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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

311 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
VIVOResource, controlled vocabulary, software application, service resource, portal, software resource, ontology, community building portal, data or information resourceOpen source semantic web application that enables the discovery of research and scholarship across disciplines at a particular institution and across institutions by creating a semantic cloud of information that can be searched and browsed. Participants include institutions with local installations of VIVO or those with research discovery and profiling applications that can provide semantic web-compliant data. The information accessible through the national network''''s search and browse capability will therefore reside and be controlled locally within institutional VIVOs or other semantic web applications. The VIVO ontology provides a set of types (classes) and relationships (properties) to represent researchers and the full context of their experience, outputs, interests, accomplishments, and associated institutions. VIVO is populated with detailed profiles of faculty and researchers including information such as publications, teaching, service, and professional affiliations. It also supports browsing and a search function which returns faceted results for rapid retrieval of desired information. The rich semantically structured data in VIVO support and facilitate research discovery. Examples of applications that consume these rich data include: visualizations, enhanced multi-site search through VIVO Search, and applications such as VIVO Searchlight, a browser bookmarklet which uses text content of any webpage to search for relevant VIVO profiles, and the Inter-Institutional Collaboration Explorer, an application which allows visualization of collaborative institutional partners, among others. Institutions are free to participate in the national network by installing and using the application. The application provides linked data via RDF data making users a part of the semantic web! or any other application that provides linked data can be used. Users can also get involved with developing applications that provide enhanced search, new collaboration capabilities, grouping, finding and mapping scientists and their sharing, network, semantic web, linked data, rdf, owl, database, people resourceSCR_005246(VIVO, RRID:SCR_005246)University of Florida; Florida; USA NCRRrelated to: Clinical and Translational Science Awards Consortium, DataStaR, CTSAconnect, CTSA ShareCenter, listed by: BioPortalLast checked upnlx_144266
FMAResource, data analysis software, data processing software, database, software application, software resource, ontology, controlled vocabulary, data or information resourceA domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Its ontological framework can be applied and extended to all other species. The description of how the OWL version was generated is in Pushing the Envelope: Challenges in a Frame-Based Representation of Human Anatomy by N. F. Noy, J. L. Mejino, C. Rosse, M. A. Musen: The Foundational Model of Anatomy ontology has four interrelated components: # Anatomy taxonomy (At), # Anatomical Structural Abstraction (ASA), # Anatomical Transformation Abstraction (ATA), # Metaknowledge (Mk), The ontology contains approximately 75,000 classes and over 120,000 terms; over 2.1 million relationship instances from over 168 relationship types link the FMA's classes into a coherent symbolic model.anatomy, informatics, model, neuroanatomy, protg, reference, standard, structural, taxonomy, owl, phenotypeSCR_003379(FMA, RRID:SCR_003379)University of Washington; Seattle; USA Intel Corporation, Microsoft, Murdock Charitable Trust, NHLBI, NLM, RSNA-NIBIB, University of Washington; Washington; USArelated to: T3DB, HIV Brain Sequence Database, CELDA Ontology, listed by: BioPortalReferences (3)Last checked upnif-0000-00066
