Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelated entities that demonstrate the network of the understanding on Alzheimer's disease and can be readily applied for text mining.
The upper level ontology upon which OBO Foundry ontologies are built.
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 main ontology in OWL. Contains all MP terms and links to other OBO ontologies
A direct translation of the AfPO (OWL edition) into OBO format
A direct translation of the AfPO (OWL edition) into OBOGraph JSON format
Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments
An ontology of environmental systems, components, and processes.
A broadly scoped ontology representing entities which bear a “food role”. It encompasses materials in natural ecosystems and agriculture that are consumed by humans and domesticated animals. This includes any generic (unbranded) raw or processed food material found in processing plants, markets, stores or food distribution points. FoodOn also imports nutritional component and dietary pattern terms from other OBO Foundry ontologies to support interoperability in diet and nutrition research
An ontology for describing the function of genes and gene products
An ontology representation of the NCBI organismal taxonomy
An integrated ontology for the description of life-science and clinical investigations
An ontology of phenotypic qualities (properties, attributes or characteristics)
A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments.
The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.
Relationship types shared across multiple ontologies
A controlled vocabulary to describe phenotypic traits in plants.
Metrical units for use in conjunction with PATO
Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.
Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics.
Contains all AgrO terms and links to other relevant ontologies.
The AISM contains terms used in insect biodiversity research for describing structures of the exoskeleton and the skeletomuscular system. It aims to serve as the basic backbone of generalized terms to be expanded with order-specific terminology.
Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)
An ontology for representing spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces
An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species
An integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies
git clone https://github.com/insect-morphology/aism
An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum).
The Amphioxus Development and Anatomy Ontology
git clone https://github.com/EBISPOT/amphx_ontology.git
A structured controlled vocabulary for the phenotypes of Ascomycete fungi
New mutant phenotype data curation system in the Saccharomyces Genome Database
An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.
The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation
Antibiotic resistance genes and mutations
CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.
An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.
Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies
An application ontology that represents comprehensive knowledge involving a variety of fields of medical and biological aspects.
Includes axioms linking to other ontologies, but no imports of those ontologies
git clone https://github.com/obophenotype/biological-spatial-ontology.git
Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.
A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures.
git clone https://github.com/BRENDA-Enzymes/BTO.git
The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources
a formalization of concepts and relations relevant to evolutionary comparative analysis
Initial Implementation of a Comparative Data Analysis Ontology
CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet.
Compositional Dietary Nutrition Ontology
A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds.
Chemical Entities of Biological Interest
git clone https://github.com/CompositionalDietaryNutritionOntology/cdno.git
Establishing a Common Nutritional Vocabulary - From Food Production to Diet
ChEBI: re-engineered for a sustainable future
ChEBI in 2016: Improved services and an expanding collection of metabolites.
Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them.
The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web
CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes.
The Human Phenotype Ontology (HPO) is a structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease.
Standard terms for annotating mammalian phenotypic data.
An ontological representation of protein-related entities
Extension of Roles in the ChEBI Ontology
CHMO, the chemical methods ontology, describes methods used to
The Coronavirus Infectious Disease Ontology (CIDO) aims to ontologically represent and standardize various aspects of coronavirus infectious diseases, including their etiology, transmission, epidemiology, pathogenesis, diagnosis, prevention, and treatment.
A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology
An ontology to capture confidence information about annotations.
The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations
The Cell Ontology is a structured controlled vocabulary for cell types in animals.
An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO).
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.
Complete ontology, plus inter-ontology axioms, and imports modules
Complete ontology, plus inter-ontology axioms, and imports modules merged in
complete CL but with no imports or external axioms
CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).
git clone https://github.com/luis-gonzalez-m/Collembola.git
An ontology to standardize and integrate cell line information and to support computer-assisted reasoning.
An ontology for describing the classification of human diseases organized by etiology.
The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle.
Clytia hemisphaerica Development and Anatomy Ontology
git clone https://github.com/EBISPOT/clyh_ontology.git
Morphological and physiological measurement records generated from clinical and model organism research and health programs.
Three ontologies to define phenotype measurement data.
