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http://www.photonisusa.com/

Commercial organization that manufactures Vacuum Electron Devices and Associated RF Circuits for Communications, Science, Radar, Industry & Directed Energy Applications. Other products include photo-detectors for scientific and medical applications and specialized material processing and plating services.

Proper citation: PHOTONIS (RRID:SCR_003853) Copy   

•   Source: SciCrunch Registry
  

http://www.nih.gov/science/amp/autoimmune.htm

The autoimmune disease arm of the Accelerating Medicine Partnership (AMP), which aims to identify and validate the most promising biological targets of disease for new diagnostic and drug development, that is focused on rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). They seek to identify shared common flaws in inflammation, particularly those that are shared with a larger number of autoimmune disorders which can cause severe disability, greatly affect quality of life, and are associated with an increased risk of death. This project aims to reveal biomarkers and biological targets for drug development, matching existing drugs to patients with specific molecular profiles who are most likely to benefit. The research plan proposes a 5 year process. Year one will include startup activities such as validation of tissue acquisition processes and analytic technologies, and the development of operating procedures. The second year will focus on identification of disease specific pathways by comparing data from patients and healthy individuals. Years 3-5 will expand the scale to include comparisons of different subsets of patients with RA or lupus to allow molecularly based patient stratification for precise treatment. The final 12 months (2019) will also include preliminary target validation. The data will be made publicly available through an internet-based information portal.

Proper citation: Accelerating Medicines Partnership Autoimmune Diseases of Rheumatoid Arthritis and Lupus (RRID:SCR_003731) Copy   

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http://www.ddmore.eu/mdl-ide

Software framework within which files containing Modelling Description Language (MDL) code can be created and edited offering a user-friendly, customizable modelling experience including syntax highlighting and on-demand model formatting. MDL model development is enhanced by productivity features such as the support for templates (re-usable blocks of MDL code that can be parameterised for ease of inclusion in multiple models) and content assist (the automatic display of possible alternatives based on the current editing location in the model). Common operations are supported by wizards which provide a step-by-step guide through the necessary functionality, while an advanced validation engine immediately highlights any inconsistencies or errors detected in the model and offers a list of suggested options to correct the problem. The MDL-IDE includes in-built functionality to convert an MDL model into the equivalent NM-TRAN control stream (.ctl file). Organizationally, it can support multiple distinct projects within a workspace, offering a natural separation between disparate models but retaining the ability to switch between the models quickly and easily. Additionally a large main window with a tabbed layout allows multiple models to be open for editing or viewing simultaneously.

Proper citation: MDL-IDE (RRID:SCR_003852) Copy   

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http://www.nce-rce.gc.ca/Programs-Programmes/BLNCE-RCEE/Index_eng.asp

Funds large-scale collaborative research networks that bring a wide range of research expertise to bear on specific challenges identified by an industrial sector. Led by a not-for-profit consortium of industrial partners, networks enhance private sector innovation by blending academic expertise with the private sector''s drive to respond to real-world challenges. BL-NCEs increase private sector investments in Canadian research, support training of skilled researchers, and accelerate the transfer of ideas from the laboratory into solutions needed by the private sector.

Proper citation: Business-Led Networks of Centres of Excellence (RRID:SCR_003730) Copy   

•   Source: SciCrunch Registry
  

http://jexpress.bioinfo.no/site/

Gene expression analysis software using Java.

Proper citation: J-Express (RRID:SCR_003609) Copy   

•   Source: SciCrunch Registry
  

http://www.ahrq.gov/data/

Agency that produces evidence to make health care safer, higher quality, more accessible, equitable, and affordable. Funding opportunities, grants, and a large collection of longitudinal hospital care data in the United States including the Systematic Review Data Repository and data sources on healthcare cost, quality, and accessibility, emergency room visits, hospitalization, and medical insurance are available. It works within the U.S. Department of Health and Human Services and with other partners to make sure that the evidence is understood and used.

Proper citation: Agency for Healthcare Research and Quality (RRID:SCR_003604) Copy   

•   Source: SciCrunch Registry
  

http://knowledgeblog.org/

Blog investigating a light-weight way of publishing scientific, academic and technical knowledge on the web where you can read about current events. It is used in a number of different ways: hosting tutorials on ontologies and bioinformatics; as a conference website; and as a mechanism for documenting Knowledge Blog. They also provide software for extending WordPress, enabling referencing, adding metadata to posts, and supporting mathematics on the web. Together, these pieces of software have had many thousands of downloads, representing 100s of installations; it can be used to provide a formal personal publication framework for the researcher. Finally, they provide Greycite, a service which provides bibliographic metadata for any website, supporting their referencing plugin, and helping authors to link to the many web archiving services, enabling increased digital preservation. Blogs and blog technology has been designed to allow people to discuss, share and disseminate their opinion in a simple and light-weight way. Adding a little formality to this, and we have a journal.

