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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

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
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
BIRNLexResource, ontology, data or information resource, controlled vocabularyTHIS RESOURCE IS NO LONGER IN SERVICE, documented on April 26, 2011. Lexicon that provides entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. These sources may include complex image databases, such as data from structural and functional magnetic resonance imaging (MRI) on human subjects involved in studies on Alzheimer''s disease or schizophrenia. The BIRNLex is a specialized vocabulary utilized by BIRN scientists in the context of their research, including common terms for neuroanatomy, molecular species, subject information, behavioral and cognitive processes, experimental practice and design, and the associated elements of primary data provenance required for large-scale data integration across disparate experimental studies.The BIRNLex offers well defined terms from several domains of importance to neuroimaging across scales.controlled vocabulary, owlSCR_007326(BIRNLex, RRID:SCR_007326)Drexel University College of Medicine; Pennsylvania; USA listed by: BioPortalLast checked downnif-0000-00199
RxNormResource, ontology, data or information resource, controlled vocabularyOntology that provides a normalized naming system for generic and branded drugs and a tool for supporting semantic interoperation between drug terminologies and pharmacy knowledge base systems. It contains the names of prescription and many over-the-counter drugs available in the United States and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software. It can mediate messages between systems not using the same software and vocabulary. * RxNorm Download Files - contain data consistent with the 2013AB UMLS Metathesaurus Release Files. * RxNorm API - web service for accessing the current RxNorm data set. * RxNorm Browser (RxNav) - a browser for several drug information sources, including RxNorm, RxTerms and National Drug File - Reference Terminology (NDF-RT) . * Current Prescribable Content - subset of currently prescribable drugs found in RxNorm. * RxTerms Drug Interface Terminology - a drug interface terminology derived from RxNorm for prescription writing or medication history recordingumls, drug, pharmacy, clinical, drug pack, medicine, unique identifier, prescribable drug, web service, metathesaurus, generic drug, branded drug, data set, web service, databaseSCR_006645(RxNorm, RRID:SCR_006645)National Library of Medicine listed by: BioPortalPMID:22426081Last checked upnif-0000-02575
Adult Mouse Anatomy OntologyResource, ontology, data or information resource, controlled vocabularyOntology that organizes anatomical structures for the adult mouse (Theiler stage 28) spatially and functionally, using ''is a'' and ''part of'' relationships. The ontology is used to describe expression data for the adult mouse and phenotype data pertinent to anatomy in standardized ways. The browser can be used to view anatomical terms and their relationships in a hierarchical display.
functionally, adult mouse, anatomical, anatomy, phenotype, postnatal, structure, theiler stage 28, obo, gene expressionSCR_006568(Adult Mouse Anatomy Ontology, RRID:SCR_006568)Gene Expression Database NHGRI, NICHD, NIHrelated to: Bgee: a dataBase for Gene Expression Evolution, listed by: BioPortalLast checked upnif-0000-10300
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
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
Experimental Factor OntologyResource, ontology, data or information resource, controlled vocabularyAn application focused ontology modelling the experimental factors in ArrayExpress and Gene Expression Atlas. It has been developed to increase the richness of the annotations that are currently made in the ArrayExpress repository, to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The ontology describes cross-product classes from reference ontologies in area such as disease, cell line, cell type and anatomy. The methodology employed in the development of EFO involves construction of mappings to multiple existing domain specific ontologies, such as the Disease Ontology and Cell Type Ontology. This is achieved using a combination of automated and manual curation steps and the use of a phonetic matching algorithm. The ontology is evaluated with use cases from the ArrayExpress repository and ArrayExpress Atlas. You may also browse the EFO in the NCBO Bioportal. Term submissions are welcome.gene expression, owl, experimental factor, disease, cell line, cell type, anatomy, gold standardSCR_003574(Experimental Factor Ontology, RRID:SCR_003574)European Bioinformatics Institute European Molecular Biology Laboratory, European Union EMERALD, European Union FELICS, European Union Gen2Phenrelated to: ArrayExpress, ArrayExpress, Gene Expression Atlas, listed by: BioPortalPMID:20200009Last checked upnlx_11363
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