The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.
COB brings together key terms from a wide range of OBO projects to improve interoperability.
Core Ontology for Biology and Biomedicine
Core Ontology for Biology and Biomedicine, main ontology
COB with native IDs preserved rather than rewired to OBO IDs
demo of COB including subsets of other ontologies (Experimental, for demo purposes only)
The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. It has been built using the Ontology Develoment Kit, with the Ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM) as a backbone.
A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability.
git clone https://github.com/data2health/contributor-role-ontology.git
An anatomical and developmental ontology for ctenophores (Comb Jellies)
The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials.
An ontology to describe entities related to cardiovascular diseases
A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum
An anatomy ontology to represent biological knowledge in Dictyostelium discoideum
A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum.
Dictyostelium discoideum phenotype ontology
git clone https://github.com/obophenotype/dicty-phenotype-ontology.git
dictyBase and the Dicty Stock Center (version 2.0) - a progress report
The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology
Drug-drug Interaction and Drug-drug Interaction Evidence Ontology
Ontology for drivers and triggers of human diseases, built to classify ExO ontology exposure stressors. An application ontology. Built in collaboration with EnvO, ExO, ECTO and ChEBI.
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data
Disease Ontology, OWL format. This file contains DO's is_a asserted hierarchy plus equivalent axioms to other OBO Foundry ontologies.
Disease Ontology, OBO format. This file omits the equivalent axioms.
An ontology of commonly encountered and/or high level Drosophila phenotypes.
git clone https://github.com/FlyBase/drosophila-phenotype-ontolog.git
A structured controlled vocabulary used for various aspects of annotation by FlyBase.
An ontology to support comparative effectiveness researchers studying claims data.
Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request
DUO is an ontology which represent data use conditions.
An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586).
The Echinoderm Anatomy and Development Ontology
git clone https://github.com/echinoderm-ontology/ecao_ontology.git
An ontology for experimental and other evidence statements.
ECO: the Evidence and Conclusion Ontology, an update for 2022.
ECO, the Evidence & Conclusion Ontology: community standard for evidence information.
Standardized description of scientific evidence using the Evidence Ontology (ECO)
Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms.
An ontology about groups of interacting organisms such as populations and communities
ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology).
Environmental conditions, treatments and exposures ontology
Vocabularies for describing exposure data to inform understanding of environmental health.
The Medical Action Ontology (MAxO) provides a broad view of medical actions and includes terms for medical procedures, interventions, therapies, treatments, and recommendations.
An ontology of human and animal behaviours and behavioural phenotypes
NCI Thesaurus (NCIt)is a reference terminology that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities. The NCIt OBO Edition aims to increase integration of the NCIt with OBO Library ontologies. NCIt OBO Edition releases should be considered experimental.
An ontology for mouse anatomy covering embryonic development and postnatal stages.
An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature
EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update
Mouse Anatomy Ontologies: Enhancements and Tools for Exploring and Integrating Biomedical Data
Textual Anatomics: the Mouse Developmental Anatomy Ontology and the Gene Expression Database for Mouse Development (GXD)
The environment ontology: contextualising biological and biomedical entities
The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation
A application driven Epilepsy Ontology with official terms from the ILAE.
A core reference ontology built upon BFO about exercise medicine and it contains the related terms for healthy people, people with chronic conditions and people living with diability to exercise.
Core reference ontology for individualized exercise prescription
A structured controlled vocabulary for the anatomy of fungi.
git clone https://github.com/obophenotype/fungal-anatomy-ontology.git
An ontology representing the gross anatomy of Drosophila melanogaster.
git clone https://github.com/FlyBase/drosophila-anatomy-developmental-ontology.git
A strategy for building neuroanatomy ontologies
The Virtual Fly Brain Browser and Query Interface
FlyBase: anatomical data, images and queries
git clone https://github.com/FlyBase/flybase-controlled-vocabulary.git
A structured controlled vocabulary of the development of Drosophila melanogaster.
git clone https://github.com/FlyBase/drosophila-developmental-ontology.git
Food-Drug interactions automatically extracted from scientific literature
Food Interactions with Drugs Evidence Ontology
Traits and phenotypes of flowering plants occurring in digitized Floras
The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants
FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data
FOBI: an ontology to represent food intake data and associate it with metabolomic data
The fobitools framework: the first steps towards food enrichment analysis
FOBI is an ontology to represent food intake data and associate it with metabolomic data
FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration
FoodOn ontology with import file references and over 9,000 food products
FoodOn core ontology (currently the same as foodon.owl)
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).
