List of all ontologies in OLS

Ontology Name Short name Description Loaded Action
Anatomical Entity Ontology AEO AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology Fri Jul 15 21:27:33 BST 2016 Search
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Adverse Event Reporting Ontology AERO The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events Mon Jun 26 01:22:18 BST 2017 Search
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Agronomy Ontology AGRO Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments Wed Jul 27 06:51:47 BST 2016 Search
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Ancestry Ontology ancestro The Ancestry Ontology (Ancestro) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies. It includes a list of countries, regions and major areas (essentially continents), as well as a fairly exhaustive list of country- or region-specific ancestral groups, uncategorised ancestral groups and population isolates. Mon May 22 01:24:47 BST 2017 Search
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Ascomycete phenotype ontology APO A structured controlled vocabulary for the phenotypes of Ascomycete fungi Mon Jul 24 01:22:08 BST 2017 Search
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Animal Trait Ontology for Livestock ATOL ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production. Tue Nov 01 14:44:05 GMT 2016 Search
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BioAssay Ontology BAO The BioAssay Ontology (BAO) describes biological 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. Fri May 26 01:18:56 BST 2017 Search
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Beta Cell Genomics Ontology BCGO An application ontology built for beta cell genomics studies. Mon Jun 26 01:42:21 BST 2017 Search
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Biological Collections Ontology BCO An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. Mon Jun 26 01:52:58 BST 2017 Search
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Basic Formal Ontology BFO The upper level ontology upon which OBO Foundry ontologies are built. Wed Mar 23 13:35:08 GMT 2016 Search
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Biological Spatial Ontology BSPO An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces Mon Jun 26 02:03:16 BST 2017 Search
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BRENDA tissue / enzyme source BTO A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures. Tue Oct 18 01:20:00 BST 2016 Search
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Common Anatomy Reference Ontology CARO An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species Mon Dec 05 01:16:32 GMT 2016 Search
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Cell Cycle Ontology CCO The Cell Cycle Ontology extends existing ontologies for cell cycle knowledge building a resource that integrates and manages knowledge about the cell cycle components and regulatory aspects. Wed Mar 23 13:43:08 GMT 2016 Search
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Comparative Data Analysis Ontology CDAO The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character. Mon Jun 05 01:52:11 BST 2017 Search
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Cephalopod Ontology CEPH An anatomical and developmental ontology for cephalopods Mon Dec 05 01:23:31 GMT 2016 Search
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Chemical Entities of Biological Interest CHEBI A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds. Tue Jul 04 02:25:40 BST 2017 Search
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chemical information ontology (cheminf) - information entities about chemical entities CHEMINF Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. Fri Feb 10 01:12:42 GMT 2017 Search
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Chemical Methods Ontology CHMO CHMO, the chemical methods ontology, describes methods used to Wed Aug 17 01:32:43 BST 2016 Search
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Confidence Information Ontology CIO An ontology to capture confidence information about annotations. Wed Jun 01 01:31:57 BST 2016 Search
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Cell Ontology CL The Cell Ontology is a structured controlled vocabulary for cell types in animals. Mon Apr 17 01:21:21 BST 2017 Search
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CLO: Cell Line Ontology CLO The Cell Line Ontology. Thu Jun 01 01:23:31 BST 2017 Search
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Clinical measurement ontology CMO Morphological and physiological measurement records generated from clinical and model organism research and health programs. Mon Jul 24 01:33:20 BST 2017 Search
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Cellular Microscopy Phenotype Ontology CMPO CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. Wed Jul 05 11:59:32 BST 2017 Search
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Rice ontology CO_320 Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables Mon Jul 17 01:47:27 BST 2017 Search
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Wheat ontology CO_321 Wheat Trait Dictionary in template v5 - CIMMYT - Nov 2016 Mon Jul 17 01:57:22 BST 2017 Search
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Maize ontology CO_322 Maize Trait Dictionary in template 5 - CIMMYT- September 2016 Mon Jul 24 01:43:16 BST 2017 Search
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Barley Trait Dictionary ontology CO_323 ICARDA - Beta Trait Dictionary v 4 Tue Jul 18 01:31:58 BST 2017 Search
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Sorghum ontology CO_324 Sorghum TDv5 - Oct 2016 Wed Jun 07 02:48:53 BST 2017 Search
