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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GeneVito Resource Report Resource Website |
GeneVito (RRID:SCR_006211) | GeneVito | data processing software, data visualization software, software application, software resource | A JAVA-based computer application that serves as a workbench for genome-wide analysis through visual interaction. GeneViTo offers an inspectional view of genomic functional elements, concerning data stemming both from database annotation and analysis tools for an overall analysis of existing genomes. The application deals with various experimental information concerning both DNA and protein sequences (derived from public sequence databases or proprietary data sources) and meta-data obtained by various prediction algorithms, classification schemes or user-defined features. Interaction with a Graphical User Interface (GUI) allows easy extraction of genomic and proteomic data referring to the sequence itself, sequence features, or general structural and functional features. Emphasis is laid on the potential comparison between annotation and prediction data in order to offer a supplement to the provided information, especially in cases of poor annotation, or an evaluation of available predictions. Moreover, desired information can be output in high quality JPEG image files for further elaboration and scientific use. GeneViTo has already been applied to visualize the genomes of two microbial organisms: the bacterion Chlamydia trachomatis and the archaeon Methanococcus jannaschii. The application is compatible with Linux or Windows ME-2000-XP operating systems, provided that the appropriate Java Runtime Environment (Java 1.4.1) is already installed in the system. | java, genome-wide analysis, genome, visualization, gene, function, structure, dna, protein sequence, genomic, proteomic | has parent organization: University of Athens Biophysics and Bioinformatics Laboratory | PMID:14594459 | Free for academic use, Acknowledgement requested | nlx_151776 | SCR_006211 | GeneVito: Genome Visualization Tool, GeneViTo (Genome Visualization Tool), Genome Visualization Tool | 2026-09-12 12:56:36 | 0 | ||||||
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Public Health Genomics Resource Report Resource Website 500+ mentions |
Public Health Genomics (RRID:SCR_006462) | data or information resource, narrative resource, organization portal, podcast, portal, radio, training resource | The Office of Public Health Genomics (OPHG) aims to integrate genomics into public health research, policy, and programs. Doing so could improve interventions designed to prevent and control the country''s leading chronic, infectious, environmental, and occupational diseases. OPHG''s efforts focus on conducting population-based genomic research, assessing the role of family health history in disease risk and prevention, supporting a systematic process for evaluating genetic tests, translating genomics into public health research and programs, and strengthening capacity for public health genomics in disease prevention programs. Goals: To improve public health interventions of diseases of major public health importance, including chronic, infectious, environmental, and occupational diseases, through six major initiatives: * Evaluation of Genomic Applications in Practice and Prevention (EGAPP), * Human Genome Epidemiology Network (HuGENet), * NHANES Collaborative Genomics Project, * Family History Public Health Initiative, * Genomics Translation Research and Programs, and, * Genomic Applications in Practice and Prevention Network (GAPPNet). | environmental, genetics, chronic, disease, genomic, health, infectious, occupational, prevention, research | has parent organization: Centers for Disease Control and Prevention | nif-0000-10186 | SCR_006462 | Genomics | 2026-09-12 12:56:40 | 885 | |||||||||
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NCBI Resource Report Resource Website 10000+ mentions |
NCBI (RRID:SCR_006472) | NCBI | nonprofit organization | A portal to biomedical and genomic information. NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information for the better understanding of molecular processes affecting human health and disease. | biomedical, genomic, molecular biology, health, disease, database, computational biology, bio.tools |
