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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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T Cell ExTRECT Resource Report Resource Website 1+ mentions |
T Cell ExTRECT (RRID:SCR_027742) | software resource, software toolkit, source code | Software R package to calculate T cell fractions from WES data from hg19 or hg38 aligned genomes. | T-cell, T cell receptor excision circle, WES data, hg19 or hg38 aligned genomes, | NCATS UL1TR000100; NCI P30CA023100; NCI R21CA177519; NCI U01CA196406; NHLBI U54HL108460; NIH Office of the Director DP5OD017937; NLM T15LM011271; NSF |
PMID:34497419 | Free, Available for download, Freely available | SCR_027742 | , T cell exome TREC, T cell exome T cell Receptor Excision Circle | 2026-09-12 01:05:35 | 1 | ||||||||
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Human Microbiome Compendium Resource Report Resource Website 1+ mentions |
Human Microbiome Compendium (RRID:SCR_026991) | data or information resource, portal, project portal | Microbial ecology dataset describing the composition of publicly available human microbiome samples deposited in INSDC databases (Sequence Read Archive, European Nucleotide Archive, Digital Data Bank of Japan). Genus-level read counts are available for more than 168,000 samples from around the world, with additional curated metadata for samples and projects. | microbiome, compendium, dataset, public data, amplicon, shotgun, metagenomics, | NLM R01LM013863 | PMID:39848248 | https://doi.org/10.5281/zenodo.8186993 | SCR_026991 | 2026-09-12 01:05:16 | 1 | |||||||||
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NetBCE Resource Report Resource Website |
NetBCE (RRID:SCR_028677) | software application, software resource, source code | Software tool used to predict linear B-cell epitopes (BCEs) from protein sequences. It helps scientists find parts of a pathogen that trigger immune responses. Interpretable deep neural network for accurate prediction of linear B-cell epitopes. | predict linear B-cell epitopes from protein sequences, find parts of pathogen, trigger immune responses, | CPRIT RP180734; CPRIT RP210045; NIDCR R01DE029818; NIDCR R01DE030122; NLM R01LM012806 |
PMID:36526218 | Free, Available for download, Freely available | SCR_028677 | 2026-09-12 01:05:57 | 0 | |||||||||
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GLIMMPSE Resource Report Resource Website 1+ mentions |
GLIMMPSE (RRID:SCR_016297) | data access protocol, software resource, web service | Web based software tool that calculates power and sample size for study designs with normally distributed outcomes. Permits power calculations for clinical trials, randomized experiments, and observational studies with clustering, repeated measures, and both, and almost any testable hypothesis. GLIMMPSE Version 3 release back end has been refactored in Python, interface has been simplified, requiring user decisions about only one topic per screen, new menu improves specification of both between-participant and within-participant hypothese, recursive algorithm permits computing covariances for up to ten levels of clustering. | power, multivariate, linear, models, Gaussian, error, Java, web, calculate | NIGMS R01 GM121081; NIGMS R25 GM111901; NLM G13 LM011879 |
PMID:24403868 PMID:40901910 |
Free, Freely available | SCR_016297 | , GLIMMPSE Version 3 | 2026-09-16 10:44:56 | 9 | ||||||||
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PubChem Resource Report Resource Website 10000+ mentions |
PubChem (RRID:SCR_004284) | data or information resource, data repository, database, service resource, storage service resource | Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI). | collection, information, data, chemical, structure, biological, property, small, molecule, siRNA reagent, bio.tools |
uses: ChEMBL is used by: NIF Data Federation is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: GEROprotectors is listed by: OMICtools is listed by: re3data.org is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is related to: NCBI Structure is related to: Molecular Libraries Program is related to: NIH Data Sharing Repositories is related to: PubChem BioAssay has parent organization: NCBI is parent organization of: PubChem Substance works with: MiMeDB |
NLM | PMID:21418625 PMID:21272340 PMID:20970519 PMID:20298522 PMID:19825798 |