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Banana ontology CO_325 Banana Trait Dictionary in template 5 - Bioversity & IITA - December 2016 - characterization and breeding variables Wed Jun 07 02:59:14 BST 2017 Search
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Pearl millet ontology CO_327 Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016 Wed Jun 07 03:09:11 BST 2017 Search
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Potato ontology CO_330 CIP - Potato ontology- TD v4 Wed Jun 07 03:18:57 BST 2017 Search
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Sweet Potato ontology CO_331 Sweet Potato Trait Dictionary in template v5 - CIP - June 2016 Wed Jun 07 03:28:34 BST 2017 Search
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Cassava ontology CO_334 Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016 Mon Jul 24 01:53:12 BST 2017 Search
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Common bean ontology CO_335 CIAT Common bean trait dictionary - version August 2014 Mon Jul 24 02:03:37 BST 2017 Search
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Soybean ontology CO_336 Soybean Trait Dictionary in template v5 - IITA - July 2015 Search
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Groundnut ontology CO_337 Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015 Mon Jul 17 02:27:50 BST 2017 Search
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Chickpea ontology CO_338 Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015 Mon Jul 17 02:37:57 BST 2017 Search
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Lentil ontology CO_339 Lentil Trait Dictionary in template v5 - ICARDA - July 2015 Tue Jul 04 02:35:40 BST 2017 Search
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Cowpea ontology CO_340 Cowpea Trait Dictionary in template v5 - IITA - August 2015 Tue Jul 04 02:45:33 BST 2017 Search
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Pigeonpea ontology CO_341 Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015 Tue Jul 04 02:55:20 BST 2017 Search
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Yam ontology CO_343 IITA - Yam trait ontology -TD v. 5.0- Feb 2017 Mon Jul 24 02:13:57 BST 2017 Search
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Brachiaria ontology CO_345 Brachiaria (forages) ontology TD v5 - Version Oct 2016 Tue Jun 13 04:25:42 BST 2017 Search
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Mungbean ontology CO_346 oct 2016 Tue Jun 27 02:53:08 BST 2017 Search
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Castor bean ontology CO_347 March 2017 version Tue Jun 27 03:02:50 BST 2017 Search
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Oat ontology CO_350 Oat trait dictionary commissioned by Oat Global (http://oatglobal.org/) to hold the traits used in the T3/Oat database (http://triticeaetoolbox.org/oat/). Mon Jul 24 02:23:41 BST 2017 Search
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Vitis ontology CO_356 Grape Ontology including OIV and bioversity descriptors. INRA July 2017 Mon Jul 24 02:33:55 BST 2017 Search
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Ctenophore Ontology CTENO An anatomical and developmental ontology for ctenophores (Comb Jellies) Thu Oct 20 01:20:09 BST 2016 Search
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Cardiovascular Disease Ontology CVDO An ontology to describe entities related to cardiovascular diseases Wed Sep 14 01:17:08 BST 2016 Search
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Dictyostelium discoideum anatomy DDANAT A structured controlled vocabulary of the anatomy of the slime-mould <i>Dictyostelium discoideum</i>. Mon Jul 24 02:43:46 BST 2017 Search
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Dictyostelium discoideum phenotype DDPHENO A structured controlled vocabulary of phenotypes of the slime-mould <i>Dictyostelium discoideum</i>. Mon Jul 24 02:54:14 BST 2017 Search
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Drug Interaction and Evidence Ontology DIDEO The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology Mon Jun 12 01:46:08 BST 2017 Search
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The Drug-Drug Interactions Ontology DINTO A formal represention for drug-drug interactions knowledge. Search
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Human Disease Ontology DOID An ontology for describing the classification of human diseases organized by etiology. Mon Jul 17 03:20:41 BST 2017 Search
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Drosophila Phenotype Ontology FBcv An ontology of commonly encountered and/or high level Drosophila phenotypes. Mon Oct 31 15:28:47 GMT 2016 Search
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The Drug Ontology DRON An ontology to support comparative effectiveness researchers studying claims data. Fri Dec 16 15:18:55 GMT 2016 Search
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The Data Use Ontology DUO DUO is an ontology which represent data use conditions. Mon Feb 20 03:08:54 GMT 2017 Search
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Evidence ontology ECO An ontology for experimental and other evidence statements. Thu Jul 20 01:34:45 BST 2017 Search
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Bioinformatics operations, data types, formats, identifiers and topics EDAM EDAM is a simple ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM provides a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use. Fri Jul 07 01:33:59 BST 2017 Search
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Experimental Factor Ontology EFO The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for external projects such as the NHGRI GWAS catalogue. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by many groups at the EBI and as the core ontology for OpenTargets.org Fri Jul 21 01:51:30 BST 2017 Search
