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Public medical school in the northwest United States, located in Seattle and affiliated with the University of Washington.
Proper citation: University of Washington School of Medicine; Washington; USA (RRID:SCR_006147) Copy
Public flagship research university in Eugene, Oregon, United States.
Proper citation: University of Oregon; Oregon; USA (RRID:SCR_006269) Copy
http://www.bioconductor.org/packages/devel/bioc/html/RUVSeq.html
Software package that implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.
Proper citation: RUVSeq (RRID:SCR_006263) Copy
The Toronto Centre for Phenogenomics (TCP) is an innovative, scientific collaboration between four research hospitals to operate a centralized, state-of-the-art research-enabling mouse facility. We conduct and support genetic research involving generation of mutant mice, physiological phenotyping, behavioural analysis, imaging, pathology and cryopreservation for storage and distribution. This joint project involving Mount Sinai Hospital, The Hospital for Sick Children, University Health Network and St. Michael''s Hospital pools resources and expertise to achieve excellence and economies of scale. The TCP opened for operations in October 2007. The centre functions as a regional, national and international resource for mouse models of human disease. This 120,000 square foot facility is located at 25 Orde Street, Toronto, and occupies four floors two below ground and two above. It houses specialized laboratories for mouse generation and analysis and, when fully occupied, it will contain approximately 36,000 cages (180,000 mice). The world-renowned scientific staff studies mammalian gene function, identifies genetic components of complex human disease, produces new mouse models of human disease, develops and tests new cell-based and gene-based therapies, and develops technologies for genome manipulation and phenotypic analysis. The TCP offers state-of-the-art mouse holding and facility support services to academic stakeholders and strategic private sector partners. It houses the Centre for Modeling Human Disease (CMHD), the Canadian Mouse Mutant Repository (CMMR), and the Mouse Imaging Centre (MICe) to provide an array of pre-clinical research services to clients. TCP Services * Phenotyping * Genetic Mapping * Pathology * Cryopreservation * Imaging * Genetically Engineered Mouse Models * Mouse Holding and Technical Services
Proper citation: Toronto Centre for Phenogenomics (RRID:SCR_006143) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 19,2021. A model of peer review, providing independent and standardized peer review that can be accepted and shared across all types of journals and distribution systems. Rubriq can provide rigorous reviews by the same qualified peers who review for journals, but with a standardized scorecard that can be used in any publishing model. The system will enable faster, more consistent reviews, and will help match papers with the right journals. Authors, reviewers and journal editors are encouraged to sign up in the earliest phases, so you can be among the first to participate and provide feedback.
Proper citation: Rubriq (RRID:SCR_006256) Copy
The CREATE consortium represents a core of major European and international mouse database holders and research groups involved in conditional mutagenesis, primarily to develop a strategy for the integration and dissemination of Cre driver strains for modelling aspects of complex human diseases in the mouse. Collectively the participants have amassed a significant number of these strains in their respective databases. Therefore one of the goals of CREATE is to provide a unified portal for worldwide access to these critical resources. The portal can either be searched through an advanced BioMart interface, by driver name, or by anatomical site of expression using Embryonic Mouse Anatomy Project (EMAP) and Mouse Anatomy (MA) ontology terms. Search results link back to the original source of the data for more detailed information and to IMSR to order mice if available. The ontology browser is particularly useful as it enables the CREATE consortium to identify cell and tissues that are not currently covered by existing lines. CREATE also aims to coordinate the production of suitable lines by the Cre generation projects described above. Through the CREATE portal, the CREATE consortium aims to develop a strategy for the production, integration and dissemination of new Cre driver strains for modelling aspects of complex human diseases in the mouse. CREATE is also developing a roadmap for harnessing emerging technologies and methods for improving Cre-mediated recombination in vivo through targeted, intensive workshops and discussion forums on the portal. This will entail review of construct design options for classical transgenic constructs (promoter/enhancer used, small size <2025 Kb) vs large transgenic constructs (BAC, P1, YAC etc.); methods used for Cre transgenic lines including random vs targeted integration, position independent expression loci, or replacement of endogenous coding sequences with Cre recombinase under the control of the endogenous locus. CREATE provides a platform for discussion of additional issues specific to inducible Cre strategies including background activity before induction, inducibility (kinetics), efficiency, and protocols used for induction of Cre recombinase activity. Additional components of the technology roadmap will be the cataloguing of other existing methodologies (rtTA, FLP, Dre) of mouse genome modification, sharing information on validated Cre mutant lines as well as identification and assessment of new methods of mutagenesis such as RNAi and other emerging technologies. Other discussion topics addressed through surveys on the CREATE portal include the characterization of Cre lines (specificity of expression/deletion; efficiency of expression/ deletion; reproducibility of deletion from animal to animal for the same floxed allele; reproducibility with different floxed alleles; timing of expression/deletion, etc.), the extent to which Cre expression changes upon backcrossing to specific genetic backgrounds through variegation and silencing; potential phenotypes caused by either integration- mediated mutagenesis or Cre ''toxicity''; and other factors affecting the specificity of Cre-mediated expression/deletion. CREATE regularly integrates common fields from the Cre-X, CreZOO and the MGI recombinase portal resources described below. The data in common consists of: * Transgene or Knock-in name. * MGI ID of allele. * Driver. * Anatomical site of expression. * Pubmed ID. * IMSR strain name and link. * Inducibility (YES/NO).
