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http://archive.gramene.org/plant_ontology/ontology_browse.html#eo

A structured controlled vocabulary for the representation of plant environmental conditions.

Proper citation: Plant Environmental Conditions (RRID:SCR_003460) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/pharmgkb-owl/

An OWL representation of the data in PharmGKB, Comparative Toxicogenomics Database (CTD) and DrugBank and linked to related ontologies: ChEBI ontology, the Human Disease Ontology (DO), the Anatomical Therapeutic Chemical Classification System (ATC) and the Medical Subject Headings Thesaurus (MESH). The combined knowledge base can be exploited using the ELK reasoner.

Proper citation: PharmGKB Ontology (RRID:SCR_003529) Copy   

•   Source: SciCrunch Registry

http://www.oae-ontology.org

Biomedical ontology in the domain of adverse events that aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. AEO is a community-based ontology. Its development follows the OBO Foundry principles.

Proper citation: Ontology of Adverse Events (RRID:SCR_003428) Copy   

•   Source: SciCrunch Registry

http://rgd.mcw.edu/tools/ontology/ont_search.cgi

Ontology that defines hierarchical display of different rat strains as derived from parental strains. Ontology Browser allows to retrieve all genes, QTLs, strains and homologs annotated to particular term. Covers all types of biological pathways including altered and disease pathways, and to capture relationships between them within hierarchical structure. Five nodes of ontology include classic metabolic, regulatory, signaling, drug and disease pathways. Ontology allows for standardized annotation of rat. Serves as vehicle to connect between genes and ontology reports, between reports and interactive pathway diagrams, between pathways that directly connect to one another within diagram or between pathways that in some fashion are globally related in pathway suites and suite networks.

Proper citation: Rat Strain Ontology (RRID:SCR_003449) Copy   

•   Source: SciCrunch Registry

http://www.violinet.org/ovae/

A biomedical ontology in the area of vaccine adverse events aimed to represent and analyze various vaccine-specific adverse events. OVAE is an extension of the Ontology of Adverse Events (OAE) and the Vaccine Ontology (VO).

Proper citation: Ontology of Vaccine Adverse Events (RRID:SCR_003442) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/omrse/

An ontology covering the domain of social entities that are related to health care, such as demographic information (social entities for recording gender (but not sex) and marital status, for example) and the roles of various individuals and organizations (patient, hospital, etc.)

Proper citation: Ontology of Medically Related Social Entities (RRID:SCR_003439) Copy   

•   Source: SciCrunch Registry

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

Ontology of Medical Dictionary for Regulatory Activities Terminology (MedDRA)

Proper citation: Medical Dictionary for Regulatory Activities (RRID:SCR_003751) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/efo/

An 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.

Proper citation: Experimental Factor Ontology (RRID:SCR_003574) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/adverse-event-reporting-ontology/

An ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events.

Proper citation: Adverse Event Reporting Ontology (RRID:SCR_003571) Copy   

•   Source: SciCrunch Registry

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

Ontology of Medical Diagnostic Categories-Diagnosis Related Groups

Proper citation: Medical Diagnostic Categories - Diagnosis Related Groups (RRID:SCR_003725) Copy   

•   Source: SciCrunch Registry

http://ncit.nci.nih.gov/

A reference terminology and core biomedical ontology for NCI that covers approximately 100,000 key biomedical concepts with terms, codes, definitions, and more than 200,000 inter-concept relationships. It is the reference terminology for NCI, NCI Metathesaurus and NCI informatics infrastructure covering vocabulary for clinical care, translational and basic research, and public information and administrative activities. It includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities; anatomy; agents, drugs and chemicals; genes and gene products and so on. In certain areas, like cancer diseases and combination chemotherapies, it provides the most granular and consistent terminology available. It combines terminology from numerous cancer research related domains, and provides a way to integrate or link these kinds of information together through semantic relationships. NCIt features: * Stable, unique codes for biomedical concepts; * Preferred terms, synonyms, definitions, research codes, external source codes, and other information; * Links to NCI Metathesaurus and other information sources; * Over 200,000 cross-links between concepts, providing formal logic-based definition of many concepts; * Extensive content integrated from NCI and other partners, much available as separate NCIt subsets * Updated frequently by a team of subject matter experts. NCIt is a widely recognized standard for biomedical coding and reference, used by a broad variety of public and private partners both nationally and internationally including the Clinical Data Interchange Standards Consortium Terminology (CDISC), the U.S. Food and Drug Administration (FDA), the Federal Medication Terminologies (FMT), and the National Council for Prescription Drug Programs (NCPDP).

Proper citation: NCI Thesaurus (RRID:SCR_003563) Copy   

•   Source: SciCrunch Registry

http://bioassayontology.org/

Ontology 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.

Proper citation: Bioassay Ontology (RRID:SCR_002638) Copy   

•   Source: SciCrunch Registry

http://www.geneontology.org/

Computable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases.

Proper citation: Gene Ontology (RRID:SCR_002811) Copy   

•   Source: SciCrunch Registry

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

An ontology to describe the entities and relationships in the SEEK database, a Systems Biology environment for the sharing and exchange of data and models. The SysMO-SEEK database contains the work of the SysMO consortium (Systems Biology of Micro-Organisms) https://seek.sysmo-db.org/

Proper citation: SysMO JERM Ontology of Systems Biology for Micro-Organisms (RRID:SCR_004569) Copy   

•   Source: SciCrunch Registry

http://www.proconsortium.org/pro/

An ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. The ontology has a meta-structure encompassing three areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp). NOTICE: The PRO ID format has changed from PRO: to PR: (e.g. PRO:000000563 is now PR:000000563).

Proper citation: PR (RRID:SCR_004964) Copy   

•   Source: SciCrunch Registry

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

A structured controlled vocabulary for describing cereal plant development and growth stages. Please note that this ontology has now been superseded by the Plant Ontology.

Proper citation: Cereal Plant Development Ontology (RRID:SCR_005095) Copy   

•   Source: SciCrunch Registry

http://omim.org

Online catalog of human genes and genetic disorders, for clinical features, phenotypes and genes. Collection of human genes and genetic phenotypes, focusing on relationship between phenotype and genotype. Referenced overviews in OMIM contain information on all known mendelian disorders and variety of related genes. It is updated daily, and entries contain copious links to other genetics resources.

Proper citation: OMIM (RRID:SCR_006437) Copy   

•   Source: SciCrunch Registry

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://purl.bioontology.org/ontology/BDO

Ontology that provides a comprehensive and formal representation of the different domain concepts involved in documenting the full complexity of the skeletal dysplasia domain. It captures and combines the genetic features that discriminate the bone dysplasias with the multitude of phenotypic characteristics manifested by patients and required to be taken into account in order to support the diagnosis process.

Proper citation: Bone Dysplasia Ontology (RRID:SCR_006588) 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