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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Sep 14, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
ERICResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceERIC is a resource of annotated enterobacterial genomes. Information is available and accessed through a open web portal uniting biological data and analysis tools. ERIC contains information on Escherichia, Shigella, Salmonella, Yersinia, and other microorgansims. ERIC has recently been moved over to PATRIC: The PATRIC BRC is now responsible for all bacterial species in the NIAID Category A-C Priority Pathogen lists for biodefense research, and pathogens causing emerging/reemerging infectious diseases. For ERIC users, we understand that the resource was valuable to your work. As such, we will be doing our very best to create a useful PATRIC resource to continue supporting your work. We realize that the transition will cause disruptions. However, it is a priority for us to work with established BRC users and communities to identify and prioritize our transition efforts. We have concentrated on the transfer of genomic data for this initial release. We anticipate adding new data, tools, and website features over the next several months. We look forward to working with you during the next 5 years.enterobacteria, enterobacteria pathogen, biodefense, disease bioinformatics, human disease, pathogen, pathogenic bacteria, cronobacter, enterobacter, erwinia, klebsiella, pectobacterium, photorhabdus, proteus, serratia, escherichia, shigella, salmonella, yersinia, citrobacterSCR_007644(ERIC, RRID:SCR_007644)Virginia Polytechnic Institute and State University; Virginia; USA NIAIDLast checked downnif-0000-02813http://www.ericbrc.org
Cryptococcus Neoformans cDNA SequencingResource, software resourceCryptococcus neoformans is an encapsulated yeast that infects the human host via the respiratory tract where it usually causes an inapparent infection. In the susceptible host, it may disseminate, typically producing a chronic and life-threatening meningitis. The Cryptococcus neoformans serotypes A and D are responsible for the overwhelming majority of pulmonary infections in AIDS patients. Cryptococcus neoformans strain H99 Latest Data Release - May 19, 2004 To date, we have isolated ca. 3750 cDNA clones from Cryptococcus neoformans strain H99 in collaboration with Drs. Juneann Murphy and Dave Dyer at the University of Oklahoma Health Sciences Center''s Department of Microbiology and Immunology in Oklahoma City and Kent Buchanan at the Tulane University Medical School, New Orleans, LA. The Cryptococcus neoformans strain H99 EST''s have been generated by Doris Kupfer, Heather Bell, Sunkyoung So, Yuong Tang, and Jennifer Lewis at the University of Oklahoma''s Advanced Center for Genome Technology, in the Department of Chemistry and Biochemistry. We now have end sequenced all available templates (ca. 7500 reactions) from both ends of the directionally cloned inserts after excision into pBlueScript SK-. . All of our data is available from our ftp site, and we now have added the ability to perform blast searches on this data. A keyword search of a blastx search of GenBank with this data also is available but we have not yet linked this to a unigene database as the number of EST''s sequenced doesn''t warrent this yet.SCR_008462(Cryptococcus Neoformans cDNA Sequencing, RRID:SCR_008462)University of Oklahoma; Oklahoma; USA NIAIDLast checked downnif-0000-30397
BEI Resource RepositoryResource, service resource, material storage repository, storage service resource, biobankCentral data repository that supplies organisms and reagents to the broad community of microbiology and infectious diseases researchers.biomaterial, material, reagent, microbiology, infectious diseasesSCR_013698(BEI Resource Repository, RRID:SCR_013698)infectious diseaseNIAIDrelated to: ATCC, NIH Data Sharing Repositories, listed by: NIH Data Sharing RepositoriesLast checked down
Type 1 Diabetes Genetics Consortium Resource, disease-related portal, topical portal, resource, research forum portal, portal, data or information resourceData and biological samples were collected by this consortium organizing international efforts to identify genes that determine an individual risk of type 1 diabetes. It originally focused on recruiting families with at least two siblings (brothers and/or sisters) who have type 1 diabetes (affected sibling pair or ASP families). The T1DGC completed enrollment for these families in August 2009. They completed enrollment of trios (father, mother, and a child with type 1 diabetes), as well as cases (people with type 1 diabetes) and controls (people with no history of type 1 diabetes) from populations with a low prevalence of this disease in January 2010. T1DGC Data and Samples: Phenotypic and genotypic data as well as biological samples (DNA, serum and plasma) for T1DGC participants have been deposited in the NIDDKCentral Repositories for future research.gene, genetics, genotyping, analytic, dna, serum, plasma, data set, biomaterial supply resource, phenotypic, genotypic, autoantibody, hla, phenotype, genotypeSCR_001557( Type 1 Diabetes Genetics Consortium , RRID:SCR_001557)Type 1 diabetes, Parent, ControlJDRF, NHGRI, NIAID, NIDDKlisted by: One Mind Biospecimen Bank Listing, NIDDK Information Network, NIDDK Central Repository, submitted by: NIDDK Information NetworkPMID:17130525Last checked downnlx_152867