is used by: NIF Data Federation is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: NCBI Viral Genomes is related to: Clone DB is related to: PubReader is related to: OMIA - Online Mendelian Inheritance in Animals is related to: European Nucleotide Archive (ENA) is related to: Plant Co-expression Annotation Resource is related to: METAGENOTE is related to: Phyutility is related to: CaspBase is related to: Prokaryotic Genomes Automatic Annotation Pipeline has parent organization: National Library of Medicine is parent organization of: MedGen is parent organization of: dbSTS is parent organization of: PubMed Health is parent organization of: BLASTP is parent organization of: GQuery is parent organization of: BLASTN is parent organization of: GTEx eQTL Browser is parent organization of: BLASTX is parent organization of: Homology Maps Page is parent organization of: PEDHUNTER is parent organization of: Conserved Domain Database is parent organization of: NCBI Genome Survey Sequences Database is parent organization of: High Throughput Genomic Sequences Division is parent organization of: AceView is parent organization of: dbMHC is parent organization of: dbSNP is parent organization of: Entrez Gene is parent organization of: NCBI Genome is parent organization of: NCBI database of Genotypes and Phenotypes (dbGap) is parent organization of: GenBank is parent organization of: International HapMap Project is parent organization of: IgBLAST is parent organization of: Lowes Syndrome Mutation Database is parent organization of: HomoloGene is parent organization of: Influenza Virus Resource is parent organization of: Distant Regulatory Elements is parent organization of: e-PCR is parent organization of: MapViewer is parent organization of: Primer-BLAST is parent organization of: dbVar is parent organization of: NCBI Taxonomy is parent organization of: NCBI Protein Database is parent organization of: Gene Reference into Function is parent organization of: Protein Clusters is parent organization of: RefSeq is parent organization of: TPA is parent organization of: GENSAT at NCBI - Gene Expression Nervous System Atlas is parent organization of: COBALT: Constraint-based Multiple Alignment Tool is parent organization of: PubMed Central is parent organization of: UniLib is parent organization of: NCBI Structure is parent organization of: PubChem is parent organization of: Anopheles gambiae (African malaria mosquito) genome view is parent organization of: UniGene is parent organization of: NLM Catalog is parent organization of: Entrez GEO Profiles is parent organization of: Nucleotide database is parent organization of: NCBI BioSystems Database is parent organization of: CBLAST is parent organization of: NCBI BioProject is parent organization of: NCBI Probe is parent organization of: PubMed is parent organization of: NCBI BioSample is parent organization of: NCBI Nucleotide is parent organization of: NCBI Structure: Cn3D is parent organization of: NCBI BLAST is parent organization of: IBIS: Inferred Biomolecular Interactions Server is parent organization of: NCBI Sequence Read Archive (SRA) is parent organization of: Gene Expression Omnibus (GEO) is parent organization of: NCBI Popset is parent organization of: PIE the search is parent organization of: Genetic Testing Registry is parent organization of: NCBI Resource List is parent organization of: NCBI dbRBC is parent organization of: NCBI YouTube Channel is parent organization of: NCBI Epigenomics is parent organization of: ClinVar is parent organization of: Genome Reference Consortium is parent organization of: GeneReviews is parent organization of: Molecular Imaging and Contrast Agent Database is parent organization of: Consensus CDS is parent organization of: UniSTS is parent organization of: HIV-1 Human Protein Interaction Database is parent organization of: Assay Guidance Manual is parent organization of: Bookshelf is parent organization of: COG is parent organization of: Gene Expression Omnibus is parent organization of: Molecular Modelling DataBase is parent organization of: Organelle Genome Resources is parent organization of: SKY/M-FISH/CGH is parent organization of: dbEST is parent organization of: JournalReview.org is parent organization of: NCBI GenBank via FTP is parent organization of: PubChem Compound is parent organization of: Molecular Modeling DataBase is parent organization of: Vector Alignment Search Tool is parent organization of: PubChem BioAssay is parent organization of: NCBI Genome Workbench is parent organization of: TBLASTN is parent organization of: TBLASTX is parent organization of: Mega BLAST is parent organization of: Genetic Codes is parent organization of: HIV-1, Human Protein Interaction Database is parent organization of: PubReader is parent organization of: PubChem Substance is parent organization of: OMIA - Online Mendelian Inheritance in Animals is parent organization of: OMIM is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: GeneTests is parent organization of: NCBI Genome Survey Sequences Database is parent organization of: MagicBlast is parent organization of: RefSeq is parent organization of: Sequin is parent organization of: Batch Entrez is parent organization of: Entrez is parent organization of: tbl2asn is parent organization of: Whole Genome Shotgun (WGS) Project is parent organization of: Digital Differential Display (DDD) is parent organization of: BLASTClust is parent organization of: PASC is parent organization of: Open Reading Frame Finder is parent organization of: Genotyping works with: Human Mouse Disease Connection works with: A plasmid Editor works with: Database of genes related to Repeat Expansion Diseases |
