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

Comprehensive hierarchical controlled vocabulary for human disease representation.Open source ontology for integration of biomedical data associated with human disease. Disease Ontology database represents comprehensive knowledge base of inherited, developmental and acquired human diseases.

Proper citation: Human Disease Ontology (RRID:SCR_000476) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Description not available.

Proper citation: Gazetteer (RRID:SCR_000473) Copy   

•   Source: SciCrunch Registry

http://www.aetionomy.eu/

Consortium founded to establish mechanism-based taxonomies for Alzheimer's and Parkinson's disease and other neurodegenerative disorders (NDD), with the goal of facilitating development of more effective and targeted treatments. To do this, the consortium collects and analyzes data to: * Create new ways to combine underutilized data currently available in the literature, public databases, and from private companies * Determine how to dynamically organize and structure different types of knowledge about NDD * Determine how to apply this knowledge to construct new patient group classification * Identify correlations between disease features at molecular, tissue or organ-specific, and clinical levels * Identify sub-groups of patients based on the molecular cause of their disease, as opposed to the nature and location of their symptoms * Deliver data, tools, and recommendations for the biomedical community in the treatment of NDD A mechanism-based taxonomy is hoped to advance the: # Description and organization of the indication-specific data # Linking of data to disease models, based on causal and correlative relationships The expected outcome of AETIONOMY is a new NDD taxonomy system that distinguishes mixed pathologies, allowing for new features or classes to be added into the taxonomy, all with the goal of aiding drug and biomarker discovery.

Proper citation: AETIONOMY (RRID:SCR_000232) Copy   

•   Source: SciCrunch Registry

http://www.du.edu/psychology/

The department of psychology at Denver University that offers degrees at the undergraduate, graduate and doctoral level. The doctoral programs have specializations such as Affect/Social, Child Clinical, Cognitive, and Developmental.

Proper citation: Denver University Department of Psychology (RRID:SCR_000474) Copy   

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http://www.ecnp.eu/

A pan-European scientific association to encourage research across the neurosciences and to translate new knowledge on fundamental disease mechanisms into new medicines and clinical applications. As an interdisciplinary forum for the science and treatment of disorders of the brain, they promote the communication and cross- fertilization of high-quality experimental and clinical research across the field of neuroscience. ECNP is a non-profit member-based association, independently governed and self-funded. ECNP is a public-interest-serving entity.

Proper citation: ECNP (RRID:SCR_000501) Copy   

•   Source: SciCrunch Registry

http://www.nationalmssociety.org/index.aspx

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Society helps people affected by Multiple Sclerosis by funding cutting-edge research, driving change through advocacy, facilitating professional education, and providing programs and services that help people with MS and their families move their lives forward.

Proper citation: National MS Society (RRID:SCR_000104) Copy   

•   Source: SciCrunch Registry

http://deweylab.biostat.wisc.edu/rsem/

Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data.

Proper citation: RSEM (RRID:SCR_000262) Copy   

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http://teddy.epi.usf.edu/

International consortium of six centers assembled to participate in the development and implementation of studies to identify infectious agents, dietary factors, or other environmental agents, including psychosocial factors, that trigger type 1 diabetes in genetically susceptible people. The coordinating centers recruit and enroll subjects, obtaining informed consent from parents prior to or shortly after birth, genetic and other types of samples from neonates and parents, and prospectively following selected neonates throughout childhood or until development of islet autoimmunity or T1DM. The study tracks child diet, illnesses, allergies and other life experiences. A blood sample is taken from children every 3 months for 4 years. After 4 years, children will be seen every 6 months until the age of 15 years. Children are tested for 3 different autoantibodies. The study will compare the life experiences and blood and stool tests of the children who get autoantibodies and diabetes with some of those children who do not get autoantibodies or diabetes. In this way the study hopes to find the triggers of T1DM in children with higher risk genes.

Proper citation: TEDDY (RRID:SCR_000383) Copy   

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http://www.tarp.nih.gov/

Trans-NIH program encouraging and facilitating the study of the underlying mechanisms controlling blood vessel growth and development. Other aims include: to identify specific targets and to develop therapeutics against pathologic angiogenesis in order to reduce the morbidity due to abnormal blood vessel proliferation in a variety of disease states; to better understand the process of angiogenesis and vascularization to improve states of decreased vascularization; to encourage and facilitate the study of the processes of lymphangiogenesis; and to achieve these goals through a multidisciplinary approach, bringing together investigators with varied backgrounds and varied interests.

Proper citation: Trans-Institute Angiogenesis Research Program (RRID:SCR_000384) Copy   

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http://tomcat.esat.kuleuven.be/MACBETH/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2023. Web service for performing microarray classification. It aims at finding the best prediction among different classification methods by using randomizations of the benchmarking dataset.

