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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Zebrafish RNAi Database Resource Report Resource Website |
Zebrafish RNAi Database (RRID:SCR_008965) | Zebrafish RNAi Database | data or information resource, data repository, organism-related portal, portal, service resource, storage service resource, topical portal | Community built zebrafish RNAi platform that contains plasmids, successfully targeted genes and shRNA sequences, and a forum for discussion. This is a true community platform with users who add data, modify entiries, request features and share using the discussion board. | plasmid, gene, shrna sequence, rnai, method | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | nlx_152032 | SCR_008965 | 2026-09-12 12:57:11 | 0 | |||||||||
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Human Variation DB Resource Report Resource Website |
Human Variation DB (RRID:SCR_009014) | Human Variation DB | data or information resource, data repository, database, service resource, storage service resource | A repository database to achieve continuous and intensive management of GWAS data and variation data identified by next generation sequencing (NGS) and data-sharing among researchers. In this database, variations including short/long insertions / deletions and structural variations related to disease susceptibility, virus resistance, and drug response are registered along with statistical genetic results and simple clinical characteristics to clarify the locus specific characteristics. Currently this database contains information extracted from scientific papers and next generation sequencing results and other small scale experimental results of several research laboratories. Mutation data submission is greatly appreciated. | gene, genome, disease, snp, next generation sequencing, gwas, genetic variation, mutation, copy number variation, insertion, deletion, structural variation | has parent organization: NBDC - National Bioscience Database Center | Japan Science and Technology Agency | PMID:19629137 PMID:21385384 |
The community can contribute to this resource | nlx_153886 | SCR_009014 | Human Genome Variation Database | 2026-09-12 12:57:11 | 0 | |||||
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BARS Resource Report Resource Website 10+ mentions |
BARS (RRID:SCR_009123) | BARS | software application, software resource | Software application that is a statistical method that bridges the gap between single-locus and haplotype-based tests of association. It is based on the non-parametric regression techniques embodied by Bayesian Adaptive Regression Splines. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, r, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154204, biotools:bars, nlx_154228, SCR_009106 | https://bio.tools/bars | SCR_009123 | Bayesian Adaptive Regression Splines | 2026-09-12 12:57:11 | 39 | ||||||
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CMAP Resource Report Resource Website 100+ mentions |
CMAP (RRID:SCR_009034) | CMap | data analysis software, data processing software, software application, software resource | Web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, unix, solaris, freebsd, linux, sequence, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SoftCite has parent organization: Generic Model Organism Database Project works with: Drug Gene Budger |
PMID:19648141 | GNU General Public License | nlx_153998, OMICS_00933 | https://sourceforge.net/projects/gmod/files/cmap/ | http://www.gmod.org/cmap/, http://gmod.org/wiki/Cmap | SCR_009034 | , GMOD Comparative Mapping (CMap) tool, Comparative Mapping tool, genetic and comparative maps | 2026-09-12 12:57:11 | 417 | ||||
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caGWAS Resource Report Resource Website |
caGWAS (RRID:SCR_009617) | caGWAS | software resource | Too that allows researchers to integrate, query, report, and analyze significant associations between genetic variations and disease, drug response or other clinical outcomes. SNP array technologies make it possible to genotype hundreds of thousands of single nucleotide polymorphisms (SNPs) simultaneously, enabling whole genome association studies. Within the Clinical Genomic Object Model (CGOM), the caIntegrator team created a domain model for Whole Genome Association Study Analysis. CGOM-caGWAS is a A semantically annotated domain model that captures associations between Study, Study Participant, Disease, SNP Association Analysis, SNP Population Frequency and SNP annotations. caGWAS APIs and web portal provide: * a semantically annotated domain model, database schema with sample data, seasoned