Public, The community can contribute to this resource | nif-0000-00139, biotools:ncbi_resources | https://bio.tools/ncbi_resources | http://www.ncbi.nih.gov/ | SCR_006472 | National Center for Biotechnology Information, NCBI - National Center for Biotechnology Information | 2026-09-12 12:56:40 | 29053 | |||||
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GeneAnswers Resource Report Resource Website 10+ mentions |
GeneAnswers (RRID:SCR_006498) | data analysis software, data processing software, data visualization software, software application, software resource | GeneAnswers provide an integrated tool for given genes biological or medical interpretation. It includes statistical test of given genes and specified categories. Microarray techniques have been widely employed in genomic scale studies for more than one decade. The standard analysis of microarray data is to filter out a group of genes from thousands of probes by certain statistical criteria. These genes are usually called significantly differentially expressed genes. Recently, next generation sequencing (NGS) is gradually adopted to explore gene transcription, methylation, etc. Also a gene list can be obtained by NGS preliminary data analysis. However, this type of information is not enough to understand the potential linkage between identified genes and interested functions. The integrated functional and pathway analysis with gene expression data would be very helpful for researchers to interpret the relationship between the identified genes and proposed biological or medical functions and pathways. The GeneAnswers package provides an integrated solution for a group of genes and specified categories (biological or medical functions, such as Gene Ontology, Disease Ontology, KEGG, etc) to reveal the potential relationship between them by means of statistical methods, and make user-friendly network visualization to interpret the results. Besides the package has a function to combine gene expression profile and category analysis together by outputting concept-gene cross tables, keywords query on NCBI Entrez Gene and application of human based Disease ontology analysis of given genes from other species can help people to understand or discover potential connection between genes and functions. Sponsors: This project was supported in part by Award Number UL1RR025741 from the National Center for Research Resources. | expression, function, gene, analysis, biological, genomic, medical, microarray, network, pathway, technique, transcription, visualization | has parent organization: Northwestern University; Illinois; USA | nif-0000-25387 | SCR_006498 | GeneAnswers | 2026-09-12 12:56:40 | 48 | |||||||||
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GMD Resource Report Resource Website 100+ mentions |
GMD (RRID:SCR_006625) | GMD | data access protocol, data or information resource, database, service resource, software resource, web service | It facilitates the search for and dissemination of mass spectra from biologically active metabolites quantified using Gas chromatography (GC) coupled to mass spectrometry (MS). Use the Search Page to search for a compound of your interest, using the name, mass, formula, InChI etc. as query input. Additionally, a Library Search service enables the search of user submitted mass spectra within the GMD. In parallel to the library search, a prediction of chemical sub-groups is performed. This approach has reached beta level and a publication is currently under review. Using several sub-group specific Decision Trees (DTs), mass spectra are classified with respect to the presence of the chemical moieties within the linked (unknown) compound. Prediction of functional groups (ms analysis) facilitates the search of metabolites within the GMD by means of user submitted GC-MS spectra consisting of retention index (n-alkanes, if vailable) and mass intensities ratios. In addition, a functional group prediction will help to characterize those metabolites without available reference mass spectra included in the GMD so far. Instead, the unknown metabolite is characterized by predicted presence or absence of functional