Tools   Select Another Resource Report Type

http://www.tidebc.org/

A collaborative care and research initiative with a focus on prevention and treatment of Intellectual disability (ID) that is due to inborn errors of metabolism (IEM), which can be treated with diet or drugs. Health care policy and institutional culture is still operating under the old premise that all ID is incurable and thus, many children born with treatable ID are at risk of not being treated. To acknowledge the multidisciplinary scope and the ways in which health care professionals and researchers will collaborate, the goals of the TIDE BC project are demonstrated within a framework of 7 Work Packages: * Implementation of a new Protocol for diagnostic evaluation of ID, focusing of treatable conditions; * Development of infrastructure to facilitate implementation, evaluation and sustainability of the Protocol; * Investments into next generation genomic technologies; * Improving evidence of and access to treatments; * Evaluation and health economy; * Knowledge dissemination; * Education and Mentoring. The objectives addressed in all Work Packages reflect a highly integrated cluster combining clinical care, research, evaluation, and knowledge dissemination.

Proper citation: TIDE BC (RRID:SCR_003924) Copy   

•   Source: SciCrunch Registry

http://www.icn.ucl.ac.uk/motorcontrol/imaging/suit.htm

High-resolution atlas template of the human cerebellum and brainstem, based on the anatomy of 20 young healthy individuals. The atlas is spatially unbiased, i.e. the location of each structure is equal to the expected location of that structure across individuals in MNI space. At the same time, the new template preserves the anatomical detail of cerebellar structures through a nonlinear atlas-generation algorithm. By using automated nonlinear normalization methods, a more accurate intersubject-alignment than current whole-brain methods can be achieved. The toolbox allows you to: * Automatically isolate cerebellar structures from the cerebral cortex based on an anatomical image * Achieve accurate anatomical normalization of cerebellar structures * Normalize functional imaging data for fMRI group analysis * Normalize focal cerebellar lesions for lesion-symptom mapping * Use Voxel-based morphometry (VBM) to determine patterns of cerebellar degeneration or growth * Use a probabilisitc atlas in SUIT space to assign locations to different cerebellar lobuli in an unbiased and informed way * Automatically define ROIs for specific cerebellar lobuli and summarize function and anatomical data * Improve normalization of the deep cerebellar nuclei using an ROI-driven normalization. The suit-toolbox requires Matlab (Version 6.5 and higher) and SPM. The newest version only supports SPM8, although it likely runs under SPM2 or 5 as well. A standalone version for the suit-toolbox is not planned. Usage of the isolation or normalization functions, however, does not require that the analysis is conducted under SPM.

Proper citation: Spatially unbiased atlas template of the cerebellum and brainstem (RRID:SCR_004969) Copy   

•   Source: SciCrunch Registry

http://www.gin.cnrs.fr/spip.php?article216

Software for automated anatomical labeling of activations in SPM (Statistical Parametric Mapping) using a macroscopic anatomical parcellation of the MNI MRI single-subject brain. The software was used for an automated anatomical parcellation of the spatially normalized single-subject high-resolution T1 volume provided by the Montreal Neurological Institute (MNI) (D. L. Collins et al., 1998, Trans. Med. Imag. 17, 463468, PubMed). Using this parcellation method, three procedures to perform the automated anatomical labeling of functional studies were proposed: (1) labeling of an extremum defined by a set of coordinates, (2) percentage of voxels belonging to each of the anatomical volumes of interest (AVOI) intersected by a sphere centered by a set of coordinates, and (3) percentage of voxels belonging to each of the AVOI intersected by an activated cluster. An interface with the Statistical Parametric Mapping package is provided as a freeware to researchers of the neuroimaging community.

Proper citation: AAL (RRID:SCR_003550) Copy   

•   Source: SciCrunch Registry

http://database.hudsen.eu/

Interactive digital atlas and movies comprising 3-D reconstructions at all stages of human development from Carnegie Stage 12 (CS12; ~26 days post conception (dpc)) to CS23 (~ 56 dpc) and anatomical annotations of the 3-D models linked to an anatomical database. The 3D models are generated using Optical Projection Tomography (OPT; Sharpe et al 2002). The digital atlas is also linked to a gene expression database that has been developed from the Edinburgh Mouse Atlas Project gene expression database (EMAGE). In the future, the HUDSEN EADHB aims to provide the wider scientific and medical communities with a dynamic tool for documenting and analyzing gene expression patterns and morphological changes in the developing human brain.

