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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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MAOS Resource Report Resource Website 10+ mentions |
MAOS (RRID:SCR_013351) | software application, software resource | Software application that implements valid and efficient statistical methods for meta-analysis of genomewide association studies with overlapping subjects. The current release performs logistic regression analysis of individual level data under the additive mode of inheritance. Data from genome-wide association studies are often analyzed jointly for the purposes of combining information from multiple studies of the same disease or comparing results across different disorders. In many instances, the same subjects appear in multiple studies. Failure to account for overlapping subjects can greatly inflate type I error when combining results from multiple studies of the same disease and can drastically reduce power when comparing results across different disorders. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++ | is listed by: Genetic Analysis Software | nlx_154452 | SCR_013351 | Meta-Analysis with Overlapping Subjects | 2026-09-12 01:02:49 | 25 | |||||||||
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Cancer Therapeutics Response Portal (CTRP) Resource Report Resource Website 1+ mentions |
Cancer Therapeutics Response Portal (CTRP) (RRID:SCR_026293) | data or information resource, portal, topical portal | Cancer Therapeutics Response Portal (CTRP) links genetic, lineage, and other cellular features of cancer cell lines to small-molecule sensitivity with the goal of accelerating discovery of patient-matched cancer therapeutics. CTRP can be mined to develop insights into small-molecule mechanisms of action and novel therapeutic hypotheses, and to support future discovery of drugs matched to patients based on predictive biomarkers. | cancer cell lines, genetic, lineage, small-molecule sensitivity, small-molecule mechanisms of action, novel therapeutics, discovery of drugs, predictive biomarkers, | Free, Freely available | SCR_026293 | 2026-09-12 01:05:01 | 1 | |||||||||||
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MACH 1.0 Resource Report Resource Website 50+ mentions |
MACH 1.0 (RRID:SCR_001759) | data analysis software, data processing software, software application, software resource | A Markov Chain based software tool for haplotyping, genotype imputation and disease association analysis that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals. | gene, genetic, genomic, haplotype, genotype, genomic analysis, imaging genomics, imputation, snp, gene, haplotyping, sequence |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Mach2dat has parent organization: University of Michigan; Ann Arbor; USA |
PMID:21058334 PMID:19715440 |
Free | nlx_154202, OMICS_00064 | SCR_001759 | MArkov Chain Haplotyper MINIMAC, MArkov Chain Haplotyping | 2026-09-12 12:55:30 | 58 | |||||||
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Phelan-McDermid Syndrome Foundation Resource Report Resource Website 10+ mentions |
Phelan-McDermid Syndrome Foundation (RRID:SCR_001707) | PMSF | community building portal, data or information resource, disease-related portal, funding resource, portal, topical portal | The Phelan-McDermid Syndrome Foundation, established in 2002, is a 501(c)3 nonprofit group that provides support services for those who have family members affected by 22q13 Deletion Syndrome / Phelan-McDermid Syndrome. It also raises money to further awareness of the syndrome through research and sponsoring an international conference every two years that brings together families, researchers and therapists. The Foundation facilitates connections between families through networking, communications and support services. We also build alliances with other rare diseases groups to expand our reach and exposure. The syndrome, which affects families worldwide, is a rare genetic occurrence and is the result of a damaged or missing protein on the 22nd chromosome. Our Foundation works with researchers who are looking into the cause and possible cure for the syndrome. PMSF's grants and fellowships program is intended to encourage research projects that will advance the development of treatments and cures for PMS. Our mission is to bring together everyone affected by 22q13 Deletion Syndrome/Phelan-McDermid Syndrome to help them through the challenges they face every day and to raise awareness in the medical and research communities. | 22q13 deletion syndrome, phelan-mcdermid syndrome, rare disease, genetic, meeting, child, chromosome 22, treatment, therapy, research, grant, fellowship | is parent organization of: Phelan-McDermid Syndrome International Registry | Phelan-McDermid Syndrome | Free, Freely Available | nif-0000-10203 | SCR_001707 | 2026-09-12 12:55:29 | 33 | |||||||
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Living Links: Center for the Advanced Study of Ape and Human Evolution Resource Report Resource Website 1+ mentions |
