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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)

Physical Resource or Software Tool Software

13 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
Human Phenotype Ontology AnnotationsResource, data set, data or information resourceDownloadable dataset of Human Phenotype Ontology (HPO) annotations. Provides standardized vocabulary of phenotypic abnormalities encountered in human disease.phenotype, genetics, hereditary disease, human disease, adult human, ontology, annotation, disease, clinicalSCR_006219(Human Phenotype Ontology Annotations, RRID:SCR_006219)HPO - Human Phenotype Ontology related to: Phenomizer, used by: NIF Data Federation, Monarch InitiativePMID:20412080Last checked downnlx_151835http://www.human-phenotype-ontology.org/contao/index.php/downloads.html
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_152691http://www.immport.org/immport-open/public/home/homehttp://www.immport.org
National Institute on Drug Abuse Center for Genetic StudiesResource, data set, service resource, data repository, storage service resource, data or information resourceSite for collection and distribution of clinical data related to genetic analysis of drug abuse phenotypes. Anonymous data on family structure, age, sex, clinical status, and diagnosis, DNA samples and cell line cultures, and data derived from genotyping and other genetic analyses of these clinical data and biomaterials, are distributed to qualified researchers studying genetics of mental disorders and other complex diseases at recognized biomedical research facilities. Phenotypic and Genetic data will be made available to general public on release dates through distribution mechanisms specified on website.drug abuse, family, family structure, genetic analysis, genetics, addiction, age, biomaterial, cell line, citation, clinical, clinical status, data, diagnosis, dna, genotyping, human, mental disorder, mutation analysis, phenotype, publications, sex, clinical data, genotype, geneSCR_013061(National Institute on Drug Abuse Center for Genetic Studies, RRID:SCR_013061) Rutgers University; New Jersey; USA , Washington University School of Medicine in St. Louis; Missouri; USA NIDA, NIH Blueprint for Neuroscience Researchrelated to: One Mind Biospecimen Bank Listing, NIH Data Sharing Repositories, recommended by: National Library of Medicine, BRAIN Initiative, listed by: One Mind Biospecimen Bank ListingLast checked downnif-0000-00181https://zork5.wustl.edu//nida/http://zork.wustl.edu/nida/
National Sleep Research Resource (NSRR) Resource, organization portal, service resource, portal, storage service resource, data repository, data or information resourceSystem for sharing sleep data. Organization portal that aggregates, harmonizes, and organizes sleep and clinical data from individuals studied as part of cohort studies or clinical trials and provides suite of tools to facilitate data exploration and data visualization. National Heart, Lung, and Blood Institute resource designed to provide big data resources to sleep research community.sleep, clinical, data, cohort, study, trial, dataset, visualization, explorationSCR_016576(National Sleep Research Resource (NSRR) , RRID:SCR_016576)sleep apneaNHLBIrecommended by: National Library of Medicine, BRAIN Initiative, lists: Apnea, Bariatric surgery, and CPAP study, Sleep Heart Health Study, Honolulu-Asia Aging Study of Sleep Apnea, Cleveland Family Study, Cleveland Children's Sleep and Health Study, Best Apnea Interventions for Research (BestAIR) sleep studyPMID:29860441Last checked downhttps://sleepdata.org/share, https://sleepdata.org/datasets
TalkBankResource, narrative resource, data or information resource, training material, databaseDatabases of transcript and media data collected from conversations with adults and older children to foster fundamental research in the study of human and animal communication. Conversations with children are available from CHILDES. All of the data is transcribed in CHAT and CA/CHAT formats. Databases of the following types are included in the collection: Aphasia patient speech, Child speech, Study of Phonological Development, Conversation Analysis, and Bilingualism and Second Language Acquisition. TalkBank will use these databases to advance the development of standards and tools for creating, sharing, searching, and commenting upon primary materials via networked computers.aphasia, aphasiabank, bilingbank, cabank, phonbank, psychology, speech, communication, clinical, transcript, audio track, video, talk, voice, language, conversation, discourse, adult human, child, second language, audiology, media, animal communication, conversation analysis, discourse analysis, gesture, code switching, bilingualism, linguistic, phonological development, danishSCR_003242(TalkBank, RRID:SCR_003242) University of Pennsylvania; Philadelphia; Pennsylvania , Carnegie Mellon University; Pennsylvania; USA Aphasia, Dementia, BilingualismNICHD, NIDCDrelated to: PhonBank, listed by: re3data.org, works_with: Child Language Data Exchange System (CHILDES)Last checked upnif-0000-00626
ClinVarResource, service resource, data or information resource, data repository, storage service resource, databaseArchive of aggregated information about sequence variation and its relationship to human health. Provides reports of relationships among human variations and phenotypes along with supporting evidence. Submissions from clinical testing labs, research labs, locus-specific databases, expert panels and professional societies are welcome. Collects reports of variants found in patient samples, assertions made regarding their clinical significance, information about submitter, and other supporting data. Alleles described in submissions are mapped to reference sequences, and reported according to HGVS standard.sequence variation, variation, phenotype, genetics, genetic variation, clinical, allele, aggregator, geneotype, gene, disease, clinical assertionSCR_006169(ClinVar, RRID:SCR_006169)NCBI used by: NIF Data Federation, Monarch Initiative, MARRVEL, listed by: OMICtoolsLast checked upnlx_151671, OMICS_00262