Free, Freely Available | biotools:pubchem, nlx_42691, nlx_29861, r3d100010538, OMICS_01587 | https://bio.tools/pubchem, https://doi.org/10.17616/R3GW37 | SCR_004284 | 2026-09-12 12:56:11 | 15598 | ||||||
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U-Compare Resource Report Resource Website 1+ mentions |
U-Compare (RRID:SCR_004911) | U-Compare | data processing software, service resource, software application, software resource, text-mining software, workflow software | An integrated text mining / natural language processing system based on the Unstructured Information Management Architecture (UIMA) Framework. It allows interoperability of text mining tools and allows the creation of text mining workflows, comparison and visualization of tools. U-Compare can be launched straight from the web or downloaded. As the name implies comparison of components and workflows is a central feature of the system. U-Compare allows sets of components to be run in parallel on the same inputs and then automatically generates statistics for all possible combinations of these components. Once a workflow has been created in U-Compare it can be exported and shared with other users or used with other UIMA compatible tools and so in addition to comparison, U-Compare also functions as a general purpose workflow creation tool. It contains a repository of 50+ biomedical text mining components. These components are included in the U-Compare single-click-to-launch package, ready to use by just drag-and-drop. You can also use this repository independent from the U-Compare system. Link with Taverna It has a link with Taverna for scientific workflows, http://bioinformatics.oxfordjournals.org/content/26/19/2486.abstract, where you can use U-Compare and its workflow from within the Taverna workflow. There are two ways, the U-Compare Taverna plugin and the U-Compare command line mode as a Taverna activity. We have recently integrated it with Peter Murray-Rust''''s OSCAR for Chemistry (see http://www.nactem.ac.uk/cheta/) Web Demo: http://www.nactem.ac.uk/software/cheta/ | statistics, text mining, natural language processing, interoperability, comparison, workflow, computational linguistics |
is listed by: FORCE11 is related to: Taverna is related to: Chemistry Using Text Annotations is related to: Oscar3 has parent organization: University of Tokyo; Tokyo; Japan has parent organization: National Centre for Text Mining has parent organization: University of Colorado Denver; Colorado; USA |
NIGMS R01 GM083649-04; NLM R01 LM008111-07; NIGMS R01GM083649; NLM R01LM008111; NLM R01LM009254 |
PMID:19414535 | nlx_87780 | SCR_004911 | 2026-09-12 12:56:18 | 5 | |||||||
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OligoGenome Resource Report Resource Website 1+ mentions |
OligoGenome (RRID:SCR_006025) | OligoGenome | data or information resource, database, resource | The Stanford Human OligoGenome Project hosts a database of capture oligonucleotides for conducting high-throughput targeted resequencing of the human genome. This set of capture oligonucleotides covers over 92% of the human genome for build 37 / hg19 and over 99% of the coding regions defined by the Consensus Coding Sequence (CCDS). The capture reaction uses a highly multiplexed approach for selectively circularizing and capturing multiple genomic regions using the in-solution method developed in Natsoulis et al, PLoS One 2011. Combined pools of capture oligonucleotides selectively circularize the genomic DNA target, followed by specific PCR amplification of regions of interest using a universal primer pair common to all of the capture oligonucleotides. Unlike multiplexed PCR methods, selective genomic circularization is capable of efficiently amplifying hundreds of genomic regions simultaneously in multiplex without requiring extensive PCR optimization or producing unwanted side reaction products. Benefits of the selective genomic circularization method are the relative robustness of the technique and low costs of synthesizing standard capture oligonucleotide for selecting genomic targets. | oligonucleotide, genome, probe, coding region, oligonucleotide sequence, chromosome | has parent organization: Stanford University; Stanford; California | NHGRI RC2 HG005570-01; NCI R21CA12848; NCI 5K08CA96879?6; NIDDK DK56339; NHGRI 2P01HG000205; NLM T15-LM007033; Doris Duke Clinical Foundation ; Reddere Foundation ; Liu Bie Ju Cha and Family Fellowship in Cancer ; Wang Family Foundation ; Howard Hughes Medical Foundation |
