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.
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
Contains all AgrO terms and links to other relevant ontologies.
Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics.
AgroFIMS enables digital collection of agronomic data that is semantically described a priori with agronomic terms from AgrO.
AgrO is being used by GARDIAN to facilitate data search within publications and datasets for use in quantitative analyses.
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 the development and anatomy of Amphioxus (Branchiostoma lanceolatum).
The Amphioxus Development and Anatomy Ontology
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
Apollo-SV terms are used in the new MIDAS portal (https://midasnetwork.us/catalog/) for making data discoverable.
A 'hospital stay dataset' reference in the midasnetwork.us resource
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
The upper level ontology upon which OBO Foundry ontologies are built.
BFO is imported by multiple OBO ontologies to standardize upper level structure
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
An ontology for representing spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces
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.
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 main release in OWL format
Compositional Dietary Nutrition Ontology additional release in OBO format
Establishing a Common Nutritional Vocabulary - From Food Production to Diet
Compositional Dietary Nutrition Ontology
A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds.
ChEBI: re-engineered for a sustainable future
ChEBI in 2016: Improved services and an expanding collection of metabolites.
Chemical Entities of Biological Interest
Rhea uses CHEBI to annotate reaction participants
Query for all usages of CHEBI:29748 (chorismate)
A curated zebrafish experiment involving exposure to (5Z,8Z,14Z)-11,12-dihydroxyicosatrienoic acid (CHEBI:63969)
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
The RDF is provided as SPARQL endpoint by Maastricht University.
PubChem uses CHEMINF in their RDF representation
Physicochemical properties are represented as classes that are typed with CHEMINF classes
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.
CHEBI Integrated Role Ontology main release in OWL format
CHEBI Integrated Role Ontology additional release in OBO format
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.
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
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.
The BICCN created a high-resolution atlas of cell types in the primary motor based on single cell transcriptomics. These cell types are represented in the brain data standards ontology which anchors to cell types in the cell ontology.
cell type card of a cell type linked to a PCL cell type (L2/3 IT primary motor cortex glutamatergic neuron) which is a subclass of cell types in CL (CL:4023041)
PCL cell type used in cell type cards linked directly to CL cell types
Brain Data Standards Ontology: A data-driven ontology of transcriptomically defined cell types in the primary motor cortex
HuBMAP develops tools to create an open, global atlas of the human body at the cellular level. The Cell Ontology is used in annotating cell types in the tools developed.
ASCT+B reporter showing CL being used to annotate cell types in the heart
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.
The single-cell transcriptomics platform CZ CELLxGENE uses CL to annotate all cell types. All datasets on CellXGene are annotated according to a standard schema that specifies the use of CL to record Cell Type.
A CELLxGENE Cell Guide entry for 'luminal adaptive secretory precursor cell of mammary gland', which includes the CL ID (CL:4033057), CL definition and a visualizer of CL hierarchy
CELLxGENE: a performant, scalable exploration platform for high dimensional sparse matrices
The Human Cell Atlas (HCA) is an international group of researchers using a combination of these new technologies to create cellular reference maps. The HCA use CL to annotate cells in their reference maps.
HCA collection studies that are related B cell (CL:0000236) that is filtered through CL annotation
The EBI single cell expression atlas is an extension to EBI expression atlas that displays gene expression in single cells. Cell types in the single cell expression atlas linked with terms from the Cell Ontology.
RNA-Seq CAGE (Cap Analysis of Gene Expression) analysis of mice cells in RIKEN FANTOM5 project annotated using cell types from CL
Expression Atlas update: from tissues to single cells
The National Human Genome Research Institute (NHGRI) launched a public research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to identify all functional elements in the human genome sequence. The ENCODE DCC uses Uberon to annotate samples
Ontology application and use at the ENCODE DCC
FANTOM5 is using Uberon and CL to annotate samples allowing for transcriptome analyses with cell-type and tissue-level specificity.
CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).
An ontology to standardize and integrate cell line information and to support computer-assisted reasoning.
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
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, 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)
Core Ontology for Biology and Biomedicine
List of ontologies using at least one COB term (See section entitled "Which ontologies use it?")
