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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GoatMap Database Resource Report Resource Website |
GoatMap Database (RRID:SCR_008144) | portal, database, service resource, storage service resource, data repository, data or information resource, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. This website contains information about the mapping of the caprine genome. It contains loci list, phenes list, cartography, gene list, and other sequence information about goats. This website contains 731 loci, 271 genes, and 1909 homologue loci on 112 species. It also allows users to summit their own data for Goatmap. ARK-Genomics is not-for-profit and has collaborators from all over the world with an interest in farm animal genomics and genetics. ARK-Genomics was initially set up in 2000 with a grant awarded from the BBSRC IGF (Investigating Gene Function) initiative and from core resources of the Roslin Institute to provide a laboratory for automated analysis of gene expression using state-of-the-art genomic facilities. Since then, ARK-Genomics has expanded considerably, building up considerable expertise and resources. | farm, gene, animal, caprine, cartography, genome, genomic, goat, homologue, locus, map, mapping, phene, sequence | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20978 | SCR_008144 | GoatMap | 2026-02-15 09:19:48 | 0 | |||||||||
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Bacterial Genomes Resource Report Resource Website 10+ mentions |
Bacterial Genomes (RRID:SCR_008141) | software application, data processing software, software resource, database, data or information resource, data analysis software | This website includes a list of projects that the Sanger Institute is currently working on or completed. All projects consist of the genomic sequencing of different bacteria. Each description of the bacteria includes its classification, a description, and the types of diseases that the bacteria is likely to cause. The Sanger Institute bacterial sequencing effort is concentrated on pathogens and model organisms. Data is accessible in a number of ways; for each organism there is a BLAST server, allowing users to search the sequences with their own query and retrieve the matching contigs. Sequences can also be downloaded directly by FTP. Data is accessible in a number of ways; for each organism there is a BLAST server, allowing you to search the sequences with your own query and retrieve the matching contigs. Sequences can also be downloaded directly by FTP. The primary sequence viewer and annotation tool, Artemis is available for download. This is a portable Java program which is used extensively within the Microbial Genomes group for the analysis and annotation of sequence data from cosmids to whole genomes. The Artemis Comparison Tool (ACT) is also useful for interactive viewing of the comparisons between large and small sequences. | bacteria, bacterial, classification, description, disease, genomic, model, organism, pathogen, sequence, sequencing, model |
is listed by: 3DVC has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
nif-0000-20963 | SCR_008141 | Bacterial Genomes | 2026-02-15 09:19:43 | 12 | |||||||||
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Bio2RDF atlas of post genomic knowledge Resource Report Resource Website 10+ mentions |
Bio2RDF atlas of post genomic knowledge (RRID:SCR_007991) | portal, blog, data or information resource, narrative resource, topical portal | This is a blog about post genomic knowledge. The website''s goal is to make public datasets from the bioinformatics community available in RDF format via standard SPARQL endpoints. | bioinformatic, community, dataset, genomic, knowledge, rdf | nif-0000-10166 | SCR_007991 | Bio2RDF | 2026-02-15 09:19:40 | 41 | ||||||||||
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Distributed Annotation System Resource Report Resource Website 10+ mentions |
Distributed Annotation System (RRID:SCR_008427) | standard specification, data or information resource, narrative resource, software resource | The Distributed Annotation System (DAS) defines a communication protocol used to exchange annotations on genomic or protein sequences. It is motivated by the idea that such annotations should not be provided by single centralized databases, but should instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is done by DAS clients. The advantages of this system are that control over the data is retained by data providers, data is freed from the constraints of specific organisations and the normal issues of release cycles, API updates and data duplication are avoided. DAS is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up sequence annotation information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers. DAS is heavily used in the genome bioinformatics community. Over the last years we have also seen growing acceptance in the protein sequence and structure communities. A DAS-enabled website or application can aggregate complex and high-volume data from external providers in an efficient manner. For the biologist, this means the ability to plug in the latest data, possibly including a user''s own data. For the application developer, this means protection from data format changes and the ability to add new