middleware, APIs, and web portal for GWAS data; * platform and disease agnostic CGOM-caGWAS model and associated APIs; * the opportunity for developers to customize the look and feel of their GWAS portal; * a foundation of open source technologies; * a well-tested and performance-enhanced platform, as the same software is being used to house the CGEMS data portal; * accelerated analysis of results from various biomedical studies; and * a single application through which researchers and bioinformaticians can access and analyze clinical and experimental data from a variety of data types, as caGWAS objects are part of the CGOM, which includes microarray, genomic, immunohistochemistry, imaging, and clinical data. | application, computational neuroscience, genetic association, genomic analysis, imaging genomics, java, snp, gene, software, web environment, microarray, genomic, immunohistochemistry, imaging, clinical |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National Cancer Institute |
BSD License | nlx_155841 | http://www.nitrc.org/projects/cagwas | SCR_009617 | caGWAS (Cancer Genome-Wide Association Studies), Cancer Genome-Wide Association Studies, CGOM-caGWAS | 2026-09-12 12:57:14 | 0 | ||||||
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AgingDB Resource Report Resource Website |
AgingDB (RRID:SCR_010226) | AgingDB | data or information resource, data repository, database, service resource, storage service resource | A database that stores information on the biomolecules which are modulated during aging and by caloric restriction (CR). To enhance its usefulness, data collected from studies of CR''''s anti-oxidative action on gene expression, oxidative stress, and many chronic age-related diseases are included. AgingDB is organized into two sections A) apoptosis and the various mitochondrial biomolecules that play a role in aging; B) nuclear transcription factors known to be_sensitive to oxidative environment. AgingDB features an imagemap of biomolecular signal pathways and visualized information that includes protein-protein interactions of biomolecules. Authorized users can submit a new biomolecule or edit an existing biomolecule to reflect latest developments. | oxidative stress, calorie restriction, pathway, biomolecule, signal pathway, interaction, gene, protein, protein-protein interaction, apoptosis, mitochondrial, nuclear transcription factor |
is related to: Gene Ontology has parent organization: Pusan National University; Busan; South Korea |
Aging | PMID:23604914 | The community can contribute to this resource | nlx_156773 | http://aging.pharm.pusan.ac.kr/AgingDB/ | SCR_010226 | Aging Database, Aging DB | 2026-09-12 12:57:15 | 0 | ||||
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Illumina Resource Report Resource Website 1000+ mentions |
Illumina (RRID:SCR_010233) | Illumina, Inc. | commercial organization | American company incorporated that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function. Provides a line of products and services that serve the sequencing, genotyping and gene expression and proteomics markets. Its headquarters are located in San Diego, California. | Commercial, organization, develope, manufacture, system, analysis, genetic, sequencing, genotyping, gene, expression, proteomic |
is related to: fermi-lite is related to: Illumina: NextSeq 2000 system is parent organization of: Strelka2 is parent organization of: Tk-GO is parent organization of: BaseSpace is parent organization of: Illumina: iSeq 100 Sequencing System |
nlx_156846, grid.185669.5, Wikidata: Q2068984, ISNI: 0000 0004 0507 3954 | https://ror.org/05k34t975 | SCR_010233 | Inc., Illumina | 2026-09-12 12:57:16 | 2543 | |||||||
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Evex Resource Report Resource Website 10+ mentions |
Evex (RRID:SCR_010509) | data or information resource, database, software application, software resource, text-mining software | EVEX is a text mining resource built on top of PubMed abstracts and PubMed Central full texts. It contains over 40 million bio-molecular events among more than 76 million automatically extracted gene/protein name mentions. The text mining data further has been enriched with gene normalization results, allowing straightforward integration with external resources. Further, gene families from Ensembl and HomoloGene provide homology-based event generalizations. EVEX presents both direct and indirect associations between genes and proteins, enabling explorative browsing of relevant literature. | gene, protein, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Ghent University; Ghent; Belgium |
biotools:evex, nlx_158731 | https://bio.tools/evex | SCR_010509 | 2026-09-12 12:57:20 | 19 | |||||||||