Proper citation: HUDSEN Electronic Atlas of the Developing Human Brain (RRID:SCR_002056) Copy   

•   Source: SciCrunch Registry

http://emsci.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. A clinical spinal cord injury network that provides a database of clinical assessment data from spinal cord injured patients. The EMSCI assessment scheme currently consists of the so called core sets: neurological (ISNCSCI), functional (10MWT, 6MWT, TUG, WISCI2) measurements and independence measures (SCIM3). Additional assessments are: neurophysiology (MEP, SSEP, NCV), pain, hand function and an urodynamics.

Proper citation: European Multicenter Study about Spinal Cord Injury (RRID:SCR_003720) Copy   

•   Source: SciCrunch Registry

http://www.btool.org/ADGO2

A web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. It provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. It screens redundant composite annotations when generating and prioritizing them. It also incorporates union and subtracted sets as well as intersection sets. Users can upload their gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets.

Proper citation: ADGO (RRID:SCR_006343) Copy   

•   Source: SciCrunch Registry

http://tbdb.org

Database providing integrated access to genome sequence, expression data and literature curation for Tuberculosis (TB) that houses genome assemblies for numerous strains of Mycobacterium tuberculosis (MTB) as well assemblies for over 20 strains related to MTB and useful for comparative analysis. TBDB stores pre- and post-publication gene-expression data from M. tuberculosis and its close relatives, including over 3000 MTB microarrays, 95 RT-PCR datasets, 2700 microarrays for human and mouse TB related experiments, and 260 arrays for Streptomyces coelicolor. (July 2010) To enable wide use of these data, TBDB provides a suite of tools for searching, browsing, analyzing, and downloading the data.

Proper citation: Tuberculosis Database (RRID:SCR_006619) Copy   

•   Source: SciCrunch Registry

https://open.med.harvard.edu/display/SHRINE/Community

Software providing a scalable query and aggregation mechanism that enables federated queries across many independently operated patient databases. This platform enables clinical researchers to solve the problem of identifying sufficient numbers of patients to include in their studies by querying across distributed hospital electronic medical record systems. Through the use of a federated network protocol, SHRINE allows investigators to see limited data about patients meeting their study criteria without compromising patient privacy. This software should greatly enable population-based research, assessment of potential clinical trials cohorts, and hypothesis formation for followup study by combining the EHR assets across the hospital system. In order to obtain the maximum number of cases representing the study population, it is useful to aggregate patient facts across as many sites as possible. Cutting across institutional boundaries necessitates that each hospital IRB remain in control, and that their local authority is recognized for each and every request for patient data. The independence, ownership, and legal responsibilities of hospitals predetermines a decentralized technical approach, such as a federated query over locally controlled databases. The application comes with the SHRINE Core Ontology but it can be used with any ontology, even one that is disease specific. The Core Ontology is designed to enable the widest range of studies possible using facts gathered in the EMR during routine patient care. SHRINE allows multiple ontologies to be used for different research purposes on the same installed systems.

Proper citation: SHRINE (RRID:SCR_006293) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/scicrunch/data/source/nlx_154697-7/search?q=*

Virtual database currently indexing interaction between genes and diseases from Online Mendelian Inheritance in Man (OMIM) and Comparative Toxicogenomics Database (CTD).

Proper citation: Integrated Gene-Disease Interaction (RRID:SCR_006173) Copy   

•   Source: SciCrunch Registry

http://app1.bioinformatics.mdanderson.org/tarhub/_design/basic/index.html

A database of miRNA-mRNA interactions. The interaction data is obtained from various external data sources and in some cases computed in-house by algorithms implemented for miRNA target prediction.

Proper citation: targetHub (RRID:SCR_006522) Copy   

•   Source: SciCrunch Registry

http://www.nlm.nih.gov/medlineplus/druginformation.html

Database of authoritative health information about diseases, conditions, and wellness issues that offers reliable, up-to-date health information for free. It contains the latest treatments, information on drugs and supplements, the meanings of words, and medical videos and illustrations. Links to the latest topic or disease specific medical research or clinical trials are also offered. * MedlinePlus pages contain carefully selected links to Web resources with health information on over 900 topics. ** The MedlinePlus health topic pages include links to current news on the topic and related information. You can also find preformulated searches of the MEDLINE/PubMed database, which allow you to find references to latest health professional articles on your topic. * The A.D.A.M. medical encyclopedia brings health consumers an extensive library of medical images and videos, as well as over 4,000 articles about diseases, tests, symptoms, injuries, and surgeries. * The Merriam-Webster medical dictionary allows you to look up definitions and spellings of medical words. * Drug and supplement information is available from the American Society of Health-System Pharmacists (ASHP) via AHFS Consumer Medication Information, and Natural Medicines Comprehensive Database Consumer Version. ** AHFS Consumer Medication Information provides extensive information about more than 1,000 brand name and generic prescription and over-the-counter drugs, including side effects, precautions and storage for each drug. ** Natural Medicines Comprehensive Database Consumer Version is an evidence-based collection of information on alternative treatments. MedlinePlus has 100 monographs on herbs and supplements. * Interactive tutorials from the Patient Education Institute explain over 165 procedures and conditions in easy-to-read language. An XML File for the MedlinePlus Health Topics is available, http://www.nlm.nih.gov/medlineplus/xmldescription.html. The ontology is available through Bioportal, http://bioportal.bioontology.org/ontologies/MEDLINEPLUS