data with minimal development cost. Here are some examples of DAS-enabled applications or websites for end users: :- Dalliance Experimental Web/Javascript based Genome Viewer :- IGV Integrative Genome Viewer java based browser for many genomes :- Ensembl uses DAS to pull in genomic, gene and protein annotations. It also provides data via DAS. :- Gbrowse is a generic genome browser, and is both a consumer and provider of DAS. :- IGB is a desktop application for viewing genomic data. :- SPICE is an application for projecting protein annotations onto 3D structures. :- Dasty2 is a web-based viewer for protein annotations :- Jalview is a multiple alignment editor. :- PeppeR is a graphical viewer for 3D electron microscopy data. :- DASMI is an integration portal for protein interaction data. :- DASher is a Java-based viewer for protein annotations. :- EpiC presents structure-function summaries for antibody design. :- STRAP is a STRucture-based sequence Alignment Program. Hundreds of DAS servers are currently running worldwide, including those provided by the European Bioinformatics Institute, Ensembl, the Sanger Institute, UCSC, WormBase, FlyBase, TIGR, and UniProt. For a listing of all available DAS sources please visit the DasRegistry. Sponsors: The initial ideas for DAS were developed in conversations with LaDeana Hillier of the Washington University Genome Sequencing Center. | annotation, database, software, genomic, protein, sequence, visualization, data, client-server, integration, bioinformatics, genome, structure, data integration |
is listed by: 3DVC has parent organization: Uppsala University; Uppsala; Sweden |
Howard Hughes Medical Institute ; NHGRI 2-P01-HG00956 |
nif-0000-30177 | SCR_008427 | BioDAS | 2026-02-15 09:19:31 | 11 | ||||||||
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Augustus Resource Report Resource Website 1000+ mentions |
Augustus (RRID:SCR_008417) | software application, sequence analysis software, data processing software, software resource, web application, data analysis software | Software for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes. | software, gene, prediction, eucaryotic, genomic, sequence |
is used by: BRAKER is used by: BRO_annotation is listed by: Debian is listed by: OMICtools is listed by: SoftCite works with: Gsnap2Augustus |
Deutsche Forschungsgemeinschaft (DFG) HO4545/1-1;; STA1009/6-1 ; Institute for Mathematics and Computer Science ; Ernst Moritz Arndt University of Greifswald |
PMID:23700307 DOI:10.1093/bioinformatics/btw494 |
Free, Available for download, Freely available | SCR_015981, OMICS_07777, nif-0000-30133 | https://sources.debian.org/src/autodock-vina/ | SCR_008417 | Augustus: Gene Prediction, WebAUGUSTUS, Augustus, Augustus [gene prediction] | 2026-02-15 09:19:50 | 3542 | |||||
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U.S. Pig Genome Project Resource Report Resource Website |
U.S. Pig Genome Project (RRID:SCR_008151) | topical portal, data or information resource, database, portal | Database and resources on the pig genome. | embryo, embryonic, environmental, exercise, exposure, fat, feed, feeding, fibroblast, food, foot and mouth disease, function, genetic, acute, additive, alcohol, alcoholism, atherosclerosis, bed, behavior, biological, bone, breed, cancer, cell, chronic, clone, degenerative, density, deposition, dermal, developmental, diabetes, dietary, digestive, disease, genome, genomic, growth, habit, healing, human, hypertension, kidney, mammal, map, melanoma, metabolism, nephropathy, nuclear, nutrition, obesity, omnivore, organ, organism, parenteral, pathogen, pattern, phenotype, phenotypic, physiology, pig, pollutant, population, porcine, prenatal, pulmonary, reproductive, respiratory, retinal, sex, shock, size, social, somatic, structure, swine, taxon, technique, tissue, tobacco, transplantation, variation, vascular, warfare, xenobiotic, model | is listed by: 3DVC | nif-0000-20986 | SCR_008151 | U.S. Pig Genome Project | 2026-02-15 09:19:48 | 0 | |||||||||
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GeneWindow Resource Report Resource Website 1+ mentions |
GeneWindow (RRID:SCR_008183) | software application, data processing software, data analysis software, software resource | Software tool for pre- and post-genetic bioinformatics and analytical work, developed and used at the Core Genotyping Facility (CGF) at the National Cancer Institute. While Genewindow is implemented for the human genome and integrated with the CGF laboratory data, it stands as a useful tool to assist investigators in the selection of variants for study in vitro, or in novel genetic association studies. The Genewindow application and source code is publicly available for use in other genomes, and can be integrated with the analysis, storage, and archiving of data generated in any laboratory setting. This can assist laboratories in the choice and tracking of information related to genetic annotations, including variations and genomic positions. Features of GeneWindow include: -Intuitive representation of genomic variation using advanced web-based graphics (SVG) -Search by HUGO gene symbol, dbSNP ID, internal CGF polymorphism ID, or chromosome coordinates -Gene-centric display (only when a gene of interest is in view) oriented 5 to 3 regardless of the reference strand and adjacent genes -Two views, a