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Gene Regulation Ontology Resource Report Resource Website |
Gene Regulation Ontology (RRID:SCR_010590) | GRO, BOOTStrep | controlled vocabulary, data or information resource, ontology | Ontology that is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes. GRO is intended to represent common knowledge about gene regulation in a formal way rather than representing extremely fine-grained classes as can be found in ontologies such as the Gene Ontology (GO) (created for data base annotation purposes) and various relevant databases. The main purpose of the ontology is to support NLP applications. It has a particular focus on the relations between processes and the molecules (participants) involved. The basic structure of the GRO is a direct acyclic graph (DAG) with ontology classes as nodes and is-a relations between classes as edges. The taxonomic backbone is further enriched by several semantic relation types (part-of, from-species, participates-in with the two sub-relations agent-of and patient-of). | owl, genomic, proteomic, biological process, gene regulation, gene expression, gene, transcription factor, process, molecule, biological_process |
is listed by: BioPortal is listed by: OBO has parent organization: European Bioinformatics Institute |
nlx_157415, nlx_46399 | http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html, http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO_latest | SCR_010590 | Gene Regulation Ontology - Ontological resource from the BOOTStrep project for the representation of gene regulation events | 2026-09-12 12:57:21 | 0 | |||||||
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miRDeep Resource Report Resource Website 100+ mentions |
miRDeep (RRID:SCR_010829) | miRDeep2 | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to identify known and novel miRNA genes in seven animal clades by analyzing sequenced RNAs. Used for discovering known and novel miRNAs from small RNA sequencing data. | miRNA, gene, animal, clade, analysis, sequence, RNA, data | is listed by: OMICtools | China Scholarship Council ; German Ministry of Education and Research ; Helmholtz Association ; Helmholtz-Alliance on Systems Biology ; Max Delbrück Centrum Systems Biology Network ; Senate of Berlin |
PMID:18392026 PMID:21911355 |
Free, Available for download, Freely available | OMICS_00373 | https://github.com/rajewsky-lab/mirdeep2 | SCR_010829 | 2026-09-12 12:57:24 | 182 | |||||
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Gene Cloud: Exploring Connections in the Mouse Genome Resource Report Resource Website 1+ mentions |
Gene Cloud: Exploring Connections in the Mouse Genome (RRID:SCR_003503) | Gene Cloud | service resource | Gene Cloud is a novel tool presenting gene-gene associations based on the scientific literature. It was developed by the Knockout Mouse Repository (www.komp.org) to help our customers find products related to other products they chose. We have built a detailed graph model of gene-gene associations based on how many times two genes are cited in the same article. If two genes are cited in many papers together, they are considered strongly connected. Each instance of Gene Cloud is centered around a specific gene. A list of the top most related genes is plotted as a branching structure from the center. A secondary branch can occur if a gene in the graph is more related a non-central gene than it is to the center gene. The font size of a branched gene indicates the relative strength of connection--always to the center gene. The distribution of genes in space is randomized each time Gene Cloud is run so a different picture will result for the same central gene. Color is used to indicate the availability of Knockout Mouse products at the KOMP Repository. If a gene is colored green in the graph there are products (mutant ES cells, sperm, embryos, or mice) ready to be ordered. Blue colored genes do not yet have products available, but you can follow the links back to the KOMP Repository and register interest to be alerted when products do become available. Gene Cloud is driven by a database of gene-gene associations that currently contains 82,000 genes and other biotypes, 113,000 annotated publications, and 467 million connections. The latest gene symbols, names and gene-publication annotation information is updated daily from the Mouse Genome Informatics database. The graphing is accomplished through the use of a modified version of jsViz. | gene, association, literature, knockout, mouse | has parent organization: University of California at Davis; California; USA | www.komp.org ; www.mousebiology.org |
