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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
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
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
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
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
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
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-0000-21104http://www.webcitation.org/getfile?fileid=6fc2d850dde348335d1ab0b66828190d475a6967
Digital Repository Infrastructure Vision for European ResearchResource, service resource, data or information resource, data repository, storage service resource, databaseCohesive, robust and flexible, pan-European infrastructure for digital repositories, offering sophisticated services and functionalities for researchers, administrators and the general public. Access the network of freely accessible digital repositories with content across academic disciplines with over 3,500,000 scientific publications, found in journal articles, dissertations, books, lectures, reports, etc., harvested regularly from more than 295 repositories, from 38 countries. DRIVER has established a network of relevant experts and Open Access repositories. DRIVER-II will consolidate these efforts and transform the initial testbed into a fully functional, state-of-the art service, extending the network to a larger confederation of repositories. It aims to optimize the way the e-Infrastructure is used to store knowledge, add value to primary research data and information making secondary research more effective, provide a valuable asset for industry, and help bridging research and education. The objectives of DRIVER-II, the second phase of the project, include efforts to expand, enrich, and strengthen the results of DRIVER, in the following areas: * strategic geographic and community expansion by means of the DRIVER confederation * establish a robust, scalable repository infrastructure accompanied by an open source software package D-Net * broader coverage of content through the use of enhanced publications * advanced end-user functionality to support scientific exploration of complex digital objects * larger outreach and advocacy programs * continued repository support * guidelines for interoperability in the larger European digital library communitydigital, publication, repository, scholarly information, publication, primary data, educational material, digital repository, infrastructure, interoperability, networkingSCR_002752(Digital Repository Infrastructure Vision for European Research, RRID:SCR_002752)University of Athens; Athens; Greece European UnionLast checked upnif-0000-24122
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/
ArrayExpressResource, database, catalog, service resource, storage service resource, data repository, data or information resourceInternational functional genomics data collection generated from microarray or next-generation sequencing (NGS) platforms. Repository of functional genomics data supporting publications. Provides genes expression data for reuse to the research community where they can be queried and downloaded. Integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. Data collected to MIAME and MINSEQE standards. Data are submitted by users or are imported directly from the NCBI Gene Expression Omnibus.gold, standard, functional, genomics, data, collection, microarray, next, generation, sequencing, NGS, repositorySCR_002964(ArrayExpress, RRID:SCR_002964)European Bioinformatics Institute European Commission, European Union, Gen2Phen, NHGRI, SLINGrelated to: DDBJ Omics Archive, MIAME, Gene Expression Atlas, Experimental Factor Ontology, Bgee: a dataBase for Gene Expression Evolution, ISA Infrastructure for Managing Experimental Metadata, FlyMine, MAGE-TAB, Experimental Factor Ontology, Magic, ArrayExpress (R), Gene Expression Database, used by: NIF Data Federation, BioSample Database at EBI, Integrated Datasets, uses: MIAME, MINSEQE, Gene Expression Omnibus, listed by: DataCite, OMICtools, re3data.orgReferences (2)Last checked upnif-0000-30123, OMICS_01023http://www.ebi.ac.uk/microarray-as/ae