HIV Sequence DatabaseResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceHIV Sequence Database is a database of annotated HIV sequences, plus a variety of tools and information for researchers studying HIV and SIV. The main aim of this website is to provide easy access to our sequence database, alignments, and the tools and interfaces we have produced. The HIV Sequence Database focuses on five primary goals: * Collecting HIV and SIV sequence data (all sequences since 1987) * Curating and annotating this data, and making it available to the scientific community * Computer analysis of HIV and related sequences * Production of software for the analysis of (sequence) data * The data and analyses on this site and published in a yearly printed publication, the HIV sequence Compendium, which is available free of charge.drug resistance, genetics, mutation, vaccine, human immunodeficiency virus, siv, sequence, alignment, simian immunodeficiency virusSCR_002906(HIV Sequence Database, RRID:SCR_002906)HIV Databases Human immunodeficiency virus, Simian immunodeficiency virusNIAIDLast checked downnif-0000-02967
Fungal Genome InitiativeResource, data set, data or information resourceProduces and analyzes sequence data from fungal organisms that are important to medicine, agriculture and industry. The FGI is a partnership between the Broad Institute and the wider fungal research community, with the selection of target genomes governed by a steering committee of fungal scientists. Organisms are selected for sequencing as part of a cohesive strategy that considers the value of data from each organism, given their role in basic research, health, agriculture and industry, as well as their value in comparative genomics.sequence, fungi, gene annotation, genomeSCR_003169(Fungal Genome Initiative, RRID:SCR_003169)Broad Institute NHGRI, NIAID, NSF, USDAlisted by: 3DVCLast checked downnif-0000-30591
Weighted Gene Co-expression Network AnalysisResource, software resource, software application, data analysis software, data processing softwareAn R package for weighted correlation network analysis. Recommended for all R users. WGCNA is also available as a point-and-click application. Unfortunately this application is not maintained anymore. It is known to have compatibility problems with R-2.8.x and newer, and the methods it implements are not all state of the art. The above R package above is recommended within the R environment.gene, co-expression, analysis, networkSCR_003302(Weighted Gene Co-expression Network Analysis, RRID:SCR_003302)University of California at Los Angeles; California; USA NCI, NIAID, NIDA, NIDCRPMID:19114008Last checked downnif-0000-31889http://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/Rpackages/WGCNA/#citation
GOEx - Gene Ontology ExplorerResource, software resourceTHIS RESOURCE IS NO LONGER AVAILABLE. Documented July 5, 2018. Gene Ontology Explorer (GOEx) combines data from protein fold changes with GO over-representation statistics to help draw conclusions in proteomic experiments. It is tightly integrated within the PatternLab for Proteomics project and, thus, lies within a complete computational environment that provides parsers and pattern recognition tools designed for spectral counting. GOEx offers three independent methods to query data: an interactive directed acyclic graph, a specialist mode where key words can be searched, and an automatic search. A recent hack included in GOEx is to load the sparse matrix index file directly into GOEx, instead of going through the report generation using the AC/T-fold methods. This makes it easy for GOEx to analyze any list of proteins as long as the list follows the index file format (described in manuscript) . Please note that if using this alternative strategy, there will be no protein fold information. Platform: Windows compatibleproteomics, visualization, statistical analysis, gene ontology, parse, pattern recognition, spectral counting, analysis, protein foldSCR_005779(GOEx - Gene Ontology Explorer, RRID:SCR_005779)The Scripps Research Institute Ary Frauzino Foundation, CAPES, CNPq, FAPERJ BBP grant, Fiocruz-INCA collaboration, genesis molecular biology laboratory, NCRR, NIAID, NIH, NIMH, PAPES, PDTISrelated to: Gene Ontology, listed by: Gene Ontology ToolsPMID:19239707Last checked downnlx_149249http://pcarvalho.com/patternlab/goex.shtml