PMID:22102592 | nlx_151422 | SCR_006025 | Stanford Human Oligo Genome Project, Human OligoGenome Resource, Stanford Human Oligo Genome, Human Oligo Genome, Human OligoGenome | 2026-09-12 12:56:34 | 2 | ||||||
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NMR Restraints Grid Resource Report Resource Website |
NMR Restraints Grid (RRID:SCR_006127) | NMR Restraints Grid | data or information resource, database, image collection | Original NMR (nuclear magnetic resonance) data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the Database Of Converted Restraints (DOCR) and the Filtered Restraints Database (FRED) respectively as described in the references. There are 9,672,968 parsed constraints in 7159 entries. (Mar. 2013) | nmr, biomolecule, structure, magnetic resonance, database of converted restraint, filtered restraints database, fred, mri, protein, nucleic acid |
is related to: NRG-CING is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Biological Magnetic Resonance Data Bank (BMRB) |
European Union FP6 contract QLG2-CT-2000-01313; NLM LM05799 |
PMID:12766409 PMID:16041478 |
Please acknowledge the references in publications where the data from this site have been utilized. | nlx_151606 | SCR_006127 | BMRB NMR Restraints Grid | 2026-09-12 12:56:35 | 0 | |||||
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Coremine Medical Resource Report Resource Website 1+ mentions |
Coremine Medical (RRID:SCR_005323) | Coremine Medical | service resource | Service to access comprehensive information on diseases, drugs, treatments and medical biology. It is ideal for those seeking an overview of a complex subject while allowing the possibility to drill down to specific details. Search results are presented in a dashboard format comprized of panels containing various categories of information ranging from introductory sources to the latest scientific articles. | disease, drug, treatment, medical biology, text mining, health, medicine, biology, network, database |
is listed by: OMICtools is related to: MeSH is related to: Entrez Gene is related to: MEDLINE is related to: PubMed is related to: DrugBank is related to: Gene Ontology is related to: UniProt has parent organization: PubGene |
NLM ; European Union FP7 ; Research Council of Norway ; Innovation Norway |
Copyrighted | OMICS_01179 | SCR_005323 | 2026-09-12 12:56:24 | 6 | |||||||
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FLASH Resource Report Resource Website 1000+ mentions |
FLASH (RRID:SCR_005531) | FLASh | data analysis software, data processing software, sequence analysis software, software application, software resource | Open source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: shovill is related to: CLIP-Explorer has parent organization: Johns Hopkins University; Maryland; USA |
NHGRI R01 HG006677; NIGMS R01 GM083873; NLM R01 LM006845 |
PMID:21903629 | Free, Available for download, Freely available | biotools:flash, OMICS_01047 | https://sourceforge.net/projects/flashpage/files/, https://bio.tools/flash, https://sources.debian.org/src/flash/ | SCR_005531 | Fast Length Adjustment of SHort reads, Fast Length Adjustment of Short reads | 2026-09-12 12:56:27 | 2461 | ||||
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Array Information Library Universal Navigator Resource Report Resource Website 1+ mentions |
Array Information Library Universal Navigator (RRID:SCR_006967) | AILUN | analysis service resource, data analysis service, data or information resource, database, production service resource, resource, service resource | Re-annotated gene expression / proteomics data from GEO by relating all probe IDs to Entrez Gene IDs once every three months, enabling you to find data from GEO, and compare them from different platforms and species. Platform Annotations adds the latest annotations to any uploaded probe / gene ID list file. Platform Comparison compares any two platforms to find corresponding probes mapping to the same gene. Cross-species mapping maps platform annotations to other species. Gene Search finds deposited platforms and samples in GEO that contain a list of genes. GPL ID Search finds the GPL ID (GEO platform ID) for your array. You can also download the latest annotations files for all arrays and their comprehensive universal gene identifier table, which relates all types of gene / protein / clone identifiers to Entrez Gene IDs for all species. Note: The database was last updated on 4/30/2011. They have successfully mapped 54932732 individual probes from 385099 GEO samples measuring 3519 GEO platforms across 217 species. | gene expression, gene, array, clone, probe, protein, proteomic, annotation, analytical service, probe id, comparison, microarray, probe sequence, gene identifier, annotation file, web service |
