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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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311 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
Ontology for MicroRNA Target PredictionResource, ontology, data or information resource, controlled vocabularyOntology to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans'' various diseases and biological processes (usually through miRs'' respective target genes). OMIT has reused and extended a set of well-established concepts from existing bio-ontologies, e.g., Gene Ontology, Sequence Ontology, Protein Ontology, NCBI Organism Taxonomy, Human Disease Ontology, Foundational Model of Anatomy, and so forth.oboSCR_010387(Ontology for MicroRNA Target Prediction, RRID:SCR_010387)listed by: BioPortalLast checked downnlx_157519
Portfolio Management ApplicationResource, ontology, data or information resource, controlled vocabularyOntology of a system for tracking grants and producing reports - Users can access grant data through a query interface and a variety of pre-defined forms and reports.owlSCR_010411(Portfolio Management Application, RRID:SCR_010411)listed by: BioPortalLast checked downnlx_157559
Semantic Web for Earth and Environment Technology OntologyResource, ontology, data or information resource, controlled vocabularyA mature foundational ontology developed at the NASA Jet Propulsion Laboratory, currently containing over 6000 concepts organized in 200 ontologies represented in OWL, whose top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research). SWEET is now officially under the governance of the ESIP foundation.owlSCR_010426(Semantic Web for Earth and Environment Technology Ontology, RRID:SCR_010426)listed by: BioPortalLast checked downnlx_157585
Taxonomic Rank VocabularyResource, ontology, data or information resource, controlled vocabularyA vocabulary of taxonomic ranks intended to replace the sets of rank terms found in the Teleost Taxonomy Ontology, the OBO translation of the NCBI taxonomy and similar OBO taxonomy ontologies. It provides terms for taxonomic ranks drawn from both the NCBI taxonomy database and from a rank vocabulary developed for the TDWG biodiversity information standards group. Cross references to appearances of each term in each source are provided. Consistent with its intended use as a vocabulary of labels, there is no relation specifying an ordering of the rank terms.oboSCR_010430(Taxonomic Rank Vocabulary, RRID:SCR_010430)listed by: BioPortalLast checked downnlx_157606
suicideoResource, ontology, data or information resource, controlled vocabularyOntology of suicidology.owlSCR_010451(suicideo, RRID:SCR_010451)listed by: BioPortalLast checked downnlx_157632
Regulation of Transcription OntologyResource, ontology, data or information resource, controlled vocabularyAn application ontology for the domain of gene transcription regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, KEGG and orthology relations.oboSCR_006238(Regulation of Transcription Ontology, RRID:SCR_006238)listed by: BioPortalLast checked downnlx_157573
Systematized Nomenclature of Medicine - Clinical TermsResource, ontology, data or information resource, controlled vocabularyOntology of SNOMED (Systematized Nomenclature of Medicine) clinical terms.umlsSCR_003915(Systematized Nomenclature of Medicine - Clinical Terms, RRID:SCR_003915)listed by: BioPortalLast checked downnlx_157603
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
Medical Diagnostic Categories - Diagnosis Related GroupsResource, ontology, data or information resource, controlled vocabularyOntology of Medical Diagnostic Categories-Diagnosis Related GroupsowlSCR_003725(Medical Diagnostic Categories - Diagnosis Related Groups, RRID:SCR_003725)listed by: BioPortalLast checked downnlx_157470
Mosquito Gross Anatomy OntologyResource, ontology, data or information resource, controlled vocabularyA structured controlled vocabulary of the anatomy of mosquitoes.oboSCR_003839(Mosquito Gross Anatomy Ontology, RRID:SCR_003839)listed by: BioPortalLast checked downnlx_157485