List of ontologies using the term 'organism' (See section entitled "Ontologies that use the Class")
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.
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.
dictyBase and the Dicty Stock Center (version 2.0) - a progress report
Dictyostelium discoideum phenotype ontology
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.
fetal alcohol syndrome, has exposure stressor some alcohol
An ontology for describing the classification of human diseases organized by etiology.
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.
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data
Alliance of Genome Resources - MGD, RGD, SGD, FlyBase, WormBase, ZFIN use DO
Human diseases annotated to over 190,000 MOD genes, alleles, disease models and human genes
The landing page for Coronavirus Infectious Disease
Antibody and T cell epitopes associated with human diseases
An ontology of commonly encountered and/or high level Drosophila phenotypes.
FlyBase uses dpo for phenotype data annotation in Drosophila
alleles and constructs annotated to pupal lethal in 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
DrOn is used for the classification of Drugs, in particular, based on RxNorm codes, in the PennTURBO project.
From the documentation: For example, the text `500 mg Tylenol po tabs` might be mapped to http://purl.obolibrary.org/obo/DRON_00073395, with the label `Acetaminophen 500 MG Oral Tablet [Tylenol]`. DrOn knows that this is a subclass of `Acetaminophen 500 MG Oral Tablet` (through its logical axiomatisation).
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
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)
ECO is used by the GO consortium for evidence on GO associations
ECO is used by the Monarch Initiative for evidence types for disease to phenotype annotations.
Parkinsonism: Characteristic neurologic anomaly resulting form degeneration of dopamine-generating cells in the substantia nigra, a region of the midbrain, characterized clinically by shaking, rigidity, slowness of movement and difficulty with walking and gait.
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species
Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms.
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 main release in OWL format
Environmental conditions, treatments and exposures ontology additional release in OBO format
Environmental conditions, treatments and exposures ontology additional release in OBOJSon format
Environmental conditions, treatments and exposures ontology
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)
An ontology of environmental systems, components, and processes.
The environment ontology: contextualising biological and biomedical entities
The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation
Pseudobarbus burchelli (Tradou Redfin) is a species of bony fishes in the family Cyprinidae. They are associated with freshwater habitat. Individuals can grow to 13.5 cm. They have sexual reproduction.
annotating datasets in data repositories
Samples collected during Tara Oceans expedition are annotated with ENVO
Sample collected during the Tara Oceans expedition (2009-2013) at station TARA_004 (latitudeN=36.5533, longitudeE=-6.5669)
Annotation of habitat of Pseudovibrio sp. FO-BEG1 to marine environment
Annotation and semantic search over microbial data sets
Example metadata of a sample of marine water near Lisboa, taken as part of the Ocean Sampling Day Project (https://www.microb3.eu/osd.html). ENVO is used for the fields environmental feature, material, and biome.
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
Vocabularies for describing exposure data to inform understanding of environmental health.
A structured controlled vocabulary for the anatomy of fungi.
An ontology for the description of sample preparation, visualization, and imaging methods used in biomedical research.
FlyBase uses FBbi to annotate its image collection.
images annotated to "scanning electron micrograph"
Virtual Fly Brain uses FBbi to annotate images.
The Cell Image Library uses FBbi to annotate images.
An image annotate with several terms from FBbi.
An ontology representing the gross anatomy of Drosophila melanogaster.
A strategy for building neuroanatomy ontologies
The Virtual Fly Brain Browser and Query Interface
FlyBase: anatomical data, images and queries
genes expressed in ring neuron R2 in VFB
Flybase uses FBbt for expression and phenotype data annotation in Drosophila
alleles, constructs and insertions annotated to neuron in FlyBase
A structured controlled vocabulary used for various aspects of annotation by FlyBase.
FlyBase uses FBcv for phenotype data annotation in Drosophila
alleles and constructs annotated to bang sensitive in FlyBase
A structured controlled vocabulary of the development of Drosophila melanogaster.
