Genes, proteins, cells, anatomy, taxonomy, investigations and bioinformatics.
The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi.
The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO).
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.
The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways.
The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.
A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO.
An ontology representing the gross anatomy of Drosophila melanogaster.
A formal ontology of phenotypes observed in fission yeast.
A structured controlled vocabulary used for various aspects of annotation by FlyBase.
PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation.
The Cell Line Ontology is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns.
Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity.
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.
A structured controlled vocabulary of the anatomy and development of the Zebrafish
An ontology for the description of sample preparation, visualization, and imaging methods used in biomedical research.
Traits and phenotypes of flowering plants occurring in digitized Floras
Precision Fermentation Ontology: An ontology for PREcision FERmentation. A ontology listed in Bioregistry, OBO Foundry, OLS (EMBL-EBI).
The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies.
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.
Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names.
Ontology about the development and life stages of the C. elegans
Ontology about C. elegans and other nematode phenotypes
A structured controlled vocabulary of the development of Drosophila melanogaster.
PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea.
OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions.
An ontology for modeling and understanding of pharmacokinetics in biological systems.
XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis.
GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations.
The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field.
The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined.
The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.
Human ancestry ontology for the NHGRI GWAS Catalog
Zebrafish developmental stages ontology: Developmental stages of the Zebrafish. A ontology listed in Bioregistry, OBO Foundry, OLS (EMBL-EBI).
AfPO is an ontology that can be used in the study of diverse populations across Africa. It brings together publicly available demographic, anthropological and genetic data relating to African people in a standardised and structured format. The AfPO can be employed to classify African study participants comprehensively in prospective research studies. It can also be used to classify past study participants by mapping them using a language or ethnicity identifier or synonyms.
The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles.
OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration).
The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.
An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies.
An ontology for mouse anatomy covering embryonic development and postnatal stages.
An ontology describing the anatomical structures and characteristics of Porifera (sponges)
The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research.
The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data.
The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. 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 the EBI Functional Genomics Team.
OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles.
FuTRES Ontology of Vertebrate Traits is an application ontology used to convert vertebrate trait data in spreadsheet to triples. FOVT leverages the BioCollections Ontology (BCO) to link observations of individual specimens to their trait values. Traits are defined in the Ontology of Biological Attributes (OBA).
The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc.
A structured controlled vocabulary for the phenotypes of Ascomycete fungi.
A structured controlled vocabulary of anatomies of the slime-mold Dictyostelium discoideum.
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The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world.
The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts.
The Vaccine Ontology (VO) is a community-based biomedical ontology in the domain of vaccines and vaccination. VO aims to standardize vaccine types and annotations, integrate various vaccine data, and support computer-assisted reasoning. The VO supports basic vaccine R&D and clinical vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities.
An ontology of commonly encountered and/or high level Drosophila phenotypes.
The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM.
FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies.
The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations.
The Radiomics Ontology aims to cover the radiomics feature domain with a strong focus on first order, shape, textural radiomics features. In addition, in the original version. it includes classes about segmentation algorithms and imaging filters. Due to a recent collaboration with the IBSI (International Biomarkers Standardization Initiative), the ontology has been expanded (v 1.6) and it includes all the entities presented in the IBSI document. Therefore, a broad coverage of not only radiomics features, but also every entity (e.g.
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds.
Ontology of species-neutral phenotypes observed in pathogen-host interactions.
The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.
The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies.
An ontology of units of measurement, used across OBO Foundry ontologies to annotate quantitative values with standard units.
An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.
COB brings together key terms from a wide range of OBO projects to improve interoperability.
A controlled vocabulary to describe phenotypic traits in plants.
An ontology that formalizes IASP's definition of pain as both an unpleasant physical and emotional experience, and it provides terms and axioms to represent the multidimensional aspects of pain, such as temporality, quality, extent, biological mechanism, and anatomical location.
RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization.
An ontology for glycans based on GlyTouCan, but organized by subsumption.
An ontology of human and animal behaviours and behavioural phenotypes
The chemical information ontology (cheminf) describes information entities about chemical entities. It provides qualitative and quantitative attributes to richly describe chemicals.
An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch.
MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation.
A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments.
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