CharProtDB: Characterized Protein DatabaseResource, data or information resource, databaseThe Characterized Protein Database, CharProtDB, is designed and being developed as a resource of expertly curated, experimentally characterized proteins described in published literature. For each protein record in CharProtDB, storage of several data types is supported. It includes functional annotation (several instances of protein names and gene symbols) taxonomic classification, literature links, specific Gene Ontology (GO) terms and GO evidence codes, EC (Enzyme Commisssion) and TC (Transport Classification) numbers and protein sequence. Additionally, each protein record is associated with cross links to all public accessions in major protein databases as ??synonymous accessions??. Each of the above data types can be linked to as many literature references as possible. Every CharProtDB entry requires minimum data types to be furnished. They are protein name, GO terms and supporting reference(s) associated to GO evidence codes. Annotating using the GO system is of importance for several reasons; the GO system captures defined concepts (the GO terms) with unique ids, which can be attached to specific genes and the three controlled vocabularies of the GO allow for the capture of much more annotation information than is traditionally captured in protein common names, including, for example, not just the function of the protein, but its location as well. GO evidence codes implemented in CharProtDB directly correlate with the GO consortium definitions of experimental codes. CharProtDB tools link characterization data from multiple input streams through synonymous accessions or direct sequence identity. CharProtDB can represent multiple characterizations of the same protein, with proper attribution and links to database sources. Users can use a variety of search terms including protein name, gene symbol, EC number, organism name, accessions or any text to search the database. Following the search, a display page lists all the proteins that match the search term. Click on the protein name to view more detailed annotated information for each protein. Additionally, each protein record can be annotated.protein, annotation, functional annotation, taxonomic classification, literature, gene ontology, evidence code, enzyme commission, transport classification, protein sequenceSCR_005872(CharProtDB: Characterized Protein Database, RRID:SCR_005872)J. Craig Venter Institute NHGRI, NIAIDrelated to: Gene OntologyPMID:22140108Last checked downnlx_149421
Influenza Research Database (IRD)Resource, data analysis service, database, analysis service resource, production service resource, service resource, storage service resource, data repository, data or information resourceThe Influenza Research Database (IRD) serves as a public repository and analysis platform for flu sequence, experiment, surveillance and related data.avian, clinical, genomic, host, influenza, isolate, mammalian, nonhuman, phenotypic, preventive, proteomic, repository, strain, epitope, surveillance, treatment, virus, protein sequence, immune, 3d protein structure, align, blast, short peptide, flu protein, sequence variation, snp, phylogenetic tree, human, 3d spacial image, image, clinical data, clinical, genomic, proteomic, phenotypeSCR_006641(Influenza Research Database (IRD), RRID:SCR_006641) Los Alamos National Laboratory , University of Texas Southwestern Medical Center; Texas; USA , Sage Analytica Influenza virus, InfluenzaNIAIDrelated to: Los Alamos National Laboratory, University of California at Davis, California, USA, Sage Analytica, J. Craig Venter InstitutePMID:17965094Last checked downnif-0000-21222
Nonhuman Primate Transplantation Tolerance Cooperative Study Group Resource, disease-related portal, topical portal, resource, research forum portal, portal, data or information resourceCooperative program for research on nonhuman primate models of kidney, islet, heart, and lung transplantation evaluating the safety and efficacy of existing and new treatment regimens that promote the immune system''''s acceptance of a transplant and to understand why the immune system either rejects or does not reject a transplant. This program bridges the critical gap between small-animal research and human clinical trials. The program supports research into the immunological mechanisms of tolerance induction and development of surrogate markers for the induction, maintenance, and loss of tolerance.transplantation, clinical, kidney, islet, tolerance, heart, lung, treatment, immune system, tolerance inductionSCR_006847( Nonhuman Primate Transplantation Tolerance Cooperative Study Group , RRID:SCR_006847)Kidney transplantation, Islet transplantation, Heart transplantation, Lung transplantationNIAID, NIDDKrelated to: NIDDK Information Network, submitted by: NIDDK Information NetworkLast checked downnlx_152728http://www.niddk.nih.gov/fund/diabetesspecialfunds/consortia/NHP.pdf