is related to: Gene Expression Omnibus is related to: Entrez Gene has parent organization: Stanford University School of Medicine; California; USA |
Lucile Packard Foundation for Childrens Health ; Howard Hughes Medical Institute ; Pharmaceutical Research and Manufacturers of America Foundation ; NLM K22 LM008261; NIDDK R01GM079719 |
PMID:17971777 | nif-0000-33004 | SCR_006967 | 2026-09-12 12:56:48 | 5 | |||||||
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Virtual Human Embryo Resource Report Resource Website 10+ mentions |
Virtual Human Embryo (RRID:SCR_006921) | VHE | data or information resource, database, image collection | A digital image database of serially sectioned human embryos from the Carnegie Collection originally developed as a collaboration between embryologist Dr. Raymond Gasser at Louisiana State University Health Science Center (LSUHSC) and the Human Developmental Anatomy Center (HDAC) in Washington D.C. The aim of the project is to increase understanding of human embryology and to encourage study of human embryonic development by providing students and researchers with reliable resources for human embryo morphology. The VHE project has several components: * DREM: The Digitally Reproduced Embryonic Morphology (DREM) project, with funding from NICHD, project has produced 27 image databases of labeled serial sections from representative human embryos at each of the 23 Carnegie stages. These databases, together with animations and reconstructions of the embryos are available on DVD and CD. * HEIRLOOM: The HEIRLOOM Collection (Human Embryo Imaging and Reconstruction, Library Of Online Media) was funded by the National Library of Medicine to provide greater access to the DREM databases. NLM provided funding to set up this website and to produce additional 3D-reconstructions and animations that are included on the DREM disks. Original website, http://virtualhumanembryo.lsuhsc.edu/HEIRLOOM/heirloom.htm * EHD: Starting in 2011, The Endowment for Human Development (EHD) will also host the VHE databases. They have made the project accessible to everyone and include a comprehensive cataloging of all the terms used to label the embryos. Their website enables users to browse through the complete VHE atlas of human embryology, http://www.ehd.org/virtual-human-embryo/ | embryo, embryonic human, development, embryology, morphology, carnegie stage, 3d-reconstruction | has parent organization: Louisiana State University Health Sciences Center New Orleans; Louisiana; USA | NICHD R01 HD37811; NLM R01 LM007591 |
nlx_152029 | SCR_006921 | Virtual Human Embryo Project | 2026-09-12 12:56:47 | 25 | |||||||
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Olfactory Receptor DataBase Resource Report Resource Website 1+ mentions |
Olfactory Receptor DataBase (RRID:SCR_007830) | ORDB | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Database of vertebrate olfactory receptors genes and proteins. It supports sequencing and analysis of these receptors by providing a comprehensive archive with search tools for this expanding family. The database also incorporates a broad range of chemosensory genes and proteins, including the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfaction receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), and fungal pheromone receptors (FPRs). ORDB currently houses chemosensory receptors for more than 50 organisms. ORDB contains public and private sections which provide tools for investigators to analyze the functions of these very large gene families of G protein-coupled receptors. It also provides links to a local cluster of databases of related information in SenseLab, and to other relevant databases worldwide. The database aims to house all of the known olfactory receptor and chemoreceptor sequences in both nucleotide and amino acid form and serves four main purposes: * It is a repository of olfactory receptor sequences. * It provides tools for sequence analysis. * It supports similarity searches (screens) which reduces duplicate work. * It provides links to other types of receptor information, e.g. 3D models. The database is accessible to two classes of users: * General public www users have full access to all the public sequences, models and resources in the database. * Source laboratories are the laboratories that clone olfactory receptors and submit sequences in the private or public database. They can search any sequence they deposited to the database against any private or public sequence in the database. This user level is suited for laboratories that are actively cloning olfactory receptors. | fungal, pheromone receptor, gene, chemosensory, chemosensory receptor, g protein-coupled receptor, olfaction receptor, protein, receptor, taste papilla receptor, vomeronasal organ receptor, olfactory receptor, nucleotide, amino acid, chemoreceptor sequence, olfactory receptor sequence, chemoreceptor, sequence |
