works_with: Genotate, CellPhoneDB, Open Regulatory Annotation DatabaseReferences (2)Last checked upnif-0000-21145, OMICS_01647
EPILEPSIE databaseResource, data or information resource, databaseA comprehensive database for human surface and intracranial EEG data that is suitable for a broad range of applications e.g. of time series analyses of brain activity. Currently, the EU database contains annotated EEG datasets from more than 200 patients with epilepsy, 50 of them with intracranial recordings with up to 122 channels. Each dataset provides EEG data for a continuous recording time of at least 96 hours (4 days) at a sample rate of up to 2500 Hz. Clinical patient information and MR imaging data supplement the EEG data. The total duration of EEG recordings included execeeds 30000 hours. The database is composed of different modalities: Binary files with EEG recording / MR imaging data and Relational database for supplementary meta data.seizure, electroencephalography, mri, eeg recording, metadata, intracranial, surface, time series analyses, brain activity, brain, clinical, image collectionSCR_003179(EPILEPSIE database, RRID:SCR_003179)University of Freiburg; Baden-Wurttemberg; Germany EpilepsyBMBF, European Union, Excellence Initiative of the German Federal and State Governments, German Science Foundationlisted by: NeuroImaging Tools and Resources Collaboratory (NITRC)PMID:22738131Last checked upnlx_156892
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 ( 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,, Integrated Manually Extracted Annotation, used by: NIF Data FederationReferences (2)Last checked upnif-0000-00064
EuroBioBankResource, biomaterial supply resource, tissue bank, data set, cell repository, material resource, data or information resourceThe EuroBioBank network is the first operating network of biobanks in Europe providing human DNA, cell and tissue samples as a service to the scientific community conducting research on rare diseases. It is the only network dedicated to rare disease research in Europe. By creating a critical mass of collections and facilitating the exchange of biological material, the EuroBioBank network helps accelerate research on these diseases. * Over 440,000 samples are available across the network and can be requested via the online catalogue. Approximately 13,000 samples are collected each year and 7,000 samples distributed in Europe and beyond. The biological samples are obtained from patients affected by rare diseases, including rare neuromuscular disorders. * The EuroBioBank Network is currently composed of 18 members, of which 16 biobanks from 8 European countries (France, Germany, Hungary, Italy, Malta, Slovenia, Spain and the United-Kingdom) as well as Israel and Canada. Goals * Identify and localize biological material of interest to researchers * Build a critical mass of rare disease sample collections * Distribute high quality material and associated data to users * Promote best-practice guidelines for biobanking activities * Disseminate knowledge and know-how to the scientific community through training courses * Enhance collaboration with the medical and scientific community in the field of rare diseases EuroBioBank acts as a clearing house or virtual bank, with all samples listed in the central online catalogue remaining in the possession of the member biobanks, where they are located and can be requested. The network was established by patients and researchers to facilitate research on rare diseases by guaranteeing quick and easy access to samples via an online catalogue. The catalogue lists the samples available throughout the EuroBioBank network by type of biomaterial. A search engine enables a search by disease or by bank contact. Once a sample has been located in the catalogue, it can be requested by email. Therefore, the biological material is exchanged faster. If a sample does not appear in the EuroBioBank catalogue, help can be provided to further search it at: eurobiobank (at) Funding and Collaboration Originally funded by the EC between 2003-2006, the EuroBioBank received further EC support between 2007-2011 within the European Network of Excellence TREAT-NMD (FP6), which covered the cost sustained by Eurordis for the network coordination and website hosting. Each biobank of the network is financed by its own Institution or charitable organization. As of January 2012, the Fondazione Telethon provides the administrative support for coordinating the EuroBioBank network and hosting the website.rare disease, catalog, cell, dna, tissue, myoblast, fibroblast, myocyte, cardiomyocyte, epithelial cell, rare disease, rare neuromuscular disorder, myasthenia gravis, inflammatory myopathy, glycogen storage disease, mitochondrial myopathy, muscular dystrophy, malignant hyperthermia, congenital myopathy, myotonic disorder, duchenne dystrophySCR_003599(EuroBioBank, RRID:SCR_003599)Telethon Foundation Rare disease, Rare neuromuscular disorder, Myasthenia gravis, Inflammatory myopathy, Glycogen storage disease, Mitochondrial myopathy, Muscular dystrophy, Malignant hyperthermia, Congenital myopathy, Myotonic disorder, Duchenne dystrophy, Etc.European Union, Treat-NMDrelated to: Treat-NMD, Movement Disorders Biobank, listed by: One Mind Biospecimen Bank Listing, affiliated with: Telethon Network of Genetic BiobanksLast checked upnlx_12526
Alzheimer EuropeResource, disease-related portal, topical portal, portal, data or information resourceA non-governmental organization aimed at raising awareness of all forms of dementia by creating a common European platform through co-ordination and co-operation between Alzheimer organizations throughout Europe. Alzheimer Europe is also a source of information on all aspects of dementia.SCR_003802(Alzheimer Europe, RRID:SCR_003802)Dementia, Alzheimer's diseaseEuropean Unionrelated to: Greek Association of Alzheimers Disease and Related Disorders, PharmaCog, EMIFLast checked upnlx_158313
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