Proper citation: MedlinePlus (RRID:SCR_006512) Copy   

•   Source: SciCrunch Registry

http://www.droidb.org

A gene and protein interactions database designed specifically for the model organism Drosophila including protein-protein, transcription factor-gene, microRNA-gene, and genetic interactions. For advanced searches and dynamic graphing capabilities the IM Browser and a DroID Cytoscape plugin are available.

Proper citation: DroID - Drosophila Interactions Database (RRID:SCR_006634) Copy   

•   Source: SciCrunch Registry

http://www.chordomafoundation.org/research/rdrepository.aspx

U-CH1 and U-CH2 are sacral-chordoma derived cell lines created by the lab of Dr. Peter Moeller at the University of Ulm, Germany. The Chordoma Foundation maintains a repository of these cell lines and makes them available to academic and industry investigators. Additionally, Notochordal tissue is available from the Congenital Defects Lab at the University of Washington. (Contact us for more information.) The following data is available: * Xenographs: The U-CH1 cell line forms tumors that resemble chordomas in NSG mice. A protocol for creating a xenograft using U-CH1 was developed by Dr. Adrienne Flanagan. * Tissue Microarrays (sacral, spine, skull base, lumbar, cervical, mobile spine, etc.) * Gene Expression Data: EBI Array Express Experiment E-MEXP-353: transcription profiling of human mesenchymal and some possibly neural crest derived neoplasms using the Affymetrix GeneChip? Human Genome HG-U133A. This data set was generated by the University College London Cancer Institute and contains 96 tissue samples including 4 chordomas. * Comparative Genomic Hybridization Data: Gene Expression Omnibus Series GSE9023: DNA copy number analysis of 21 fresh frozen chordoma biopsies, and the respective relapse in four of them, using 32k and 1Mb array CGH. Cases 1-11 were analyzed using 32k array CGH and male genomic DNA (Promega) was used as reference. Cases 17-26, and the respective relapse in four of these tumors, were analyzed with 1 Mb array CGH, using sex matched controls. All cases showed copy number alterations and primarily deletions of chromosomal regions were found. Particularly, the CDKN2A and CDKN2B loci in 9p21 were homo- or heterozygously lost in 70% of the tumors.

Proper citation: Chordoma Foundation Biobank (RRID:SCR_006425) Copy   

•   Source: SciCrunch Registry

http://wavi.bioinfo.cnio.es/

A versatile web-server application for the analysis and visualization of array-CGH data.

Proper citation: waviCGH (RRID:SCR_006662) Copy   

•   Source: SciCrunch Registry

http://epi.grants.cancer.gov/CFR/

The Breast Cancer Family Registry (Breast CFR) and the Colon Cancer Family Registry (Colon CFR) were established by the National Cancer Institute (NCI) as a unique resource for investigators to use in conducting studies on the genetics and molecular epidemiology of breast and colon cancer. Known collectively as the CFRs, they share a central goal: the translation of research to the clinical and prevention settings for the benefit of Registry participants and the general public. The CFRs are particularly interested in: * Identifying and characterizing cancer susceptibility genes; * Defining gene-gene and gene-environment interactions in cancer etiology; and * Exploring the translational, preventive, and behavioral implications of research findings. The CFRs do not provide funding for studies; however, researchers can apply to access CFR data and biospecimens contributed by thousands of families from across the spectrum of risk for these cancers and from population-based or relative controls. Special features of the CFRs include: * Population-based and clinic-based ascertainment; * Systematic collection of validated family history; * Epidemiologic risk factor , clinical, and followup data; * Biospecimens (including tumor blocks and Epstein-Barr virus (EBV)-transformed cell lines); * Ongoing molecular characterization of the participating families; and * A combined informatics center.

