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on page 1 showing 20 out of 56 results

Cite this (1000 Functional Connectomes Project, RRID:SCR_005361)

URL: http://fcon_1000.projects.nitrc.org/

Resource Type: Resource, database, image collection, catalog, service resource, storage service resource, image repository, data repository, data or information resource

Database of resting state fMRI (R-fMRI) datasets collected from sites around the world. It demonstrates open sharing of R-fMRI data and aims to emphasize the aggregation and sharing of well-phenotyped datasets.

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    ASAP

Cite this (ASAP, RRID:SCR_001849)

URL: https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Database and web interface developed to store, update and distribute genome sequence data and gene expression data. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments. Use of some of this preliminary data is conditional, and it is the users responsibility to read the data release policy and to verify that any use of specific data obtained through ASAP is consistent with this policy. There are four main routes to viewing the information in ASAP: # a summary page, # a form to query the genome annotations, # a form to query strain collections, and # a form to query the experimental data. Navigational buttons appear on every page allowing users to jump to any of these four points.

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    ASPGD

Cite this (ASPGD, RRID:SCR_002047)

URL: http://www.aspgd.org/

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Database of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus including information about genes and proteins of Aspergillus nidulans and Aspergillus fumigatus; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Sgenus species. Also available are Gene Ontology (GO) and community resources. Based on the Candida Genome Database, the Aspergillus Genome Database is a resource for genomic sequence data and gene and protein information for Aspergilli. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). Search options allow you to: *Search AspGD database using keywords. *Find chromosomal features that match specific properties or annotations. *Find AspGD web pages using keywords located on the page. *Find information on one gene from many databases. *Search for keywords related to a phenotype (e.g., conidiation), an allele (such as veA1), or an experimental condition (e.g., light). Analysis and Tools allow you to: *Find similarities between a sequence of interest and Aspergillus DNA or protein sequences. *Display and analyze an Aspergillus sequence (or other sequence) in many ways. *Navigate the chromosomes set. View nucleotide and protein sequence. *Find short DNA/protein sequence matches in Aspergillus. *Design sequencing and PCR primers for Aspergillus or other input sequences. *Display the restriction map for a Aspergillus or other input sequence. *Find similarities between a sequence of interest and fungal nucleotide or protein sequences. AspGD welcomes data submissions.

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Cite this (BEI Resource Repository, RRID:SCR_013698)

URL: https://www.beiresources.org/

Resource Type: Resource, service resource, material storage repository, storage service resource, biobank

Central data repository that supplies organisms and reagents to the broad community of microbiology and infectious diseases researchers.

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Cite this (Berkeley Bioinformatics Open-Source Projects, RRID:SCR_006704)

URL: http://www.berkeleybop.org/

Resource Type: Resource, software resource, topical portal, portal, data or information resource

The BBOP, located at the Lawrence Berkeley National Labs, is a diverse group of scientific researchers and software engineers dedicated to developing tools and applying computational technologies to solve biological problems. Members of the group contribute to a number of projects, including the Gene Ontology, OBO Foundry, the Phenotypic Quality Ontology, modENCODE, and the Generic Model Organism Database Project. Our group is focused on the development, use, and integration of ontolgies into biological data analysis. Software written or maintained by BBOP is accessible through the site.

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    BioGRID

Cite this (BioGRID, RRID:SCR_007393)

URL: http://www.thebiogrid.org/

Resource Type: Resource, database, service resource, storage service resource, software resource, data repository, data or information resource

A curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts.

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Cite this (Biologic Specimen and Data Repository Information Coordinating Center, RRID:SCR_013142)

URL: https://biolincc.nhlbi.nih.gov/home/

Resource Type: Resource, data or information resource, database, biomaterial supply resource, biospecimen repository, service resource, storage service resource, data repository, material resource, material storage repository

Repository that serves to coordinate searches across data and biospecimen collections from participants in numerous clinical trials and epidemiologic studies and to provide an electronic means for requests for additional information and the submission of requests for collections. The collections, comprising data from more than 80 trials or studies and millions of biospecimens, are available to qualified investigators under specific terms and conditions consistent with the informed consents provided by the individual study participants. Some datasets are presented with studies and supporting materials to facilitate their use in reuse and teaching. Datasets support basic research, clinical studies, observational studies, and demonstrations. Researchers wishing to apply to submit biospecimen collections to the NHLBI Biorepository for sharing with qualified investigators may also use this website to initiate that process.