Proper citation: CREATE (RRID:SCR_006133) Copy
http://purl.bioontology.org/ontology/RSA
An ontology for sequence annotations and how to preserve them with reference sequences.
Proper citation: Reference Sequence Annotation (RRID:SCR_006095) Copy
The John Templeton Foundation serves as a philanthropic catalyst for discoveries relating to the Big Questions of human purpose and ultimate reality. We support research on subjects ranging from complexity, evolution, and infinity to creativity, forgiveness, love, and free will. We encourage civil, informed dialogue among scientists, philosophers, and theologians and between such experts and the public at large, for the purposes of definitional clarity and new insights. Our vision is derived from the late Sir John Templeton''s optimism about the possibility of acquiring new spiritual information and from his commitment to rigorous scientific research and related scholarship. The Foundation''s motto, How little we know, how eager to learn, exemplifies our support for open-minded inquiry and our hope for advancing human progress through breakthrough discoveries. Our Core Funding Areas cover the full range of the Foundation''s activities and grantmaking. Science and the Big Questions is the largest of these Core Funding Areas and is further divided into several subfields. The descriptions and illustrative grants attached to the Core Funding Areas are not meant to be exhaustive, but they should give potential applicants a general understanding of the sorts of activities that the Foundation does and does not fund. Core Funding Areas: * Science and the Big Questions ** Mathematical and Physical Sciences ** Life Sciences ** Human Sciences ** Philosophy and Theology ** Science in Dialogue * Character Development * Freedom and Free Enterprise * Exceptional Cognitive Talent and Genius * Genetics
Proper citation: John Templeton Foundation (RRID:SCR_006092) Copy
A comprehensive encyclopedia of genomic functional elements in the model organisms C. elegans and D. melanogaster. modENCODE is run as a Research Network and the consortium is formed by 11 primary projects, divided between worm and fly, spanning the domains of gene structure, mRNA and ncRNA expression profiling, transcription factor binding sites, histone modifications and replacement, chromatin structure, DNA replication initiation and timing, and copy number variation. The raw and interpreted data from this project is vetted by a data coordinating center (DCC) to ensure consistency and completeness. The entire modENCODE data corpus is now available on the Amazon Web Services EC2 cloud. What this means is that virtual machines and virtual compute clusters that you run within the EC2 cloud can mount the modENCODE data set in whole or in part. Your software can run analyses against the data files directly without experiencing the long waits and logistics associated with copying the datasets over to your local hardware. You may also view the data using GBrowse, Dataset Search, or download the data via FTP, as well as download pre-release datasets.
Proper citation: modENCODE (RRID:SCR_006206) Copy
A clustering and visualization tool that enables the interactive exploration of genome-wide data, with a specialization in epigenomics data. Spark is also available as a service within the Epigenome toolset of the Genboree Workbench. The approach utilizes data clusters as a high-level visual guide and supports interactive inspection of individual regions within each cluster. The cluster view links to gene ontology analysis tools and the detailed region view connects to existing genome browser displays taking advantage of their wealth of annotation and functionality.
Proper citation: Spark (RRID:SCR_006207) Copy
PhenomeNet is a cross-species phenotype similarity network. It contains the experimentally observed phenotypes of multiple species as well as the phenotypes of human diseases. PhenomeNet provides a measure of phenotypic similarity between the phenotypes it contains. The latest release (from 22 June 2012) contains 124,730 complex phenotype nodes taken from the yeast, fish, worm, fly, rat, slime mold and mouse model organism databases as well as human disease phenotypes from OMIM and OrphaNet. The network is a complete graph in which edge weights represent the degree of phenotypic similarity. Phenotypic similarity can be used to identify and prioritize candidate disease genes, find genes participating in the same pathway and orthologous genes between species. To compute phenotypic similarity between two sets of phenotypes, we use a weighted Jaccard index. First, phenotype ontologies are used to infer all the implications of a phenotype observation using several phenotype ontologies. As a second step, the information content of each phenotype is computed and used as a weight in the Jaccard index. Phenotypic similarity is useful in several ways. Phenotypic similarity between a phenotype resulting from a genetic mutation and a disease can be used to suggest candidate genes for a disease. Phenotypic similarity can also identify genes in a same pathway or orthologous genes. PhenomeNet uses the axioms in multiple species-dependent phenotype ontologies to infer equivalent and related phenotypes across species. For this purpose, phenotype ontologies and phenotype annotations are integrated in a single ontology, and automated reasoning is used to infer equivalences. Specifically, for every phenotype, PhenomeNet infers the related mammalian phenotype and uses the Mammalian Phenotype Ontology for computing phenotypic similarity. Tools: * PhenomeBLAST - A tool for cross-species alignments of phenotypes * PhenomeDrug - method for drug-repurposing
Proper citation: phenomeNET (RRID:SCR_006165) Copy
Open, web-based platform providing bioinformatics tools and services for data intensive genomic research. Platform may be used as a service or installed locally to perform, reproduce, and share complete analyses. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Community has created Galaxy instances in many different forms and for many different applications including Galaxy servers, cloud services that support Galaxy instances, and virtual machines and containers that can be easily deployed for your own server.The Galaxy team is a part of BX at Penn State, and the Biology and Mathematics and Computer Science departments at Emory University.Training Infrastructure as a Service (TIaaS) is a service offered by some UseGalaxy servers to specifically support training use cases.
