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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Oct 12, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
KI Biobank - HARMONYResource, disease-related portal, topical portal, research forum portal, biomaterial supply resource, portal, material resource, data or information resourceA twin study characterizing the importance of genetic factors for dementia and using discordant twin pairs to study other putative risk factors which control for genetic propensity to develop the disease. Molecular genetic studies have identified a number of mutations and other markers associated with early age of onset Alzheimer''''s disease. However, most cases of late age of onset dementia are considered sporadic, that is, without a clear genetic basis. Twin studies provide a unique opportunity to characterize the importance of genetic factors for dementia. Discordant twin pairs additionally provide the opportunity to study other putative risk factors which controlling for genetic propensity to develop the disease. In the first wave of the Study of Dementia in Swedish Twins, all SATSA twins born before 1935 have been screened for dementia symptoms. Over 190 suspects have been identified. This pilot study has been expanded to the entire registry in the study known as HARMONY. All twins aged 65 and older were invited to participate in a computer assisted telephone screening interview. A total of 13,519 individuals completed the interview (response rate = 75.9%). Dementia screening was based on the TELE, which includes the 10-item MSQ, other cognitive items (counting backwards, recalling three words, and similarities), and questions about health and daily functioning; or on Blessed scores obtained from a proxy interview. Among those screened, 1565 were positive for suspicion of dementia and were referred for complete clinical evaluation by a physician and a nurse. Once the preliminary in-person evaluation suggested that the suspected case was demented, the twin partner was also invited for an identical clinical work-up. Response rate for clinical evaluations is 71.4%. Approximately half of those visited for evaluation have been diagnosed as demented according to DSM-IV criteria, of which two-thirds have Alzheimer''''s disease. An extensive assessment of probable risk exposure is also included. Longitudinal follow-up is yet another feature of the study. Association studies with candidate genes are also being performed. Types of samples * DNA Number of sample donors * 1154 (sample collection completed)interview, late adult human, clinical evaluation, association study, candidate gene, gene, risk factor, twin, longitudinalSCR_008884(KI Biobank - HARMONY, RRID:SCR_008884)Karolisnka Biobank Dementia, Alzheimer''''s disease, Discordant twin, AgingNIHrelated to: Swedish Twin Registry, KI Biobank - SATSA, listed by: One Mind Biospecimen Bank ListingLast checked downnlx_151298
OrbitProjectResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented on May 29, 2014. The orbit project was a registry of biomedical resources.SCR_010463(OrbitProject, RRID:SCR_010463)National Library of Medicine NIHLast checked downnlx_157692
National Centers for Biomedical ComputingResource, organization portal, portal, data or information resourceThe NCBCs are a set of networked computation core facilities for biomedical infrastructure funded under the NIH Common Fund, the National Program of Excellence in Biomedical Computing (NPEBC). There are seven funded Centers that cover systems biology, image processing, biophysical modeling, biomedical ontologies, information integration, and tools for gene-phenotype and disease analysis. The centers will create innovative software programs and other tools that enable the biomedical community to integrate, analyze, model, simulate, and share data on human health and disease. Each Center has Cores that are focused on (1) computational science, (2) biomedical computational science and (3) driving biological projects whose intent is to drive the interaction between computational and biomedical computational science. In addition to the Centers, the NIH has a number of active program announcements to develop collaborations with the biomedical research community??this includes announcements from the Biomedical Information Science and Technology Initiative (BISTI) and the Program for Collaborations with National Centers for Biomedical Computing. There are numerous efforts in education and training that emanate from the Centers and there is an annual all hands meeting.nih (common fund)SCR_010635(National Centers for Biomedical Computing, RRID:SCR_010635)National Institutes of Health NIHrelated to: iDASH, iTools, Center for Computational Biology at UCLA, i2b2 Research Data Warehouse, Informatics for Integrating Biology and the Bedside, National Alliance for Medical Image Computing, Simbios, National Center for Biomedical Ontology, National Center for Integrative Biomedical Informatics, MAGNet - Multiscale Analysis of Genomic and Cellular Networks, iDASHLast checked downnlx_62048