eagle-i research resource ontologyResource, source code, data repository, database, software application, service resource, storage service resource, software resource, ontology, controlled vocabulary, data or information resourceOntology that models research resources such as instruments, protocols, reagents, animal models and biospecimens. It has been developed in the context of the eagle-i project ( and consists of over 3451 classes of which over 1200 were created within the ERO namespace, while the rest come from existent ontologies such as the Ontology for Biomedical Investigation (OBI), the uber-anatomy ontology (Uberon), VIVO, the Ontology for Clinical Research (OCRe), the Sequence Ontology (SO), the Software Ontology (SWO) and we include terms from the NCBI Taxonomy as well. The main ontology can be browsed in OntoBee. All purls resolve to OntoBee.research, resource, biomedical, owlSCR_008784(eagle-i research resource ontology, RRID:SCR_008784) Google Code , Eagle I ARRA, NCRRrelated to: Ontobee, CTSA ShareCenter, listed by: BioPortalLast checked upnlx_144312
Zebrafish Anatomical OntologyResource, ontology, data or information resource, controlled vocabularyA structured controlled vocabulary of the anatomy and development of the Zebrafish (Danio rerio). It includes a list of structures, organized hierarchically into an ontology, with descriptions of each structure. The current version is being written by a consortium of researchers, each serving as an expert for a particular set of anatomical structures. Additional anatomical information derived from the current literature is provided by the ZFIN curation group. Development of a complete and uniform anatomical ontology for the zebrafish is vital to the success of zebrafish science. The anatomical ontology is necessary for: * Effective data dissemination and informatics. * A reference framework. * Interoperability.anatomy, structure, anatomical structure, oboSCR_005887(Zebrafish Anatomical Ontology, RRID:SCR_005887)Zebrafish Information Network related to: OBO, Bgee: a dataBase for Gene Expression Evolution, used by: Teleost Anatomy Ontology, recommended by: Zebrafish Brain Atlas, listed by: BioPortalLast checked upnlx_149454
EDAM OntologyResource, ontology, data or information resource, controlled vocabularyAn ontology of bioinformatics operations (tool, application, or workflow functions), types of data including identifiers, topics (application domains), and data formats. The applications of EDAM are within organizing tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web.bioinformatics, operation, data, topic, type, identifier, format, semantic annotation, obo format, owlSCR_006620(EDAM Ontology, RRID:SCR_006620)European Bioinformatics Institute related to: DRCAT Resource Catalogue, bioDBcore, listed by: BioPortalLast checked upnlx_151281
EnvOResource, ontology, data or information resource, controlled vocabularyCommunity ontology for the concise, controlled description of environmental features and habitats. It provides a structured vocabulary that is designed to support the annotation of any organism or biological sample with environment descriptors. EnvO contains terms for biomes, environmental features, and environmental material.biome, environmental feature, environmental material, environment, habitatSCR_000182(EnvO, RRID:SCR_000182)related to: Gramene, listed by: BioPortalLast checked upnlx_153832
Teleost Taxonomy OntologyResource, ontology, data or information resource, controlled vocabularyAn ontology of taxonomic terms (names of taxonomic groups) used in the systematics of fish, including non-teleost groups such as Chondrichthys (sharks and rays), Sarcopterygii (lungfish and coelacanths), lampreys, and hagfish. It contains (as of August 2010) over 38,500 names, and over 44,000 taxonomic synonyms. A majority of the taxonomic names and synonyms were made available from the Catalog of Fishes. In July 2010 they added nearly 15,000 common names provided by Fishbase. Additional names and synonyms are added as a result of their curation activities. The ontology is being used to facilitate annotation of phenotypes, particularly for taxa that are not covered by NCBI because no submissions of molecular data have been made. Taxonomy ontologies can also be valuable in annotating legacy data, where authors make phenotype or ecological assertions (e.g., host-parasite associations) that refer to groups that are reorganized or no longer recognized. The taxonomy ontology serves as the source of taxa for their project's use for identifying evolutionary changes that match the phenotype of a zebrafish mutant.taxonomy, term, name, group, fish, phenotype, oboSCR_001611(Teleost Taxonomy Ontology, RRID:SCR_001611)Phenoscape Knowledgebase related to: Catalog of Fishes, FishBase, used by: Vertebrate Taxonomy Ontology, listed by: BioPortalLast checked upnlx_153877