nif-0000-37178 | SCR_003503 | 2026-09-12 12:55:59 | 1 | ||||||||
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JISTIC Resource Report Resource Website 1+ mentions |
JISTIC (RRID:SCR_003482) | JISTIC | software resource | Software tool for analyzing datasets of genome-wide copy number variation to identify driver aberrations in cancer. | copy number variation, candidate gene, gene |
is listed by: OMICtools has parent organization: Columbia University; New York; USA |
Cancer | PMID:20398270 | Free, Public | OMICS_02297 | SCR_003482 | 2026-09-12 12:55:59 | 2 | ||||||
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ProbeMatchDB 2.0 Resource Report Resource Website |
ProbeMatchDB 2.0 (RRID:SCR_003433) | ProbeMatchDB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Matches a list of microarray probes across different microrarray platforms (GeneChip, EST from different vendors, Operon Oligos) and species (human, mouse and rat), based on NCBI UniGene and HomoloGene. The capability to match protein sequence IDs has just been added to facilitate proteomic studies. The ProbeMatchDB is mainly used for the design of verification experiments or comparing the microarray results from different platforms. It can be used for finding equivalent EST clones in the Research Genetics sequence verified clone set based on results from Affymetirx GeneChips. It will also help to identify probes representing orthologous genes across human, mouse and rat on different microarray platforms. | experiment, human, microarray, mouse, oligo, operon, platform, probe, protein, proteomic, rate, sequence, study, gene, est, cdna, sts marker, orthologous gene, ortholog, microarray probe, nucleotide sequence |
is related to: UniGene is related to: HomoloGene has parent organization: University of Michigan; Ann Arbor; USA |
University of Michigan Microarray Network ; Nancy Pritzker Depression Research Network ; Department of Psychiatry pilot study ; NIMH L99 MH60398; NIDA R21 DA13754-01 |
PMID:11934751 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33156 | SCR_003433 | 2026-09-12 12:55:58 | 0 | ||||||
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MARCAR Resource Report Resource Website 1+ mentions |
MARCAR (RRID:SCR_003755) | MARCAR | consortium, data or information resource, organization portal, portal | Consortium to identify early biological indicators (biomarkers) that can be used to predict the development of cancer, as an unintended and adverse response to a new drug. The use of these biomarkers that detect early carcinogenicity will hopefully accelerate drug development and increase patient safety. The project focuses on non-genotoxic carcinogenesis (NGC) specifically looking at the role of epigenetic effects that could be caused as unintended consequences of new drugs. Using a combination of molecular analysis technologies, the consortium combines expertise in the field of biomarkers, human and rodent cancer models, imaging, molecular profiling and bioinformatics. Participants will focus on liver tumors, the organ most affected by non-genotoxic carcinogenesis, during the preclinical safety evaluations of candidate-medicines. Their findings aim to facilitate tumor identification in other organs as well, in hopes of providing insights in the mechanisms of tumor growth. The main objectives of the consortium are to: * Identify early biomarkers for predicting which compounds have a potential for later cancer development * Improve the scientific basis for assessing carcinogenic potential of non-genotoxic (NGC) drugs * Identify the molecular response to NGC exposure that underpins development of early exposure biomarkers * Improve drug safety and the efficiency of drug development by advancing the development of alternative research methods | biomarker, tumor classification, non genotoxic carcinogen, drug-induced tumor, safety, drug development, drug, consortium, carcinogen, adverse response, liver, mri, gene interaction, dna modification, drug exposure, gene expression, mutation, nuclear receptor, drug safety, biological process, gene, imaging, molecular profiling |
is listed by: Consortia-pedia has parent organization: University of Dundee; Scotland; United Kingdom |
Innovative Medicines Initiative | nlx_157986 | SCR_003755 | MARCAR - towards novel biomarkers for cancer risk assessment, bioMARkers and molecular tumor classification for non-genotoxic CARcinogenesis | 2026-09-12 12:56:02 | 6 | |||||||
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Blueprint Epigenome Resource Report Resource Website 100+ mentions |