eVOCResource, ontology, data or information resource, controlled vocabularyTHIS RESOURCE IS NO LONGER SUPPORTED, documented September 6, 2016. Set of orthogonal controlled vocabularies that unifies gene expression data by facilitating a link between the genome sequence and expression phenotype information. The system associates labelled target cDNAs for microarray experiments, or cDNA libraries and their associated transcripts with controlled terms in a set of hierarchical vocabularies. eVOC consists of four orthogonal controlled vocabularies suitable for describing the domains of human gene expression data including Anatomical System, Cell Type, Pathology and Developmental Stage. The four core eVOC ontologies provide an appropriate set of detailed human terms that describe the sample source of human experimental material such as cDNA and SAGE libraries. These expression terms are linked to libraries and transcripts allowing the assessment of tissue expression profiles, differential gene expression levels and the physical distribution of expression across the genome. Analysis is currently possible using EST and SAGE data, with microarray data being incorporated. The eVOC data is increasingly being accepted as a standard for describing gene expression and eVOC ontologies are integrated with the Ensembl EnsMart database, the Alternate Transcript Diversity Project and the UniProt Knowledgebase. Several groups are currently working to provide shared development of this resource such that it is of maximum use in unifying transcript expression information.mouse, mapping, cdna, development, microarray, expression, expressed sequence, anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation, treatment, gene expression, genome sequence, expression phenotype, genome, sequence, phenotype, anatomical system, cell type, pathology, anatomySCR_010704(eVOC, RRID:SCR_010704)University of the Western Cape; Bellville; South Africa European Union, South African Department of Arts Culture Science and Technology, South African National Research Foundation, Wellcome Trustrelated to: OBO, Bgee: a dataBase for Gene Expression EvolutionPMID:12799354Last checked downnlx_84448
HOMERResource, software resource, software application, sequence analysis software, data analysis software, data processing softwareSoftware tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.motif, discovery, next, generation, sequencing, analysis, genomic, dataSCR_010881(HOMER, RRID:SCR_010881)University of California at San Diego; California; USA Foundation Leducq Transatlantic Network Grant, NCI, NIDDK, NIGMS, NIH, NURSA consortium grantrelated to:, listed by: OMICtoolsPMID:20513432Last checked downOMICS_00483
The Immunology Database and Analysis Portal (ImmPort)Resource, disease-related portal, topical portal, data repository, database, service resource, portal, storage service resource, ontology, controlled vocabulary, data or information resourceData sharing repository of clinical trials, associated mechanistic studies, and other basic and applied immunology research programs. Platform to store, analyze, and exchange datasets for immune mediated diseases. Data supplied by NIAID/DAIT funded investigators and genomic, proteomic, and other data relevant to research of these programs extracted from public databases. Provides data analysis tools and immunology focused ontology to advance research in basic and clinical immunology.immunology, basic, clinical, data, share, store, analyze, exchange, dataset, immune, mediated, disease, analysis, toolSCR_012804(The Immunology Database and Analysis Portal (ImmPort), RRID:SCR_012804)Immune mediated diseaseDAIT, NIAID, NIHrelated to: MetaCyto, The 10000 Immunomes, NIAID, recommended by: National Library of Medicine, BRAIN Initiative, listed by: NIDDK Research Resources, affiliated with: Cytokine RegistryPMID:24791905Last checked downnlx_152691
Colon Therapy Research Consortium (COLTHERES)Resource, organization portal, portal, consortium, data or information resourceThe Colon Therapy Research (COLTHERES) consortium brings together clinical centers and translational researchers funded in the European Union to define and perform biomarker driven clinical trials to improve cancer therapy outcomes. This 4-year consortium will use comprehensively molecularly-annotated colon cancers as a "test-bed" to define specific biomarkers of response or resistance to signaling pathway agents.translational, clinical, colon cancer, colon, biomarkersSCR_013690(Colon Therapy Research Consortium (COLTHERES), RRID:SCR_013690)European UnionLast checked down