Living Links: Center for the Advanced Study of Ape and Human Evolution (RRID:SCR_001776) | data or information resource, portal, topical portal | The primary mission of the Living Links Center is to study human evolution by investigating our close genetic, anatomical, cognitive, and behavioral similarities with great apes. The Living Links Center was established for primate studies that shed light on human behavioral evolution. It is an integrated part of the Yerkes National Primate Research Center, which is the nation's oldest and largest primate center. The Living Links Center is home to two socially housed groups of chimpanzees and two socially housed groups of capuchin monkeys. The research conducted in this center is broken down into four categories: - Chimpanzees: Chimpanzee research at the Living Links Center is conducted at the Yerkes Field Station, which is home to two socially housed chimpanzee groups known as FS1 and FS2. Each mixed gender group of 12 individuals lives in a large outdoor enclosure with wooden climbing structures and play objects attached to an indoor sleeping area. FS1 and FS2 can hear, but not see each other because their enclosures are ~200m apart and separated by a small hill. Chimpanzee research is conducted on a volunteer basis with members of each group. - Elephants: This newly found presence of mirror self-recognition in elephants, previously predicted due to their well-known social complexity, is thought to relate to empathetic tendencies and the ability to distinguish oneself from others. As a result of this study, the elephant now joins a cognitive elite among animals commensurate with its well-known complex social life and high level of intelligence. Although elephants are far more distantly related to us than the great apes, they seem to have evolved similar social and cognitive capacities making complex social systems and intelligence part of this picture. These parallels between humans and elephants suggest a convergent cognitive evolution possibly related to complex sociality and cooperation. - Capuchin Monkeys: Though there are several different species of capuchin monkey, the one most widely studied in captivity by Living Links, is the brown, or tufted, capuchin (Cebus apella). - Collaborative Projects: projects with collaborators around the world. Sponsors: This center is supported by the Yerkes National Primate Research Center. | elephant, evolution, gender, genetic, anatomical, animal, behavioral, capuchin monkey, cebus apella, chimpanzee, cognitive, convergent, great ape, human, primate, specie | has parent organization: Emory University; Georgia; USA | Free, Freely available | nif-0000-10280 | SCR_001776 | Living Links | 2026-09-12 12:55:31 | 2 | ||||||||
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GATK Resource Report Resource Website 10000+ mentions |
GATK (RRID:SCR_001876) | GATK | data analysis software, data processing software, software application, software library, software resource, software toolkit | A software package to analyze next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. This software library makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. (entry from Genetic Analysis Software) | gene, genetic, genomic, next-generation resequencing, bio.tools |
is used by: Halvade Somatic is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: SnpEff is related to: GATK HaplotypeCaller is related to: GATK VariantFiltration has parent organization: Broad Institute |
PMID:21478889 | Free, Available for download, Freely available | nlx_154324, OMICS_00286, biotools:gatk | http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit, https://bio.tools/gatk | SCR_001876 | Genome Analysis ToolKit | 2026-09-12 12:55:33 | 18211 | |||||
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MouseCyc Resource Report Resource Website 10+ mentions |
MouseCyc (RRID:SCR_001791) | MouseCyc | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A manually curated database of both known and predicted metabolic pathways for the laboratory mouse. It has been integrated with genetic and genomic data for the laboratory mouse available from the Mouse Genome Informatics database and with pathway data from other organisms, including human. The database records for 1,060 genes in Mouse Genome Informatics (MGI) are linked directly to 294 pathways with 1,790 compounds and 1,122 enzymatic reactions in MouseCyc. (Aug. 2013) BLAST and other tools are available. The initial focus for the development of MouseCyc is on metabolism and includes such cell level processes as biosynthesis, degradation, energy production, and detoxification. MouseCyc differs from existing pathway databases and software tools because of the extent to which the pathway information in MouseCyc is integrated with the wealth of biological knowledge for the laboratory mouse that is available from the Mouse Genome Informatics (MGI) database. | energy production, biosynthesis, cell, cellular, degradation, detoxification, metabolism, mouse, physiological, enzymatic reaction, gene, disease, genome, metabolic pathway, pathway, compound, enzymatic reaction, protein, rna, reaction, blast, human, mammal, genetic, genomic |