Proper citation: Knowledge Blog (RRID:SCR_003603) Copy   

•   Source: SciCrunch Registry
  

http://omop.org/

Initiative to improve the safety of drugs on the market that utilized information drawn from patient medical record databases and health insurance claims to develop and test methods to detect and evaluate drug safety issues over time. The OMOP pilot project focused on the following objectives: * Defining and evaluating analytical methods that can be used to identify associations between drugs and health-related conditions. * Developing tools for organizing access to and evaluating the usefulness of multiple observational datasets. * Study how information from analyses of observational data can be used to inform ongoing pharmacovigilence efforts. The software tools - packaged as the OMOP Web RL Platform was developed and made available to the public, https://github.com/OMOP . In addition to these data tools, this collaborative research effort discovered methods for using data to reliably identify correlations between individual medical interventions and specific health outcomes. These insights are being used to help inform the FDA Sentinel Initiative as part of the Innovation in Medical Evidence Development and Surveillance (IMEDS) program. The achievements of the program include: * Establishment of a common data model and creation of data characterization tools, and vocabulary mappings * Implementation of Health Outcome of Interest definitions, including a program to implement these definitions as part of the Regularized Identification of Cohorts (RICO) * Release of 14 analysis methods to evaluate the performance of methods and data in identifying drug safety issues

Proper citation: Observational Medical Outcomes Partnership (RRID:SCR_003724) Copy   

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http://www.calliope-network.eu/

Consortium to act as a forum for the diversity of stakeholders in the implementation of electronic health systems. It comprises a dedicated forum where decision makers, implementers, professionals, patients and other stakeholders can share visions, experiences and good practices on how to establish interoperable eHealth services. The process of consensus-building has reached six main achievements. # Offering support to European decision-makers with regard to EU level actions on eHealth. # Enlarging active representation of EU and European Free Trade Association (EFTA) activities. CALLIOPE established a roster of 22 national members in 2010 # Enlarging active involvement of European eHealth stakeholder organizations. # Developing and validating an open working method among stakeholders # Creating a working collaboration method between the appropriate eHealth large-scale pilot(s) and a wider range of Member States & and sta-keholders CALLepSO collaboration # Building an eHealth Interoperability roadmapping process. A full iterative cycle of the Roadmapping process has been now completed and the second issue of the EU eHealth Interoperability Roadmap has been delivered.

Proper citation: CALLIOPE Network (RRID:SCR_003845) Copy   

•   Source: SciCrunch Registry
  

http://www.blueprint-epigenome.eu/

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.

Proper citation: Blueprint Epigenome (RRID:SCR_003844) Copy   

•   Source: SciCrunch Registry
  

http://medschool.umaryland.edu/btbank/

The objective of this human tissue repository is to systematically collect, store, and distribute brain and other tissues for research dedicated to the improved understanding, care, and treatment of individuals with developmental disorders. Brain sections are primarily frozen in isopentane / dry ice. Tissues are stored in 10% formalin and frozen at -85 degrees C. Of special interest are individuals with Down syndrome and other chromosomal defects, mitochondrial encephalopathies, phenylketonuria and other aminoacidopathies, maternal PKU, Rett syndrome, leukodystrophies, lysosomal disorders, dyslexia, autism, and other neurodevelopmental disorders. The brain and tissue banks have extensive experience in arranging for the rapid retrieval of tissue upon the death of individuals who die while at home, in hospitals or hospice care. As a special service, the brain and tissue banks are able to assist researchers who are working with patients who intend to donate tissues at the time of their death. Immediately after retrieval of the tissue, the brain and tissue banks will forward needed tissue to the referring investigators and ensure proper storage and cataloging of any additional tissues as part of the brain and tissue banks. The recipient of tissue and the brain and tissue banks are required to sign a Tissue Transfer Agreement before any tissues are transferred.

Proper citation: NICHD Brain and Tissue Bank for Developmental Disorders (RRID:SCR_003601) Copy   

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http://eagl.unige.ch/GOCat/

Software tool that uses a machine learning (ML) approach to classify text, based on the Gene Ontology. It relies on a k-Nearest Neighbours algorithm, a simple algorithm which assigns to a new text the categories that are the most prevalent among the k most similar instances contained in the knowledge base. The ML classifier operates in two steps and combines two components. First, a related article search engine retrieves instances (i.e. abstracts) in the knowledge base that are the most similar to the input text (its nearest neighbours); second, a score computer infers the functional profile from the k most similar instances.