Proper citation: Galaxy (RRID:SCR_006281) Copy
http://compbio.charite.de/phenexplorer/
The PhenExplorer allows you to browse the Human Phenotype Ontology (HPO) in different ways, using the tabs ''''by features'''', ''''by disease'''', ''''by ontology'''' or ''''by genes''''. Clicking on a particular phenotypic feature (HPO-term) you can get a list of disease entries that are linked to it (i.e. diseases that are annotated with this HPO-term). You can also visualize this term in the context of the ontological structure. Finally, a lists of genes can be displayed, that are known to cause (when mutated) the linked diseases mentioned above. For each disease you can get the list of linked HPO-terms and genes. You can also search for specific genes and explore to which HPO-terms and diseases they are linked.
Proper citation: Phenexplorer (RRID:SCR_006156) Copy
An open-membership International community to promote mechanisms that standardize the description of genomes and the exchange and integration of genomic data. Community-driven standards have the best chance of success if developed within the auspices of international working groups. Participants in the GSC include biologists, computer scientists, those building genomic databases and conducting large-scale comparative genomic analyses, and those with experience of building community-based standards. The mission of the GSC is to work with the wider community towards: * the implementation of new genomic standards * methods of capturing and exchanging metadata * harmonization of metadata collection and analysis efforts across the wider genomics community
Proper citation: Genomic Standards Consortium (RRID:SCR_006273) Copy
University in Norway, located in Oslo. Its faculties include Lutheran Theology, Law, Medicine, Humanities, Mathematics, natural sciences, social sciences, Dentistry, and Education.
Proper citation: University of Oslo; Oslo; Norway (RRID:SCR_006275) Copy
Collegiate university based in Dunedin, Otago, New Zealand.
Proper citation: University of Otago; Dunedin; New Zealand (RRID:SCR_006276) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented on December 13, 2012. Cell Press continues to evolve the way scientific information is conveyed, and has made Article of the Future available for all review article formats, in addition to the research article format launched in January. With this latest release, all articles are also now more customizable, giving users added flexibility and control over how they read research and reviews. Readers can now: * Adjust the widths of the text and figure panels using a horizontal slider, allowing text and figures to be viewed side-by-side in a way that best suits the readers' needs. (Available in the Summary and Main Text tabs for reviews, and in the Results tab for research articles) * Easily identify proteins and small molecules and access additional information about these compounds with Reflect, winner of the 2009 Elsevier Grand Challenge * Reveal greater detail in figures with improved zoom functionality * Search across all tabs within an article * View the article in the standard, linear format with one click
Proper citation: Article of the Future (RRID:SCR_006270) Copy
http://www.australianphenomics.org.au/
Mouse models for the study of human and animal disease for Australian and international researchers. It has reduced the cost to researchers of accessing mouse models of disease, and provides equipment and expertise to undertake characterization and further research of these models. The APN brought together mouse production, strain storage and pathology capabilities, later extending the core services of the network, and include new services (RNAi and genomics services). Twelve Australian facilities and institutions currently constitute the APN. The APN partners contribute their expertise and infrastructure for the production of mouse models, as well as providing cryopreservation and pathology services. * Walter and Eliza Hall Institute of Medical Research * Monash University * Queensland Institute of Medical Research * Animal Resources Centre * Institute of Medical and Veterinary Science * University of Melbourne * Institute of Molecular Bioscience * Menzies Research Institute * Peter MacCallum Cancer Centre * Australian National University * Western Australian Institute of Medical Research * Centenary Institute In addition, the APN is working with the Atlas of Living Australia to develop a framework for Australia''''s e-science infrastructure to improve the capture, annotation and dissemination of research data. The APN''''s core expertise and infrastructure is also extended by key national and international partnerships. These include the Garvan Institute, the National Institutes of Health (United States), the Wellcome Trust (United Kingdom), and the University of Manitoba (Canada). Services * ES Cell to Mouse: Create a mouse model from embryonic stem cells * RNAi: Screen full genomes to identify novel gene targets * ENU Mutagenesis - Produce chemically-induced mouse models * Pathology - Investigate mouse models using clinical and histopathology * Genomics - Further mouse mutant identification via new discovery pipeline * NHMRC Australian PhenomeBank - a non-profit repository of mouse strains used in Medical Research.
Proper citation: Australian Phenomics Network (RRID:SCR_006150) Copy
http://purl.bioontology.org/ontology/VO
A biomedical ontology in the vaccine domain
Proper citation: Vaccine Ontology (RRID:SCR_006271) Copy
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