Locus Overview, which varies in size depending on the gene or genomic region being viewed and, below it, a Sequence View displaying 2000 base pairs within the overview -Navigate the genome by clicking along the gene in the Locus Overview to change the Sequence View, expand or contract the genomic interval, or shift the view in the 5 or 3 direction (relative to the current gene) -Lists of available genomic features -Search for sequence matches in the Locus Overview -Genomic features are represented by shape, color and opacity with contextual information visible when the user moves over or clicks on a feature -Administrators can insert newly-discovered polymorphisms into the Genewindow database by entering annotations directly through the GUI -Integration with a Laboratory Information Management System (LIMS) or other databases is possible | gene, genetic, analysis, annotation, archive, bioinformatic, cancer, genome, genomic, genotype, genotyping, human, human genome databases, maps, polymorphism, position, variation, data set |
is listed by: 3DVC has parent organization: National Cancer Institute |
nif-0000-21173 | SCR_008183 | GeneWindow | 2026-02-15 09:19:44 | 1 | |||||||||
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HAP-SAMPLE Resource Report Resource Website 1+ mentions |
HAP-SAMPLE (RRID:SCR_009234) | HAP-SAMPLE | software application, data analysis service, software resource, service resource, production service resource, analysis service resource | Web application for simulating SNP genotypes for case-control and affected-child trio studies by resampling from Phase I/II HapMap SNP data. The user provides a list of SNPs to be genotyped, along with a disease model file that describes causal SNPs and their effect sizes. The simulation tool is appropriate for candidate regions or whole-genome scans. (entry from Genetic Analysis Software) | gene, genetic, genomic, web-based | is listed by: Genetic Analysis Software | nlx_154392 | SCR_009234 | 2026-02-15 09:19:59 | 4 | |||||||||
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R/QTLBIM Resource Report Resource Website 1+ mentions |
R/QTLBIM (RRID:SCR_009375) | software application, software library, software toolkit, software resource | Software library for QTL Bayesian Interval Mapping that provides a Bayesian model selection approach to map multiple interacting QTL. It works on experimentally inbred lines and performs a genome-wide search to locate multiple potential QTL. The package can handle continuous, binary and ordinal traits. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154597, biotools:qtlbim | http://www.ssg.uab.edu/qtlbim/index.jsp https://cran.r-project.org/src/contrib/Archive/qtlbim/ https://bio.tools/qtlbim |
http://www.qtlbim.org/ | SCR_009375 | 2026-02-15 09:20:01 | 2 | ||||||||
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Arvados Resource Report Resource Website 1+ mentions |
Arvados (RRID:SCR_002223) | arvados | service resource, storage service resource, data repository | Bioinformatics platform for storing, organizing, processing, and sharing genomic and other biomedical big data. Designed to make it easier for bioinformaticians to develop analyses, developers to create genomic web applications and IT administers to manage large-scale compute and storage genomic resources. Designed to run on top of cloud operating systems such as Amazon Web Services and OpenStack. Currently, there are implementations that work on AWS and Xen+Debian/Ubuntu. Functionally, Arvados has two major sets of capabilities: (a) data management and (b) compute management. | mapreduce/hadoop, genomic, biomedical, data sharing, compute, data management, cloud | is listed by: Debian | Free, Freely available | OMICS_01835 | https://sources.debian.org/src/arvados/ | SCR_002223 | 2026-02-15 09:18:15 | 3 | |||||||
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ARK-Genomics: Centre for Functional Genomics Resource Report Resource Website 10+ mentions |
ARK-Genomics: Centre for Functional Genomics (RRID:SCR_002214) | ARK Genomics | organization portal, portal, database, service resource, core facility, data or information resource, access service resource | Portal for studies of genome structure and genetic variation, gene expression and gene function. Provides services including DNA sequencing of model and non-model genomes using both Next Generation and Sanger sequencing , Gene expression analysis using both microarrays and Next Generation Sequencing, High throughput genotyping of SNP and copy number variants, Data collection and analysis supported in-house high performance computing facilities and expertise, Extensive EST clone collections for a number of animal species, all of commercially available microarray tools from Affymetrix, Illumina, Agilent and Nimblegen, Parentage testing using microsatellites and smaller SNP panels. ARK-Genomics has developed network of researchers whom they support through each stage of their genomics research, from grant application, experimental design and technology selection, performing wet laboratory protocols, through to analysis of data often in conjunction with commercial partners. | gene expression, farm, function, gene, genetic, animal, dna, genome, genomic, genotype, knowledge base, model, structure, variation, job, comparative genome hybridization, parentage testing, microsatellite |