Blueprint Epigenome (RRID:SCR_003844) | BLUEPRINT | consortium, data or information resource, organization portal, portal, protocol | Consortium to further the understanding of how genes are activated or repressed in both healthy and diseased human cells with a focus on distinct types of haematopoietic cells from healthy individuals and on their malignant leukemic counterparts. They will generate at least 100 reference epigenomes and study them to advance and exploit knowledge of the underlying biological processes and mechanisms in health and disease. Reference epigenomes will be generated by state-of-the-art technologies from highly purified cells for a comprehensive set of epigenetic marks in accordance with quality standards set by International Human Epigenome Consortium (IHEC). Access to the data is provided as well as the protocols used to collect the different blood cell types, to perform the different types of epigenomic analyses, etc.). This resource-generating activity will be complemented by hypothesis-driven research into blood-based diseases, including common leukemias and autoimmune disease (Type 1 Diabetes), by discovery and validation of epigenetic markers for diagnostic use and by epigenetic target identification. Since epigenetic changes are reversible, they can be targets for the development of novel and more individualized medical treatments. The involvement of companies will energize epigenomic research in the private sector by the development of smart technologies for better diagnostic tests and by identifying new targets for compounds. Thus the results of the project may lead to targeted diagnostics, new treatments and preventive measures for specific diseases in individual patients, an approach known as "personalized medicine". The Blueprint Data Access Committee will consider applications for access to data sets stored in the European Genome-phenome Archive (EGA) when authorized to do so by the Blueprint consortium and the holders of the original consent documents. Access is conditional upon availability of samples and/or data and signed agreement by the researcher(s) and the responsible employing Institution to abide by policies related to publication, data disposal, ethical approval and confidentiality. At EBI, the ftp site with the data can be found. You can either opt to link to the track hubs yourself or you can add the track hub to a genome browser - UCSC or ENSEMBL. Also Meta Data files and README are available. The data can also be accessed via the BIOMART system. | epigenome, hematopoiesis, gene, data set, biomaterial supply resource, antibody, blood cell, blood, cord blood precursor cell, cell, cord blood, bone marrow, rna-seq, dname-seq, dnasei-seq, chip-seq, monocyte, granulocyte neutrophil, eosinophil, macrophage, m0, m1, m2, naive cd4+, naive cd8+, pathway |
uses: European Genome phenome Archive uses: European Bioinformatics Institute uses: BioMart Project uses: UCSC Genome Browser uses: Ensembl is used by: Deep Blue Epigenomic Data Server is listed by: Consortia-pedia is listed by: One Mind Biospecimen Bank Listing has parent organization: Radboud University; Nijmegen; The Netherlands |
Leukemia, Blood disease, Autoimmune disease, Type 1 diabetes, Diabetes | European Union FP7 282510 | Authorization required, Application required, Data Access Agreement, Acknowledgement required | nlx_158155 | SCR_003844 | BLUEPRINT - A BLUEPRINT of Haematopoietic Epigenomes | 2026-09-12 12:56:03 | 123 | |||||
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Alzheimers Disease Genetics Consortium Resource Report Resource Website 10+ mentions |
Alzheimers Disease Genetics Consortium (RRID:SCR_004004) | ADGC | consortium, data or information resource, data set, organization portal, portal | Consortium to conduct genome-wide association studies (GWAS) to identify genes associated with an increased risk of developing late-onset Alzheimer''''s disease (LOAD). The goal of the ADGC is to identify genetic variants associated with risk for AD. It plans to do this through the following collaborative goals: # Identify genes responsible for AD susceptibility # Identify AD sub-phenotype genes rate-of-progression plaque / tangle load / distribution biomarker variability # Generate a genetic data resource for the AD research community Data generated by ADGC is available at the following website: https://www.niagads.org/content/alzheimers-disease-genetics-consortium-adgc-collection | genome-wide association study, gene, biomarker, basic science, genetic variant, genetics, african-american, caucasian |