NHS Quality IndicatorsResource, ontology, data or information resource, controlled vocabularyOntology to organise a 2009 set of over 200 NHS quality indicators from different sources. Relationships between indicators, a basic set of inclusion / exclusion criteria, clinical pathway, clinical code and purpose (per 1992 Institute of Medicine, originally intended to categorise clinical guidelines) are identifies and made searchable.protegeSCR_004005(NHS Quality Indicators, RRID:SCR_004005)listed by: BioPortalLast checked downnlx_157491
PATOResource, ontology, data or information resource, controlled vocabularyOntology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation. The new PATO differs from the old in that the system of attributes and values has been abandoned in favor of a single hierarchy of qualities. PATO is designed to be used in conjunction with ontologies of quality-bearing entities. An example of such an entity is an insect eye (taken from the fly_anatomy ontology), which could be the bearer of the quality ''red'' (PATO:0000322). This combination is the red eye phenotype. We say that the phenotype term is ''post-coordinated'', as it is formed by coordinating two terms together. This is in contrast to ontologies of pre-coordinated phenotypes, such as the Mammalian Phenotype (MP) ontology. PATO is independent of any exchange format or database schema. One way of expressing phenotype annotation using PATO is pheno-syntax, or pheno-xml. They will also post recommendations for representing phenotypes using OWL. All representations share the same basic formal underpinnings, a combination of quality-bearing entity and a quality (the EQ model).plant trait, mammalian, phenotype, obo, quality, phenotypic qualitySCR_004782(PATO, RRID:SCR_004782)OBO used by: Morpholino Database, listed by: BioPortalLast checked downnlx_77534http://obofoundry.org/wiki/index.php/PATO:Main_Page
BFOResource, ontology, data or information resource, controlled vocabularyA small, upper level ontology that is designed for use in supporting information retrieval, analysis and integration in scientific and other domains. BFO is a genuine upper integration in scientific and other domains. Thus it does not contain physical, chemical, biological or other terms which would properly fall within the coverage domains of the special sciences.owl, gold standardSCR_004818(BFO, RRID:SCR_004818)IFOMIS Volkswagen Foundationused by: Beta Cell Genomics Ontology, listed by: BioPortalLast checked downnlx_80606http://bioportal.bioontology.org/ontologies/BFO
PhenomeBLAST OntologyResource, ontology, data or information resource, controlled vocabularyA cross-species phenotype and anatomy ontology resulting from combining available anatomy and phenotype ontologies and their definitions. The ontology includes phenotype definitions for yeast, mouse, fish, worm, fly and human phenotypes and diseases.owlSCR_005139(PhenomeBLAST Ontology, RRID:SCR_005139)listed by: BioPortalLast checked downnlx_157549
Nursing Interventions ClassificationResource, ontology, data or information resource, controlled vocabularyOntology of nursing interventions classification.umlsSCR_000911(Nursing Interventions Classification, RRID:SCR_000911)listed by: BioPortalLast checked downnlx_157512
Regulation of Gene Expression OntolologyResource, ontology, data or information resource, controlled vocabularyAn application ontology for the domain of gene expression regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, KEGG and orthology relations.oboSCR_006124(Regulation of Gene Expression Ontolology, RRID:SCR_006124)listed by: BioPortalLast checked downnlx_157572
Brucellosis OntologyResource, ontology, data or information resource, controlled vocabularyA biomedical ontology in the domain of zoonotic disease brucellosis that is caused by Brucella, a facultative intracellular baterium.owlSCR_006795(Brucellosis Ontology, RRID:SCR_006795)Zoonotic disease brucellosislisted by: BioPortalLast checked downnlx_157345http://www.phidias.us/bbp/idobru/index.php
C. elegans Development VocabularyResource, ontology, data or information resource, controlled vocabularyA structured controlled vocabulary of the development of Caenorhabditis elegans.oboSCR_006811(C. elegans Development Vocabulary, RRID:SCR_006811)WormBase listed by: BioPortalLast checked downnlx_157346
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 Spanish.adult, 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
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-0000-00199http://xwiki.nbirn.net:8080/xwiki/bin/view/%20BIRN-OTF-Public/
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