AnoBase: An Anopheles databaseResource, data or information resource, databaseA database containing genomic/biological information on anopheline mosquitoes, with an emphasis on Anopheles gambiae, the world''''s most important malaria vector. AnoBase is an integrated, relational database of basic biological and genetic data on anopheline species, with a particular emphasis on Anopheles gambiae. It has been designed as an information source and research support tool for the broad vector biology community. Although AnoBase is not a primary genomic database that develops and provides tools to access the genome of the malaria mosquito, it nevertheless contains several sections that offer data of genomic interest such as in situ hybridization images, an integrated gene tool and direct online access to AnoXcel, the proteomic database of An. gambiae. Moreover, AnoBase also contains information on non-gambiae mosquito species and a novel section on studies related to insecticide resistance.gene, genetic, anopheles gambiae, anopheline, biological, biology, community, genomic, in-situ hybridization, insecticide, invertebrate databases, malaria, mosquito, proteomic, specie, vector, imageSCR_008166(AnoBase: An Anopheles database, RRID:SCR_008166)Foundation for Research and Technology-Hellas; Heraklion; Greece NIAIDrelated to: VectorBaseLast checked downnif-0000-21031http://www.anobase.org/
Induced Mutant ResourceResource, organism supplier, production service resource, biomaterial supply resource, material service resource, service resource, storage service resource, material resource, biomaterial manufacture, material storage repositoryTHIS RESOURCE IS NO LONGER IN SERVICE, documented on June 08, 2012. The function of the IMR is to select, import, cryopreserve, maintain, and distribute these important strains of mice to the research community. To improve their value for research, the IMR also undertakes genetic development of stocks, such as transferring mutant genes or transgenes to defined genetic backgrounds and combining transgenes and/or targeted mutations to create new mouse models for research. The function of the IMR is to: * select biomedically important stocks of transgenic, chemically induced, and targeted mutant mice * import these stocks into the Jackson Laboratory by rederivation procedures that rid them of any pathogens they might carry * cryopreserve embryos from these stocks to protect them against accidental loss and genetic contamination * backcross the mutation onto an inbred strain, if necessary * distribute them to the scientific community More than 1000 mutant stocks have been accepted by the IMR from 1992 through December 2006. Current holdings include models for research on cancer; breast cancer; immunological and inflammatory diseases; neurological diseases; behavioral, cardiovascular and heart diseases; developmental, metabolic and other diseases; reporter (e.g., GFP) and recombinase (e.g., cre/loxP) strains. About eight strains a month are being added to the IMR holdings. Research is being conducted on improved methods for assisted reproduction and speed congenic production. Most of the targeted mutants arrive on a mixed 129xC57BL/6 genetic background, and as many of these as possible are backcrossed onto an inbred strain (usually C57BL/6J). In addition, new mouse models are being created by intercrossing carriers of specific transgenes and/or targeted mutations. Simple sequence length polymorphism DNA markers are being used to characterize and evaluate differences between inbred strains, substrains, and embryonic stem cell lines.embryo, genetic, behavioral, biomedical, breast cancer, cancer, cardiovascular, chemical, cre, cryopreserved, developmental, disease, distribution, dna, gfp, heart, immunological, inflammatory, loxp, marker, metabolic, model, mouse, mutation, neurological, pathogen, polymorphism, recombinase, research, stock, targeting, transgeneSCR_008366(Induced Mutant Resource, RRID:SCR_008366)Jackson Laboratory American Cancer Society, American Heart Association, Amyotrophic Lateral Sclerosis Association, Cystic Fibrosis Foundation, Department of the Army Breast Cancer Research Initiative., Howard Hughes Medical Institute, March of Dimes Birth Defects Foundation, National Multiple Sclerosis Society, NCRR, NIAID, NIAMSLast checked downnif-0000-25566
Immune Disorder OntologyResource, ontology, data or information resource, controlled vocabularyOntology generated as part of the Bioinformatics Integration Support Contract (BISC) that is based on the National Library of Medicine (NLM) Medical Subject Headings; National Cancer Institute Thesaurus; International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM); ICD-10; and other open source public databases. Specific information may be available about a class, including Preferred_Name, DEFINITION, Synonym, etc.obo, health, immunologySCR_010344(Immune Disorder Ontology, RRID:SCR_010344)Division of Allergy Immunology and Transplantation, NIAIDlisted by: BioPortalLast checked downnlx_157438