BRENDAResource, data analysis service, database, analysis service resource, production service resource, service resource, storage service resource, data repository, data or information resourceMain database of functional biochemical and molecular enzyme data that provides access to seven interconnected databases. It contains 2.7 million manually annotated data on enzyme occurrence, function, kinetics and molecular properties. The majority of the data are manually extracted from the primary literature. Each entry is connected to a reference and the source organism. Enzyme ligands are stored with their structures and can be accessed via their names, synonyms or via a structure search. FRENDA (Full Reference ENzyme DAta) and AMENDA (Automatic Mining of ENzyme DAta) are based on text mining methods and represent a complete survey of PubMed abstracts with information on enzymes in different organisms, tissues or organelles. The supplemental database DRENDA provides more than 910 000 new EC number-disease relations in more than 510 000 references from automatic search and a classification of enzyme-disease-related information. KENDA (Kinetic ENzyme DAta), a new amendment extracts and displays kinetic values from PubMed abstracts. The integration of the EnzymeDetector offers an automatic comparison, evaluation and prediction of enzyme function annotations for prokaryotic genomes. The biochemical reaction database BKM-react contains non-redundant enzyme-catalyzed and spontaneous reactions and was developed to facilitate and accelerate the construction of biochemical models. The content covers information on function, structure, occurrence, preparation and application of enzymes as well as properties of mutants and engineered variants. BRENDA provides viewing options such as the display of the statistics of functional parameters and the 3D view of protein sequence and structure features. Furthermore a ligand summary shows comprehensive information on the BRENDA ligands. The enzymes are linked to their respective pathways and can be viewed in pathway maps. The disease text mining part is strongly enhanced. It is possible to submit new, not yet classified enzymes to BRENDA, which then are reviewed and classified by the International Union of Biochemistry and Molecular Biology. A new SBML output format of BRENDA kinetic data allows the construction of organism-specific metabolic models. The enzymes are classified according to the Enzyme Commission list of enzymes. Some 5000 different enzymes are covered. Frequently enzymes with very different properties are included under the same EC number. Although they intend to give a representative overview on the characteristics and variability of each enzyme the Handbook is not a compendium. The reader will have to go to the primary literature for more detailed information. Naturally it is not possible to cover all the numerous literature references for each enzyme (for some enzymes up to 40000) if the data representation is to be concise as is intended. The data collection is being developed into a metabolic network information system with links to Enzyme expression and regulation information. BRENDA SOAP Webservice is available.enzyme, metabolic pathway, protein sequence, protein structure, genome, structure, function, annotation, kinetics, molecular property, occurrence, preparation, application, mutant, variant, pathway, ligand, web service, sequence, substructureSCR_002997(BRENDA, RRID:SCR_002997)Technical University of Braunschweig; Braunschweig; Germany European Unionrelated to: ENZYMEReferences (6)Last checked upnif-0000-30222http://www.brenda-enzymes.info/http://www.brenda.uni-koeln.de/
ProteomeXchangeResource, organization portal, database, consortium, catalog, service resource, portal, storage service resource, data repository, data or information resourceA data repository for proteomic data sets. The ProteomeExchange consortium, as a whole, aims to provide a coordinated submission of MS proteomics data to the main existing proteomics repositories, as well as to encourage optimal data dissemination. ProteomeXchange provides access to a number of public databases, and users can access and submit data sets to the consortium's PRIDE database and PASSEL/PeptideAtlas.consortium, database, proteomics, MS proteomics, protein, mass spectrometrySCR_004055(ProteomeXchange, RRID:SCR_004055)European Bioinformatics Institute European Unionrelated to: PRIDE, PeptideAtlas, SIB Swiss Institute of Bioinformatics, massIVE, European Bioinformatics Institute, uses: PRIDE, PeptideAtlas, affiliated with: Omics Discovery IndexLast checked upnlx_158620http://proteomecentral.proteomexchange.org