A collection of biological attributes (traits) covering all kingdoms of life.
FYPO is a formal ontology of phenotypes observed in fission yeast.
FYPO: The Fission Yeast Phenotype Ontology.
Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls.
An ontology covering the anatomy of the taxon Porifera (sponges)
A gazetteer constructed on ontological principles. The countries are actively maintained.
An ontology to represent genomics cohort attributes
The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks.
An integrated ontology for representing the genetic variations described in genotypes, and their causal relationships to phenotype and diseases.
git clone https://github.com/monarch-initiative/GENO-ontology.git
GlyTouCan provides stable accessions for glycans described at varyious degrees of characterization, including compositions (no linkage) and topologies (no carbon bond positions or anomeric configurations). GNOme organizes these stable accessions for interative browsing, for text-based searching, and for automated reasoning with well-defined characterization levels.
Glycan Naming and Subsumption Ontology (GNOme)
git clone https://github.com/glygen-glycan-data/GNOme.git
GNOme - Glycan Naming and Subsumption Ontology
Glycan Naming and Subsumption Ontology, OWL format (primary)
Glycan Naming and Subsumption Ontology, OBO format (automated conversion from OWL)
Glycan Naming and Subsumption Ontology, JSON format (automated conversion from OWL)
The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments.
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
The Gene Ontology resource: enriching a GOld mine
The main ontology in OWL. This is self contained and does not have connections to other OBO ontologies
Equivalent to go.owl, in obograph json format
The main ontology plus axioms connecting to select external ontologies, with subsets of those ontologies
The main ontology plus axioms connecting to select external ontologies, excluding the external ontologies themselves
As go-plus.owl, in obographs json format
Basic version of the GO, filtered such that the graph is guaranteed to be acyclic and annotations can be propagated up the graph. The relations included are is a, part of, regulates, negatively regulates and positively regulates. This version excludes relationships that cross the 3 GO hierarchies.
GO-Basic, Filtered, for use with legacy tools
GO-Basic, Filtered, for use with legacy tools (JSON)
Classes added to ncbitaxon for groupings such as prokaryotes
Equivalent to go.owl, but released daily. Note the snapshot release is not archived.
GO (OWL edition), daily snapshot release
GO (OBO Format edition), daily snapshot release
The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies.
A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog
The full version of HANCESTRO in OWL format, with BFO upper hierarchy for easier integration with other ontologies
A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)
git clone https://github.com/hymao/hao.git
A gross anatomy ontology for hymenoptera
This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.
git clone https://github.com/BgeeDB/homology-ontology.git
An ontology to clarify homology-related concepts
The health Surveillance Ontology (HSO) focuses on "surveillance system level data", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance.
An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines
An ontology based on a theory of document acts describing what people can do with documents
ICEO is an integrated biological ontology for the description of bacterial integrative and conjugative elements (ICEs).
Integrative and Conjugative Element Ontology
ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements
An ontology of clinical informed consents
A set of interoperable ontologies that will together provide coverage of the infectious disease domain. IDO core is the upper-level ontology that hosts terms of general relevance across the domain, while extension ontologies host terms to specific to a particular part of the domain.
The Infectious Disease Ontology in the age of COVID-19
An ontology of interactions and interaction networks
Development and application of an Interaction Network Ontology for literature mining of vaccine-associated gene-gene interactions
LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents.
An ontology for representing treatment of disease and diagnosis and on carcinomas and other pathological entities
An ontological version of MIABIS (Minimum Information About BIobank data Sharing)
The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations.