is related to: Mouse Genome Informatics (MGI) is related to: Gene Ontology has parent organization: Jackson Laboratory |
NHGRI HG003622 | PMID:19682380 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10303 | SCR_001791 | MouseCyc database, Mouse Genome Informatics: MouseCyc database | 2026-09-12 12:55:31 | 10 | |||||
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SNAP - SNP Annotation and Proxy Search Resource Report Resource Website 100+ mentions |
SNAP - SNP Annotation and Proxy Search (RRID:SCR_002127) | SNAP | analysis service resource, data analysis service, production service resource, service resource, software application, software resource | A computer program and web-based service for the rapid retrieval of linkage disequilibrium proxy single nucleotide polymorphism (SNP) results given input of one or more query SNPs and based on empirical observations from the International HapMap Project and the 1000 Genomes Project. A series of filters allow users to optionally retrieve results that are limited to specific combinations of genotyping platforms, above specified pairwise r2 thresholds, or up to a maximum distance between query and proxy SNPs. SNAP can also generate linkage disequilibrium plots | gene, genetic, genomic, r, oracle, single nucleotide polymorphism, linkage disequilibrium, genotypeing array, physical distance, membership, proxy, plot |
is listed by: OMICtools is listed by: Genetic Analysis Software is related to: International HapMap Project is related to: 1000 Genomes: A Deep Catalog of Human Genetic Variation has parent organization: Broad Institute |
NHLBI N01-HC-65226 | PMID:18974171 | Free, Freely Available | OMICS_01927, nlx_154638 | http://www.broad.mit.edu/mpg/snap/ | SCR_002127 | SNAP (SNP Annotation and Proxy Search), SNAP 2, SNP Annotation and Proxy Search | 2026-09-12 12:55:37 | 146 | ||||
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Rice Genome Research Project Resource Report Resource Website 1+ mentions |
Rice Genome Research Project (RRID:SCR_002268) | data or information resource, database, portal, topical portal | Rice Genome Research Program (RGP) is an integral part of the Japanese Ministry of Agriculture, Forestry and Fisheries (MAFF) Genome Research Project. RGP now aims to completely sequence the entire rice genome and subsequently to pursue integrated goals in functional genomics, genome informatics and applied genomics. It is jointly coordinated by the National Institute of Agrobiological Sciences (NIAS), a government research institute under MAFF and the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF), a semi-private research organization managed and supported by MAFF and a consortium of some twenty Japanese companies. The research is funded with yearly grants from MAFF and additional funds from the Japan Racing Association (JRA). It is now the leading member of the International Rice Genome Sequencing Project (IRGSP), a consortium of ten countries sharing the sequencing of the 12 rice chromosomes. The IRGSP adopts the clone-by-clone shotgun sequencing strategy so that each sequenced clone can be associated with a specific position on the genetic map and adheres to the policy of immediate release of the sequence data to the public domain. In December 2004, the IRGSP completed the sequencing of the rice genome. The high-quality and map-based sequence of the entire genome is now available in public databases. | fishery, forestry, functional, genetic, agriculture, chromosome, clone, genome, genomic, informatic, map, rice, sequence, sequencing, shotgun | PMID:9482829 | Free, Freely available | nif-0000-20992 | SCR_002268 | Rice Genome Research Project | 2026-09-12 12:55:38 | 4 | ||||||||
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Genetic Maps of the Rat Genome Resource Report Resource Website |
Genetic Maps of the Rat Genome (RRID:SCR_002266) | Genetic Maps of the Rat | data or information resource, data set, image collection | Data set of pictures representing genetic linkage maps of the rat resulting from the integration of two F2 intercrosses (SHRSP x BN and FHH x ACI). Markers in common between the two crosses are connected by a line to define integration points. There are a total of 4,786 markers on these maps; 4375 WIBR/MIT CGR markers; 223 markers from the previously released Mit/Mgh rat maps and 188 markers from the National Institute of Arthritis and Musculoskeletal and Skin Diseases Arb rat maps. Pictures are drawn to a scale of 5cm (Kosombi) per inch. The changes in color of the backbone of the chromosome for each cross represents the space between any two framework loci. Markers in blue type are framework loci. Markers in green type are unique placement loci. Markers in black type are bouncy placement loci. | f2, genetic, backbone, chromosome, cross, intercross, linkage, locus, map, marker, rat, genome | has parent organization: Broad Institute | nif-0000-20990 | SCR_002266 | 2026-09-12 12:55:38 | 0 | |||||||||