is used by: NIF Data Federation is listed by: 3DVC is related to: Odor Molecules DataBase is related to: Integrated Manually Extracted Annotation has parent organization: Yale School of Medicine; Connecticut; USA |
Aging | Human Brain Project ; NIMH ; NIA ; NICD ; NINDS ; Multidisciplinary University Research Initiative ; National Aeronautics and Space Administration ; NIDCD RO1 DC 009977; NIDCD P01 DC 04732; NLM G08 LM05583 |
PMID:11752336 PMID:9847223 PMID:9218144 |
Public, Private, Acknowledgement requested, The community can contribute to this resource | nif-0000-03213 | SCR_007830 | Olfactory Receptors Database | 2026-09-12 12:56:57 | 4 | ||||
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REBASE Resource Report Resource Website 100+ mentions |
REBASE (RRID:SCR_007886) | REBASE | data or information resource, database | Database of information about restriction enzymes and related proteins containing published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included. Several tools are available including REBsites, BLAST against REBASE, NEBcutter and REBpredictor. Putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed. REBASE is updated daily and is constantly expanding. Users may submit new enzyme and/or sequence information, recommend references, or send them corrections to existing data. The contents of REBASE may be browsed from the web and selected compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly updates can be requested via email., | endonuclease, enzyme, genome, archaeal, bacterial, cleavage, crystal, dna, individual protein family databases, isochizomer, methylation, methyltransferase, modification, protein, recognition, restriction, restriction enzyme, sensitivity, sequence, site, methylase, cleavage site, restriction-modification, blast, FASEB list |
has parent organization: New England Biolabs works with: Webcutter |
New England Biolabs Inc ; NLM LM04971 |
PMID:19846593 PMID:17202163 |
r3d100012171, nif-0000-03391 | http://rebase.neb.com, https://doi.org/10.17616/R3J930 | http://www.neb.com/rebase | SCR_007886 | The Restriction Enzyme Database, Restriction Enzyme Database | 2026-09-12 12:56:57 | 261 | ||||
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GeneTests Resource Report Resource Website 10+ mentions |
GeneTests (RRID:SCR_010725) | GeneTests | analysis service resource, biomaterial analysis service, data or information resource, database, material analysis service, narrative resource, portal, production service resource, service resource, topical portal, training material | The GeneTests Web site, a publicly funded medical genetics information resource developed for physicians, other healthcare providers, and researchers, is available at no cost to all interested persons. By providing current, authoritative information on genetic testing and its use in diagnosis, management, and genetic counseling, GeneTests promotes the appropriate use of genetic services in patient care and personal decision making. At This Site: * GeneReviews: Expert-authored peer-reviewed disease descriptions * Laboratory Directory: International directory of genetic testing laboratories * Clinic Directory: International directory of genetics and prenatal diagnosis clinics * Educational Materials: Illustrated glossary, information on genetic services, PowerPoint presentations, annotated Internet resources We comply with the HONcode standard for trustworthy health information. |
has parent organization: University of Washington; Seattle; USA has parent organization: NCBI |
NCI ; NHGRI 1 P41 LM/HG 06029; NLM 1 P41 LM/HG 06029; NLM contract N01-LM-4-3505; NLM 5 P41 LM07242; NLM 2 P41 LM 06001; DOE DE-FG03-02ER63301/A00 |
nlx_94696 | SCR_010725 | GeneTests: Clinical Genetic Information Resource | 2026-09-12 12:57:22 | 12 | ||||||||