groups. For power users this functionality presented here is exposed as soap based web services. Functional group prediction of compounds by means of GC-EI-MS spectra using Microsoft analysis service decision trees All currently available trained decision trees and sub-structure predictions provided by the GMD interface. Table describes the functional group, optional use of an RI system, record date of the trained decision tree, number of MSTs with proportion of MSTs linked to metabolites with the functional group present for each tree. Average and standard deviation of the 50-fold CV error, namely the ratio false over correctly sorted MSTs in the trained DT, are listed. The GMD website offers a range of mass spectral reference libraries to academic users which can be downloaded free of charge in various electronic formats. The libraries are constituted by base peak normalized consensus spectra of single analytes and contain masses in the range 70 to 600 amu, while the ubiquitous mass fragments typically generated from compounds carrying a trimethylsilyl-moiety, namely the fragments at m/z 73, 74, 75, 147, 148, and 149, were excluded. | drug, expression, functional, gas chromatography, gene, general chemistry databases, bioinformatic, biological extract, biology, biotechnology, compound, genomic, herbicide, mass spectra, mass spectrometry, metabolism, metabolite, metabolomics, organism, profiling, protein, spectral, system, FASEB list | has parent organization: Max Planck Institute of Molecular Plant Physiology; Golm; Germany | PMID:15613389 PMID:15733837 PMID:18501684 PMID:20526350 |
r3d100011046, nif-0000-21180 | http://csbdb.mpimp-golm.mpg.de/csbdb/gmd/gmd.html, https://doi.org/10.17616/R3MC9K | SCR_006625 | Golm Metabolome Data Base, The Golm Metabolome Database, Golm Metabolome Database | 2026-09-12 12:56:42 | 192 | ||||||
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Influenza Research Database (IRD) Resource Report Resource Website 50+ mentions |
Influenza Research Database (IRD) (RRID:SCR_006641) | IRD | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | The 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, phenotype |
is recommended by: NIDDK Information Network (dkNET) is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing is related to: Los Alamos National Laboratory is related to: University of California at Davis; California; USA is related to: Sage Analytica is related to: J. Craig Venter Institute has parent organization: University of Texas Southwestern Medical Center; Texas; USA has parent organization: Los Alamos National Laboratory has parent organization: Sage Analytica |
Influenza virus, Influenza | NIAID | PMID:17965094 | Acknowledgement requested, The community can contribute to this resource | DOI:10.25504/FAIRsharing.ws7cgw, nif-0000-21222, DOI:10.17616/R3S634, DOI:10.35094, r3d100011558 | https://www.fludb.org/, https://doi.org/10.17616/R3S634, https://doi.org/10.17616/r3s634, https://doi.org/10.35094/, https://dx.doi.org/10.35094/, https://fairsharing.org/10.25504/FAIRsharing.ws7cgw, https://doi.org/10.17616/R3S634 | http://www.fludb.org/brc/home.do?decorator=influenza | SCR_006641 | , Influenza Research Database, IRD | 2026-09-12 12:56:43 | 55 | ||
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Descriptions of Plant Viruses Resource Report Resource Website 10+ mentions |
Descriptions of Plant Viruses (RRID:SCR_006656) | data or information resource, database, portal, topical portal | DPVweb provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences are provided. The database also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. For comparative purposes, it also contains a single representative sequence of all other fully sequenced virus species with an RNA or single-stranded DNA genome. The start and end positions of each feature (gene, non-translated region and the like) have been recorded and checked for accuracy. As far as possible, nomenclature for genes and proteins are standardized within genera and families. Sequences of features (either as DNA or amino acid sequences) can be directly downloaded from the website in FASTA format. The sequence information can also be accessed via client software for PC computers (freely downloadable from the website) that enable users to make an easy selection of sequences and features of a chosen virus for further analyses. The public sequence databases contain vast amounts of data on virus genomes but accessing and comparing the data, except for relatively small sets of related viruses can be very time consuming. The procedure is made difficult because some of the sequences on these databases are incorrectly named, poorly annotated or redundant. The NCBI Reference Sequence