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Biomedical ontology in the domain of adverse events that aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. AEO is a community-based ontology. Its development follows the OBO Foundry principles.
Proper citation: Ontology of Adverse Events (RRID:SCR_003428) Copy
Private comprehensive research university in South Korea. Starting as a church-run kindergarten in 1918, CAU transformed into a school for female kindergarten teachers in 1922 and was granted university status in 1953.
Proper citation: Chung-Ang University; Seoul; South Korea (RRID:SCR_003547) Copy
A web based social authoring and publishing environment that adheres to open standards and RESTful design principals. It provides wiki-like ease of use with a sophisticated web services framework for rapid application development, creating flexible workflows and rapid integration. MindTouch creates a vibrant real-time information fabric by federating content from across enterprise silos, such as CRM, ERP, file servers, email, databases, web services and more.
Proper citation: Mindtouch DekiWiki (RRID:SCR_003425) Copy
http://www.nanostring.com/products/nSolver
Data analysis software program that offers nCounter users the ability to QC, normalize, and analyze data without having to purchase additional software packages.
Proper citation: nSolver Analysis Software (RRID:SCR_003420) Copy
http://portal.ncibi.org/gateway/mimiplugin.html
The Cytoscape MiMI Plugin is an open source interactive visualization tool that you can use for analyzing protein interactions and their biological effects. The Cytoscape MiMI Plugin couples Cytoscape, a widely used software tool for analyzing bimolecular networks, with the MiMI database, a database that uses an intelligent deep-merging approach to integrate data from multiple well-known protein interaction databases. The MiMI database has data on 119,880 molecules, 330,153 interactions, and 579 complexes. By querying the MiMI database through Cytoscape you can access the integrated molecular data assembled in MiMI and retrieve interactive graphics that display protein interactions and details on related attributes and biological concepts. You can interact with the visualization by expanding networks to the next nearest neighbors and zooming and panning to relationships of interest. You also can perceptually encode nodes and links to show additional attributes through color, size and the visual cues. You can edit networks, link out to other resources and tools, and access information associated with interactions that has been mined and summarized from the research literature information through a biology natural language processing database (BioNLP) and a multi-document summarization system, MEAD. Additionally, you can choose sub-networks of interest and use SAGA, a graph matching tool, to match these sub-networks to biological pathways.
Proper citation: MiMI Plugin for Cytoscape (RRID:SCR_003424) Copy
http://graphml.graphdrawing.org/
A file format for graphs that consists of a language core to describe the structural properties of a graph and a flexible extension mechanism to add application-specific data. It is based on XML and is ideally suited as a common denominator for all kinds of services generating, archiving, or processing graphs. Its main features include support of * directed, undirected, and mixed graphs, * hypergraphs, * hierarchical graphs, * graphical representations, * references to external data, * application-specific attribute data, and * light-weight parsers.
Proper citation: GraphML (RRID:SCR_003545) Copy
http://www.broadinstitute.org/mpg/magenta/
A computational tool that tests for enrichment of genetic associations in predefined biological processes or sets of functionally related genes, using genome-wide genetic data as input.
Proper citation: MAGENTA (RRID:SCR_003422) Copy
http://cran.r-project.org/web/packages/NAPPA/
Software that enables the processing and normalization of the standard mRNA data output from the Nanostring nCounter software.
Proper citation: NAPPA (RRID:SCR_003419) Copy
http://rgd.mcw.edu/tools/ontology/ont_search.cgi
Ontology that defines hierarchical display of different rat strains as derived from parental strains. Ontology Browser allows to retrieve all genes, QTLs, strains and homologs annotated to particular term. Covers all types of biological pathways including altered and disease pathways, and to capture relationships between them within hierarchical structure. Five nodes of ontology include classic metabolic, regulatory, signaling, drug and disease pathways. Ontology allows for standardized annotation of rat. Serves as vehicle to connect between genes and ontology reports, between reports and interactive pathway diagrams, between pathways that directly connect to one another within diagram or between pathways that in some fashion are globally related in pathway suites and suite networks.