is listed by: ScienceExchange is related to: Roslin Institute Labs and Facilities has parent organization: Roslin Institute works with: University of Edinburgh GenePool Next Generation Sequencing and Bioinformatics |
BBSRC | Free, Freely available | nif-0000-20966, SciEx_157 | https://genomics.ed.ac.uk/ | SCR_002214 | ARK Genomics, Roslin Institute ARK-Genomics | 2026-02-15 09:18:15 | 12 | |||||
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La Jolla Interdisciplinary Neurosciences Center Resource Report Resource Website |
La Jolla Interdisciplinary Neurosciences Center (RRID:SCR_002772) | La Jolla Neuroscience Center Cores | material service resource, service resource, production service resource, material analysis service, access service resource, biomaterial analysis service, analysis service resource | Our NINDS Center Core Grant supports centralized resources and facilities shared by investigators with existing NINDS-funded research projects. Our Center is composed of three research cores, each of which will enrich the effectiveness of ongoing research, and promote new research directions. The three Core facilities support Electrophysiology, Neuropathology / Histology, and High-Throughput/High-Content Chemical and Genomic Library screening. By making these important Core Services available to the local Neuroscience community, the La Jolla Neurosciences Program hopes to promote the study of how the nervous system works and develop treatments for nervous system diseases. The cores and their services are available to La Jolla neuroscientists. Core services are available to NINDS-supported neuroscience projects from local investigators as well as young neuroscientists prior to obtaining their first NIH-funded grant. * Electrophysiology: SBMRI Electrophysiology ** The Electrophysiology Core consists of the Sanford-Burnham Electrophysiology Facility. This facility can perform patch-clamp intracellular and extracellular field recordings on a range of material including cultured cells and brain slices. The Sanford-Burnham facility emphasizes electrophysiological analysis of cultured cells and the detailed electrical properties of channels, receptors and recombinant proteins expressed in Xenopus oocytes or mammalian cells. * Neuropathology: UCSD Neuropathology ** The Neuropathology laboratory applies immunocytochemistry, neurochemistry, molecular genetics, transgenic models of disease, and imaging by scanning laser confocal microscopy to analysis of neurological disease in animal models. * Chemical Library Screening: SBIMR Assay Development, SBIMR Chemical Library Screening, SBIMR Cheminformatics, SBIMR High-content Screening ** The Chemical Library Screening core offers high-throughput screening (HTS) of biochemical and cell-based array using traditional HTS readouts and automated microscopy for high-content screening (HCS)> These facilities also offer array development and screening, as well as cheminformatics and medicinal chemistry., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026. | neuroscience, nervous system, electrophysiology, neuropathology, histology, high-throughput screening, high-content screening, chemical, genomic, chemical library screening, cheminformatics, medicinal chemistry |
has parent organization: University of California at San Diego; California; USA has parent organization: Sanford Burnham Prebys Medical Discovery Institute |
Nervous system disease | NINDS ; NIH Blueprint for Neuroscience Research |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00436 | SCR_002772 | La Jolla Interdisciplinary Neuroscience Center Core (Burnham-Salk-Scripps-UCSD) | 2026-02-15 09:18:22 | 0 | |||||
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Macaque.org Resource Report Resource Website 1+ mentions |
Macaque.org (RRID:SCR_002767) | Macaque.org | organization portal, portal, laboratory portal, research forum portal, data or information resource, topical portal, disease-related portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on June 8, 2020.Macaque genomic and proteomic resources and how they are providing important new dimensions to research using macaque models of infectious disease. The research encompasses a number of viruses that pose global threats to human health, including influenza, HIV, and SARS-associated coronavirus. By combining macaque infection models with gene expression and protein abundance profiling, they are uncovering exciting new insights into the multitude of molecular and cellular events that occur in response to virus infection. A better understanding of these events may provide the basis for innovative antiviral therapies and improvements to vaccine development strategies. | genomic, hiv, infection, proteomic, virus, simian immunodeficiency virus, influenza virus, animal model | has parent organization: University of Washington; Seattle; USA | Viral infection, Infectious disease | NCRR ; NIAID ; NHLBI ; NIDA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-24370 | SCR_002767 | Macaque.org | 2026-02-15 09:18:22 | 3 | |||||
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Sal-Site Resource Report Resource Website 50+ mentions |