Ontology for Modeling and Representation of Social Entities
The Ontology of Precision Medicine and Investigation (OPMI) aims to ontologically represent and standardize various entities and relations associated with precision medicine and related investigations at different conditions.
Ontology of Precision Medicine and Investigation
LABO: An Ontology for Laboratory Test Prescription and Reporting
The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research. LEPAO is developed in part by BIOfid (The Specialised Information Service Biodiversity Research).
A structured controlled vocabulary of the adult anatomy of the mouse (Mus).
git clone https://github.com/monarch-initiative/MAxO.git
Microbial Conditions Ontology is an ontology...
An ontology of prokaryotic phenotypic and metabolic characters
Ontology of Prokaryotic Phenotypic and Metabolic Characters
Ontology to establish data exchange standards and common data elements in the microRNA (miR) domain
An ontology of phenotypes covering microbes
Experimental conditions applied to zebrafish, developed to facilitate experiment condition annotation at ZFIN
Zebrafish Experimental Conditions Ontology
An ontology representing the structure of model card reports - reports that describe basic characteristics of machine learning models for the public and consumers.
The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community.
Toward a standard formal semantic representation of the model card report
The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning.
An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings.
An ontology to describe and classify mental diseases such as schizophrenia, annotated with DSM-IV and ICD codes where applicable
A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions.
Molecular Interactions Controlled Vocabulary
An application ontology to formalize annotation of phylogenetic data.
Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)
A representation of the variety of methods used to make clinical and phenotype measurements.
PSI-MOD is an ontology consisting of terms that describe protein chemical modifications
The PSI-MOD community standard for representation of protein modification data
A global community effort to harmonize multiple disease resources to yield a coherent merged ontology.
Mondo: Integrating Disease Terminology Across Communities
Mondo: Unifying diseases for the world, by the world
The main ontology classes and their hierarchies, without references to external terms.
Expanding and refining the Mammalian Phenotype Ontology to enhance disease model discovery
The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data
Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens
The main ontology in OWL. Contains all MP terms and links to other OBO ontologies.
A direct translation of the MP (OWL edition) into OBO format.
For a description of the format see https://github.com/geneontology/obographs.
The main ontology plus axioms connecting to select external ontologies, excluding axioms from the the external ontologies themselves.
A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes
An ontology of minimum information regarding potential drug-drug interaction information.
An ontology for Major Histocompatibility Complex (MHC) restriction in experiments
A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry.
The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.
Analyzing gene expression data in mice with the Neuro Behavior Ontology
A direct transformation of the standard NCIt content using OBO-style term and ontology IRIs and annotation properties.
An ontology for non-coding RNA, both of biological origin, and engineered.
ncro-devel@googlegroups.com, ncro-discuss@googlegroups.com
The Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management.
NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature.
NOMEN - A nomenclatural ontology for biological names
git clone https://github.com/SpeciesFileGroup/nomen.git
A biomedical ontology in the domain of adverse events
OArCS is an ontology describing the Arthropod ciruclatory system.
Ontology of Arthropod Circulatory Systems
The Ontology of Biological Attributes (OBA) - computational traits for the life sciences
A biomedical ontology in the domain of biological and clinical statistics.
Ontology of Biological and Clinical Statistics
The Ontology for Biomedical Investigations
A collection of important high-level terms and their relations from OBI and other ontologies
An ontology built for annotation and modeling of biobank repository and biobanking administration
An ontology representing occupations. It is designed to facilitate harmonization of existing occupation standards, such as the US Bureau of Labor Statistics Standard Occupational Classification (US SOC), the International Standard Classification of Occupations (ISCO), the UK National Statistics Standard Occupational Classification (UK SOC), and the European Skills, Competences, Qualifications and Occupations (ESCO) of the European Union.
A formal ontology of genes and genomes of biological organisms.
Toward an ontological treatment of disease and diagnosis
Biomarkers in the Ontology for General Medical Science
The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies.
Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology
The Ontology of Host-Microbiome Interactions aims to ontologically represent and standardize various entities and relations related to microbiomes, microbiome host organisms (e.g., human and mouse), and the interactions between the hosts and microbiomes at different conditions.