ECOResource, ontology, data or information resource, controlled vocabularyA controlled vocabulary that describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about research subjects that result from scientific research, such as scientific conclusions, gene annotations, or other statements of fact. ECO comprises two high-level classes, evidence and assertion method, where evidence is defined as a type of information that is used to support an assertion, and assertion method is defined as a means by which a statement is made about an entity. Together evidence and assertion method can be combined to describe both the support for an assertion and whether that assertion was made by a human being or a computer. However, ECO can not be used to make the assertion itself; for that, one would use another ontology, free text description, or other means. ECO was originally created around the year 2000 to support gene product annotation by the Gene Ontology. Today ECO is used by many groups concerned with provenance in scientific research. ECO is used in AmiGO 2evidence, assertion, assertion method, gene product, obo, evidence code, experiment, similarity, provenanceSCR_002477(ECO, RRID:SCR_002477) Google Code , University of Maryland School of Medicine; Maryland; USA NIGMSrelated to: AmiGO, Gene Ontology, listed by: BioPortalLast checked upnlx_155860,
Bioassay OntologyResource, ontology, data or information resource, controlled vocabularyOntology to describe and categorize chemical biology and drug screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. BAO is an extensible, knowledge-based, highly expressive (currently SHOIQ(D)) description of biological assays making use of descriptive logic based features of the Web Ontology Language (OWL). BAO currently has over 700 classes and also makes use of several other ontologies. It describes several concepts related to biological screening, including Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint. Perturbagens are perturbing agents that are screened in an assay; they are mostly small molecules. Assay Meta Target describes what is known about the biological system and / or its components interrogated in the assay (and influenced by the Perturbagen). Meta target can be directly described as a molecular entity (e.g. a purified protein or a protein complex), or indirectly by a biological process or event (e.g. phosphorylation). Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. The assay Design describes the assay methodology and implementation of how the perturbation of the biological system is translated into a detectable signal. Detection Technology relates to the physical method and technical details to detect and record a signal. Endpoints are the final HTS results as they are usually published (such as IC50, percent inhibition, etc). BAO has been designed to accommodate multiplexed assays. All main BAO components include multiple levels of sub-categories and specification classes, which are linked via object property relationships forming an expressive knowledge-based representation.chemical biology, drug screening, assay, perturbation, high-throughput screening, owlSCR_002638(Bioassay Ontology, RRID:SCR_002638)used by: LINCS Information Framework, listed by: BioPortalLast checked downnlx_156065
MeGOResource, ontology, data or information resource, controlled vocabularyA Gene Ontology dedicated to the functions of mobile genetic elements. The terms defined are used to annotate phage and plasmid protein families in ACLAME. Note: The phage ontology PhiGO has now been incorporated in MeGO and can thus be accessed in MeGO version 1.0 and up.phage, plasmid, protein family, mobile genetic element, oboSCR_000110(MeGO, RRID:SCR_000110)A Classification of Mobile genetic Elements related to: OBO, AmiGO, Gene Ontology, listed by: BioPortalLast checked upnlx_156939
Vertebrate Trait OntologyResource, ontology, data or information resource, controlled vocabularyA controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.trait, morphology, physiology, development, oboSCR_003214(Vertebrate Trait Ontology, RRID:SCR_003214)SourceForge related to: monarch-ontologies, Rat Genome Database (RGD), Animal QTLdb, Mouse Phenome Database (MPD), listed by: BioPortalPMID:23937709Last checked upnlx_156940
ABA Adult Mouse Brain OntologyResource, ontology, data or information resource, controlled vocabularyAllen Brain Atlas P56 Mouse OntologyowlSCR_010286(ABA Adult Mouse Brain Ontology, RRID:SCR_010286)Allen Institute for Brain Science listed by: BioPortalLast checked upnlx_157311
AEOResource, ontology, data or information resource, controlled vocabularyAn ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology, to about 200 classes using the is_a relationship; it thus provides a detailed type classification for tissues. The new classes were chosen for their use in categorizing the major vertebrate and invertebrate anatomy ontologies at a granularity adequate for tissues of a single cell type. The ontology should be useful in increasing the amount of knowledge in anatomy ontologies, facilitating annotation and enabling interoperability across anatomy ontologiesoboSCR_010287(AEO, RRID:SCR_010287)OBO listed by: BioPortalLast checked downnlx_157312
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