Proper citation: Rat Strain Ontology (RRID:SCR_003449) Copy
https://code.google.com/p/fade/
A software package designed to determine the methylation parameter at each cytosine or cytosine-guanine position in the human genome. FadE uses color reads produced by the SOLiD sequencer or nucleotide reads produced by the Illumina or 454 sequencing platforms.
Proper citation: FadE (RRID:SCR_003448) Copy
A biomedical ontology in the area of vaccine adverse events aimed to represent and analyze various vaccine-specific adverse events. OVAE is an extension of the Ontology of Adverse Events (OAE) and the Vaccine Ontology (VO).
Proper citation: Ontology of Vaccine Adverse Events (RRID:SCR_003442) Copy
https://code.google.com/p/proteomecommons-tranche/
A distributed file storage system that you can upload files to and download files from. All files uploaded to the repository are replicated several times to protect against their accidental loss. Files uploaded to the repository can be of any size, can be of any file type, and can be encrypted with a passphrase of your choosing. The Proteome Commons Tranche repository is the first instance of a Tranche repository. Tranche, was created so that anybody can take it and make their own Tranche repository. This is the first implementation of the Tranche software, and is useful as a test bed for the software. This repository relies on educational institutions to provide the hardware and facilities for Tranche servers. While we maintain a set of servers, the continued growth of this public resource will rely on the generosity of the institutions that use the repository most.
Proper citation: Proteome Commons Tranche repository (RRID:SCR_003441) Copy
http://www.compgen.org/tools/metagen
Software program providing a method for meta-analysis of case-control genetic association studies using random-effects logistic regression.
Proper citation: metagen (RRID:SCR_003443) Copy
http://www.physiol.ucl.ac.uk/research/silver_a/nclamp/
Data acquisition software that runs in conjunction with neuromatic. configured to work with Igor Pro on PC or Mac, instrutech or national instrument acquisition devices. Funded by The Medical Research Council (UK) Compatibility with WaveMetrics Igor Pro 5 and 6. Compatibility with Mac or PC. NIDAQ interfacing multifunction DAQ boards from National Instruments. Requires Igor NIDAQ Tools MX. ITC interfacing - data acquisition systems from InstruTech / Heka. Requires Igor ITC XOPs. Episodic acquisition (stim and sample). Continuous acquisition (currently for ITC users only). Online analysis, with ability to create your own analysis functions. Notes and Log Files which can be displayed within a table or notebook. Automatic saving of data and log folders to your hard drive. Flexible stimulus pulse generator with ability to use your own pulse waveforms. Instant accessibility to all of NeuroMatics and Igor Pros pre-existing data analysis functions.
Proper citation: Nclamp - data acquisition software for electrophysiology (RRID:SCR_003750) Copy
Initiative to improve health by speeding up the development of, and patient access to, innovative medicines, particularly in areas where there is an unmet medical or social need. It does this by initiating and managing consortia composed of the key players involved in healthcare research, including universities, the pharmaceutical and other industries, small and medium-sized enterprises (SMEs), patient organizations, and medicines regulators. IMI is a public-private partnership between the European Union and the European pharmaceutical industry, represented by the European Federation of Pharmaceutical Industries and Associations (EFPIA), with a timeframe separated into two phases (2008-2013, 2014-2024) that are each defined by unique research agendas. The first phase (2008 2013) had four pillars that defined the focus of its research agenda: * Predicting safety: evaluating the safety of a compound during the pre-clinical phase of the development process and the later phases in clinical development. * Predicting efficacy: improving the ability to predict how a drug will interact in humans and how it may produce a change in function. * Knowledge management: utilization of information and data for predicting safety and efficacy. * Education and training: closing existing training gaps in the drug development process. Some of the consortia managed under IMI focused on specific health issues while others focused on broader challenges in drug development. Additionally, IMI launched a number of education and training projects during its first phases. The goal of the second phase (IMI2, 2014-2024) is to develop next generation vaccines and drugs. The focus is on delivering the right prevention and treatment for the right patient at the right time. There is a strong focus on the development of new medicines with an emphasis on tools and methods that accelerate patient access to new medicines. IMI2's agenda can be defined by four axes of research: * target validation and biomarker research (efficacy and safety) * adoption of innovative clinical trial paradigms * innovative medicines * patient-tailored adherence programs As part of its distinct goals, IMI2 aims to deliver: * 30% better success rate in clinical trials of priority medicines identified by the WHO; clinical proof of concept in immunological, respiratory, neurological and neurodegenerative diseases in five years; * new and approved diagnostic markers for four of these diseases and at least two new medicines which could either be new antibiotics or new therapies for Alzheimer's disease.