Proper citation: GOCat (RRID:SCR_003608) Copy   

•   Source: SciCrunch Registry
  

http://www.alsace-biovalley.com/en/

A French world-class cluster dedicated to therapeutic innovations, it is the one-stop contact to optimize any R&D development or business project in Europe, both in drug development and medical technologies. Located in Alsace region, part of the famous French-German-Swiss BioValley and with a unique concentration of international life sciences & healthcare players, Alsace BioValley helps any Life Sciences & Healthcare companies interested in new projects and partnerships in Europe: * to search outstanding scientific or industrial partners to develop very innovative R&D projects * to find the best innovative technology, patent or scientific expertise * to set up and locate in Alsace region

Proper citation: Alsace BioValley (RRID:SCR_003729) Copy   

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http://purl.bioontology.org/ontology/SNMI

Ontology of systematized nomenclature of human and veterinary medicine: SNOMED International. Cote, Roger A., editor. Northfield (IL): College of American Pathologists; Schaumburg (IL): American Veterinary Medical Association, Version 3.5, 1998.

Proper citation: Systematized Nomenclature of Medicine - International Version (RRID:SCR_003849) Copy   

•   Source: SciCrunch Registry
  

http://c-path.org/programs/pstc/

A public-private partnership to identify new and improved translational safety testing methods for use in nonclinical and clinical studies and submit them for formal regulatory qualification by the FDA (Food and Drug Administration), EMA (European Medicines Agency), and PMDA (Japanese Pharmaceutical and Medical Devices Agency). The current 19 corporate members of the consortium share internal experience with nonclinical and clinical safety biomarkers in six working groups: cardiac hypertrophy, nephrotoxicity, hepatotoxicity, skeletal myopathy, testicular toxicity, and vascular injury. The ultimate goal of the consortium is to improve the current approach to drug safety testing and offer assurance to the drug developers that these approaches will be accepted by the regulatory authorities in their drug development programs. Through PSTC, members are able to share their expertise, resources, data, and internally developed approaches in a neutral, precompetitive, confidential environment. There are more than 250 participating scientists and C-Path serves as the trusted third party, leading the collaborative process by collecting and summarizing the data, and leading the interactions with global health authorities.

Proper citation: Predictive Safety Testing Consortium (RRID:SCR_003727) Copy   

•   Source: SciCrunch Registry
  

http://www.chem21.eu/

A European public-private consortium examining ways to make chemical research and the pharmaceutical industry more sustainable and environmentally friendly with the aim of developing sustainable biological and chemical alternatives to finite materials, such as precious metals, which are currently used as catalysts in the manufacture of medicines. The project has looked at the industry and identified needs and barriers, and is now working to develop methods to navigate around them to reduce costs for companies and thus reduce prices for patients. Chem21 also involves an educational training component that will help instill the project's results in the next wave of scientists. The project has four focus areas that are driving it toward the desired impact on the 21st century pharmaceuticals industry: * New, more efficient catalyst classes made available for greening processes and the generation of novel molecules * Alternative methodologies clearly described to allow broader use * New modified microorganisms for preparing pharma building blocks disclosed * Training materials developed for driving longer-term innovation

Proper citation: CHEM21 (RRID:SCR_003848) Copy   

•   Source: SciCrunch Registry
  

http://www.europeanlung.org/en/

Foundation with aim of bringing together patients, the public and respiratory professionals to positively influence lung health and respiratory medicine. ELF aims to communicate respiratory science to those outside of the respiratory field, to ensure that people with lung diseases and the general public have a chance to influence respiratory research and guidelines at a European level.

Proper citation: European Lung Foundation (RRID:SCR_003842) Copy   

•   Source: SciCrunch Registry
  

http://www.treat-nmd.eu/about/related-projects/bioimage-nmd/

Project whose objective is to deliver combined structural and molecular imaging biomarkers with proven utility for the detection of therapeutic effects in patients with rare neuromuscular diseases (NMD). The project has three specific objectives: # To develop a new generation of muscle diffusion Magnetic Resonance Imaging (MRI). This diffusion imaging technology will be used to augment a state of the art simultaneous MRI / Magnetic Resonance Spectroscopic Imaging (MRSI) protocol for quantitative muscle imaging. # To provide a proof of principle in Duchenne Muscular Dystrophy (DMD) that simultaneous MRI/MRSI can be used as a biomarker to monitor therapeutic efficacy in clinical trials in neuromuscular diseases. # To develop a novel simultaneous Positron Emission Tomography (PET)/MRI technology to advance innovative drug development programs for personalized medicines based on Antisense Oligonucleotide technology

Proper citation: BIOIMAGE-NMD (RRID:SCR_003840) Copy   

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http://purl.bioontology.org/ontology/MFO

A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.

Proper citation: Medaka Fish Anatomy and Development Ontology (RRID:SCR_003719) Copy   

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http://www.siaf.uzh.ch/

Originally established as a research institute for tuberculosis, it now performs applied, basic research in the field of allergies and asthma. Research activities are focused on immune-pathological mechanisms of allergic, asthmatic and cutaneous inflammations and the structural basis and peculiarities of allergens, as well as development of novel tools for the diagnosis and treatment of allergic disease.

Proper citation: Swiss Institute of Allergy and Asthma Research (RRID:SCR_003835) Copy   

•   Source: SciCrunch Registry