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Protein Information Resource Resource Report Resource Website 50+ mentions |
Protein Information Resource (RRID:SCR_002837) | PIR | data or information resource, portal, topical portal | Integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies. Provides databases and protein sequence analysis tools to scientific community, including Protein Sequence Database which grew out from the Atlas of Protein Sequence and Structure. Conducts research in biomedical text mining and ontology, computational systems biology, and bioinformatics cyberinfrastructure. In 2002 PIR, along with its international partners, EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics), were awarded a grant from NIH to create UniProt, a single worldwide database of protein sequence and function, by unifying the PIR-PSD, Swiss-Prot, and TrEMBL databases. Currently, PIR major activities include: i) UniProt (Universal Protein Resource) development, ii) iProClass protein data integration and ID mapping, iii) PRO protein ontology, and iv) iProLINK protein literature mining and ontology development. The FTP site provides free download for iProClass, PIRSF, and PRO. | annotation, genomic, mining, protein, protein bioinformatics, proteomic, research, sequence, structure, systems biology, gold standard, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: NCBI Protein Database has parent organization: University of Delaware; Delaware; USA has parent organization: Georgetown University; Washington D.C.; USA is parent organization of: PRO is parent organization of: PIRSF is parent organization of: PR is parent organization of: UniProt |
NLM P41 LM05798 | PMID:12520019 | Free, Freely available | biotools:pir, nif-0000-21327, nif-0000-00143, SCR_008229 | https://bio.tools/pir, http://pir.georgetown.edu/ | SCR_002837 | PIR - Protein Information Resource | 2026-09-12 12:55:47 | 85 | ||||
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ClinicalTrials.gov Resource Report Resource Website 10000+ mentions |
ClinicalTrials.gov (RRID:SCR_002309) | ClinicalTrials.gov | catalog, clinical trial, data or information resource, data repository, database, service resource, storage service resource | Registry and results database of federally and privately supported clinical trials conducted in United States and around world. Provides information about purpose of trial, who may participate, locations, and phone numbers for more details. This information should be used in conjunction with advice from health care professionals.Offers information for locating federally and privately supported clinical trials for wide range of diseases and conditions. Research study in human volunteers to answer specific health questions. Interventional trials determine whether experimental treatments or new ways of using known therapies are safe and effective under controlled environments. Observational trials address health issues in large groups of people or populations in natural settings. ClinicalTrials.gov contains trials sponsored by National Institutes of Health, other federal agencies, and private industry. Studies listed in database are conducted in all 50 States and in 178 countries. | clinical trial, intervention, treatment, therapy, observation, drug, adverse event, result, outcome, data set, FASEB list |
is used by: NIF Data Federation is used by: Patients to Trials Consortium is used by: Corengi is used by: Biomarkers of Anti-TNF Treatment Efficacy in Rheumatoid Arthritis - Unresponsive Populations is used by: Limited Access Datasets From NIMH Clinical Trials is used by: Integrated Clinical Trials is used by: Integrated Datasets is used by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases lists: Epidemiology of Diabetes Interventions and Complications lists: Behavior Enhances Drug Reduction of Incontinence lists: Diabetes Prevention Program lists: Diabetes Prevention Program Outcomes Study lists: Folic Acid for Vascular Outcome Reduction in Transplantation lists: Family Investigation of Nephropathy of Diabetes lists: Frequent Hemodialysis Network Daily Trial lists: HALT PKD lists: HEALTHY study lists: RiVuR lists: Study of Nutrition in Acute Pancreatitis lists: TINSAL-T2D lists: Treatment Options for type 2 Diabetes in Adolescents and Youth lists: TOMUS lists: TRIGR lists: CATIE - Alzheimers Disease lists: CATIE - Clinical Antipsychotic Trials in Intervention Effectiveness lists: Gastroparesis Clinical Research Consortium