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

Ontology for representing events, time, and their relationships.

Proper citation: Time Event Ontology (RRID:SCR_000310) Copy   

•   Source: SciCrunch Registry

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

An ontology for standardized, systematic description of effects, consequences and mechanisms of variations.

Proper citation: Variation Ontology (RRID:SCR_000311) Copy   

•   Source: SciCrunch Registry

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

An ontology for DICOM as used in the SeDI project.

Proper citation: Semantic DICOM Ontology (RRID:SCR_000309) Copy   

•   Source: SciCrunch Registry

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

Comprehensive hierarchical controlled vocabulary for human disease representation.Open source ontology for integration of biomedical data associated with human disease. Disease Ontology database represents comprehensive knowledge base of inherited, developmental and acquired human diseases.

Proper citation: Human Disease Ontology (RRID:SCR_000476) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Description not available.

Proper citation: Gazetteer (RRID:SCR_000473) Copy   

•   Source: SciCrunch Registry

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

Ontology for Phylogenetic Analysis

Proper citation: Phylogenetic Ontology (RRID:SCR_000912) Copy   

•   Source: SciCrunch Registry

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

An application ontology devoted to the standardized recording of phenotypic data related to hemorrhagic disorders.

Proper citation: Bleeding History Phenotype Ontology (RRID:SCR_001165) Copy   

•   Source: SciCrunch Registry

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

A taxonomy of Amphibia

Proper citation: Amphibian Taxonomy Ontology (RRID:SCR_000906) Copy   

•   Source: SciCrunch Registry

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

A comprehensive lexicon - a unified language of anatomic pathology terms - for standardized indexing and retrieval of anatomic pathology information resources.

Proper citation: Anatomic Pathology Lexicon (RRID:SCR_000907) Copy   

•   Source: SciCrunch Registry

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

Ontology that encompasses all knowledge about HIV

Proper citation: HIV ontology (RRID:SCR_000908) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/ICD11-BODYSYSTEM

Ontology of a set of body-system terms used in the ICD (International Classification of Diseases) 11 revision

Proper citation: Body System Terms from ICD11 (RRID:SCR_001252) Copy   

•   Source: SciCrunch Registry

https://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology

A multi-species anatomy ontology for teleost fishes. It was originally seeded from ZFA, but covers terms relevant to other taxa. The TAO uses terms from the Common Anatomy Reference Ontology (CARO) as a template for its upper level nodes, and the Vertebrate Skeletal Anatomy Ontology (VSAO) for general skeletal anatomy classes. Growth of the TAO is enabled by contributions from data curators and the ichthyological community. The TAO can be browsed by using the NCBO BioPortal and data annotated using TAO terms can be queried using the Phenoscape Knowedgebase.

Proper citation: Teleost Anatomy Ontology (RRID:SCR_001610) Copy   

•   Source: SciCrunch Registry

http://www.biopax.org/

Community standard for pathway data sharing. Standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Supports data exchange between pathway data groups and thus reduces complexity of interchange between data formats by providing accepted standard format for pathway data. Open and collaborative effort by community of researchers, software developers, and institutions. BioPAX is defined in OWL DL and is represented in RDF/XML format.Uses W3C standard Web Ontology Language, OWL.

Proper citation: Biological Pathways Exchange (RRID:SCR_001681) 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/LIPRO

An ontology that describes the LIPIDMAPS nomenclature classification explicitly using description logics (OWL-DL). Lipid classes are organized hierarchically with the super-classes restricted by generic necessary conditions. More specific necessary conditions are used to define membership requirements for sub classes of lipid according to appropriate functional groups. Lipid research is increasingly integrated within systems level biology such as lipidomics where lipid classification is required before appropriate annotation of chemical functions can be applied.

Proper citation: Lipid Ontology (RRID:SCR_003349) Copy   

•   Source: SciCrunch Registry

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

A structured controlled vocabulary for the phenotypes of Ascomycete fungi.

Proper citation: Ascomycete Phenotype Ontology (RRID:SCR_003254) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/bcgo-ontology/

An application ontology built for the Beta Cell Genomics database aiming to support database annotation, complicated semantic queries, and automated cell type classification. The ontology is developed using Basic Formal Ontology (BFO) as upper ontology, Ontology for Biomedical Investigations (OBI) as ontology framework and integrated subsets of multiple OBO Foundry (candidate) ontologies. Current the BCGO contains 2383 classes including terms referencing to 24 various OBO Foundry ontologies including CL, CLO, UBERON, GO, PRO, UO, etc.

Proper citation: Beta Cell Genomics Ontology (RRID:SCR_003259) Copy   

•   Source: SciCrunch Registry

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

A structured controlled vocabulary of the anatomy of the slime-mould Dictyostelium discoideum.

Proper citation: Dictyostelium Discoideum Anatomy Ontology (RRID:SCR_003309) Copy   

•   Source: SciCrunch Registry

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

Ontology developed as an application ontology as part of the Biocode Commons project whose goal is to support the interoperability of biodiversity data, including data on museum collections, environmental and metagenomic samples, and ecological surveys. It includes consideration of the distinctions between individuals, organisms, voucher specimens, lots, and samples the relations between these entities, and processes governing the creation and use of samples. Within scope as well are properties including collector, location, time, storage environment, containers, institution, and collection identifiers.

Proper citation: Biological Collections Ontology (RRID:SCR_003262) Copy   

•   Source: SciCrunch Registry