Sal-Site (RRID:SCR_002850) | Sal-Site | portal, data analysis service, database, organism-related portal, service resource, production service resource, data or information resource, image collection, topical portal, analysis service resource | Portal that supports Ambystoma-related research and educational efforts. It is composed of several resources: Salamander Genome Project, Ambystoma EST Database, Ambystoma Gene Collection, Ambystoma Map and Marker Collection, Ambystoma Genetic Stock Center, and Ambystoma Research Coordination Network. | gene, genomic, expressed sequence tag, blast, model organism, genome, salamander, animal model, genetic map, genetic marker, gene expression, limb regeneration, microarray, quantitative-pcr, rna-seq, nanostring, husbandry, embryo, limb, mutant, strain, neural, olfaction, phentotype, regeneration, renal, retina, sequence, vision, human, chicken, xenopus tropicalis, FASEB list | has parent organization: University of Kentucky; Kentucky; USA | NSF OB0242833; NSF DBI0443496; NCRR R24 RR016344; NIH Office of the Director R24 OD010435 |
PMID:16359543 | Free, Freely available | nif-0000-25309 | https://orip.nih.gov/comparative-medicine/programs/vertebrate-models | SCR_002850 | Ambystoma Resources for Model Amphibians Database | 2026-02-15 09:18:25 | 92 | ||||
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GenePattern Resource Report Resource Website 1000+ mentions |
GenePattern (RRID:SCR_003201) | GenePattern | software application, data processing software, data analysis software, software resource | A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. | gene expression, analysis, genomic, pattern, proteomics, silico, snp, workflow, analysis pipeline, flow cytometry, rna-seq, data processing, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is affiliated with: GenePattern Notebook is related to: TIGRESS has parent organization: Broad Institute |
NCI ; NIGMS |
PMID:16642009 | Free, Freely available | biotools:genepattern, OMICS_01855, nif-0000-30654 | https://bio.tools/genepattern | SCR_003201 | 2026-02-15 09:18:28 | 1078 | |||||
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UCSC Genome Browser Resource Report Resource Website 10000+ mentions Rating or validation data |
UCSC Genome Browser (RRID:SCR_005780) | portal, database, service resource, project portal, data or information resource | Portal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data. | Reference, sequence, assembly, collection, genome, visualize, genomic, data, ENCODE, Neanderthal, project, sequencing |
is used by: VizHub is used by: Blueprint Epigenome is used by: QmRLFS-finder is used by: International Human Epigenome Consortium Data Portal is used by: iPiG is listed by: re3data.org is listed by: OMICtools is listed by: Educational Resources in Neuroscience is listed by: SoftCite is related to: HEXEvent is related to: PicTar is related to: Phenotree is related to: Enhancer Trap Line Browser is related to: CistromeFinder is related to: ENCODE is related to: Human Epigenome Atlas is related to: ENCODE is related to: BigWig and BigBed is related to: PhenCode is related to: doRiNA is related to: ISCA Consortium is related to: WashU Epigenome Browser is related to: CRISPOR is related to: liftOver is related to: kent has parent organization: University of California at Santa Cruz; California; USA works with: TarBase |
UC BIOTEuropean UnionH ; Alfred P. Sloan Foundation ; David and Lucille Packard Foundation ; NIH ; HHMI ; CISI ; NHGRI ; DOE ; NSF DBI 9809007; NIGMS GM52848 |
PMID:12045153 PMID:22908213 PMID:23155063 |
OMICS_00926, SCR_017502, nif-0000-03603, SciEx_217, SCR_012479, r3d100010243 | http://genome.cse.ucsc.edu https://doi.org/10.17616/R3RK5C |
SCR_005780 | The Human Genome Browser at UCSC, UCSC Genome Browser Group, University of California at Santa Cruz Genome Browser, UCSC Genome Bioinformatics | 2026-02-15 09:19:03 | 10026 | ||||||
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GeneVito Resource Report Resource Website |
GeneVito (RRID:SCR_006211) | GeneVito | software application, data visualization software, data processing software, 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 | 2026-02-15 09:19:22 | 0 | ||||||
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GMD Resource Report Resource Website 100+ mentions |
GMD (RRID:SCR_006625) | GMD | database, software resource, data access protocol, web service, service resource, data or information resource | 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 | 2026-02-15 09:19:32 | 157 | ||||||
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Public Health Genomics Resource Report Resource Website 500+ mentions |
Public Health Genomics (RRID:SCR_006462) | organization portal, portal, training resource, data or information resource, narrative resource, podcast, radio | 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 | 2026-02-15 09:19:16 | 772 | |||||||||
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Influenza Research Database (IRD) Resource Report Resource Website 10+ mentions |
Influenza Research Database (IRD) (RRID:SCR_006641) | IRD | data analysis service, database, service resource, storage service resource, data repository, production service resource, data or information resource, analysis 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:10.35094, DOI:10.17616/R3S634, 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 | 2026-02-15 09:19:32 | 28 |
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