NASCResource, database, biomaterial supply resource, service resource, storage service resource, material storage repository, material resource, data or information resourceThe Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. NASC now maintains over 500,000 accessions of Arabidopsis thaliana (and a small number of other related species), including Characterized lines, Mapping populations, and Insertion lines. You may browse or search the catalog. NASC was established in April 1991 as part of the Plant Molecular Biology initiative of the Agricultural and Food Research Council (AFRC). Its activities are coordinated with those of the Arabidopsis Biological Resource Center, (ABRC) based at Ohio State University, USA. This facilitates a unified and efficient service for the research community. The stock centers have a distribution agreement. NASC distributes to Europe and ABRC distributes to North America. Laboratories in other locations may establish their primary affiliation with either center. Stocks include over 200 well-characterized hormone, flowering, biochemical, form mutants and multiple marker lines, many of which were received from Maarten Koornneef. We also stock several hundred form and color mutants as well as 300 ecotypes donated by Professor Kranz. Our total of ecotypes representing a reservoir of natural variation, now stands at ~1300 bulk (original collection) and single seed "purified" lines. For mapping purposes we stock: * 300 recombinant inbred lines derived from a cross between Landsberg erecta and Columbia, donated by Caroline Dean and Clare Lister. * A set of 146 recombinant inbreds produced from a cross between Wassileweskija and W100F and donated by Pablo Scolnik. * A population of Cvi-0 (Cape Verde Islands) x Landsberg erecta lines (162 in total) developed by Maarten Koornneef. * A population of Nd (Niederzenz) x Columbia (100 lines) developed by Eric Holub, Jim Beynon, and Ian Crute (HRI Wellsbourne, UK). * A population generated from a cross between Landsberg and Columbia quartet mutants qrt1-1 and qrt1-2 NASC stocks a large number of T-DNA and transposon insertion lines which can be used for both forward and reverse genetics. Many thanks to all of the researchers who have donated material to NASC. We are always happy to receive new donations. If you would like to donate stocks to NASC, please fill in the donation form and send your seeds to NASC.seed, arabidopsisSCR_004576(NASC, RRID:SCR_004576)University of Nottingham; Nottingham; United Kingdom BBSRC, European Union, University of Nottingham; Nottingham; United Kingdomlisted by: One Mind Biospecimen Bank ListingLast checked upnlx_56885
PDBe - Protein Data Bank in EuropeResource, service resource, data or information resource, data repository, storage service resource, databaseThe European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - they work to collate, maintain and provide access to the global repository of macromolecular structure data. The main objectives of the work at PDBe are: * to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces. * to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data). * to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites. Several sophisticated tools are also available for the structural analysis of macromolecules.x-ray, nmr, cryo-em, hybrid method, dna, protein, rna, sugar, ligand, virus, compound, fold, enzyme, 3d spatial image, structure, macromolecule, protein-protein interaction, gold standardSCR_004312(PDBe - Protein Data Bank in Europe, RRID:SCR_004312)European Bioinformatics Institute BBSRC, CCP4, European Molecular Biology Laboratory; Heidelberg; Germany, European Union, MRC, NIH, Wellcome Trustrelated to: Research Collaboratory for Structural Bioinformatics Protein Data Bank, DDBJ - DNA Data Bank of Japan, EMDataBank.org: Unified Data Resource for Cryo Electron Microscopy, Worldwide Protein Data Bank , Biological Magnetic Resonance Data Bank, DDBJ - DNA Data Bank of Japan, Worldwide Protein Data Bank , PDBj - Protein Data Bank Japan, Research Collaboratory for Structural Bioinformatics Protein Data Bank, RCSB PDB, listed by: re3data.orgReferences (3)Last checked upnlx_32372
FishBaseResource, topical portal, database, organism-related portal, service resource, portal, storage service resource, image repository, data repository, data or information resourceA global species database and encyclopedia of over 32,800 species and subspecies of fishes that is searchable by common name, genus, species, geography, family, ecosystem, references literature, tools, etc. It links to other, related databases such as the Catalog of Fishes, GenBack, and LarvalBase. It is associated with a partner journal, Acta Ichthyologica et Piscatoria. It is available in English, Greek, Spanish, Portuguese, French, Dutch, Italian, and German. Photo and video submissions are welcome. FishBase 2004 is also available on DVD or CD-ROMs with full information on 28,500 species. It comes together with the FishBase 2000 book and can be ordered for 95 US$ including air-mail.forum, blog, photo, book, image, ichthyologySCR_004376(FishBase, RRID:SCR_004376)European Unionrelated to: Teleost Taxonomy Ontology, Phenoscape Knowledgebase, listed by: re3data.orgLast checked upnlx_39009