project (1) provides a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA) and protein products, for major research organisms. This now includes curated information for a single sequence of each fully sequenced virus species. While this is a welcome development, it can only deal with complete sequences. An important feature of DPV is the opportunity to access genes (and other features) of multiple sequences quickly and accurately. Thus, for example, it is easy to obtain the nucleotide or amino acid sequences of all the available accessions of the coat protein gene of a given virus species or for a group of viruses. To increase its usefulness further, DPVweb also contains a single representative sequence of all other fully sequenced virus species with an RNA or single-stranded DNA (ssDNA) genome. Sponsors: This site is supported by the Association of Applied Biologists and the Zhejiang Academy of Agricultural Sciences, Hangzhou, People''s Republic of China. | family, fungi, gene, amino acid, comparative, development, dna, genome, genomic, genus, nomenclature, non-translated, nucleotide, organism, plant, product, protein, protozoa, region, rna, satellite, sequence, single, specie, taxonomic, transcript, viral databases, viroid, virus, bio.tools |
is listed by: bio.tools is listed by: Debian |
nif-0000-21127, biotools:dpvweb | https://bio.tools/dpvweb | SCR_006656 | DPV | 2026-09-12 12:56:43 | 15 | ||||||||
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InParanoid: Eukaryotic Ortholog Groups Resource Report Resource Website 100+ mentions |
InParanoid: Eukaryotic Ortholog Groups (RRID:SCR_006801) | InParanoid | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Collection of pairwise comparisons between 100 whole genomes generated by a fully automatic method for finding orthologs and in-paralogs between TWO species. Ortholog clusters in the InParanoid are seeded with a two-way best pairwise match, after which an algorithm for adding in-paralogs is applied. The method bypasses multiple alignments and phylogenetic trees, which can be slow and error-prone steps in classical ortholog detection. Still, it robustly detects complex orthologous relationships and assigns confidence values for in-paralogs. The original data sets can be downloaded. | protein, ortholog, genome, drosophila pseudoobscura, duplication, entamoeba histolytica, escherichia colik12, eukaryotic, gasterosteus aculeatus, gene, aedes aegypti, apis mellifera, bos taurus, caenorhabditis remanei, candida glabrata, canis familiaris, ciona intestinalis, cryptococcus neoformans, debaromyces hansenii, dictyostelium discoideum, genomic, homolog, inparalog, kluyveromyces lactis, macaca mulatta, monodelphis domestica, orthology, oryza sativa, outparalog, proteome, tetraodon nigroviridis, xenopus tropicalis, blast, proteome, ortholog cluster, cluster, in-paralog, paralog, automatic clustering, genome comparison, FASEB list | has parent organization: Stockholm University; Stockholm; Sweden | Swedish Research Council ; Karolinska Institutet; Stockholm; Sweden ; Pfizer Corporation |
PMID:19892828 PMID:18055500 PMID:15608241 PMID:11743721 |
Acknowledgement requested | nif-0000-03024 | http://www.cgb.ki.se/inparanoid/ | SCR_006801 | Inparanoid eukaryotic ortholog database | 2026-09-12 12:56:45 | 189 | ||||
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Mouse Biomedical Informatics Research Network Resource Report Resource Website |
Mouse Biomedical Informatics Research Network (RRID:SCR_003392) | MouseBIRN, mBIRN | atlas, data or information resource, data set, reference atlas | Animal model data primarily focused on mice including high resolution MRI, light and electron microscopic data from normal and genetically modified mice. It also has atlases, and the Mouse BIRN Atlasing Toolkit (MBAT) which provides a 3D visual interface to spatially registered distributed brain data acquired across scales. The goal of the Mouse BIRN is to help scientists utilize model organism databases for analyzing experimental data. Mouse BIRN has ended. The next phase of this project is the Mouse Connectome Project (https://www.nitrc.org/projects/mcp/). The Mouse BIRN testbeds initially focused on mouse models of neurodegenerative diseases. Mouse BIRN testbed partners provide multi-modal, multi-scale reference image data of the mouse brain as well as genetic and genomic information linking genotype and brain phenotype. Researchers across six groups are pooling and analyzing multi-scale structural and functional data and integrating it with genomic and gene expression data acquired from the mouse brain. These correlated multi-scale analyses of data are providing a comprehensive basis upon which to interpret signals from the whole