SBOResource, database, ontology, data or information resource, controlled vocabularyA set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling. The ontology consists of seven orthogonal vocabularies defining: the roles of reaction participants (eg. substrate), quantitative parameters (eg. Michaelis constant), a precise classification of mathematical expressions that describe the system (eg. mass action rate law), the modeling framework used (eg. logical framework), and a branch each to describe entity (eg. macromolecule) and interaction (eg. process) types, and a branch to define the different types of metadata that may be present within a model. SBO terms can be used to introduce a layer of semantic information into the standard description of a model, or to annotate the results of biochemical experiments in order to facilitate their efficient reuse. SBO is an Open Biomedical Ontologies (OBO) candidate ontology, and is free for use. A programmatic access to the content of the Systems Biology Ontology is provided by Web biology, computational modeling, web service, obo, gold standardSCR_006753(SBO, RRID:SCR_006753)European Bioinformatics Institute NIGMSrelated to:, OBO, listed by: BioPortalPMID:17118155Last checked upnlx_66206
NEMO OntologyResource, database, ontology, portal, data or information resource, controlled vocabularyOntology that describes classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, and functional (cognitive / behavioral) attributes, and data-level attributes (acquisition and analysis parameters). Its aim is to support data sharing, logic-based queries and mapping/integration of patterns across data from different labs, experiment paradigms, and modalities (EEG/MEG).eeg, meg, owl, event-related potential, cognitive, behavioral, data sharing, erpSCR_003386(NEMO Ontology, RRID:SCR_003386)Neural ElectroMagnetic Ontologies (NEMO) , SourceForge NIHrelated to: NEMO Analysis Toolkit, listed by: BioPortalLast checked upnif-0000-32927
WHO Adverse Reaction TerminologyResource, data or information resource, controlled vocabularyOntology of the WHO adverse reaction terminology, 1997.umlsSCR_010447(WHO Adverse Reaction Terminology, RRID:SCR_010447)World Health Organization listed by: BioPortalLast checked upnlx_157628
MeSHResource, data or information resource, controlled vocabularyA controlled vocabulary thesaurus that consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. MeSH, in machine-readable form, is provided at no charge via electronic means. MeSH descriptors are arranged in both an alphabetic and a hierarchical structure. At the most general level of the hierarchical structure are very broad headings such as Anatomy or Mental Disorders. More specific headings are found at more narrow levels of the twelve-level hierarchy, such as Ankle and Conduct Disorder. There are 27,149 descriptors in 2014 MeSH. There are also over 218,000 entry terms that assist in finding the most appropriate MeSH Heading, for example, Vitamin C is an entry term to Ascorbic Acid. In addition to these headings, there are more than 219,000 headings called Supplementary Concept Records (formerly Supplementary Chemical Records) within a separate thesaurus. The MeSH thesaurus is used by NLM for indexing articles from 5,400 of the world''''s leading biomedical journals for the MEDLINE/PubMED database. It is also used for the NLM-produced database that includes cataloging of books, documents, and audiovisuals acquired by the Library. Each bibliographic reference is associated with a set of MeSH terms that describe the content of the item. Similarly, search queries use MeSH vocabulary to find items on a desired topic.umls, database, health, thesaurus, medical, gold standardSCR_004750(MeSH, RRID:SCR_004750)National Library of Medicine related to: MEDLINE, Public Health Image Library, MEDLINE, DermAtlas., Coremine Medical, Unified Medical Language System, I3-CRB: Interoperable IT Infrastructure for Biological Resources Centres / Biobanks - France, Robert Hoehndorf Version of MeSH, PharmGKB Ontology, Linked Neuron Data, PubMed, used by: Nowomics, Cytokine Registry, listed by: BioPortalLast checked upnlx_75424
MedlinePlusResource, data or information resource, video resource, databaseDatabase 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, The ontology is available through Bioportal,, herb, medication, over-the-counter, prescription, supplement, health, clinical trial, disease, condition, image, test, symptom, injury, surgery, generic drug, umls, ontology, gold standardSCR_006512(MedlinePlus, RRID:SCR_006512)National Library of Medicine related to: EBIMed, MalaCards, listed by: BioPortalLast checked upnif-0000-10315