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VAAST Resource Report Resource Website 10+ mentions |
VAAST (RRID:SCR_002179) | VAAST, VAAST 2 | data analysis software, data processing software, sequence analysis software, software application, software resource, standalone software | A probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST combines elements of phylogenetic conservation, amino acid substitution, and aggregative approaches to variant prioritization into a single unified likelihood-framework that allows users to accurately identify damaged genes and deleterious variants. The software can score both coding (SNV, indel and splice site) and non-coding variants (SNV), evaluating the cumulative impact of both types of variants simultaneously. It can identify rare variants causing rare genetic diseases and can also use both rare and common variants to identify genes responsible for common diseases. | sequence analysis software, genetic, variant classifier, amino acid substitution, disease, genome interpretation, variant prioritization, disease gene prioritization, genomic variation, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is related to: Opal Research has parent organization: Yandell Lab Portal |
PMID:23836555 PMID:21700766 |
Free, Freely available | SciRes_000138, nlx_154686, biotools:vaast, OMICS_02134 | https://bio.tools/vaast | SCR_002179 | Variant Annotation Analysis and Search Tool, Variant Annotation Analysis & Search Tool | 2026-09-12 12:55:37 | 32 | |||||
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Autosomal Recessive Polycystic Kidney Disease Mutation Database Resource Report Resource Website 10+ mentions |
Autosomal Recessive Polycystic Kidney Disease Mutation Database (RRID:SCR_002290) | data or information resource, data repository, database, service resource, storage service resource | Catalog of all changes detected in PKHD1 (Polycystic Kidney and Hepatic Disease 1) in a locus specific database. Investigators are invited to submit their novel data to this database. These data should be meaningful for clinical practice as well as of relevance for the reader interested in molecular aspects of polycystic kidney disease (PKD). There are also some links and information for ARPKD patients and their parents. Autosomal recessive polycystic kidney disease (ARPKD/PKHD1) is an important cause of renal-related and liver-related morbidity and mortality in childhood. This study reports mutation screening in 90 ARPKD patients and identifies mutations in 110 alleles making up a detection rate of 61%. Thirty-four of the detected mutations have not been reported previously. Two underlying mutations in 40 patients and one mutation in 30 cases are disclosed, and no mutation was detected on the remaining chromosomes. Mutations were found to be scattered throughout the gene without evidence of clustering at specific sites. PKHD1 mutation analysis is a powerful tool to establish the molecular cause of ARPKD in a given family. Direct identification of mutations allows an unequivocal diagnosis and accurate genetic counseling even in families displaying diagnostic challenges. | clinical, gene, genetic, mutation, protein, recessive, renal | has parent organization: RWTH Aachen University; Aachen; Germany | Autosomal recessive polycystic kidney disease, Polycystic kidney disease | PMID:16199545 PMID:11919560 |
Permission required, Terms of use | nif-0000-21038 | http://www.humgen.rwth-aachen.de/index.asp?subform=database.html&nav=database_nav.html | SCR_002290 | Mutation Database Autosomal Recessive Polycystic Kidney Disease (ARPKD/PKHD1) | 2026-09-12 12:55:39 | 14 | |||||
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HuGE Navigator - Human Genome Epidemiology Navigator Resource Report Resource Website 100+ mentions |
HuGE Navigator - Human Genome Epidemiology Navigator (RRID:SCR_003172) | HuGE Navigator | bibliography, data computation service, data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. Knowledge base of genetic associations and human genome epidemiology including information on population prevalence of genetic variants, gene-disease associations, gene-gene and gene- environment interactions, and evaluation of genetic tests. This tool explores HuGENet, the Human Genome Epidemiology Network, which is a global collaboration of individuals and organizations committed to the assessment of the impact of human genome variation on population health and how genetic information can be used to improve health and prevent disease. What does HuGE Navigator offer? *HuGEpedia - an encyclopedia of human genetic variation in health and disease, includes, Phenopedia and Genopedia. Phenopedia allows you to look up gene-disease association summaries by disease, and Genopedia allows you to look up gene-disease association summaries by gene. In general, HuGEpedia is a searchable database that summarizes published articles about human disease and