lists: Diabetes Control and Complications Trial lists: Efficacy and Mechanisms of Glutamine Dipeptide in the Surgical Intensive Care Unit lists: Evaluating Predictors and Interventions in Sphincter of Oddi Dysfunction lists: Frequent Hemodialysis Network Nocturnal Trial lists: Minimally Invasive Surgical Therapies Treatment Consortium for Benign Prostatic Hyperplasia lists: Focal Segmental Glomerulosclerosis in Children and Young Adults Interventional Study lists: Complementary and Alternative Medicine for Urological Symptoms lists: Program to Reduce Incontinence by Diet and Exercise lists: TEDDY lists: Diabetes Prevention Type 1 lists: HALT-C Trial lists: Viral Resistance to Antiviral Therapy of Chronic Hepatitis C lists: Medical Therapy of Prostatic Symptoms is listed by: OMICtools is related to: NIMH Clinical Trials is related to: cthist is related to: Clinical Trials Viewer has parent organization: National Library of Medicine is parent organization of: LinkedCT is parent organization of: Functional Dyspepsia Treatment Trial is parent organization of: High-dose Ursodiol Therapy of Primary Sclerosing Cholangitis is parent organization of: Peginterferon and Ribavirin for Pediatric Patients with Chronic Hepatitis C is parent organization of: Maryland Genetics of Interstitial Cystitis is parent organization of: Treatment of SSRI-resistant Depression in Adolescents (TORDIA) is parent organization of: Systematic Treatment Enhancement Program for Bipolar Disorder (STEP-BD) is parent organization of: TADS - Treatment for Adolescents with Depression Study is parent organization of: Biomarkers of Anti-TNF Treatment Efficacy in Rheumatoid Arthritis - Unresponsive Populations is parent organization of: Renin Angiotensin System Study |
NIH ; NLM |
PMID:27631620 | Free, Freely available | OMICS_01792, r3d100010211, nif-0000-21091 | https://doi.org/10.17616/R3H887 | SCR_002309 | Clinical Trials Database, ClinicalTrials.gov, Clinicaltrials.gov: A Service Of The National Institutes Of Health, ClinicalTrials, Clinical Trials gov | 2026-09-12 12:55:39 | 54250 | ||||
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dbSNP Resource Report Resource Website 5000+ mentions |
dbSNP (RRID:SCR_002338) | dbSNP | data or information resource, data repository, database, service resource, storage service resource | General database of genetic variations maintained by the NCBI. Database as central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Distinguishes report of how to assay SNP from use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay SNP will often be accompanied by SNP experiments measuring allele occurrence in individuals and populations. Community can contribute to this resource. | insertion, polymorphism, short, deletion, single, nucleotide, genetic, variation, genomics, genotype, disease, allele, microsatellite, marker, multinucleotide, heterozygous, sequence, gold standard, bio.tools |
is used by: ExAc is used by: GEMINI is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Ensembl Variation is related to: GWAS Central is related to: TopoSNP is related to: GWAS Central is related to: dbSNP151 has parent organization: NCBI has parent organization: National Human Genome Research Institute works with: Open Regulatory Annotation Database |
NLM | PMID:21154707 | Free, Freely available | nif-0000-02734, biotools:dbsnp, OMICS_00264, r3d100010652 | http://www.ncbi.nlm.nih.gov/projects/SNP/, https://bio.tools/dbsnp, https://doi.org/10.17616/R3XG81 | SCR_002338 | dbSNP: Database for Short Genetic Variations, Entrez SNP - Single Nucleotide Polymorphism, SNV Database, NCBI SNV Database, NCBI Short Genetic Variations Database, NCBI Short Genetic Variations, NCBI Single Nucleotide Polymorphism, Entrez SNP, dbSNP, NCBI Short Genetic Variations (SNV) database | 2026-09-12 12:55:39 | 9088 | ||||
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LONI Visualization Tool Resource Report Resource Website |