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Cite this (Candida Genome Database, RRID:SCR_002036)

URL: http://www.candidagenome.org/

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Database of genetic and molecular biological information about Candida albicans, a yeast that is an opportunistic pathogen of humans, and about other Candida-related species, such as Candida glabrata. It contains information about genes and proteins; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information. Each CGD gene or open reading frame has an individual Locus Page. Genetic loci that are not tied to a DNA sequence also have Locus Pages. The Locus Page is the central clearinghouse for all information specific to that gene and tools for its analysis, including: * gene name, synonyms, and systematic name * Gene Ontology (GO) annotations * descriptions of the gene and gene product * phenotype of mutations in the gene * chromosomal and contig coordinates * interactive graphical chromosome map and browsing tool * tools for retrieval and analysis of the gene and protein sequences * a curated collection of literature CGD also provides a Gene Ontology, GO, to all its users. GO is a collaborative project involving CGD and other model organism databases to provide controlled vocabularies that are used to describe the molecular function and cellular location of gene products and the biological process in which they are involved. The three ontologies that comprise GO (Molecular Function, Cellular Component, and Biological Process) are used by multiple databases to annotate gene products, so that this common vocabulary can be used to compare gene products across species. The development of the ontologies is ongoing in order to incorporate new information. Data submissions are welcome.

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Cite this (CardioVascular Research Grid, RRID:SCR_004472)

URL: http://www.cvrgrid.org/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, service resource, storage service resource, image repository, data repository

An infrastructure for sharing cardiovascular data and data analysis tools. CVRG tools are developed using the Software as a Service model, allowing users to access tools through their browser, thus eliminating the need to install and maintain complex software. A human ExVivo heart data set and canine ExVivo normal and failing heart data sets are available. The canine hearts have an atlas available, in Analyze 7.5 format. There are also human InVivo atlases, in Analyze 7.5 format, showing end systole and end diastole data. * ECG: The ECGrid Toolkit is able to handle a number of different ECG file formats. * Ex vivo data: The CVRG has several sets of canine and human imaging sets available for public use. * Ex vivo atlas data: The CVRG has atlases with analysis of canine heart fiber and sheet angles available for public use. * In vivo data: These datasets include Ischemic (ICM) and non-ischemic cardiomyopathy (NICM) Data. * Protein Microarray data: The following datasets are supporting information for publications which reported on new experimental approaches for using reverse-phase protein microarrays to map the left ventricular transmural proteome. Web services: The CVRG is committed to the delivery of tools, for sharing and analyzing cardiovascular data. Four different groups of tools are under development or have been deployed. These are: 1) an ECG storage and analysis interface; 2) a customized instance of XNAT for cardiovascular imaging & imaging analysis; 3) an optimized representation tool for clinical data; and 4) a workflow tool for data retrieval & analysis. Within these groups, data and analytical services are combined to meet the needs of the Driving Biomedical Projects. Ontologies: CVRG ontology development and application focuses in three major areas. They have developed a preliminary ontology for describing all aspects of ECG data collection, ECG waveform features, and ECG data analysis. They coupled ontology development with the development of an ECG data model. The CVRG award supports the ECG ontology and data model development. The project is based at the Institute for Computational Medicine at the Johns Hopkins University, in collaboration with the Center for Comprehensive Informatics at Emory University, the Image Lab at Wake Forest University and the Computation Institute at The University of Chicago.

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Cite this (Database of Interacting Proteins, RRID:SCR_003167)

URL: http://dip.doe-mbi.ucla.edu/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, storage service resource, data repository, data or information resource

Database to catalog experimentally determined interactions between proteins combining information from a variety of sources to create a single, consistent set of protein-protein interactions that can be downloaded in a variety of formats. The data were curated, both, manually and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Because the reliability of experimental evidence varies widely, methods of quality assessment have been developed and utilized to identify the most reliable subset of the interactions. This CORE set can be used as a reference when evaluating the reliability of high-throughput protein-protein interaction data sets, for development of prediction methods, as well as in the studies of the properties of protein interaction networks. Tools are available to analyze, visualize and integrate user's own experimental data with the information about protein-protein interactions available in the DIP database. The DIP database lists protein pairs that are known to interact with each other. By interact they mean that two amino acid chains were experimentally identified to bind to each other. The database lists such pairs to aid those studying a particular protein-protein interaction but also those investigating entire regulatory and signaling pathways as well as those studying the organization and complexity of the protein interaction network at the cellular level. Registration is required to gain access to most of the DIP features. Registration is free to the members of the academic community. Trial accounts for the commercial users are also available.