genetic variation, including primary studies, reviews, and meta-analyses. It provides links to Pubmed abstracts, researcher contact info, trends, and more. *HuGEtools - searching and mining the literature in human genome epidemiology, includes, HuGE Literature Finder, HuGE Investigator Browser, Gene Prospector, HuGE Watch, Variant Name Mapper, and HuGE Risk Translator. *HuGE Literature Finder finds published articles in human genome epidemiology since 2001. The search query can include genes, disease, outcome, environmental factors, author, etc. Results can be filtered by these categories. It is also possible to see all articles in the database for a particular topic, such as genotype prevalence, pharmacogenomics, or clinical trial. *HuGE Investigator Browser finds investigators in a particular field of human genome epidemiology. This info is obtained using a behind-the-scenes tool that automatically parses PubMed affiliation data. *Gene Prospector is a gateway for evaluating genes in relation to disease and risk factors. This tool allows you to enter a disease or risk factor and then supplies you with a table of genes associated w/your query that are ranked based on strength of evidence from the literature. This evidence is culled from the HuGE Literature Finder and NCBI Entrez Gene - And you're given the scoring formula. The Gene Prospector results table provides access to the Genopedia entry for each gene in the list, general info including links to other resources, SNP info, and associated literature from HuGE, PubMed, GWAS, and more. It is a great place to locate a lot of info about your disease/gene of interest very quickly. *HuGE Watch tracks the evolution of published literature, HuGE investigators, genes studied, or diseases studied in human genome epidemiology. For example, if you search Trend/Pattern for Diseases Studied you'll initially get a graph and chart of the number of diseases studied per year since 1997. You can refine these results by limiting the temporal trend to a category or study type such as Gene-gene Interaction or HuGE Review. *Variant Name Mapper maps common names and rs numbers of genetic variants using information from SNP500Cancer, SNPedia, pharmGKB, ALFRED, AlzGene, PDGene, SZgene, HuGE Navigator, LSDBs, and user submissions. *HuGE Risk Translator calculates the predictive value of genetic markers for disease risk. To do so, users must enter the frequency of risk variant, the population disease risk, and the odds ratio between the gene and disease. This information is necessary in order to yield a useful predictive result. *HuGEmix - a series of HuGE related informatics utilities and projects, includes, GAPscreener, HuGE Track, Open Source. GAPscreener is a screening tool for published literature on human genetic associations; HuGE Track is a custom track built for HuGE data in the UCSC Genome Browser; and Open Source is infrastructure for managing knowledge and information from PubMed. | environment, epidemiology, gene, genetic, genetic associations, genetic markers, genome, disease, human, human disease, predictive value, prevalence, publications, risk factors, test evaluations, variance, FASEB list |
has parent organization: Centers for Disease Control and Prevention works with: Kinase Associated Neural Phospho Signaling |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00573 | http://hugenavigator.net/HuGENavigator/home.do | SCR_003172 | 2026-09-12 12:55:53 | 117 | |||||||
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QGene Resource Report Resource Website 100+ mentions |
QGene (RRID:SCR_003209) | QGene | data analysis software, data processing software, simulation software, software application, software resource, source code | A free, open-source, computationally efficient Java program for comparative analyses of QTL mapping data and population simulation that runs on any computer operating system. (entry from Genetic Analysis Software) It is written with a plug-in architecture for ready extensibility. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Source code is available on request. | gene, genetic, genomic, java, qtl mapping, trait analysis, trait, population, simulation, map, quantitative trait locus, comparison, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Kansas State University; Kansas; USA |
NSF DBI 0109879; USDA-NRI Applied Plant Genomics Program 2004-35317-14867 |
PMID:18940826 | Free, Available for download, Freely available | biotools:qgene, nif-0000-31383 | https://bio.tools/qgene | http://coding.plantpath.ksu.edu/qgene | SCR_003209 | QGene - Software for QTL data exploration | 2026-09-12 12:55:53 | 129 | |||
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University of Leicester; Leicester; United Kingdom Resource Report Resource Website |
University of Leicester; Leicester; United Kingdom (RRID:SCR_004900) | university | Public research university based in Leicester, England. Famous for the discovery of genetic fingerprinting and contributing to the discovery and identification of the remains of King Richard III. | public, research, university, England, discovery, genetic, fingerprinting |