is listed by: Consortia-pedia is related to: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA is related to: Icahn School of Medicine at Mount Sinai; New York; USA is related to: University of Washington; Seattle; USA is related to: Boston University; Massachusetts; USA is related to: Washington University in St. Louis; Missouri; USA is related to: Vanderbilt University; Tennessee; USA is related to: Oregon Health and Science University; Oregon; USA is related to: Columbia University; New York; USA is related to: University of Miami; Florida; USA is related to: Banner Alzheimer's Institute; Arizona; USA is related to: Indiana University; Indiana; USA is related to: University of Toronto; Ontario; Canada is related to: Mayo Clinic Florida; Florida; USA is related to: Johns Hopkins University; Maryland; USA is related to: Albert Einstein College of Medicine; New York; USA is related to: Genentech is related to: University of Gothenburg; Gothenburg; Sweden is related to: University of North Texas; Texas; USA is related to: University of Kentucky; Kentucky; USA is related to: University of Chicago; Illinois; USA is related to: University of Michigan; Ann Arbor; USA is related to: University of Virginia; Virginia; USA is related to: Florida Alzheimer's Disease Research Center is related to: Mayo Clinic is related to: Emory University; Georgia; USA is related to: New York University; New York; USA is related to: Stanford University; Stanford; California is related to: Northwestern University Feinberg School of Medicine; Illinois; USA is related to: University of Alabama; Alabama; USA is related to: University of Arkansas for Medical Sciences; Arkansas; USA is related to: University of San Diego; California; USA is related to: University of California at Irvine; California; USA is related to: University of California at Los Angeles; California; USA is related to: University of California at San Diego; California; USA is related to: University of California at San Francisco; California; USA is related to: University of Pittsburgh; Pennsylvania; USA is related to: University of Southern California; Los Angeles; USA is related to: University of Texas Southwestern Medical Center; Texas; USA is related to: National Alzheimer's Coordinating Center is related to: Childrens Hospital of Philadelphia - Research Institute; Pennsylvania; USA is related to: National Institute on Aging is related to: University of California at Davis; California; USA is related to: Mayo Clinic College of Medicine is related to: Wake Forest University; North Carolina; USA is related to: National Cell Repository for Alzheimer's Disease is related to: International Genomics of Alzheimers Project is related to: National Alzheimer's Coordinating Center has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA |
NIA UO1AG032984 | nlx_158415 | SCR_004004 | Alzheimer''''s Disease Genetics Consortium (ADGC), Alzheimer''''s Disease Genetics Consortium | 2026-09-12 12:56:06 | 12 | |||||||
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International AMD Genetics Consortium Resource Report Resource Website 10+ mentions |
International AMD Genetics Consortium (RRID:SCR_004009) | IAMDGC | consortium, data or information resource, organization portal, portal | Consortium aiming to identify the remaining genetic risk variants for Age-related Macular Degeneration (AMD). To increase the statistical power needed to identify genes that have small, yet significant contributions to AMD, the consortium is conducting a meta-analysis on 15 Genome Wide Association Studies (GWAS) pooled from consortium members representing over 8,000 patients with advanced AMD (dry type, neovascular, or both) and 50,000 controls. In addition to verifying known genes, the consortium identified 19 new gene variants. The genes identified in these studies function in the immune system, cholesterol transport and metabolism, and formation and maintenance of connective tissue. This study provides a nearly complete picture of genetic heritability for AMD. | genetic variant, genome-wide association study, gene, risk factor, genetics, visual system, eye, late adult human, basic science, biomarker |
is related to: National Eye Institute (NEI) Commons is related to: Boston University; Massachusetts; USA is related to: University of Regensburg; Bavaria; Germany is related to: Vanderbilt University; Tennessee; USA is related to: Case Western Reserve University; Ohio; USA is related to: University of Pittsburgh; Pennsylvania; USA is related to: Harvard Medical School; Massachusetts; USA is related to: University of Edinburgh; Scotland; United Kingdom is related to: Queens University Belfast; Ireland; United Kingdom is related to: Columbia University; New York; USA is related to: Johns Hopkins University; Maryland; USA is related to: University of Cambridge; Cambridge; United Kingdom is related to: University of Southampton; Southampton; United Kingdom is related to: University College London; London; United Kingdom is related to: University of Athens; Athens; Greece is related to: University of Thessaly; Thessaly; Greece is related to: University of Sydney; Sydney; Australia is related to: University of Melbourne; Victoria; Australia is related to: Flinders University; Adelaide; Australia is related to: Lions Eye Institute for Transplant and Research is related to: University of Western Australia; Perth; Australia is related to: National Institute of Health and Medical Research; Rennes; France is related to: Centre dEtude du Polymorphisme Humain is related to: University of Pennsylvania; Philadelphia; USA is related to: University of Miami; Florida; USA is related to: Texas Biomedical Research Institute; Texas; USA is related to: University of Utah; Utah; USA is related to: University of California at San Diego; California; USA is related to: University of California at Los Angeles; California; USA is related to: Oregon Health and Science University; Oregon; USA is related to: University of Michigan; Ann Arbor; USA has parent organization: Case Western Reserve University; Ohio; USA has parent organization: National Eye Institute (NEI) Commons |
NEI | nlx_158429, SCR_013676 | SCR_004009 | International Age-related Macular Degeneration Genetics Consortium | 2026-09-12 12:56:07 | 13 | |||||||
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WholeCellKB Resource Report Resource Website 1+ mentions |
WholeCellKB (RRID:SCR_004104) | WholeCellKB | data access protocol, data or information resource, database, model, software resource, source code, web service | A collection of free, open-source model organism databases designed specifically to enable comprehensive, dynamic simulations of entire cells and organisms. WholeCellKB provides comprehensive, quantitative descriptions of individual species including: * Their subcellular organization, * Their chromosome sequences, * The essentiality, location, length, direction, and homologs of each gene, * The organization and promoter of each transcription unit, * The expression and degradation rate of each RNA gene product, * The specific folding and maturation pathway of each RNA and protein species including the localization, N-terminal cleavage, signal sequence, prosthetic groups, disulfide bonds, and chaperone interactions of each protein species, * The subunit composition of each macromolecular complex, * Their genetic code, * The binding sites and footprint of every DNA-binding protein, * The structure, charge, and hydrophobicity of every metabolite, * The stoichiometry, catalysis, coenzymes, energetics, and kinetics of every chemical reaction, * The regulatory strength of each transcription factor on each promoter, * Their chemical composition, and * The composition of its typical SP-4 laboratory growth medium. WholeCellKB currently contains a single database of Mycoplasma genitalium, an extremely small gram-positive bacterium and common human pathogen. This database is the most comprehensive description of any single organism to date, and was used to develop the first whole-cell computational model. Users can download the WholeCellKB source code and content to create and customize - including the content, data model, and user interface - their own model organism database. | model organism, whole-cell model, gene, protein, reaction, pathway, phenotype, genotype, simulation, cell, organism | has parent organization: Stanford University; Stanford; California | PMID:23175606 PMID:22817898 |
Free, Open unspecified license, Acknowledgement requested, The community can contribute to this resource | nlx_158579 | http://wholecellkb.stanford.edu | SCR_004104 | Mycoplasma genitalium database, WholeCellKB-MG, Whole Cell KB | 2026-09-12 12:56:09 | 1 | |||||
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International Genomics of Alzheimers Project Resource Report Resource Website |
International Genomics of Alzheimers Project (RRID:SCR_004029) | IGAP | consortium, data or information resource, data set, organization portal, portal | Consortium to discover and map the genes that contribute to Alzheimer's disease and completely understand the role inheritance plays. To achieve this goal, they will work to identify all the genes that contribute to the risk of developing this disease. Investigators will have access to combined genetic data from a large number of Alzheimer's disease subjects and compare it to genetic data from an equally large number of elderly people who do not have Alzheimer's. In the initial phase of the work, more than 20,000 people with Alzheimer's and about 