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Human developmental anatomy, abstract EHDAA2 A structured controlled vocabulary of stage-specific anatomical structures of the developing human. Mon Nov 14 01:36:11 GMT 2016 Search
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Mouse gross anatomy and development, timed EMAP A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus). Mon Jul 24 03:05:40 BST 2017 Search
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Mouse gross anatomy and development, timed EMAPA Abstract (i.e. non-stage specific) stage-specific anatomical structures of the mouse. Mon Jul 24 03:15:50 BST 2017 Search
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eNanoMapper Ontology ENM The eNanoMapper project (www.enanomapper.net) is creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. > This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO. Tue Jan 24 01:23:11 GMT 2017 Search
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Environment Ontology ENVO Ontology of environmental features and habitats Tue Jun 27 03:44:23 BST 2017 Search
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Plant Environment Ontology EO A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments. Wed Jun 07 06:22:50 BST 2017 Search
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Environment Ontology for Livestock EOL L'ontologie EOL décrit les conditions d'environnement des élevages d'animaux domestiques. Elle décrit plus particulièrement les modalités de l'alimentation, de l'environnement, de la structure des élevages et des systèmes d'élevage Tue Nov 01 14:50:32 GMT 2016 Search
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Epidemiology Ontology EPO An ontology designed to support the semantic annotation of epidemiology resources Wed Mar 23 14:27:13 GMT 2016 Search
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eagle-i resource ontology ERO An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens. Wed Jul 27 07:04:31 BST 2016 Search
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Exposure ontology EXO Vocabularies for describing exposure data to inform understanding of environmental health. Mon Nov 07 01:48:42 GMT 2016 Search
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Fungal gross anatomy FAO A structured controlled vocabulary for the anatomy of fungi. Wed Sep 14 16:05:43 BST 2016 Search
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Biological imaging methods FBbi A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. Mon Jul 24 03:26:13 BST 2017 Search
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Drosophila gross anatomy FBbt An ontology representing the gross anatomy of Drosophila melanogaster. Thu May 04 01:48:11 BST 2017 Search
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FlyBase Controlled Vocabulary FBcv A structured controlled vocabulary used for various aspects of annotation by FlyBase. Thu Jul 06 01:57:01 BST 2017 Search
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Drosophila development FBdv A structured controlled vocabulary of the development of Drosophila melanogaster. Mon Oct 17 02:16:09 BST 2016 Search
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Physico-chemical methods and properties FIX An ontology of physico-chemical methods and properties. Mon Nov 14 01:50:01 GMT 2016 Search
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Flora Phenotype Ontology FLOPO Traits and phenotypes of flowering plants occurring in digitized Floras Mon May 16 05:11:19 BST 2016 Search
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Influenza ontology FLU The influenza ontology is an application ontology that covers the natural, experimental and clinical realms related to influenza virus life cycle, infection and disease. It is an extension of the infectious disease ontology (IDO). Tue Feb 21 01:49:17 GMT 2017 Search
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Foundational Model of Anatomy (subset) FMA This is currently a slimmed down version of FMA Mon Jul 24 03:40:52 BST 2017 Search
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FOODON FOODON A broadly scoped ontology representing entities which bear a “food role”. It encompasses materials in natural ecosystems and food webs as well as human-centric categorization and handling of food. Fri Jun 16 02:16:40 BST 2017 Search
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Fission Yeast Phenotype Ontology FYPO FYPO is a formal ontology of phenotypes observed in fission yeast. Mon Jul 24 03:51:34 BST 2017 Search
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Gazetteer GAZ A gazetteer constructed on ontological principles Wed Mar 23 14:57:07 GMT 2016 Search
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Genomic Epidemiology Ontology GENEPIO The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks. Mon Apr 10 02:35:33 BST 2017 Search
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Genotype Ontology GENO An integrated ontology for representing the genetic variations described in genotypes, and their causal relationships to phenotype and diseases. Fri Jun 16 02:25:42 BST 2017 Search
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Geographical Entity Ontology GEO An ontology of geographical entities Wed Sep 14 16:17:48 BST 2016 Search
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Gene Expression Ontology GeXO Gene Expression Ontology Thu Apr 20 01:35:44 BST 2017 Search
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Gene Ontology GO An ontology for describing the function of genes and gene products Mon Jul 24 04:06:15 BST 2017 Search
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Hymenoptera Anatomy Ontology HAO A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants) Thu May 19 12:32:47 BST 2016 Search