LONI Visualization Tool (RRID:SCR_000765) | LONI Viz, LONI_Viz, LOVE | data processing software, data visualization software, software application, software resource | A versatile 1D, 2D and 3D data viewer geared for cross-platform visualization of stereotactic brain data. It is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views. It reads Analyze, Raw-binary and NetCDF volumetric data, as well as, Multi-Contour Files (MCF), LWO/LWS surfaces, atlas hierarchical brain-region labelings ( Brain Trees). It is a portable Java-based software, which only requires a Java interpreter and a 64 MB of RAM memory to run on any computer architecture. LONI_Viz allows the user to interactively overlay and browse through several data volumes, zoom in and out in the axial, sagittal and coronal views, and reports the intensities and the stereo-tactic voxel and world coordinates of the data. Expert users can use LONI_Viz to delineate structures of interest, e.g., sulcal curves, on the 3 cardinal projections of the data. These curves then may be use to reconstruct surfaces representing the topological boundaries of cortical and sub-cortical regions of interest. The 3D features of the package include a SurfaceViewer and a full real-time VolumeRenderer. These allow the user to view the relative positions of different anatomical or functional regions which are not co-planar in any of the axial, sagittal or coronal 2D projection planes. The interactive part of LONI_Viz features a region drawing module used for manual delineation of regions of interest. A series of 2D contours describing the boundary of a region in projection planes (axial, sagittal or coronal) could be used to reconstruct the surface-representation of the 3D outer shell of the region. The latter could then be resliced in directions complementary to the drawing-direction and these complementary contours could be loaded in all tree cardinal views. In addition the surface object could be displayed using the SurfaceViewer. A pre-loading data crop and sub-sampling module allows the user to load and view practically data of any size. This is especially important when viewing cryotome, histological or stained data-sets which may reach 1GB (109 bytes) in size. The user could overlay several pre-registered volumes, change intensity colors and ranges and the inter-volume opacities to visually inspect similarities and differences between the different subjects/modalities. Several image-processing aids provide histogram plotting, image-smoothing, etc. Specific Features: * Region description DataBase * Moleculo-genetic database * Brain anatomical data viewer * BrainMapper tool * Surface (LightWave objects/scenes) and Volume rendering tools * Interactive Contour Drawing tool Implementation Issues: * Applet vs. Application - the software is available as both an applet and a standalone application. The former could be used to browse data from within the LONI database, however, it imposes restrictions on file-size, Internet connection and network-bandwidth and client/server file access. The later requires a local install and configuration of the LONI_Viz software * Extendable object-oriented code (Java), computer architecture independent * Complete online software documentation is available at http://www.loni.ucla.edu/LONI_Viz and a Java-Class documentation is available at http://www.loni.ucla.edu/~dinov/LONI_Vis.dir/doc/LONI_Viz_Java_Docs.html | brain, atlas, visualization, gene mapping, atlas application, magnetic resonance, surface analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: Laboratory of Neuro Imaging |
Aging | NIA P50 AG16570; NLM 2R01 LM05639-06; NIA K08 AG100784; NCRR 2 P41 RR13642; NIMH 5 P01 MN52176; NSF DUE 0442992; NCRR U52 RR021813 |
PMID:16598642 | Free, Available for download, Freely available | nif-0000-23313 | http://www.nitrc.org/projects/incf_loni-viz | http://www.loni.ucla.edu/Software/LOVE | SCR_000765 | LONI Visualization Environment, LONI Viz environment, LOVE | 2026-09-12 12:55:14 | 0 | ||
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Hanalyzer Resource Report Resource Website |
Hanalyzer (RRID:SCR_000923) | software application, software resource, source code | An open-source data integration system designed to assist biologists in explaining the results observed in genome-scale experiments as well as generating new hypotheses. It combines information extraction techniques, semantic data integration, and reasoning and facilitates network visualization. The Hanalyzer source code and binaries are available for download. | genomic, visualization, reading, reasoning, reporting, throughput analyzer, data network |
has parent organization: University of Colorado Denver; Colorado; USA has parent organization: SourceForge |
NIDCR R01DE15191; NLM R01LM008111; NLM R01LM009254; NIGMS R01GM083649; NLM T15LM009451; NHGRI 5R01HG004483-09 |
PMID:19325874 | nlx_48287 | SCR_000923 | Hanalyzer: A 3R System | 2026-09-12 01:01:21 | 0 |
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