Physician Data QueryResource, ontology, database, people resource, registry, controlled vocabulary, clinical trial, data or information resourceNCI''s comprehensive cancer database that contains summaries on a wide range of cancer topics; a registry of 8,000+ open and 19,000+ closed cancer clinical trials from around the world; a directory of professionals who provide genetics services; the NCI Dictionary of Cancer Terms, with definitions for 6,800+ cancer and medical terms; and the NCI Drug Dictionary, which has information on 2,300+ agents used in the treatment of cancer or cancer-related conditions. The PDQ cancer information summaries are peer reviewed and updated monthly by six editorial boards comprised of specialists in adult treatment, pediatric treatment, supportive care, screening and prevention, genetics, and complementary and alternative medicine. The Boards review current literature from more than 70 biomedical journals, evaluate its relevance, and synthesize it into clear summaries. Many of the summaries are also available in, pediatric, child, alternative, breast, clinical trial, colorectal, hypercalcemia, legal, lung, medicine, medullary, nausea, ovarian, pain, pathophysiology, pediatric, pharmaceutical, physician, prevention, prognosis, prostate, psychosocial, query, risk factor, screening, social, syndrome, thyroid, treatment, umls, genetics, medical, drug, peer reviewSCR_006833(Physician Data Query, RRID:SCR_006833)National Cancer Institute Cancer, Cancer-related conditionNCIlisted by: BioPortalLast checked downnif-0000-21318
Neural Motor Recovery OntologyResource, ontology, data or information resource, controlled vocabularyOntology of neural functional motor recovery.owlSCR_010377(Neural Motor Recovery Ontology, RRID:SCR_010377)listed by: BioPortalLast checked upnlx_157505
Reproductive Trait and Phenotype OntologyResource, ontology, data or information resource, controlled vocabularyOntology for livestock reproductive traits and phenotypesowlSCR_006245(Reproductive Trait and Phenotype Ontology, RRID:SCR_006245)listed by: BioPortalLast checked upnlx_157574
Dengue Fever OntologyResource, ontology, data or information resource, controlled vocabularyAn ontology for dengue fever.owlSCR_010304(Dengue Fever Ontology, RRID:SCR_010304)Dengue feverlisted by: BioPortalLast checked upnlx_157383
Amphibian Gross Anatomy OntologyResource, ontology, data or information resource, controlled vocabularyA structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon.oboSCR_010291(Amphibian Gross Anatomy Ontology, RRID:SCR_010291)listed by: BioPortalLast checked downnlx_157316
Bone and Cartilage Tissue Engineering OntologyResource, ontology, data or information resource, controlled vocabularyOntology that describes the field of Tissue Engineering for what concerns bone and cartilage tissues.oboSCR_006595(Bone and Cartilage Tissue Engineering Ontology, RRID:SCR_006595)listed by: BioPortalLast checked upnlx_157341
Image and Data Quality Assessment OntologyResource, ontology, data or information resource, controlled vocabularyOntology for Image and Data Quality Assessment for scientific data management.oboSCR_010343(Image and Data Quality Assessment Ontology, RRID:SCR_010343)listed by: BioPortalLast checked upnlx_157437
BioModels OntologyResource, ontology, data or information resource, controlled vocabularyOWL Representation of the models in the BioModels repository.owlSCR_010125(BioModels Ontology, RRID:SCR_010125)listed by: BioPortalLast checked upnlx_157326
InterNano Nanomanufacturing TaxonomyResource, ontology, data or information resource, controlled vocabularyA custom-built terminology to describe the nanomanufacturing enterprise.owlSCR_010346(InterNano Nanomanufacturing Taxonomy, RRID:SCR_010346)NSFlisted by: BioPortalLast checked upnlx_157442
Semantic Types OntologyResource, ontology, data or information resource, controlled vocabularyOntology of semantic types.umlsSCR_010425(Semantic Types Ontology, RRID:SCR_010425)listed by: BioPortalLast checked upnlx_157584
Tick Gross Anatomy OntologyResource, ontology, data or information resource, controlled vocabularyAnatomy Ontology of the Tick, Families: Ixodidae, ArgassidaeoboSCR_010433(Tick Gross Anatomy Ontology, RRID:SCR_010433)listed by: BioPortalLast checked downnlx_157609
Medaka Fish Anatomy and Development OntologyResource, ontology, data or information resource, controlled vocabularyA structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.oboSCR_003719(Medaka Fish Anatomy and Development Ontology, RRID:SCR_003719)listed by: BioPortalLast checked upnlx_157469
Mouse Gross Anatomy and Development OntologyResource, ontology, data or information resource, controlled vocabularyA structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus).oboSCR_003891(Mouse Gross Anatomy and Development Ontology, RRID:SCR_003891)listed by: BioPortalLast checked upnlx_157488
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