is related to: Predict-TB is related to: GetReal is related to: READNA is related to: EMIF is related to: Collaborative Computing Project for NMR is parent organization of: Virtual Genetics Education Centre is parent organization of: CCLG is parent organization of: cafe variome is parent organization of: GWAS Central is parent organization of: Database of Osteogenesis Imperfecta and Type III Collagen Variants is parent organization of: GWAS Central is parent organization of: CCLG Tissue Bank is parent organization of: University of Leicester Advanced Imaging Facility |
nlx_20502 | SCR_004900 | The University of Leicester, University of Leicester | 2026-09-12 12:56:18 | 0 | |||||||||
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SMART Resource Report Resource Website 5000+ mentions |
SMART (RRID:SCR_005026) | SMART | analysis service resource, data access protocol, data analysis service, data or information resource, database, production service resource, service resource, software resource, web service | Software tool for identification and annotation of genetically mobile domains and analysis of domain architectures. | extracellular, gene, genetic, genetically, genome, architecture, chromatin, domain, mobile, phyletic, protein, proteome, signaling, structure, taxonomic, tertiary, bio.tools, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is listed by: bio.tools is listed by: Debian is related to: Eukaryotic Linear Motif is related to: Conserved Domain Database is related to: GOTaxExplorer has parent organization: EMBL - Bork Group |
European Union | PMID:18978020 PMID:16381859 PMID:14681379 PMID:10592234 PMID:9847187 PMID:9600884 |
Free, Freely available | nif-0000-03471, biotools:smart | http://smart.embl-heidelberg.de/, https://bio.tools/smart | SCR_005026 | Simple Modular Architecture Research Tool | 2026-09-12 12:56:19 | 8432 | ||||
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tranSMART Resource Report Resource Website 10+ mentions |
tranSMART (RRID:SCR_005586) | tranSMART | software resource | tranSMART is a knowledge management platform that enables scientists to develop and refine research hypotheses by investigating correlations between genetic and phenotypic data, and assessing their analytical results in the context of published literature and other work. tranSMART is licensed through GPL 3. The integration, normalization, and alignment of data in tranSMART permits users to explore data very efficiently to formulate new research strategies. Some of tranSMART''s specific applications include: * Revalidating previous hypotheses * Testing and refining novel hypotheses * Conducting cross-study meta-analysis * Searching across multiple data sources to find associations of concepts, such as a gene''s involvement in biological processes or experimental results * Comparing biological processes and pathways among multiple data sets from related diseases or even across multiple therapeutic areas Data Repository The tranSMART Data Repository combines a data warehouse with access to federated sources of open and commercial databases. tranSMART accommodates: * Phenotypic data, such as demographics, clinical observations, clinical trial outcomes, and adverse events * High content biomarker data, such as gene expression, genotyping, pharmacokinetic and pharmaco-dynamics markers, metabolomics data, and proteomics data * Unstructured text-data, such as published journal articles, conference abstracts and proceedings, and internal studies and white papers * Reference data from sources such as MeSH, UMLS, Entrez, GeneGo, Ingenuity, etc. * Metadata providing context about datasets, allowing users to assess the relevance of results delivered by tranSMART Data in tranSMART is aligned to allow identification and analysis of associations between phenotypic and biomarker data, and it is normalized to conform with CDISC and other standards to facilitate search and analysis across different data sources. tranSMART also enables investigators to search published literature and other text sources to evaluate their analysis in the context of the broader universe of reported research. External data can also be integrated into the tranSMART data repository, either from open data projects like GEO, EBI Array Express, GCOD, or GO, or from commercially available data sources. Making data accessible in tranSMART enables organizations to leverage investments in manual curation, development costs of automated ETL tools, or commercial subscription fees across multiple research groups. Dataset Explorer tranSMART''s Dataset Explorer provides flexible, powerful search and analysis capabilities. The core of the Dataset Explorer integrates and extends the open source i2b2 application, Lucene text indexing, and GenePattern analytical tools. Connections to other open source and commercial analytical tools such as Galaxy, Integrative Genomics Viewer, Plink, Pathway Studio, GeneGo, Spotfire, R, and SAS can be established to expand tranSMART''s capabilities. tranSMART''s design allows organizations flexibility in selecting analytical tools accessible through the Dataset Explorer, and provides file export capabilities to enable researchers to use tools not accessible in the tranSMART portal. | source code, genetic, phenotype, gene, data storage repository, data analysis service |