Ontology of Host-Microbiome Interactions
OHPI is a community-driven ontology of host-pathogen interactions (OHPI) and represents the virulence factors (VFs) and how the mutants of VFs in the Victors database become less virulence inside a host organism or host cells. It is developed to represent manually curated HPI knowledge available in the PHIDIAS resource.
Victors: a web-based knowledge base of virulence factors in human and animal pathogens
The ontology of medically related social entities: recent developments
An ontology to standardize research output of nutritional epidemiologic studies.
An ontology for description of concepts in the nutritional studies domain.
ONS: an ontology for a standardized description of interventions and observational studies in nutrition
OntoAvida develops an integrated vocabulary for the description of the most widely-used computational approach for studying evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment).
OntoAvida: ontology for Avida digital evolution platform
The Gender, Sex, and Sexual Orientation (GSSO) ontology has terms for annotating interdisciplinary information concerning gender, sex, and sexual orientation for primary usage in the biomedical and adjacent sciences.
Gender, Sex, and Sexual Orientation (GSSO) ontology
STATO is a general-purpose STATistics Ontology. Its aim is to provide coverage for processes such as statistical tests, their conditions of application, and information needed or resulting from statistical methods, such as probability distributions, variables, spread and variation metrics. STATO also covers aspects of experimental design and description of plots and graphical representations commonly used to provide visual cues of data distribution or layout and to assist review of the results.
Ontology for the Avida digital evolution platform
Equivalent to ontoavida.owl, in obo format
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.
OntONeo: The Obstetric and Neonatal Ontology
Formal Ontologies in Knowledge Organization within the Obstetric and Neonatal Domain
The full version of ONTONEO in OWL format
An ontology built for representating the organizational components of trauma centers and trauma systems.
Ontology of Organizational Structures of Trauma centers and Trauma systems
A reference ontology for parasite life cycle stages.
An application ontology designed to annotate next-generation sequencing experiments performed on RNA.
A biomedical ontology in the domain of vaccine adverse events.
The anatomy of phenotype ontologies: principles, properties and applications
Using ontologies to describe mouse phenotypes
Cell types that are provisionally defined by experimental techniques such as single cell or single nucleus transcriptomics rather than a straightforward & coherent set of properties.
A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases.
An ontology to describe entities related to prescription of drugs
The Prescription of Drug Ontology 2.0 (PDRO): More Than the Sum of Its Parts
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.
PHIPO is a formal ontology of species-neutral phenotypes observed in pathogen-host interactions.
Pathogen Host Interaction Phenotype Ontology
PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions
PLANA, the planarian anatomy ontology, encompasses the anatomy and life cycle stages for both __Schmidtea mediterranea__ biotypes.
Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms
Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea.
The plant ontology as a tool for comparative plant anatomy and genomic analyses.
The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology
An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales.
Protein Ontology (PRO): enhancing and scaling up the representation of protein entities
PRO after reasoning has been applied, OWL format. Add '.gz' for compressed.
PRO after reasoning has been applied, OBO format.
PRO without reasoning applied, OWL format. Add '.gz' for compressed.
PRO without reasoning applied, OBO format.
PROCO covers process chemistry, the chemical field concerned with scaling up laboratory syntheses to commercially viable processes.
Terms commonly used in Systems Biology, and in particular in computational modeling.
Ontology to reproducibly study visualizations of clinical performance
The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter.
A controlled vocabulary for annotating gene products to pathways.
The pathway ontology - updates and applications.
RBO is an ontology for the effects of radiation on biota in terrestrial and space environments.
The obo edition is less expressive than the OWL, and has imports merged in
Minimal subset intended to work with BFO-classes
Axioms defined within RO and to be used in imports for other ontologies
For use in ecology and environmental science
Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD.
Connects organic name reactions to their roles in an organic synthesis and to processes in MOP
An ontology for representing the provenance of scientific claims and the evidence that supports them.
Scientific Evidence and Provenance Information Ontology
git clone https://github.com/monarch-initiative/SEPIO-ontology.git
The Space Life Sciences Ontology is an application ontology and is intended to support the operation of NASA's Life Sciences Data Archive and other systems that contain space life science research data.