brain relative to the tissue and cellular alterations characteristic of the modeled disorder. BIRN's infrastructure is providing the collaborative tools to enable researchers with unique expertise and knowledge of the mouse an opportunity to work together on research relevant to pre-clinical mouse models of neurological disease. The Mouse BIRN also maintains a collaborative Web Wiki, which contains announcements, an FAQ, and much more. | electron microscopy, expression, functional, gene, 3-dimentional, brain, cellular, disorder, genomic, genotype, mouse, neurodegenerative disease, phenotype, molecular neuroanatomy resource, mri, light microscopy, model organism, gene expression, atlas data, imaging genomics, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Mouse BIRN Atlasing Toolkit is related to: Mouse Connectome Project has parent organization: Biomedical Informatics Research Network |
Normal, Neurodegenerative disease, Multiple Sclerosis, Alzheimer's disease, Parkinson's disease | NIH ; Collaborative Tools Support Network Award ; NCRR 1U24-RR025736; NCRR U24-RR021992; NCRR U24-RR021760; NCRR 1U24-RR026057-01 |
Free, Available for download, Freely available | nif-0000-00200 | https://loni.usc.edu/research/software?name=MBATWA | http://www.loni.ucla.edu/BIRN/Projects/Mouse/index.shtml | SCR_003392 | Mouse BIRN | 2026-09-12 12:55:57 | 0 | |||
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Comprehensive Biomarker Center Resource Report Resource Website |
Comprehensive Biomarker Center (RRID:SCR_003901) | CBC | commercial organization | Commercial organization that discovers, validates & analyzes genomic biomarkers with a focus on body fluid samples. Take advantage of their proven expertise in biomarker signature development and speed up your biomarker studies. | biomarker, clinical research organization, genomic biomarker, genomic, diagnostic, testing, bodily fluid, clinical, dna, rna, dna extraction, rna extraction, microarray, next-generation sequencing, validation, microrna | is related to: READNA | nlx_158236 | SCR_003901 | febit, febit GmbH, Comprehensive Biomarker Center Gmbh | 2026-09-12 12:56:04 | 0 | ||||||||
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AirPROM Resource Report Resource Website |
AirPROM (RRID:SCR_003827) | AirPROM | consortium, data or information resource, organization portal, portal | Consortium focused on developing computer and physical models of the airway system for patients with asthma and chronic obstructive pulmonary disease (COPD). Developing accurate models will better predict how asthma and COPD develop, since current methods can only assess the severity of disease. They aim to bridge the gaps in clinical management of airways-based disease by providing reliable models that predict disease progression and the response to treatment for each person with asthma or COPD. A data management platform provides a secure and sustainable infrastructure that semantically integrates the clinical, physiological, genetic, and experimental data produced with existing biomedical knowledge from allied consortia and public databases. This resource will be available for analysis and modeling, and will facilitate sharing, collaboration and publication within AirPROM and with the broader community. Currently the AirPROM knowledge portal is only accessible by AirPROM partners. | model, airway system, lung, consortium, clinical, imaging, respiratory system, tissue sample, airway model, genomic, gas diffusion mri, airway development, function, physiological, genetic, computational model, gene-environment interaction |
is listed by: Consortia-pedia has parent organization: European Lung Foundation |
European Union FP7 | nlx_158142 | SCR_003827 | Airway Disease Predicting Outcomes through Patient Specific Computational Modelling | 2026-09-12 12:56:03 | 0 | |||||||
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Cohorts for Heart and Aging Research in Genomic Epidemiology Resource Report Resource Website 10+ mentions |
Cohorts for Heart and Aging Research in Genomic Epidemiology (RRID:SCR_004034) | CHARGE Consortium, CHARGE | bibliography, consortium, data or information resource, organization portal, portal | Consortium formed to facilitate genome-wide association study meta-analyses and replication opportunities among multiple large and well-phenotyped longitudinal cohort studies. A bibliography of CHARGE publications is available. Its founding member cohorts include: * Age, Gene, Environment, Susceptibility Study -- Reykjavik * Atherosclerosis Risk in Communities Study * Cardiovascular Health Study * Framingham Heart Study * Rotterdam Study Additional core cohorts include: * Coronary Artery Risk Development in Young Adults * Family Heart Study * Health, Aging, and Body Composition Study * Jackson Heart Study * Multi-Ethnic Study of Atherosclerosis | genome-wide association study, genomic, epidemiology, phenotype, longitudinal | is related to: International Genomics of Alzheimers Project | Aging, Heart disease | PMID:20031568 | nlx_158460 | SCR_004034 | 2026-09-12 12:56:07 | 19 | |||||||