Proper citation: M(at)CBETH (RRID:SCR_000265) Copy   

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http://www.nitrc.org/projects/mri_lbptop/

The packaged tools perform Local Binary Pattern on Three Orthogonal Planes (LBP-TOP) analysis on MR brain images. One can use them to extract LBP texture features for machine learning applications or other advance analysis. Bash scripts performing simple preprocessing with FSL and AFNI as well as LBP mapping programs written by Java are both including in this package. The output is the histogram describing the brain morphology.

Proper citation: Local Binary Pattern Analysis Tools for MR Brain Images (RRID:SCR_000412) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/PSCBS/

Software R package for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.

Proper citation: PSCBS (RRID:SCR_000417) Copy   

•   Source: SciCrunch Registry

http://www.opencolleges.edu.au/

A resource for online accredited courses in a wide variety of areas, including accounting, animal care, beauty, building and construction, business, education, design and writing. This resource is based in Australia.

Proper citation: Open Colleges (RRID:SCR_000418) Copy   

•   Source: SciCrunch Registry

http://micro-manager.org

Software package for control of automated microscopes. Cross-platform desktop application, to control motorized microscopes, scientific cameras, stages, illuminators, and other microscope accessories.

Proper citation: uManager (RRID:SCR_000415) Copy   

•   Source: SciCrunch Registry

https://github.com/BenLangmead/bsmooth-align

Software statistics and alignment pipeline that performs the alignment of bisulfite sequence reads and tabulates read-level methylation measurements.

Proper citation: BSmooth-align (RRID:SCR_000013) Copy   

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http://srf.sourceforge.net/

A generic format for DNA sequence data. The primary motivation for creating SRF has been to enable a single format capable of storing data generated by any DNA sequencing technology.

Proper citation: Sequence Read Format (RRID:SCR_000132) Copy   

•   Source: SciCrunch Registry

http://scicrunch.org/Aging

Portal devoted to aging relevant scientific data and resources.

Proper citation: Aging Portal (RRID:SCR_000496) Copy   

•   Source: SciCrunch Registry

http://www.epilepsygenetics.eu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Group of clinical care and epilepsy research centers who are committed to improving the lives of people with epilepsy through an understanding of the genetics of epilepsy. The consoritum was in an effort to speed discovery to epilepsy genetics by pooling the resources of several research centres., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: EPIGEN (RRID:SCR_000093) Copy   

•   Source: SciCrunch Registry

http://gtr.rcuk.ac.uk/project/239F234A-6BF7-4E28-8964-E882BAA8EB77

Project aiming to establish a range of new technologies to enable the synthesis of a range of chemicals from sugar beet pulp (SBP) in a cost-effective and sustainable manner. The chemical and pharmaceutical industries are currently reliant on petrochemical derived intermediates for the synthesis of a wide range of valuable products. Decreasing petrochemical reserves and concerns over costs and greenhouse gas emissions are driving the search for renewable sources of organic synthons. The UK is self-sufficient in the production of SBP which is a by-product of sugar beet production (8 million tonnes grown per year) and processing. The ability to convert SBP into chemicals and pharmaceutical intermediates will therefore have significant economic and environmental benefits. SBP is rich in carbohydrate (nearly 80% by weight) which is made up of roughly equal proportions of 2 biological polymers; cellulose and pectin. To be cost-effective it will be necessary to find uses for each of these substances. The consortium will develop a biorefinery approach for the selective breakdown of both polymers, purification of the breakdown compounds and their use to synthesize a range of added value products such as speciality chemicals, pharmaceuticals and biodegradable polymers. It is already known that cellulose can be broken down into hexose sugars and fermented to ethanol for use in biofuels. The focus is on the release of galacturonic acid and arabinose (from pectin) and their conversion, by chemical or enzymatic means, into added value products. Synthetic Biology methods will also be explored to test the feasibility of metabolically engineering microbial cells to simultaneously breakdown the polymeric feed material and synthesize a desired product, such as aromatic compounds, in a single integrated process. In conducting this research the consortium will adopt a holistic, systems-led, approach to biorefinery design and operation. Computer-based modelling tools will be used to assess the efficiency of raw material, water and energy utilization. Economic and Life Cycle Analysis (LCA) approaches will then be employed to identify the most cost-effective and environmentally benign product and process combinations. The project is supported by a range of industrial partners from raw material producer to intermediate technology providers and end-user chemical and pharmaceutical companies. This is crucial in providing business and socio-economic insights regarding the adoption of renewable resources into their current product portfolios. The company partners will also provide the material and equipment resources for the large-scale verification of project outcomes and their ultimate transition into commercial manufacture. The Intellectual Property (IP) expected to be generated by the consortium will most likely be related to new biocatalysts, synthetic routes, USD devices and modelling software. The data is accessible programmatically using one of three application programming interfaces GtR, GtR-2 and CERIF.