NanomaterialsResourceData-driven tool aimed at providing researchers with a convenient data management and sharing plan. it has developed a data model for data collection and sharing in the nanotechnology field. It facilitates data validation and data quality sharing, data managementSCR_013700(Nanomaterials, RRID:SCR_013700)NIHLast checked down
OpenAIREResource, project portal, portal, data or information resourceA research portal to share and obtain research data and journal articles openly accessible to all disciplines. Established to support the Open Access Policy, as set out by the ERC Scientific Council Guidelines for Open Access and the Open Access pilot launched by the European access, Europe, repository networks, project portal, research data, journal articlesSCR_013740(OpenAIRE, RRID:SCR_013740)European Unionrelated to: ZENODOLast checked down
Nanomaterial RegistryResource, data or information resource, databaseAn online registry that archives curated nanomaterial research data and their biological and environmental implications. The Registry provides data management plans for researchers, and accepts users' public-ready data, archive them, integrate them into the registry, allowing for the data to be shared publicly. Users can request more information on specific nanomaterial records, compare multiple nanomaterials, and export data to their desktop.registry, information resource, nanomaterial, data managementSCR_013793(Nanomaterial Registry, RRID:SCR_013793)NIHlisted by: NIH Data Sharing RepositoriesDOI:10.1109/BIBMW.2012.6470258Last checked down
National Database for Clinical Trials related to Mental IllnessResource, data resourceA database which houses human subjects clinical trial data. NDCT currently contains data on 13,409 subjects and has access to data on 100,500 subjects from the NIMH Data Archive. Users can also sign up for news updates and watch video tutorials.database, human, clinical trial, mental health, mental illnessSCR_013795(National Database for Clinical Trials related to Mental Illness, RRID:SCR_013795)NIHrelated to: NIMH Data Archive, RDoCdb, RDoCdb, uses: NIMH Data Archive, RDoCdb, listed by: NIH Data Sharing RepositoriesLast checked down
Pubmed CommonsResource, narrative resource, discussion, forum, data or information resourceA forum where authors who have published in PubMed may comment on any publication in PubMed. Members of PubMed Commons are not anonymous and must agree to certain terms and guidelines concerning appropriate and inapproriate, PubMed, commuicationSCR_014021(Pubmed Commons, RRID:SCR_014021)NIH, NLMrelated to: PubMed, Connected Researchers, listed by: Connected ResearchersLast checked down
NRF ContactsResource, data set, people resource, data or information resourceThis resource provides a list of federal program officials in the neurosciences. An informal compendium of names and contact information for nearly 300 research grant and scientific review administrators in 21 organizational units.director, military, neurodegenerative disease, program officer, 2008, neuroscienceSCR_001473(NRF Contacts, RRID:SCR_001473)Society for Neuroscience NIH, NIMH, U.S. Department of Health and Human ServicesLast checked downnif-0000-09488
Mouse Thalamic Projectome DatasetResource, data set, data or information resourceData set of thalamo-centric mesoscopic projection maps to the cortex and striatum. The maps are established through two-color, viral (rAAV)-based tracing images and high throughout imaging.jpeg image data set, projection map, thalamocortical map, viral (rAAV)-based tracing, thalamo-centric mesoscopic projection mapSCR_015702(Mouse Thalamic Projectome Dataset, RRID:SCR_015702)NIDA, NIDDK, NIH, NINDSsubmitted by: Resource Identification PortalReferences (2)Last checked down
Glyco-CDResource, data set, data or information resourceManually curated, comprehensive repository of clusters of differentiation (CDs) which are a) defined as distinct oligosaccharide sequences as part of either glycoproteins and/or glycosphingolipids and b) defined as proteins which have carbohydrate recognition sites (CRDs) or as carbohydrate binding lectins. The data base is generated by exhaustive search of literature and other online data banks related to carbohydrates and proteins. This data bank is the beginning of an effort to provide concise, relevant information of carbohydrate-related CDs in a user- friendly manner. For users convenience the data bank under menu browse of GlycoCD is arranged in two section namely carbohydrate recognition CDs (CRD CD) and glycan CD. The carbohydrate recognition CD part is the collection of proteins which recognize glycan structures by means of the CRDs. Glycan CD is the part in which CDs are summarized which characterize specific oligosaccharide structures. The GlycoCD databank has been developed with the aim to assist the immunologist, cell biologist as well as the clinician who wants to keep up with the present knowledge in this field of glycobiology.carbohydrate, glycobiology, glycan, lectin, antigen, interaction, protein, cell surface molecule, microarray, carbohydrate recognition, cluster of differentiation, oligosaccharide sequence, glycoprotein, glycosphingolipid, carbohydrate recognition site, leukocyte, antibody, endothelial cell, epithelial cellSCR_001574(Glyco-CD, RRID:SCR_001574) European UnionPMID:22847935Last checked downnlx_152887