RHEAResource, service resource, data or information resource, data repository, storage service resource, databaseManually annotated reaction database where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest) which provides detailed information about structure, formula and charge. Rhea provides built-in validations that ensure both elemental and charge balance of the reactions. The database has been populated with the reactions found in the Enzyme Commission (EC) list (and in the IntEnz and ENZYME databases), extending it with additional known reactions of biological interest. While the main focus of Rhea is enzyme-catalyzed reactions, other biochemical reactions are also included. Rhea is a manually annotated resource and it provides: stable reaction identifiers for each of its reactions; directionality information if the physiological direction of the reaction is known; the possibility to link several reactions together to form overall reactions; extensive cross-references to other resources including enzyme-catalyzed and other metabolic reactions, such as the EC list (in IntEnz), KEGG, MetaCyc and UniPathway; and chemical substructure and similarity searches on compounds in Rhea.biochemical reaction, reaction, enzyme-catalyzed reaction, spontaneous reaction, enzyme, chemical reaction, gold standardSCR_004713(RHEA, RRID:SCR_004713)SIB Swiss Institute of Bioinformatics EMBL, European Union, Swiss Federal Government SERI, Swiss Initiative in Systems Biology, SystemsX.chrelated to: European Bioinformatics Institute, uses: CHEBI, listed by: re3data.orgPMID:27789701Last checked upnlx_70986
Zebrafish Brain AtlasResource, reference atlas, service resource, storage service resource, atlas, image repository, data repository, data or information resourceCollates and curates neuroanatomical data and information generated both in-house and by community to communicate current state of knowledge about neuroanatomical structures in developing zebrafish. Most of data come from high resolution confocal imaging of intact brains in which neuroanatomical structures are labelled by combinations of transgenes and antibodies. Community repository for image based data related to neuroanatomy of zebrafish.brain, neuroanatomy, developing, transgene, antibody, confocal, section, reconstruction, high-resolution, developmental stage, embryo, brain structure, confocal imaging, comparative anatomy, transgenic, 3d spatial image, video, embryonic zebrafish, development, annotation, narrative resource, training material, cell repositorySCR_000606(Zebrafish Brain Atlas, RRID:SCR_000606)University College London; London; United Kingdom BBSRC, European Union, Wellcome Trustrecommends: Zebrafish Anatomical Ontology, listed by: One Mind Biospecimen Bank ListingLast checked upnlx_149455http://zebrafishucl.org/
UMD-BRCA1/ BRCA2 databasesResource, service resource, data or information resource, data repository, storage service resource, databaseThe UMD-BRCA1/BRCA2 databases have been set up in a joined national effort through the network of 16 diagnostic laboratories to provide up-to-date information about mutations of the BRCA1 and BRCA2 genes identified in patients with breast and/or ovarian cancer. These databases currently contain published and unpublished information about the BRCA1/BRCA2 mutations reported in French diagnostic laboratories. This database includes 28 references and 5530 mutations (1440 different mutations and 786 protein variants) The databases of BRCA1 and BRCA2 mutations were built using the Universal Mutation Database tool. For each mutation, information is provided at several levels: * at the gene level: exon and codon number, wild type and mutant codon, mutation event, mutation name and, * at the protein level: wild type and mutant amino acid, binding domain, affected domain. If you want to submit a mutation, please contact R. Lidereau., S. Caputo. or E. Rouleau.cancer, gene, mutation, exon, codon, wild type, mutant, mutation, protein, amino acid, binding domain, affected domain, brca1, brca2, variant, polymorphism, unclassified variant, unknown variant, female, womanSCR_006128(UMD-BRCA1/ BRCA2 databases, RRID:SCR_006128)National Institute of Health and Medical Research; Rennes; France Breast cancer, Ovarian cancerAssociation dAide a la Recherche Cancerologique de Saint Cloud, European Union, French National Cancer InstitutePMID:22144684Last checked upnlx_151608