20,000 healthy elderly subjects will be compared. As the study progresses, 10,000 additional people with Alzheimer's and the same number of healthy elderly subjects will be added to the study. The subjects for these studies come from different Alzheimer research project locations across Europe, the UK, the US, and Canada. Data is available from their 2014 publication in Translational Psychiatry at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3944635/ (http://www.ncbi.nlm.nih.gov/pubmed/24495969) Currently, there is no public access to the raw individual level genetic data because of privacy considerations. Researchers working with US cohorts deposit data in the database of genotypes and phenotypes (dbGaP), where it is available to all researchers who can show that they are able to guarantee the security of the data. After scanning the DNA of over 74,000 patients and controls from 15 countries, the IGAP consortium reported 11 new regions of the genome involved in late-onset Alzheimer's disease. IGAP published its results in Nature Genetics on October 27, http://www.ncbi.nlm.nih.gov/pubmed/24162737 | gene, inheritance, late adult human, genome-wide association study, database, basic science, biomarker, dna, data sharing |
uses: NCBI database of Genotypes and Phenotypes (dbGap) is listed by: Consortia-pedia is related to: Alzheimers Association is related to: Alzheimer's Plan Foundation is related to: Makray Family Foundation is related to: Alzheimers Disease Genetics Consortium is related to: Cohorts for Heart and Aging Research in Genomic Epidemiology is related to: Boston University School of Medicine; Massachusetts; USA is related to: Cardiff University; Wales; United Kingdom is related to: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA is related to: Pasteur Institute of Lille; Lille; France is related to: National Institute on Aging is related to: Lille 2 University of Health and Law; Lille; France has parent organization: Pasteur Institute of Lille; Lille; France has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA has parent organization: Boston University School of Medicine; Massachusetts; USA has parent organization: Cardiff University; Wales; United Kingdom |
alz.org ; Alzheimers Plan Foundation ; Jim Prugh ; Diane Fatheree ; Makray Family Foundation |
nlx_158457 | SCR_004029 | International Genomics of Alzheimer's Project | 2026-09-12 12:56:07 | 0 | |||||||
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Centre for Modeling Human Disease Gene Trap Resource Resource Report Resource Website 1+ mentions |
Centre for Modeling Human Disease Gene Trap Resource (RRID:SCR_002785) | CMHD Gene Trap Resource | biomaterial manufacture, material service resource, production service resource, service resource | Generate gene trap insertions using mutagenic polyA trap vectors, followed by sequence tagging to develop a library of mutagenized ES cells freely available to the scientific community. This library is searchable by sequence or key word searches including gene name or symbol, chromosome location, or Gene Ontology (GO) terms. In addition,they offer a custom email alert service in which researchers are able to submit search criteria. Researchers will receive automated e-mail notification of matching gene trap clones as they are entered into the library and database. The resource features the use of complementary second and third generation polyA trap vectors developed by the Stanford lab and the laboratory of Professor Yasumasa Ishida of the Nara Institute of Science and Technology (NAIST) in Japan to mutagenize murine embryonic stem (ES) cells. CMHD gene trap clones are distributed by the Canadian Mouse Mutant Repository(CMMR). Information about ordering, services, and pricing can be found on their web site (http://www.cmmr.ca/services/index.html)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026. | embryonic stem cell, polya trap vector, gene trap, insertion, mutagenic polya trap vector, sequence, expression, mutagenesis, gene, mutation, expression profile, phenotype, database, gene expression, vector insertion, expressed sequence tag, blast, clone |
is related to: Gene Ontology is related to: CMMR - Canadian Mouse Mutant Repository is related to: International Gene Trap Consortium has parent organization: CMHD - Centre for Modeling Human Disease |
Canadian Institutes of Health Research ; Genome Canada ; Genome Prairie ; NIH |
PMID:14681480 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02891 | http://www.cmhd.ca/sub/genetrap.asp | SCR_002785 | Centre for Modeling Human Disease (CMHD) Gene Trap Resource | 2026-09-12 12:55:46 | 3 |
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