Proper citation: Innovative Medicines Initiative (RRID:SCR_003754) Copy
A consortium that focuses their efforts on discovering and developing new pharmaceutical drugs, vaccines (both preventive and therapeutic) and diagnostics against the infectious diseases that are prevalent in developing countries. The initial targets are those disorders designated by WHO as neglected tropical diseases prevalent in developing nations. The consortium aims to facilitate international partnerships that enable Japanese technology, innovations, and insights to play a more direct role in improving global health. Another goal of GHIT is to develop a new drug-discovery screening platform to assist the screening of compound libraries housed within Japanese companies and academic institutions. The vision is to have Japanese research organizations donate compounds, with the Fund reimbursing screening costs and leveraging screening programs of existing product-development partners.
Proper citation: Global Health Innovative Technology Fund (RRID:SCR_003753) Copy
http://purl.bioontology.org/ontology/MEDDRA
Ontology of Medical Dictionary for Regulatory Activities Terminology (MedDRA)
Proper citation: Medical Dictionary for Regulatory Activities (RRID:SCR_003751) Copy
https://services.healthtech.dtu.dk/
Center for Biological Sequence Analysis of the Technical University of Denmark conducts basic research in the field of bioinformatics and systems biology and directs its research primarily towards topics related to the elucidation of the functional aspects of complex biological mechanisms. A large number of computational methods have been produced, which are offered to others via WWW servers. Several data sets are also available. The center also has experimental efforts in gene expression analysis using DNA chips and data generation in relation to the physical and structural properties of DNA. The on-line prediction services at CBS are available as interactive input forms. Most of the servers are also available as stand-alone software packages with the same functionality. In addition, for some servers, programmatic access is provided in the form of SOAP-based Web Services. The center also educates engineering students in biotechnology and systems biology and offers a wide range of courses in bioinformatics, systems biology, human health, microbiology and nutrigenomics.
Proper citation: DTU Center for Biological Sequence Analysis (RRID:SCR_003590) Copy
Project focused on developing cutting edge tools to speed up and improve the testing and monitoring of vaccine safety, both before and after release to the market. The three specific objectives of the project are: * the characterization of early inflammation induced by vaccines currently on the market and the identification and validation of biomarkers of early inflammation and allergic responses; * the identification and validation of early biomarkers of autoimmunity and their use to help identifying population at risk of developing autoimmunity; * the analysis of the incidence and epidemiology of autoimmune disease in the general population and the link to genetic background or previous events in the life of patients, including severe effects, such as anaphylactic shock.
Proper citation: BioVacSafe (RRID:SCR_003745) Copy
http://www.coca-colacompany.com/
An American multinational beverage corporation and manufacturer, retailer and marketer of nonalcoholic beverage concentrates and syrups, which is headquartered in Atlanta, Georgia. (Wikipedia) It is the world's largest beverage company, refreshing consumers with more than 500 sparkling and still brands.
Proper citation: Coca-Cola Company (RRID:SCR_003749) Copy
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