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Virus Pathogen Resource (ViPR) Resource Report Resource Website 100+ mentions |
Virus Pathogen Resource (ViPR) (RRID:SCR_012983) | ViPR | data or information resource, data processing software, data repository, data visualization software, database, service resource, software application, software resource, storage service resource | Provides searchable public repository of genomic, proteomic and other research data for different strains of pathogenic viruses along with suite of tools for analyzing data. Data can be shared, aggregated, analyzed using ViPR tools, and downloaded for local analysis. ViPR is an NIAID-funded resource that support the research of viral pathogens in the NIAID Category A-C Priority Pathogen lists and those causing (re)emerging infectious diseases. It provides a dedicated gateway to SARS-CoV-2 data that integrates data from external sources (GenBank, UniProt, Immune Epitope Database, Protein Data Bank), direct submissions, analysis pipelines and expert curation, and provides a suite of bioinformatics analysis and visualization tools for virology research. | flu, gene, bioinformatic, database, diagnostic, genomic, health, human, influenza, pathogen, protein, research, strain, therapeutic, tool, vaccine, virus, visualization, FASEB list |
is recommended by: National Library of Medicine is listed by: Data and Computational Resources to Address COVID-19 is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing has parent organization: University of Texas Southwestern Medical Center; Texas; USA |
COVID-19 | NIAID | Restricted | nif-0000-25312, DOI:10.35083, DOI:10.35084, DOI:10.17616/R30P93, DOI:10.25504/FAIRsharing.2qx8n8 | http://www.viprbrc.org/, https://doi.org/10.17616/r30p93, https://doi.org/10.35083/, https://doi.org/10.35084/, https://dx.doi.org/10.35083/, https://dx.doi.org/10.35084/, https://fairsharing.org/10.25504/FAIRsharing.2qx8n8 | SCR_012983 | Virus Pathogen Resource, ViPR | 2026-09-12 12:57:56 | 173 | ||||
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PIAGE Resource Report Resource Website |
PIAGE (RRID:SCR_013124) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software program that performs estimation of power and sample sizes required to detect genetic and environmental main, as well as gene-environment interaction (GxE) effects in indirect matched case-control studies (1:1 matching). When the hypothesis of GxE is tested, power/sample size will be estimated for the detection of GxE, as well as for the detection of genetic and environmental marginal effects. Furthermore, power estimation is implemented for the joint test of genetic marginal and GxE effects (Kraft P et al., 2007). Power and sample size estimations are based on Gauderman''s (2002) asymptotic approach for power and sample size estimations in direct studies of GxE. Hardy-Weinberg equilibrium and independence of genotypes and environmental exposures in the population are assumed. The estimates are based on genotypic codes (G=1 (G=0) for individuals who carry a (non-) risk genotype), which depend on the mode of inheritance (dominant, recessive, or multiplicative). A conditional logistic regression approach is used, which employs a likelihood-ratio test with respect to a biallelic candidate SNP, a binary environmental factor (E=1 (E=0) in (un)exposed individuals), and the interaction between these components. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, ms-windows, linux | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154534, SCR_009372, nlx_154594 | SCR_013124 | R/PIAGE, Power of Indirect Association Studies of Gene-Environment Interactions | 2026-09-12 12:57:59 | 0 | ||||||||
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BOOST Resource Report Resource Website 10+ mentions |
BOOST (RRID:SCR_013133) | BOOST | data analysis software, data processing software, software application, software resource | Software application (entry from Genetic Analysis Software) for a method for detecting gene-gene interactions. It allows examining all pairwise interactions in genome-wide case-control studies. | gene, genetic, genomic, logistic regression model, gene-gene interactions | is listed by: Genetic Analysis Software | Free, Available for download | nlx_154249 | SCR_013133 | BOolean Operation based Screening and Testing | 2026-09-12 12:57:59 | 33 | |||||||