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Homology Ontology HOM This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology. Mon Nov 14 02:28:13 GMT 2016 Search
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human phenotype ontology HP A structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease. Mon Jul 03 18:37:59 BST 2017 Search
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Human Developmental Stages HSAPDV Life cycle stages for Human Mon Jul 24 04:15:56 BST 2017 Search
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Information Artifact Ontology IAO An ontology of information entities. Mon Mar 27 02:15:02 BST 2017 Search
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Informed Consent Ontology ICO The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field. Fri May 12 02:10:25 BST 2017 Search
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Infectious disease IDO Fri Jul 08 17:41:23 BST 2016 Search
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Malaria Ontology IDOMAL An application ontology to cover all aspects of malaria as well as the intervention attempts to control it. Mon Nov 14 02:41:04 GMT 2016 Search
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Kinetic Simulation Algorithm Ontology KISAO A classification of algorithms available for the simulation of models in biology. Wed Jul 19 02:56:04 BST 2017 Search
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Livestock Breed Ontology LBO A vocabulary for cattle, chicken, horse, pig, and sheep breeds. Tue Jul 18 02:20:06 BST 2017 Search
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Mouse adult gross anatomy MA A structured controlled vocabulary of the adult anatomy of the mouse (Mus). Wed Feb 08 02:04:29 GMT 2017 Search
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Mathematical Modelling Ontology MAMO The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. Tue Feb 21 02:33:19 GMT 2017 Search
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Mental Functioning Ontology MF Wed Mar 23 15:36:06 GMT 2016 Search
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Mammalian Feeding Muscle Ontology MFMO The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors. Wed Mar 23 15:38:20 GMT 2016 Search
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Emotion Ontology MFOEM An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings. Wed May 17 11:27:21 BST 2017 Search
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Molecular Interactions MI A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. Mon Jul 10 02:47:18 BST 2017 Search
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Minimum Information for A Phylogenetic Analysis (MIAPA) Ontology MIAPA The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies. This ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA. Tue May 09 01:35:20 BST 2017 Search
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microRNA Ontology MIRNAO An application ontology for use with miRNA databases. Wed Mar 23 15:47:05 GMT 2016 Search
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Mosquito insecticide resistance MIRO Application ontology for entities related to insecticide resistance in mosquitos Mon Nov 14 03:00:31 GMT 2016 Search
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Measurement method ontology MMO A representation of the variety of methods used to make clinical and phenotype measurements. Mon Mar 20 03:21:21 GMT 2017 Search
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Mouse Developmental Stages MMUSDV Life cycle stages for Mus Musculus Mon Jul 24 04:25:36 BST 2017 Search
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Protein modification MOD PSI-MOD is an ontology consisting of terms that describe protein chemical modifications Mon Jul 24 04:35:58 BST 2017 Search
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Monarch Disease Ontology MONDO a semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology Wed May 17 19:09:07 BST 2017 Search
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Molecular Process Ontology MOP Processes at the molecular level Wed Aug 17 02:18:57 BST 2016 Search
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The Mammalian Phenotype Ontology MP The Mammalian Phenotype Ontology is being developed by Cynthia L. Smith, Susan M. Bello, Carroll W. Goldsmith and Janan T. Eppig, as part of the Mouse Genome Database (MGD) Project, Mouse Genome Informatics (MGI), The Jackson Laboratory, Bar Harbor, ME. This file contains pre-coordinated phenotype terms, definitions and synonyms that can be used to describe mammalian phenotypes. The ontology is represented as a directed acyclic graph (DAG). It organizes phenotype terms into major biological system headers such as nervous system and respiratory system. This ontology is currently under development. Weekly updates are available at the Mouse Genome Informatics (MGI) ftp site (ftp://ftp.informatics.jax.org/pub/reports/index.html#pheno) as well as the OBO Foundry site (http://obofoundry.org/). Questions, comments and suggestions are welcome, and should be directed to pheno@jax.org, Susan.Bello@jax.org or to GitHub tracker (https://github.com/obophenotype/mammalian-phenotype-ontology/issues) MGD is funded by NIH/NHGRI grant HG000330. Fri Jul 14 02:42:02 BST 2017 Search
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Mouse pathology MPATH A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes Mon Jul 24 04:45:50 BST 2017 Search
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MHC Restriction Ontology MRO The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions. Fri Dec 16 03:04:56 GMT 2016 Search
