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http://edamontology.org/

An 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.

Proper citation: EDAM Ontology (RRID:SCR_006620) Copy   

•   Source: SciCrunch Registry

http://www.nlm.nih.gov/research/umls/rxnorm/

Ontology 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 recording

Proper citation: RxNorm (RRID:SCR_006645) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/RPO

A controlled vocabulary of ontology class structures and entities of observed phenotypic terms for primary immunodeficiency diseases (PIDs) that facilitate global sharing and free exchange of PID data with users'' communities

Proper citation: Resource of Asian Primary Immunodeficiency Diseases Phenotype Ontology (RRID:SCR_006776) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/WB-LS

A structured controlled vocabulary of the development of Caenorhabditis elegans.

Proper citation: C. elegans Development Vocabulary (RRID:SCR_006811) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/MCBCC

Ontology covering a comprehensive list of cell lines derived from breast tissue, both normal and pathological. The ontology in built in OWL with cross relation to classes- genetic variation, pathological condition, genes, chemicals and drugs. The relations built enable semantic query across different classes

Proper citation: Breast Tissue Cell Lines Ontology (RRID:SCR_006686) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/WB-BT

A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.

Proper citation: C. elegans Gross Anatomy Vocabulary (RRID:SCR_006835) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/IDOBRU

A biomedical ontology in the domain of zoonotic disease brucellosis that is caused by Brucella, a facultative intracellular baterium.

Proper citation: Brucellosis Ontology (RRID:SCR_006795) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/EP

Ontology that contains terms describing single-channel electrophysiological experiments and data obtained using voltage-clamp, current clamp and fluorescence imaging techniques applied at the cell level and multi-channel fluorescence imaging techniques applied at the cell, tissue and whole heart levels.

Proper citation: Cardiac Electrophysiology Ontology (RRID:SCR_007065) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/GRO-CPGA

A structured controlled vocabulary for the anatomy of Gramineae. Please note that this ontology has now been superseded by the Plant Ontology, http://bioportal.bioontology.org/ontologies/1587.

Proper citation: Cereal Plant Gross Anatomy Ontology (RRID:SCR_007061) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/WB-PHENOTYPE

A structured controlled vocabulary of Caenorhabditis elegans phenotypes.

Proper citation: C. elegans Phenotype Vocabulary (RRID:SCR_006924) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/CCON

Ontology of Cerrado wood plant dynamics to represent the set of concepts about the dynamics, that is, changes over time of the wood vegetation structure, of Cerrado. Ccon describes the main parameters used to measure the changes, such as mortality rate and recruitment rate.

Proper citation: Cerrado concepts and plant community dynamics (RRID:SCR_007174) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/CNO

A controlled vocabulary of terms used in Computational Neurosciences to describe models of the nervous system. This first release of CNO is an alpha version and should be further aligned with other ontologies accessible on Bioportal and should be made compliant with the OBO foundry recommendations.

Proper citation: Computational Neuroscience Ontology (RRID:SCR_007289) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/CCONT

ontology for the formal representation of cell lines and their correspnding culture conditions.

Proper citation: Cell Culture Ontology (RRID:SCR_007096) Copy   

•   Source: SciCrunch Registry

http://bioportal.bioontology.org/annotator

A Web service that annotates textual metadata (e.g. journal abstract) with relevant ontology concepts. NCBO uses this Web service to annotate resources in the NCBO Resource Index. They also provide this Web service as a stand-alone service for users. This Web service can be accessed through BioPortal or used directly in your software. Currently, the annotation workflow is based on syntactic concept recognition (using concept names and synonyms) and on a set of semantic expansion algorithms that leverage the semantics in ontologies (e.g., is_a relations). Their service methodology leverages ontologies to create annotations of raw text and returns them using semantic web standards.

Proper citation: NCBO Annotator (RRID:SCR_005329) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/CABRO

A web ontology for the semantic representation of the computer assisted brain trauma rehabilitation domain. This is a novel and emerging domain, since it employs the use of robotic devices, adaptation software and machine learning to facilitate interactive, adaptive and personalized rehabilitation care, patient monitoring and assisted living.

Proper citation: Computer Assisted Brain Injury Rehabilitation Ontology (RRID:SCR_005288) Copy   

•   Source: SciCrunch Registry

http://bmir.stanford.edu/

Mark Musen''s laboratory studies components for building knowledge-based systems, controlled terminologies and ontologies, and technology for the Semantic Web. For more than two decades, Musen''s group has worked to elucidate reusable building blocks of intelligent systems, and to develop scalable computational architectures for systems with significant applications in biomedicine. Informatics is the study of information: its structure, its communication, and its use. As society becomes increasingly information intensive, the need to understand, create, and apply new methods for modeling, managing, and acquiring information has never been greater especially in biomedicine. BMIR is home to world class scientists and trainees developing cutting-edge ways to acquire, represent, process, and manage knowledge and data related to health, health care, and the biomedical sciences. Our faculty, students, and staff are committed to ensuring the biomedical community is properly equipped for the information age, and believe our efforts will provide the structure for the burgeoning revolution of health care and the biomedical sciences.

Proper citation: Stanford Center for Biomedical Informatics Research (RRID:SCR_005698) Copy   

•   Source: SciCrunch Registry

http://www.clo-ontology.org/

A community-driven ontology that is developed to standardize and integrate cell line information and support computer-assisted reasoning. Its focus is on permanent cell lines from culture collections. Upper ontology structures that frame the skeleton of CLO include Basic Formal Ontology and Relation Ontology. Cell lines contained in CLO are associated with terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology for Biomedical Investigation. A common design pattern for the cell line is used to model cell lines and their attributes, the Jurkat cell line provides ane xample. Currently CLO contains over 36,000 cell line entries obtained from ATCC, HyperCLDB, Coriell, and bymanual curation. The cell lines are derived from 194 cell types, 656 anatomical entries, and 217 organisms. The OWL-based CLO is machine-readable and can be used in various applications. The CLO development has become a community effort with international collaborations. The development consortium includes experts from all over the world: the USA, Europe, and Japan.

Proper citation: Cell Line Ontology (RRID:SCR_005840) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/RCD

Ontology of clinical terms Version 3 (CTV3) (Read Codes) (Q199): National Health Service National Coding and Classification Centre

Proper citation: Read Codes Clinical Terms Version 3 (RRID:SCR_006055) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/RCTONT

Ontology specifically for Randomized Controlled Trials in order to facilitate the production of systematic reviews and metaanalysis.

Proper citation: Randomized Controlled Trials Ontology (RRID:SCR_005992) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/RETO

An 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.

Proper citation: Regulation of Transcription Ontology (RRID:SCR_006238) Copy   

•   Source: SciCrunch Registry