The Sequence Ontology: a tool for the unification of genome annotations.
Evolution of the Sequence Ontology terms and relationships.
This subset includes only locatable sequence features and is designed for use in such outputs as GFF3
Sequence Ontology Feature Annotation (SOFA) subset (OWL)
Sequence Ontology Feature Annotation (SOFA) subset (OBO Format)
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).
The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with Cross-Disciplinary Data
Experiment design driven FAIRification of omics data matrices, an exemplar
Semantic concept schema of the linear mixed model of experimental observations
The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation
An ontology of disease symptoms, with symptoms encompasing perceived changes in function, sensations or appearance reported by a patient indicative of a disease.
GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database
A terminology for the skills necessary to make data FAIR and to keep it FAIR.
EOSC Co-creation funded project 074: Delivery of a proof of concept for terms4FAIRskills: Technical report
This community view of T4FS makes the ontology available in OWL without upper-level ontology (ULO) terms to give the user community a simpler view of the term hierarchy.
This community view of T4FS makes the ontology available in OBO format without upper-level ontology (ULO) terms to give the user community a simpler view of the term hierarchy.
This community view of T4FS makes the ontology available in JSON format without upper-level ontology (ULO) terms to give the user community a simpler view of the term hierarchy.
A vocabulary of taxonomic ranks (species, family, phylum, etc)
The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes
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.
An ontology covering the taxonomy of teleosts (bony fish)
TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity.
Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management
git clone https://github.com/obophenotype/uberon.git
Uberon, an integrative multi-species anatomy ontology
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon
Axioms defined within Uberon and to be used in imports for other ontologies
Uberon edition that excludes external ontologies and most relations
Uberon and all metazoan ontologies with redundant species-specific terms removed
The Units Ontology: a tool for integrating units of measurement in science
The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.
The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics
Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species
Phenotype Ontologies Traversing All The Organisms (POTATO) workshop: 2nd edition
uPheno 1 is no longer actively maintained, please start using uPheno 2 (see below).
The new version of uPheno, along with species independent phenotypes and additional phenotype relations. The ontology is still in Beta status, but we recommend users to migrate their infrastructures to uPheno 2 as uPheno 1 is no longer actively maintained.
Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names.
The Vertebrate Breed Ontology: Toward Effective Breed Data Standardization
VO is a biomedical ontology in the domain of vaccine and vaccination.
Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses
Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology
An ontology of traits covering vertebrates
svn co http://phenotype-ontologies.googlecode.com/svn/trunk/src/ontology/vt
Comprehensive hierarchy of extinct and extant vertebrate taxa.
A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.
git clone https://github.com/obophenotype/c-elegans-gross-anatomy-ontology.git
Building a cell and anatomy ontology of Caenorhabditis elegans
A structured controlled vocabulary of the development of Caenorhabditis elegans.
git clone https://github.com/obophenotype/c-elegans-development-ontology.git
WormBase: a modern Model Organism Information Resource
A structured controlled vocabulary of Caenorhabditis elegans phenotypes
git clone https://github.com/obophenotype/c-elegans-phenotype-ontology.git
Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community.
XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis.
An ontology for Xenopus anatomy and development.
Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase.
A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.
HUPO-PSI cross-linking and derivatization reagents controlled vocabulary
XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis.
The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development.
A structured controlled vocabulary of the anatomy and development of the Zebrafish
Zebrafish anatomy and development ontology
The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio.
The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism.
git clone https://github.com/Superraptor/GSSO.git
The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease.
The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.
Simple, manually curated version of the ontology without the use of a reasoner, and without any imported terms, in obographs JSON format.
Official HPO release in obographs JSON format
Simple, manually curated version of the ontology without the use of a reasoner, and without any imported terms, in OBO file format.
Manually classified version of the ontology without the use of a reasoner, with imported terms, in OWL format (RDF/XML).
Manually curated version of the ontology without the use of a reasoner, with references to imported terms, in obographs JSON file format.
HPO base release in obographs JSON format
Manually curated version of the ontology without the use of a reasoner, with references to imported terms, in OBO file format.