European Mouse Mutant ArchiveResource, organism supplier, biomaterial supply resource, biospecimen repository, service resource, storage service resource, cell repository, material resource, material storage repositoryNon-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. Users may browse by strain, gene, phenotype, or human disease. Its primary objective is to establish and manage a unified repository for maintaining medically relevant mouse mutants and making them available to the scientific community. Therefore, EMMA archives mutant strains and distributes them to requesting researchers. EMMA also hosts courses in cryopreservation, to promote the use and dissemination of frozen embryos and spermatozoa. Dissemination of knowledge is further fostered by a dedicated resource database. Anybody who wants their mutant mouse strains cryopreserved may deposit strains with EMMA. However depositors must be aware that these strains become freely available to other researchers after being deposited.mutant cell repository, mouse, cell repository, mutant strain, mutant mouse strainSCR_006136(European Mouse Mutant Archive, RRID:SCR_006136)Helmholtz Center Munich Institute of Experimental Genetics European Union, national research programmes, partner institutionsrelated to: European Conditional Mouse Mutagenesis Program, International Knockout Mouse Consortium, Monarch Initiative, Federation of International Mouse Resources, MGI strains, used by: EUCOMMTOOLS, listed by: One Mind Biospecimen Bank ListingReferences (2)Last checked upnlx_151625
PathbaseResource, ontology, data access protocol, database, web service, image collection, service resource, storage service resource, software resource, image repository, data repository, controlled vocabulary, data or information resourceDatabase of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice. The database currently holds more than 1000 images of lesions from mutant mice and their inbred backgrounds and further images are being added continuously. Images can be retrieved by searching for specific lesions or class of lesion, by genetic locus, or by a wide set of parameters shown on the Advanced Search Interface. Its two key aims are: * To provide a searchable database of histopathology images derived from experimental manipulation of the mouse genome or experiments conducted on genetically manipulated mice. * A reference / didactic resource covering all aspects of mouse pathology Lesions are described according to the Pathbase pathology ontology developed by the Pathbase European Consortium, and are available at the site or on the Gene Ontology Consortium site - OBO. As this is a community resource, they encourage everyone to upload their own images, contribute comments to images and send them their feedback. Please feel free to use any of the SOAP/WSDL web services. (under development)histopathology, photomicrograph, macroscopic, mutant, genetically manipulated, pathology, transgenic, rodent, mpath ontology, mouse pathology ontology, skinbase, genotype, skin, gene, tissue, hair, mutant mouse strainSCR_006141(Pathbase, RRID:SCR_006141)University of Cambridge; Cambridge; United Kingdom Lesion, Mutant mouse strain, Inbred mouse strainEllison Medical Foundation, European Union, NCI, NCRR, NIH, North American Hair Research Societyrelated to: Gene OntologyReferences (3)Last checked upnlx_151637
European Nucleotide ArchiveResource, service resource, data or information resource, data repository, storage service resource, databasePublic archive providing a comprehensive record of the world''''s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. All submitted data, once public, will be exchanged with the NCBI and DDBJ as part of the INSDC data exchange agreement. The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources including submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centers and routine and comprehensive exchange with their partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature. ENA is made up of a number of distinct databases that includes the EMBL Nucleotide Sequence Database (Embl-Bank), the newly established Sequence Read Archive (SRA) and the Trace Archive. The main tool for downloading ENA data is the ENA Browser, which is available through REST URLs for easy programmatic use. All ENA data are available through the ENA Browser. Note: EMBL Nucleotide Sequence Database (EMBL-Bank) is entirely included within this resource.analysis, bioinformatics, dna, nucleotide, sequencing, web service, rna, molecular biology, nucleotide sequence, protein, gene expression, gene, genome, biochemistry, molecular structure, metabolite, protein binding, chemogenomics, gold standardSCR_006515(European Nucleotide Archive, RRID:SCR_006515)European Bioinformatics Institute EMBL, European Union, Wellcome Trustrelated to: NCBI Sequence Read Archive, ENA Sequence Version Archive, VBASE2, DDBJ Sequence Read Archive, ISA Infrastructure for Managing Experimental Metadata, DDBJ - DNA Data Bank of Japan, DDBJ - DNA Data Bank of Japan, NCBI, INSDC, INSDC, NCBI Assembly Archive Viewer, used by: BioSample Database at EBI, listed by: 3DVC, re3data.org, OMICtoolsPMID:20972220Last checked upnif-0000-32981, OMICS_01029http://www.ebi.ac.uk/embl/
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