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Mass spectrometry ontology MS A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry. Wed Jul 12 04:43:07 BST 2017 Search
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Neuro Behavior Ontology NBO Fri Mar 10 02:25:31 GMT 2017 Search
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NCBI organismal classification NCBITaxon An ontology representation of the NCBI organismal taxonomy Fri May 05 05:09:28 BST 2017 Search
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Non-Coding RNA Ontology NCRO An ontology for non-coding RNA, both of biological origin, and engineered. Wed Mar 23 17:07:15 GMT 2016 Search
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OAE: Ontology of Adverse Events OAE The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc. Mon May 08 03:19:32 BST 2017 Search
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Ontology of Arthropod Circulatory Systems OARCS OArCS is an ontology describing the Arthropod ciruclatory system. Wed Mar 08 03:09:22 GMT 2017 Search
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Ontology of Biological Attributes OBA A collection of biological attributes (traits) covering all kingdoms of life. Fri Mar 10 02:45:12 GMT 2017 Search
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Ontology of Biological and Clinical Statistics OBCS OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012. Tue May 02 02:07:54 BST 2017 Search
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Ontology for Biomedical Investigation OBI The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific. Wed Mar 22 02:56:59 GMT 2017 Search
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Ontology for BIoBanking (OBIB) OBIB An ontology built for annotation and modeling of biobank repository and biobanking administration Mon Jul 03 19:39:12 BST 2017 Search
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OGG: Ontology of Genes and Genomes OGG OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets. Mon Dec 05 02:44:27 GMT 2016 Search
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Ontology for genetic interval OGI OGI formalized the genomic element by defining an upper class 'genetic interval'. The definition of 'genetic interval' is "the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic Acid Base Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture." Related paper: 1. Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology” Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology) Yu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval(OGI) to Sequence Assembly – Ontology apply to next generation sequencing” Proceeding of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam, Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf) Yu Lin, Peter Simons (2010) “DNA sequence from below: A Nominalist Approach” Interdisciplinary Ontology Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF) Wed Mar 23 17:37:20 GMT 2016 Search
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Ontology for General Medical Science OGMS An ontology for representing treatment of disease and diagnosis and on carcinomas and other pathological entities Mon May 16 06:37:52 BST 2016 Search
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Ontology of Genetic Susceptibility Factors (OGSF) OGSF The Ontology of Genetic Susceptibility Factors (OGSF) is an ontology that represents various types of genetic susceptibility and genetic susceptibility factors and their relations with different diseases and pathological bodily processes (e.g., vaccine adverse events). Wed Mar 23 17:45:31 GMT 2016 Search
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The Oral Health and Disease Ontology OHD The Oral Health and Disease Ontology was created, initially, to represent the content of dental practice health records. Wed Jan 04 01:12:12 GMT 2017 Search
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OHMI: Ontology of Host-Microbiome Interactions OHMI OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions. Wed May 17 12:09:33 BST 2017 Search
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Medaka Developmental Stages OLATDV Life cycle stages for Medaka Mon Jul 24 04:55:24 BST 2017 Search
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Ontologized MIABIS OMIABIS An ontological version of MIABIS (Minimum Information About BIobank data Sharing) Mon May 23 07:23:55 BST 2016 Search
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Ontology for MIRNA Target OMIT Mon May 08 11:39:20 BST 2017 Search
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Ontology of Microbial Phenotypes OMP An ontology of phenotypes covering microbes Mon Jul 10 03:15:23 BST 2017 Search
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Ontology of Medically Related Social Entities OMRSE This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations. Fri Jun 09 02:59:55 BST 2017 Search
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Obstetric and Neonatal Ontology ONTONEO The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby. Mon Mar 06 03:16:12 GMT 2017 Search
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Ontology of Organizational Structures of Trauma centers and Trauma Systems OOSTT An ontology built for representating the organizational components of trauma centers and trauma systems. Thu Jul 13 03:12:57 BST 2017 Search
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Ontology for Parasite LifeCycle OPL A reference ontology for parasite life cycle stages. Wed Mar 23 18:09:15 GMT 2016 Search