Proper citation: NCI Breast and Colon Cancer Family Registries (RRID:SCR_006664) Copy   

•   Source: SciCrunch Registry

http://www.mappd.org/

A database of experimental behavioral data from > 170 aphasia patients who exhibited language impairments secondary to chronic left hemisphere stroke. The core of the database is individual-trial performance data from picture naming. Picture naming is a primary test of lexical processing. The task taps a critical juncture in the language system because naming mediates between high-level conceptual and syntactic processing and low-level phonological processing. Difficulty in this task is present to varying degrees in nearly all aphasic individuals. This site allows researchers to search through naming data from over 170 patients. Searches can narrow in on data subsets based on patient characteristics (e.g. time since aphasia onset, clinical diagnosis), stimulus characteristics (e.g. semantic category, lexical frequency) and task performance (e.g. error type). The data available on this site can be used to test hypotheses about naming impairment and aphasic impairment generally. Once the basic analysis tools of the site are exhausted, users can export the raw data for further analysis and visualization. The web database represents years of data collection. Most were recruited to the research program at Moss Rehabilitation Research Institute (MRRI).

Proper citation: Moss Aphasia Psycholinguistics Project Database (RRID:SCR_006265) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/books/NBK1116/

Provides clinically relevant and medically actionable information for inherited conditions in standardized journal-style format, covering diagnosis, management, and genetic counseling for patients and their families. Searchable book of expert-authored, peer-reviewed disease descriptions presented in standardized format and focused on clinically relevant and medically actionable information on diagnosis, management, and genetic counseling of patients and families with specific inherited conditions.

Proper citation: GeneReviews (RRID:SCR_006560) Copy   

•   Source: SciCrunch Registry

http://decipher.sanger.ac.uk/

Interactive database which incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance. Used to enhance clinical diagnosis by retrieving information from bioinformatics resources relevant to the imbalance found in the patient. Contributing to the DECIPHER database is a Consortium, comprising an international community of academic departments of clinical genetics. Each center maintains control of its own patient data (which are password protected within the center''''s own DECIPHER project) until patient consent is given to allow anonymous genomic and phenotypic data to become freely viewable within Ensembl and other genome browsers. Once data are shared, consortium members are able to gain access to the patient report and contact each other to discuss patients of mutual interest, thus facilitating the delineation of new microdeletion and microduplication syndromes.

Proper citation: DECIPHER (RRID:SCR_006552) Copy   

•   Source: SciCrunch Registry

http://biogps.org/

An extensible and customizable gene annotation portal that emphasizes community extensibility and user customizability. It is a complete resource for learning about gene and protein function. Community extensibility reflects a belief that any BioGPS user should be able to add new content to BioGPS using the simple plugin interface, completely independently of the core developer team. User customizability recognizes that not all users are interested in the same set of gene annotation data, so the gene report layouts enable each user to define the information that is most relevant to them. Currently, BioGPS supports eight species: Human (Homo sapiens), Mouse (Mus musculus), Rat (Rattus norvegicus), Fruitfly (Drosophila melanogaster), Nematode (Caenorhabditis elegans), Zebrafish (Danio rerio), Thale-cress (Arabidopsis thaliana), Frog (Xenopus tropicalis), and Pig (Sus scrofa). BioGPS presents data in an ortholog-centric format, which allows users to display mouse plugins next to human ones. Our data for defining orthologs comes from NCBI's HomoloGene database.

Proper citation: BioGPS: The Gene Portal Hub (RRID:SCR_006433) Copy   

•   Source: SciCrunch Registry

http://www.druginteractioninfo.org/

The Database is a research and analysis tool developed at the University of Washington, in the Department of Pharmaceutics. It contains in vitro and in vivo information on drug interactions in humans from the following sources: * 9648 peer-reviewed journal articles referenced in PubMed * 102 New Drug Applications (NDAs) * 411 excerpts of FDA Prescribing Information * In-depth analyses of drug-drug interactions in the context of 40 diseases / co-morbidities. In addition, the database also provides PK Profiles of drugs, QT Prolongation data, including results of TQT studies from recent NDAs, as well as Regulatory Guidances and Editorial Summaries/Syntheses relevant to advances in the field of drug interactions. Access to the Database is licensed by UW Center for Commercialization (C4C) to organizations interested in in-depth information on drug interactions. The Database is particularly useful to scientists/clinicians working in drug discovery and drug development. Database users can search for information using several families of pre-formulated queries based on drug name, enzyme name, transporter name, therapeutic area, and more.

Proper citation: Metabolism and Transport Drug Interaction Database (RRID:SCR_006550) Copy   

•   Source: SciCrunch Registry