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Cite this (DictyBase, RRID:SCR_006643)

URL: http://dictybase.org/

Resource Type: Resource, data analysis service, organism supplier, database, analysis service resource, biomaterial supply resource, biospecimen repository, production service resource, service resource, storage service resource, material storage repository, material resource, data or information resource

Model organism database for the social amoeba Dictyostelium discoideum that provides the biomedical research community with integrated, high quality data and tools for Dictyostelium discoideum and related species. dictyBase houses the complete genome sequence, ESTs, and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome to provide a ''''reference genome'''' in the Amoebozoa clade. They highlight several new features in the present update: (i) new annotations; (ii) improved interface with web 2.0 functionality; (iii) the initial steps towards a genome portal for the Amoebozoa; (iv) ortholog display; and (v) the complete integration of the Dicty Stock Center with dictyBase. The Dicty Stock Center currently holds over 1500 strains targeting over 930 different genes. There are over 100 different distinct amoebozoan species. In addition, the collection contains nearly 600 plasmids and other materials such as antibodies and cDNA libraries. The strain collection includes: * strain catalog * natural isolates * MNNG chemical mutants * tester strains for parasexual genetics * auxotroph strains * null mutants * GFP-labeled strains for cell biology * plasmid catalog The Dicty Stock Center can accept Dictyostelium strains, plasmids, and other materials relevant for research using Dictyostelium such as antibodies and cDNA or genomic libraries.

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    EcoCyc

Cite this (EcoCyc, RRID:SCR_002433)

URL: http://ecocyc.org/

Resource Type: Resource, data or information resource, database

Database for the bacterium Escherichia coli K-12 MG1655, the EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways. The long-term goal of the project is to describe the molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli. EcoCyc is an electronic reference source for E. coli biologists, and for biologists who work with related microorganisms.

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    ECO

Cite this (ECO, RRID:SCR_002477)

URL: http://www.evidenceontology.org

Resource Type: Resource, ontology, data or information resource, controlled vocabulary

A controlled vocabulary that describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about research subjects that result from scientific research, such as scientific conclusions, gene annotations, or other statements of fact. ECO comprises two high-level classes, evidence and assertion method, where evidence is defined as a type of information that is used to support an assertion, and assertion method is defined as a means by which a statement is made about an entity. Together evidence and assertion method can be combined to describe both the support for an assertion and whether that assertion was made by a human being or a computer. However, ECO can not be used to make the assertion itself; for that, one would use another ontology, free text description, or other means. ECO was originally created around the year 2000 to support gene product annotation by the Gene Ontology. Today ECO is used by many groups concerned with provenance in scientific research. ECO is used in AmiGO 2

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Cite this (EuPathDB - Eukaryotic Pathogen Database Resources, RRID:SCR_004512)

URL: http://eupathdb.org/eupathdb/

Resource Type: Resource, topical portal, data access protocol, database, web service, service resource, portal, storage service resource, software resource, data repository, data or information resource

EuPathDB Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Diseases is a portal for accessing genomic-scale datasets associated with the eukaryotic pathogens (Babesia, Cryptosporidium, Encephalitozoon, Entamoeba, Enterocytozoon, Giardia, Leishmania, Neospora, Plasmodium, Theileria, Toxoplasma, Trichomonas and Trypanosoma). It provides a unified entry point for the Eukaryotic Pathogen integrating AmoebaDB, CryptoDB, GiardiaDB, MicrosporidiaDB, PiroplasmaDB, PlasmoDB, ToxoDB, TrichDB, and TriTrypDB. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. EuPathDB currently supports more than 80 searches and the recently-implemented "search strategy" system enables users to construct complex multi-step searches via a graphical interface. Search results are dynamically displayed as the strategy is constructed or modified, and can be downloaded, saved, revised, or shared with other database users. EuPathDB provides programmatic access to its searches, via REST Web Services

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Cite this (FITBIR Informatics System, RRID:SCR_006856)

URL: https://fitbir.nih.gov/

Resource Type: Resource, topical portal, database, standard specification, narrative resource, service resource, portal, storage service resource, data repository, data or information resource

An extensible, scalable informatics platform for TBI relevant data and for all data types (text, numeric, image, time series, etc.). This informatics system was developed to share data across the entire TBI research field and to facilitate collaboration between laboratories and interconnectivity between informatics platforms. FITBIR implements the interagency Common Data Elements for TBI research and provides tools and resources to extend the data dictionary. It has also established a two-tiered submission strategy to ensure high quality and to provide maximum benefit to investigators. Qualified researchers can request access to data stored in FITBIR and/or data stored at federated repositories.

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    FlyBase

Cite this (FlyBase, RRID:SCR_006549)

URL: http://flybase.org/

Resource Type: Resource, topical portal, organism-related portal, analysis service resource, database, data analysis service, service resource, portal, production service resource, storage service resource, data repository, data or information resource

Database of Drosophila genetic and genomic information with information about stock collections and fly genetic tools. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. Additionally, FlyBase accepts data submissions. FlyBase can be searched for genes, alleles, aberrations and other genetic objects, phenotypes, sequences, stocks, images and movies, controlled terms, and Drosophila researchers using the tools available from the "Tools" drop-down menu in the Navigation bar.