Manually curated version of the ontology without the use of a reasoner, with references to imported terms, in OWL (RDF/XML) file format.
Version of the ontology automatically classified with the use of a reasoner, including all imported terms, in obographs JSON file format.
HPO full release in obographs JSON format
Version of the ontology automatically classified with the use of a reasoner, including all imported terms, in OBO file format.
Version of the ontology automatically classified with the use of a reasoner, including all imported terms, in OWL (RDF/XML) file format.
Version of the ontology corresponding to the primary release (hp.owl), with translated labels, synonyms, and definitions, in obographs JSON file format.
HPO International Edition in obographs JSON format
Version of the ontology corresponding to the primary release (hp.owl), with translated labels, synonyms, and definitions, in OBO file format.
Version of the ontology corresponding to the primary release (hp.owl), with translated labels, synonyms, and definitions, in OWL (RDF/XML) file format.
Simple, manually curated version of the ontology without the use of a reasoner, and without any imported terms, in obographs JSON file format.
HPO simple, manually classified, without imports in obographs JSON format
HPO simple, manually classified, without imports in OBO format
Simple, manually curated version of the ontology without the use of a reasoner, and without any imported terms, in OWL (RDF/XML) file format.
HPO simple, manually classified, without imports in OWL format
A classification of algorithms for simulating biology, their parameters, and their outputs
Controlled vocabularies and semantics in systems biology
An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease.
An ontology is developed to support Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org).
An application ontology to cover all aspects of malaria as well as the intervention attempts to control it.
git clone https://github.com/scdodev/scdo-ontology.git
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation.
The Sickle Cell Disease Ontology: Enabling Collaborative Research and Co-Designing of New Planetary Health Applications.
The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation.
An ontology of physico-chemical methods and properties.
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.
An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time.
git clone https://github.com/obophenotype/sibo.git
Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations.
Variation Ontology for annotation of variation effects and mechanisms
Malaria study data integration and information retrieval based on OBO Foundry ontologies.
A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.
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.
An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process.
Ontology of Genetic Susceptibility Factor
Life cycle stages for Platynereis dumerilii
AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology
git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git
An anatomical and developmental ontology for cephalopods
A structured controlled vocabulary of stage-specific anatomical structures of the developing human.
A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20).
This is currently a slimmed down version of FMA
Foundational Model of Anatomy Ontology (subset)
Translating the Foundational Model of Anatomy into OWL
The foundational model of anatomy in OWL: Experience and perspectives
Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study
Application ontology for entities related to insecticide resistance in mosquitos
Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures.
git clone https://github.com/BGSU-RNA/rnao.git
The anatomy of the Tick, Families: Ixodidae, Argassidae
A structured controlled vocabulary of the anatomy of mosquitoes.
A manually curated resource for the representation and annotation of metabolic pathways
UniPathway: a resource for the exploration and annotation of metabolic pathways
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
An application ontology built for beta cell genomics studies.
A formal represention for drug-drug interactions knowledge.
DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug–Drug Interactions and Their Mechanisms.
Human developmental anatomy, timed version
Human developmental anatomy, abstract version
A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus).
Mouse gross anatomy and development, timed
Ontologies as integrative tools for plant science.
An ontology designed to support the semantic annotation of epidemiology resources
An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens.
eVOC (Expressed Sequence Annotation for Humans)
The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.
Molecule role (INOH Protein name/family name ontology)
An ontology representation of the LIPIDMAPS nomenclature classification.
A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.
An application ontology for use with miRNA databases.
A standardized description of a microarray experiment in support of MAGE v.1.
Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation.
NMR-instrument specific component of metabolomics investigations
An ontology that formalizes the genomic element by defining an upper class genetic interval
For the description of covalent bonds in proteins.
A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments.
Sample processing and separation techniques
SEP developers via the PSI and MSI mailing lists
Terminology of Anatomy of Human Embryology
Terminology of Anatomy of Human Histology
Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa
The teleost anatomy ontology: anatomical representation for the genomics age
Vertebrate Homologous Ontology Group Ontology