Proper citation: Bio-derived Feedstocks for Sustainable UK-Based Manufacture of Chemicals and Pharmaceutical Intermediates (RRID:SCR_000490) Copy   

•   Source: SciCrunch Registry

http://neuroshare.sourceforge.net/index.shtml

Neuroshare aims to develop a standard for accessing neurophysiological data from any vendor's acquisition device or software. An API is defined, and vendors and communities are encouraged to provide implementations of a library of functions that can read data files collected with that vendor's instrument or software. The neuroshare.org website is a collaborative, vendor-neutral area dedicated to public domain standards and software for neurophysiology.This website is part of an SBIR program funded by the National Institute for Neural Disorders and Stroke and it is currently being administered by Bionic Technologies, LLC. The goals of the SBIR program are to (Phase I) create open library and format standards for neurophysiological experiment data and (Phase II) create a set of free, open-source software tools for low-level handling and processing of neurophysiological data. Upon completion of Phase I and II, neuroshare.org will be maintained by a yet to be determined consortium of government, academic and industry partners. The SBIR was awarded in the fall of 2001 and Phase I officially began in Dec, 2001. The detailed goals of the program are summarized below:Phase I goals :(1) Establish a working group to develop and define the API library of functions.(2) A vendor-neutral web site to facilitate the development of the standards and software and publish the completed products. This site has been dubbed Neuroshare. The home page can be found at neuroshare.sourceforge.net.(3) An open, standardized API library definition for accessing neurophysiology data files. This will allow developers to produce analysis programs that can access a variety of proprietary data formats through libraries supplied by the data format owners. The manner of support will be completely determined by the research groups and vendors that supply the libraries. The Phase I standard was created by a working group consisting of international members from industry and academia. Draft standards were published for public review and comment on the neuroshare web site and revised by the working group.The grant has been awarded as a fast-track program so that Phase II begins immediately upon completion of the Phase I milestones in June 2002. Phase II will produce :(1) A set of neuroshare-compliant API libraries for existing data formats developed in collaboration with individual equipment vendors and research groups.(2) A utility for analyzing compliant API libraries for integrity and specification conformance, as well as for error checking imported data files.(3) A set of template programs in C that are meant to be used as an example on how to create a Neuroshare API compliant library and how to call it from an application,(4) An open, standardized file format for neurophysiological experiment data. This format will provide research groups and vendors with a file format for exchanging and/or publishing neural data. The format will also be powerful enough for use as a native format for researchers or vendors that wish to support it in data acquisition hardware/software.(5) Import filters that interface neuroshare-compliant API libraries to Visual Basic, MATLAB, and LabVIEW, NeuroExplorer, and Stranger analysis environments.(6) A utility program for quick header information viewing and searching to aid the organization and management of data files in the standard and proprietary formats.(7) A data file editing program for reviewing, editing, annotating, and splicing neural data files through the neuroshare API libraries and/or standard file formats. The suite will be developed in C, optimized for speed, and will run within 32-bit Windows operating systems. The availability of source code will enable eventual ports to Unix/Linux if desired(8) An add-on for the editing program that will allow review and real-time playback of multi-modal data accessible through the API and/or standard file format. These modes will include neurophysiological signals such as spikes, local field potentials and EEG, as well as experimental signals such as kinematics, stimulation, audio, video, and imaging data.(9) C and MATLAB framework programs for detection and classification of extracellular spikes in the standard data files based on classical and user-supplied algorithms.(10) A complete MATLAB application for reading data from the standard format and performing reverse correlation analysis. This program will serve as a tutorial and modifiable template for users performing analysis in MATLAB.(11) A set of export filters for creating neurophysiological data files with the neural simulation environments NEURON, NEOSIM, GENESIS, and NSL.(12) A comprehensive documentation, and help file set for all of the developed applications.Phase II will require two years of development work and software products will be made available as they are completed. As stated above, the Phase II software products will be made available as free, open-source tools. We have not decided on a license model yet, but are currently leaning towards the GNU General Public License. Revisions and bug-fixes will be maintained through the neuroshare.org website. The mission of neuroshare.org is very focused, but the specific goal list of Phase II may evolve somewhat as software is released and user feedback is received. We very interested in public suggestions about how to improve this development effort and web site. Please direct your feedback to commentsneuroshare.org or refer to our contacts page for other addresses.BackgroundThis endeavor grew out of a meeting held at the Society for Neuroscience 2000 Annual Conference in New Orleans (agenda posted here) to discuss the development of standard data formats for neuroscience. From this meeting, it was clear that although everyone supported the idea of better data portability, many vendors present wanted a standardized API (Application Program Interface) library rather than a universal data format. Based on this meeting, we submitted an SBIR application (with letters of support from key attendants of the SFN meeting) to fund the development of a standardized API definition, data format, and a suite of open source data handling and review tools.

Proper citation: Neuroshare - Open data specifications and software for neurophysiology (RRID:SCR_000005) Copy   

•   Source: SciCrunch Registry