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Orphanet Rare Disease Ontolog ORDO The Orphanet Rare Disease ontology (ORDO) is jointly developed by Orphanet and the EBI to provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It derived from the Orphanet database (www.orpha.net ) , a multilingual database dedicated to rare diseases populated from literature and validated by international experts. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA),databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) or classifications (ICD10). Thu Jul 06 02:56:07 BST 2017 Search
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OVAE: Ontology of Vaccine Adverse Events OVAE OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE). Mon Apr 25 02:43:14 BST 2016 Search
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Phenotypic quality PATO An ontology of phenotypic qualities (properties, attributes or characteristics) Tue Jul 11 02:21:43 BST 2017 Search
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Population and Community Ontology PCO A taxon-neutral ontology of material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. Thu Dec 15 03:21:59 GMT 2016 Search
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The Prescription of Drugs Ontology PDRO An ontology to describe entities related to prescription of drugs Mon Feb 20 05:01:43 GMT 2017 Search
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Platynereis Developmental Stages PDUMDV Life cycle stages for Platynereis dumerilii Mon Jul 24 05:05:09 BST 2017 Search
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planaria-ontology PLANA planaria-ontology is an ontology for planarian anatomy and developmental stages of S.med Wed Mar 22 03:03:50 GMT 2017 Search
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Plant Ontology PO The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. Fri Feb 03 02:33:59 GMT 2017 Search
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Porifera (sponge) ontology PORO An ontology describing the anatomical structures and characteristics of Porifera (sponges) Thu Sep 15 03:05:04 BST 2016 Search
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Plant Phenology Ontology PPO An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales. Mon Jul 24 05:14:40 BST 2017 Search
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PRotein Ontology (PRO) PR An ontological representation of protein-related entities Thu Apr 27 03:11:17 BST 2017 Search
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PRIDE Controlled Vocabulary PRIDE The PRIDE PRoteomics IDEntifications (PRIDE) database is a centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. Mon Dec 05 02:52:47 GMT 2016 Search
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Probability Distribution Ontology PROBONTO ProbOnto, is an ontology-based knowledge base of probability distributions, featuring more than eighty uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulas. Wed May 17 12:18:40 BST 2017 Search
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Pathway ontology PW A controlled vocabulary for annotating gene products to pathways. Mon Oct 24 02:03:43 BST 2016 Search
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Regulation of Transcription Ontology ReTO Regulation of Transcription Thu Jan 19 03:18:16 GMT 2017 Search
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Physico-chemical process REX An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. Mon Jul 24 05:24:18 BST 2017 Search
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Regulation of Gene Expression Ontology ReXO Regulation of Gene Expression Thu Jan 19 03:44:34 GMT 2017 Search
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The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data RNAO Tue Nov 08 03:21:05 GMT 2016 Search
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OBO Relations Ontology RO The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. Thu Jul 20 03:03:53 BST 2017 Search
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Rat Strain Ontology RS Ontology of rat strains Wed Jul 19 04:12:00 BST 2017 Search
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Name Reaction Ontology RXNO Connects organic name reactions to their roles in an organic synthesis and to processes in MOP Wed Aug 17 04:10:49 BST 2016 Search
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Systems Biology SBO Terms commonly used in Systems Biology, and in particular in computational modeling. Mon Jul 24 05:34:21 BST 2017 Search
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Sickle Cell Disease Ontology SCDO The Sickle Cell Disease Ontology (SCDO) project is a collaboration between H3ABioNet (Pan African Bioinformatics Network) and SPAN (Sickle Cell Disease Pan African Network). The SCDO is currently under development and its purpose is to 1) establish community standardized SCD terms and descriptions, 2) establish canonical and hierarchical representation of knowledge on SCD and 3) link to other ontologies and bodies of work such as DO, PhenX MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM. Fri Jul 07 02:35:53 BST 2017 Search
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Sample processing and separation techniques SEP A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments. Tue Nov 08 03:28:36 GMT 2016 Search
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Scientific Evidence and Provenance Information Ontology SEPIO An ontology for representing the provenance of scientific claims and the evidence that supports them. Search
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Social Insect Behavior Ontology SIBO Social Behavior in insects Wed Mar 23 20:03:52 GMT 2016 Search
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Semanticscience Integrated Ontology SIO The Semanticscience Integrated Ontology (SIO) provides a simple, integrated ontology of types and relations for rich description of objects, processes and their attributes. Mon Feb 13 03:06:12 GMT 2017 Search