Clinical Genomic DatabaseResource, data or information resource, databaseManually curated database of all conditions with known genetic causes, focusing on medically significant genetic data with available interventions. Includes gene symbol, conditions, allelic conditions, inheritance, age in which interventions are indicated, clinical categorization, and general description of interventions/rationale. Contents are intended to describe types of interventions that might be considered. Includes only single gene alterations and does not include genetic associations or susceptibility factors related to more complex diseases.genomic sequencing, genome, clinical, pediatric, adult human, young human, genomic medicine, whole-genome sequencing, gene, organ system, intervention, gene symbol, condition, allelic condition, clinical categorization, manifestation, inheritance, age group, genetic variant, pathogenic mutationSCR_006427(Clinical Genomic Database, RRID:SCR_006427)National Human Genome Research Institute NHGRIused by: Monarch Initiative, NIF Data FederationPMID:23696674Last checked upnlx_152872
OrphanetResource, service resource, topical portal, database, portal, data or information resourceEuropean website providing information about orphan drugs and rare diseases. It contains content both for physicians and for patients. Reference portal for rare diseases and orphan drugs to help improve diagnosis, care and treatment of patients with rare diseases.drug, clinical, diagnostic, test, rare, disease, molecule, gene, orphan, drugSCR_006628(Orphanet, RRID:SCR_006628)National Institute of Health and Medical Research; Rennes; France European Union, France, French Directorate General for Health, National Institute of Health and Medical Research, Rennesrelated to: Disease core ontology applied to Rare Diseases, phenomeNET, used by: NIF Data Federation, HmtPhenome, listed by: OMICtoolsLast checked upnif-0000-21306
Chemical Effects in Biological Systems (CEBS)Resource, service resource, data or information resource, data repository, storage service resource, databaseRepository for toxicogenomics data, including study design and timeline, clinical chemistry and histopathology findings and microarray and proteomics data. Data derived from studies of chemicals and of genetic alterations, and is compatible with clinical and environmental studies. Data relating to environmental health, pharmacology, and toxicology. It is not necessary to have microarray data, but study design and phenotypic anchoring data are required.CEBS contains raw microarray data collected in accordance with MIAME guidelines and provides tools for data selection, pre-processing and analysis resulting in annotated lists of genes of interest. Biomedical Investigation Database is another component of CEBS system. used to load and curate study data prior to export to CEBS, in addition to capturing and displaying novel data types such as PCR data, or additional fields of interest, including those defined by the HESI Toxicogenomics Committee. BID has been shared with Health Canada and the US Environmental Protection Agency.caenorhabditis elegans, chemical study, microarray, genetic alteration, toxicogenomics, environmental health, study design, timeline, clinical chemistry, histopathology, proteomics, chemical, clinical, microarray hybridization, gel image, phenotype, pharmacology, toxicologySCR_006778(Chemical Effects in Biological Systems (CEBS), RRID:SCR_006778)National Institute of Environmental Health Sciences NIEHS, NIGMSrecommended by: National Library of Medicine, BRAIN InitiativePMID:17962311Last checked upnif-0000-02649
L1000 Fireworks DisplayResource, software resource, data visualization software, software application, data processing software, web applicationWeb application that provides interactive visualization of drug and small-molecule induced gene expression signatures. L1000FWD enables coloring of signatures by different attributes such as cell type, time point, concentration, as well as drug attributes such as MOA and clinical phase.drug, small molecule, gene, expression, signature, moa, clinical, phaseSCR_016175(L1000 Fireworks Display, RRID:SCR_016175)Icahn School of Medicine at Mount Sinai; New York; USA submitted by: NIDDK Information NetworkPMID:29420694Last checked up
InxightResource, organization portal, data or information resource, portal, databasePortal of NCATS (the National Center for Advancing Translational Sciences) for drug development information including:US approved drugs, marketed drugs, investigational drugs. Provides manually curated data supplied by the FDA and private companies. Provides drugs marketing and regulatory status, drug ingredient definitions, biological activity and clinical use.drug, development, information, approved, marketed, investigational, data, supply, FDA, company, regulatory, status, ingredient, definition, biological, activity, clinical, useSCR_016490(Inxight, RRID:SCR_016490)NIHLast checked up
Attie Lab Diabetes DatabaseResource, database, data or information resourceInteractive database of gene expression and diabetes related clinical phenotypes. Allows to search gene expression in tissues as a function of obesity, strain, and age, in a mouse.interactive, database, gene, expression, diabetes, related, clinical, phenotype, mouseSCR_016639(Attie Lab Diabetes Database, RRID:SCR_016639)University of Wisconsin-Madison; Wisconsin; USA diabeteslisted by: OMICtoolsLast checked up
dcmqiResource, data processing software, software library, software application, software resource, software toolkit, image processing softwareSoftware library to help with the conversion between imaging research formats and the standard DICOM representation for image analysis results. Used to implement conversion of the data stored in commonly used research formats into the standard DICOM representation. Available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer.DICOM, converter, medical, image, computing, quantitative, analysis, clinical, data, metadata, radiology, standardSCR_016933(dcmqi, RRID:SCR_016933)NCI, NIBIBrelated to: Harvard University, Cambridge, United States, submitted by: Resource Identification PortalPMID:29092948Last checked up
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