The Immunology Database and Analysis Portal (ImmPort)Resource, disease-related portal, topical portal, data repository, database, the community can contribute to this resource, availability annotation standard, nif annotation standard, narrative resource, service resource, portal, standard specification, storage service resource, ontology, controlled vocabulary, data or information resourcePlatform for integrated research and data sharing to store, analyze, and exchange datasets for immune mediated diseases. Data supplied by NIAID/DAIT funded investigators and genomic, proteomic, and other data relevant to the research of these programs extracted from public databases. Provides data analysis tools and an immunology focused ontology to advance research in basic and clinical immunology.immunology, basic, clinical, data, share, store, analyze, exchange, dataset, immune, mediated, disease, analysis, toolSCR_012804(The Immunology Database and Analysis Portal (ImmPort), RRID:SCR_012804)Immune mediated diseaseDAIT, NIAID, NIHrelated to: MetaCyto, The 10000 Immunomes, NIAID, listed by: NIDDK Research Resources, affiliated with: Cytokine RegistryPMID:24791905Last checked downnlx_152691http://www.immport.org/immport-open/public/home/home
Collaboratory of AIDS Researchers for Eradciation (CARE)Resource, organization portal, portal, consortium, data or information resourceThe Collaboratory of AIDS Researchers for Eradication (CARE) is a consortium of scientific experts in the field of HIV latency from several U.S. and European academic research institutions as well as Merck Research Laboratories working together to find a cure for HIV.AIDS, HIV, drug development, data-sharing enablerSCR_013681(Collaboratory of AIDS Researchers for Eradciation (CARE), RRID:SCR_013681)NIAID, NIMHrelated to: University of North Carolina at Chapel Hill School of Medicine, North Carolina, USA, Gladstone Institute of Neurological Disease, UCSF School of Medicine, California, USA, Case Western Reserve University, Ohio, USA, Merck, UC Davis School of Medicine, California, USA, University of California at San Diego, California, USA, University of Utah School of Medicine, Utah, USA, University of Minnesota Twin Cities, Minnesota, USALast checked down
Pathogen PortalResource, portal, data or information resourceA set of web-based resources provided by the Bioinformatics Resource Centers (BRCs), focusing on organisms considered as potential agents of biowarfare or bioterrorism or causing emerging or re-emerging diseases. It provides data sets of host responses to pathogens and genome data, as well as tools to analyze host responses to pathogens.microbiome, portal, pathogen, web based, bioinformatics, bioware, bioterrorism, disease, emerging diseaseSCR_014603(Pathogen Portal, RRID:SCR_014603)NIAIDlisted by: Human Microbiome Project, hosted by: Virginia Bioinformatics InstituteLast checked downhttp://hmpdacc.org/resources/tools_protocols.php
MS-GF+Resource, software resourceSoftware that performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.protein idenitification, peptide sequence, ms, ms spectrum, proteomicSCR_015646(MS-GF+, RRID:SCR_015646)Pacific Northwest National Laboratory NCRR, NIAID, W.R. Wiley Environmental Molecular Science Laboratorysubmitted by: Resource Identification PortalPMID:25358478Last checked downhttps://github.com/sangtaekim/msgfplus
Center for Expanded Data Annotation and RetrievalOrganization, ontology, portal, data or information resource, controlled vocabularyOrganization that develops information technologies that make authoring complete metadata more manageable. Its products aim to facilitate using the metadata in further research.metadata, biomedical, research, data, file, software, applicationSCR_016269(Center for Expanded Data Annotation and Retrieval, RRID:SCR_016269)NIAIDLast checked down
Pathosystems Resource Integration CenterResource, data analysis service, production service resource, analysis service resource, database, service resource, bioinformatics resource center, data or information resourceA Bioinformatics Resource Center bacterial bioinformatics database and analysis resource that provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data) and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. The PATRIC project includes three primary collaborators: the University of Chicago, the University of Manchester, and New City Media. The University of Chicago is providing genome annotations and a PATRIC end-user genome annotation service using their Rapid Annotation using Subsystem Technology (RAST) system. The National Centre for Text Mining (NaCTeM) at the University of Manchester is providing literature-based text mining capability and service. New City Media is providing assistance in website interface development. An FTP server and download tool are available.genomics, genome, transcriptomics, protein-protein interaction, sequence typing, proteobacteria, brucella, rickettsia, coxiella, coronavirus, calicivirus, lyssavirus, virus, hepatitis a, hepatitis e, pathway, proteome, metabolic pathway, drug, vaccine, diagnosticsSCR_004154(Pathosystems Resource Integration Center, RRID:SCR_004154)Virginia Polytechnic Institute and State University; Virginia; USA NIAIDlisted by: OMICtoolsReferences (2)Last checked downnlx_17476, OMICS_01658http://patricbrc.vbi.vt.edu/portal/portal/patric/Homehttp://patric.vbi.vt.edu/
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