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PlasmoDB Resource Report Resource Website 1000+ mentions |
PlasmoDB (RRID:SCR_013331) | analysis service resource, data access protocol, data analysis service, data or information resource, data repository, database, production service resource, service resource, software resource, storage service resource, web service | Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene. | Functional, genomic, database, malaria, parasite, data, analysis, visualization, gene, genome, annotation, transcription, proteomics, protein, evolution, FASEB list |
uses: SynView is related to: GeneDB Pfalciparum has parent organization: Eukaryotic Pathogen Database Resources has parent organization: Pennsylvania State University has parent organization: University of Georgia; Georgia; USA |
malaria | NIAID | PMID:18957442 | nif-0000-03314, SCR_017665, r3d100011569 | SCR_013331 | PlasmoDB, Plasmodium Genomics Resource, PlasmoDB 5.5, Plasmodium genome-resource | 2026-09-12 12:58:02 | 1324 | ||||||
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R/FEST Resource Report Resource Website 1+ mentions |
R/FEST (RRID:SCR_013347) | software application, software resource | An R package for simulations and likelihood calculations of pair-wise family relationships using DNA marker data. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154111, SCR_000830, nlx_154582 | SCR_013347 | FEST | 2026-09-12 12:58:02 | 2 | |||||||||
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Informatics for Integrating Biology and the Bedside Resource Report Resource Website 10+ mentions |
Informatics for Integrating Biology and the Bedside (RRID:SCR_013629) | i2b2 | data or information resource, data set, organization portal, portal, software resource, training resource | i2b2 (Informatics for Integrating Biology and the Bedside) is an NIH-funded National Center for Biomedical Computing based at Partners HealthCare System. The i2b2 Center is developing a scalable informatics framework that will enable clinical researchers to use existing clinical data for discovery research and, when combined with IRB-approved genomic data, facilitate the design of targeted therapies for individual patients with diseases having genetic origin. For some resources (e.g. software) the use of the resource requires accepting a specific (e.g. OpenSource) license. | genetic, biology, biomedical, computing, genomic, health, healthcare, informatic, origin, patient, therapy, predoctoral, postdoctoral |
is related to: National Centers for Biomedical Computing is parent organization of: i2b2 Cross-Institutional Clinical Translational Research project is parent organization of: Smoking NLP Challenge Data |
NLM U54LM008748 | Free, Public, Acknowledgement requested | nif-0000-33133 | SCR_013629 | 2026-09-12 12:58:06 | 30 | |||||||
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Velvet Resource Report Resource Website 1000+ mentions |
Velvet (RRID:SCR_010755) | Velvet | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package as de novo genomic assembler for short read sequencing technologies using de Bruijn graphs. Takes in short read sequences, removes errors, then produces high quality unique contigs, retrieves repeated areas between contigs. Can leverage very short reads in combination with read pairs to produce useful assemblies. Operating system Unix/Linux., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | de novo, genomic, assembly, short, read, sequencing, de Bruijn, graph, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Velvet-SC is related to: shovill has parent organization: European Bioinformatics Institute |
EMBL | PMID:18349386 DOI:10.1101/gr.074492.107 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00038, biotools:velvet | https://www.ebi.ac.uk/~zerbino/velvet/, https://bio.tools/velvet, https://sources.debian.org/src/velvet/ | SCR_010755 | 2026-09-12 12:57:22 | 1039 | |||||
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HOMER Resource Report Resource Website 5000+ mentions |
HOMER (RRID:SCR_010881) | HOMER | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++. | motif, discovery, next, generation, sequencing, analysis, genomic, data |
is listed by: OMICtools is related to: findMotif.pl has parent organization: University of California at San Diego; California; USA |
Foundation Leducq Transatlantic Network Grant ; NCI CA52599; NIDDK DK063491; NIGMS P50 GM081892; NIH HC088093; NURSA consortium grant |
PMID:20513432 | OMICS_00483 | http://biowhat.ucsd.edu/homer/index.html | SCR_010881 | HOMER, Hypergeometric Optimization of Motif EnRichment, Homer, Homer v4.5 | 2026-09-12 12:57:25 | 5929 |
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