GOTrackResource, web service, software resource, data or information resource, data access protocol, databaseOpen source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis.database, system, access, historical, monitor, record, gene, genomic, data, analysis, ontology, annotation, bioinformaticsSCR_016399(GOTrack, RRID:SCR_016399)Canadian Foundation for Innovation infrastructure, CIHR, NIH, NSERC Discovery Grantrelated to: University of British Columbia, British Columbia, Canada, listed by: OMICtoolsDOI:10.1101/320861Last checked down,
Kids First Data Resource PortalResource, disease-related portal, topical portal, database, organization portal, service resource, portal, storage service resource, data repository, data or information resourcePortal for analysis and interpretation of pediatric genomic and clinical data to advance personalized medicine for detection, therapy, and management of childhood cancer and structural birth defects. For patients, researchers, and clinicians to create centralized database of well curated clinical and genetic sequence data from patients with childhood cancer or structural birth defects.pediatric, genomic, clinical, disease, data, children, cancer, birth, defect, analysisSCR_016493(Kids First Data Resource Portal, RRID:SCR_016493)pediatric cancer, birth defectNIH, the Common Fund’s Gabriella Miller Kids First Pediatric Research Programrecommended by: National Library of Medicine, BRAIN InitiativeLast checked downSCR_016553,,
iMITSResource, catalog, data or information resource, databaseSoftware tool for the planning of all IMPC mouse production. Allows IMPC production centers to record the progress of mouse production, cre-excision and to summarise the progress of phenotype data collection and transfer to the IMPC DCC. Stores all the mutation molecular structures made for the IKMC, catalogs of all IKMC, tracking, system, mouse, production, data, store, catalog, phenotype, collection, mutation, molecular, structure, IKMC, IMPCSCR_016552(iMITS, RRID:SCR_016552)European Union, NIHaffiliated with: IMPC, submitted by: Resource Identification PortalLast checked down
Cleveland Family StudyResource, disease-related portal, topical portal, portal, data or information resourcePortal for family based study of sleep apnea. Contains data for quantifying the familial aggregation of sleep apnea. The polysomnographic (PSG) montage signals: EEG, ECG, EOG, EMG, SpO2, plethysmography, airflow (thermistor), nasal pressure, respiratory effort, position,, polysomnography, sleep apnea, family, familial aggregation, EEG, ECG, longitudinalSCR_016585(Cleveland Family Study, RRID:SCR_016585)sleep disorderNCRR, NHLBI, NIHlisted by: National Sleep Research Resource (NSRR), submitted by: Resource Identification PortalPMID:7881656Last checked down
Functional Anatomy of the Cerebro-Cerebellar System (FACCS)Resource, data analysis service, production service resource, analysis service resource, database, service resource, storage service resource, data repository, data or information resourcePublic neuroscience database providing a collection of published data describing structure and structure-function relationships in one of the largest projection systems of the brain: the cerebro-cerebellar system. It also gives access to a suite of tools that allow the user to visualize and analyze any selected combination of data sets. Contact them if you are interested in contributing data. The overall goal is to improve communication of results and permit re-use of previously published data in new contexts. FACCS is a part of the Rat Brain WorkBench, a new research and development project funded by The Research Council of Norway, the Centre for Molecular Biology and Neuroscience, and the European Union. The project is directed by Jan G. Bjaalie, Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.axonal tracer, axon tracing, brain, cerebellum, cerebral cortex, cerebro-cerebellar function, cerebro-cerebellar structure, cerebro-cerebellar system, injection, injection site, labeled cells, labeled fibers, pontine nuclear complex, pontine nuclei, video, cerebellar cortexSCR_001661(Functional Anatomy of the Cerebro-Cerebellar System (FACCS), RRID:SCR_001661)University of Oslo; Oslo; Norway Centre for Molecular Biology and Neuroscience, European Union, Research Council of NorwayReferences (2)Last checked downnif-0000-02317
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