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Sequence types and features SO A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases. Thu Jul 20 03:24:32 BST 2017 Search
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Spider Ontology SPD An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow). Wed Jan 25 02:46:47 GMT 2017 Search
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STATO: the statistical methods ontology STATO STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots. Wed Mar 23 20:17:03 GMT 2016 Search
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Bioinformatics operations, data types, formats, identifiers and topics SWO Mon Feb 13 03:14:15 GMT 2017 Search
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Symptom Ontology SYMP An ontology of disease symptoms, with symptoms encompasing perceived changes in function, sensations or appearance reported by a patient indicative of a disease. Wed May 03 02:25:52 BST 2017 Search
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Tick gross anatomy TADS The anatomy of the Tick, <i>Families: Ixodidae, Argassidae</i> Tue Nov 08 03:49:22 GMT 2016 Search
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Taxonomic rank vocabulary TAXRANK A vocabulary of taxonomic ranks (species, family, phylum, etc) Mon Apr 18 14:03:17 BST 2016 Search
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Terminology for Description of Dynamics TEDDY TEDDY is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems and Synthetic Biology. Tue Feb 21 02:56:26 GMT 2017 Search
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Mosquito gross anatomy TGMA A structured controlled vocabulary of the anatomy of mosquitoes. Tue Nov 08 03:56:14 GMT 2016 Search
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Plant Trait Ontology TO A controlled vocabulary of describe phenotypic traits in plants. Fri Feb 03 02:59:20 GMT 2017 Search
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Pathogen Transmission Ontology TRANS An ontology representing the disease transmission process during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host. Wed Mar 22 03:39:48 GMT 2017 Search
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Teleost taxonomy TTO An ontology covering the taxonomy of teleosts (bony fish) Tue Dec 20 03:28:43 GMT 2016 Search
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Uber-anatomy ontology UBERON Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. Wed Apr 26 04:27:40 BST 2017 Search
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Unimod protein modification database for mass spectrometry UNIMOD Unimod is a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, an d site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide). Mon May 08 12:06:54 BST 2017 Search
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Units of measurement UO Metrical units for use in conjunction with PATO Mon Jul 24 05:44:03 BST 2017 Search
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Variation Ontology VARIO Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations. Wed Feb 08 02:27:47 GMT 2017 Search
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Vaccine Ontology VO The Vaccine Ontology (VO) is a biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine annotation, integrate various vaccine data, and support computer-assisted reasoning. VO supports basic vaccine R&D and clincal vaccine usage. VO is initiated and primarily developed by Dr. Yongqun "Oliver" He at the University of Michigan Medical School. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities. Tue May 02 02:32:54 BST 2017 Search
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Vertebrate trait VT An ontology of traits covering vertebrates Fri Dec 02 03:12:13 GMT 2016 Search
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Vertebrate Taxonomy Ontology VTO Comprehensive hierarchy of extinct and extant vertebrate taxa. Mon Jul 17 06:17:09 BST 2017 Search
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C. elegans gross anatomy WBBT A structured controlled vocabulary of the anatomy of <i>Caenorhabditis elegans</i>. Mon Nov 28 03:46:27 GMT 2016 Search
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C. elegans development WBLS A structured controlled vocabulary of the development of <i>Caenorhabditis elegans</i>. Mon Jul 24 05:53:36 BST 2017 Search
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C. elegans phenotype WBPHENOTYPE A structured controlled vocabulary of <i>Caenorhabditis elegans</i> phenotypes Mon Jul 24 06:02:53 BST 2017 Search
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Xenopus anatomy and development XAO Anatomy and development of the African clawed frog (<i>Xenopus laevis</i>). Mon Feb 27 03:52:27 GMT 2017 Search
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Experimental condition ontology XCO Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms. Mon Jul 24 06:12:06 BST 2017 Search
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Cross-linker reagents ontology XL A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry. Search
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Zebrafish Experimental Conditions Ontology ZECO Experimental conditions applied to zebrafish, developed to facilitate experiment condition annotation at ZFIN Tue Nov 22 02:30:42 GMT 2016 Search
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Zebrafish anatomy and development ZFA A structured controlled vocabulary of the anatomy and development of the Zebrafish Mon Jul 24 06:21:48 BST 2017 Search
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Zebrafish developmental stages ZFS Developmental stages of the Zebrafish Mon Jul 24 06:31:02 BST 2017 Search
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