is used by: eTRIKS is used by: RanchoBiosciences |
nlx_146211 | http://www.transmartproject.org/ | SCR_005586 | 2026-09-12 12:56:28 | 13 | ||||||||
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Genentech Resource Report Resource Website 1000+ mentions |
Genentech (RRID:SCR_003997) | Genentech | commercial organization | A biotechnology corporation that uses human genetic information to discover, develop, manufacture and commercialize medicines to treat patients with serious or life-threatening medical conditions. | drug, genetic, medicine, biotechnology, oncology, immunology, tissue growth, tissue repair, neuroscience, infectious disease, microbiology, medical imaging |
is related to: Alzheimers Disease Genetics Consortium has parent organization: Roche is parent organization of: GMAP |
Infectious disease, Cancer | nlx_158417 | SCR_003997 | Genentech Inc, F. Hoffmann-La Roche Ltd / Genentech | 2026-09-12 12:56:06 | 3311 | |||||||
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Alzheimers Association Research Roundtable Resource Report Resource Website |
Alzheimers Association Research Roundtable (RRID:SCR_004007) | Research Roundtable | consortium, data or information resource, meeting resource, organization portal, portal, training resource | A consortium aiming to facilitate the development and implementation of new treatments for Alzheimer's disease by collectively addressing obstacles to research and development, clinical care and public health education. The Roundtable convenes twice each year for a two-day presentation and discussion of specific topics within Alzheimer's research. Topics are selected from a list proposed and voted on by members. Roundtable members explore a broad range of Alzheimer's science topics, including: * New data and technologies that may improve the diagnosis of Alzheimer's disease, especially in its earliest and mildest stages. * Neuropsychological testing, genetic factors, and biochemical and neuroimaging biomarkers that could contribute to an earlier and more accurate Alzheimer's diagnosis. * Lessons learned about clinical trial design that may help shape future clinical trials of drugs aimed at slowing or stopping the progression of Alzheimer's. * The pros and cons of various scales as outcomes measures of clinical trials. The outputs of Roundtable meetings are published as articles in the Alzheimer's Association's journal, Alzheimer's & Dementia. The Research Roundtable also sponsors Alzheimer's Association grants. The chosen project is named Research Roundtable Sponsored Grant and the principal investigator of the project is invited to give a progress report at a Roundtable meeting. | drug, drug development, tool development, product development, discussion, funding resource, diagnosis, neuropsychological testing, genetic, biochemical, neuroimaging, clinical trial, outcome |
is listed by: Consortia-pedia is related to: AbbVie has parent organization: Alzheimers Association |
nlx_158423 | SCR_004007 | Alzheimer's Association Research Roundtable | 2026-09-12 12:56:07 | 0 | ||||||||
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VIROME Resource Report Resource Website 10+ mentions |
VIROME (RRID:SCR_004362) | VIROME | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A web-application designed for scientific exploration of metagenome sequence data collected from viral assemblages occurring within a number of different environmental contexts. The VIROME informatics pipeline focuses on the classification of predicted open-reading frames (ORFs) from viral metagenomes. The portal allows you to submit your viral metagenome to be processed through the VIROME analysis pipeline, and enable you to investigate your data via the VIROME user interface., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | open-reading frame, metagenome, virus, environment, sequence, library, genetic, polymorphism, orfan, environmental sequencing, shotgun metagenomics, viral ecology, function, taxonomy, peptide, blast |
is listed by: OMICtools is related to: UniRef is related to: CAMERA is related to: Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis has parent organization: University of Delaware; Delaware; USA has parent organization: University of Maryland School of Medicine; Maryland; USA |
Gordon and Betty Moore Foundation ; NSF award 0959894 |
PMID:23407591 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01506 | SCR_004362 | Viral Informatics Resource for Metagenome Exploration, Viral Informatics Resource for Metagenome Exploration - VIROME | 2026-09-12 12:56:12 | 22 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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