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Cite this (GeneDB Lmajor, RRID:SCR_004613)

URL: http://www.genedb.org/Homepage/Lmajor

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

Database of the most recent sequence updates and annotations for the L. major genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Trypanosomatid research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The Pathogen Genomics group at the Wellcome Trust Sanger Institute played a major role in sequencing the genome of Leishmania major (see Ivens et al.) Details of the centres involved and which chromosomes they sequenced, are given. The sequence data were obtained by adopting several parallel approaches, including complete cosmid sequencing, whole chromosome shotguns and/or BAC sequencing/skimming. The Leishmania parasite is an intracellular pathogen of the immune system targeting macrophages and dendritic cells. The disease Leishmaniasis affects the populations of 88 counties worldwide with symptoms ranging from disfiguring cutaneous and muco-cutaneous lesions that can cause widespread destruction of mucous membranes to visceral disease affecting the haemopoetic organs. In collaboration with GeneDB, the EuPathDB genomic sequence data and annotations are regularly deposited on TriTrypDB where they can be integrated with other datasets and queried using customized queries.

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Cite this (GeneDB Pfalciparum, RRID:SCR_006567)

URL: http://www.genedb.org/Homepage/Pfalciparum

Resource Type: Resource, data or information resource, database

Database of the most recent sequence updates and annotations for the P. falciparum genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Plasmodium research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. The P. falciparum 3D7 nuclear genome is 23.3 Mb in size, with a karyotype of 14 chromosomes. The G+C content is approximately 19%. The P. falciparum genome is undergoing re-annotation. This process started in October 2007 with a weeklong workshop co-organized by staff from the Wellcome Trust Sanger Intistute and the EuPathDB team. Ongoing curation and sequence checking is being carried out by the Pathogen Genomics group. Plasmodium falciparum is the most deadly of the five Plasmodium species that cause human malaria. Malaria has a massive impact on human health; it is the worlds second biggest killer after tuberculosis. Around 300 million clinical cases occur each year resulting in between 1.5 - 2.7 million deaths annually, the majority in sub-saharan Africa. It is estimated that 3,000 children under the age of five years fall victim to malaria each day. Around 40% of the worlds population are at risk. In collaboration with EuPathDB, genomic sequence data and annotations are regularly deposited on PlasmoDB where they can be integrated with other datasets and queried using customized queries.

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Cite this (GeneDB Tbrucei, RRID:SCR_004786)

URL: http://www.genedb.org/Homepage/Tbruceibrucei927

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

Database of the most recent sequence updates and annotations for the T. brucei genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Trypanosomatid research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. T. brucei possesses a two-unit genome, a nuclear genome and a mitochondrial (kinetoplast) genome with a total estimated size of 35Mb/haploid genome. The nuclear genome is split into three classes of chromosomes according to their size on pulsed-field gel electrophoresis, 11 pairs of megabase chromosomes (0.9-5.7 Mb), intermediate (300-900 kb) and minichromosomes (50-100 kb). The T. brucei genome contains a ~0.5Mb segmental duplication affecting chromosomes 4 and 8, which is responsible for some 75 gene duplicates unique to this species. A comparative chromosome map of the duplicons can be accessed here (PubmedID 18036214). Protozoan parasites within the species Trypanosoma brucei are the etiological agent of human sleeping sickness and Nagana in animals. Infections are limited to patches of sub-Saharan Africa where insects vectors of the Glossina genus are endemic. The most recent estimates indicate between 50,000 - 70,000 human cases currently exist, with 17 000 new cases each year (WHO Factsheet, 2006). In collaboration with GeneDB, the EuPathDB genomic sequence data and annotations are regularly deposited on TriTrypDB where they can be integrated with other datasets and queried using customized queries.

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Cite this (GeneNetwork, RRID:SCR_002388)

URL: http://www.genenetwork.org/

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

A group of linked data sets and tools used to study complex networks of genes, molecules, and higher order gene function and phenotypes. It combines more than 25 years of legacy data generated by hundreds of scientists together with sequence data (SNPs) and massive transcriptome data sets (expression genetic or eQTL data sets). The quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. GeneNetwork can be used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Most of these population data sets are linked with dense genetic maps (genotypes) that can be used to locate the genetic modifiers that cause differences in expression and phenotypes, including disease susceptibility. Users are welcome to enter their own private data directly into GeneNetwork to exploit the full range of analytic tools and to map modulators in a powerful environment. This combination of data and fast analytic functions enable users to study relations between sequence variants, molecular networks, and function. What can be done with GeneNetwork? * QTL Mapping: ** Interval Mapping ** Simple interval mapping ** Composite interval mapping ** Pair-scan * Correlation Analysis ** Correlation Matrix / Principal Components Analysis ** QTL Heatmaps ** Compare Correlates ** Network Graph * Systems Genetics and Complex Trait Analysis Source code is available and is written in Python, C, and JavaScript. The QTL Reaper module of GeneNetwork that is used by several mapping modules of GeneNetwork is also available.

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