Used to record stages in expression and phenotype curation
Expression of DLP in embryonic/larval midgut primordium at embryonic stage 13 (http://purl.obolibrary.org/obo/FBdv_00005328) (Khare and Baumgartner, 2000)
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 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
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
FoodOn ontology with import file references and over 9,000 food products
FoodOn core ontology (currently the same as foodon.owl)
FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration
FoodData Central nutrition database web portal provided by USDA Agricultural Research Service.
An entry for 'Apples, fuji, with skin, raw' from the FoodData Central nutrition database which is annotated with the term FOODON:00002862.
FDA GenomeTrackr surveillance program for reporting foodborne pathogen biosamples.
An entry from NCBI Biosample that describes a *Samonella enterica* sample extracted from Chicken and annotated with the term FOODON:03411457.
Wiki database consolidating over 30 global food composition databases.
An entry from WikiFCD that describes Walnuts and is annotated with the term FOODON:03301364.
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).
FuTRES Ontology of Vertebrate Traits main release in OWL format
FuTRES Ontology of Vertebrate Traits additional release in OBO format
FYPO is a formal ontology of phenotypes observed in fission yeast.
FYPO: The Fission Yeast Phenotype Ontology.
Pombase uses fypo for phenotype data annotation in fission yeast
genotypes annotated to abnormal mitotic cell cycle in fission yeast
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.
A gazetteer constructed on ontological principles. The countries are actively maintained.
An ontology to represent genomics cohort attributes
IHCC uses GECKO to standardize data from various cohorts for the IHCC cohort browser
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.
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, 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)
GNOme - Glycan Naming and Subsumption Ontology
Glycan Naming and Subsumption Ontology (GNOme)
GlyGen - Computational and Informatics Resources for Glycoscience
GNOme attributes and related glycans on glycan pages
ChEBI - Chemical Entities of Biological Interest
The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments.
An ontology for describing the function of genes and gene products
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
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
The Gene Ontology resource: enriching a GOld mine
The GO ontology is used by the GO consortium for functional annotation of genes
Uniprot uses GO to show the function of proteins
functional annotations of human Sonic hedgehog protein
Reactome annotates activities, pathways, and cellular localization using GO
protein tyrosine kinase activity of an EGFR complex
The Alliance of Genome Resources uses GO for model organism gene function annotation
Functional summary of C elegans nsy-1 gene
Gene Ontology Causal Activity Models for C elegans nsy-1 gene
Rhea uses GO to describe individual biochemical reactions
Glutamine scyllo-inositol transaminase reaction and associated GO term
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.
The full version of HANCESTRO in OWL format, with BFO upper hierarchy for easier integration with other ontologies
A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog
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.
Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data
FoodOn (http://foodon.org) is a consortium-driven project to build 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.
A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)
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.
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
IAO is used widely by multiple OBO ontologies for information representation.
ICEO is an integrated biological ontology for the description of bacterial integrative and conjugative elements (ICEs).
ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements
Integrative and Conjugative Element Ontology
An ontology of clinical informed consents
tracking informed consent in the kidney precision medicine project that has over 20 institutes involved.
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.
LABO: An Ontology for Laboratory Test Prescription and Reporting
LABO is a part of a core ontological model of medical knowledge in the PARS3 data platform.
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).
The Medical Action Ontology (MAxO) provides a broad view of medical actions and includes terms for medical procedures, interventions, therapies, treatments, and recommendations.
Medical Action Ontology main release in OWL format
Medical Action Ontology additional release in OBO format
Medical Action Ontology additional release in OBOJSon format
MAxO is used to capture disease-treatment relations from the scientific literature.
Bardet-biedl Syndrome 1 (MONDO:0008854) is treated through dietary interventions (MAXO:0000088) according to Forsyth et al 2003 (PMID:20301537)
Microbial Conditions Ontology is an ontology...
An ontology representing the structure of model card reports - reports that describe basic characteristics of machine learning models for the public and consumers.
Toward a standard formal semantic representation of the model card report
Demonstration of Java-based library utilizing MCRO to output RDF-based model card reports
Application of an ontology for model cards to generate computable artifacts for linking machine learning information from biomedical research
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.
The main ontology classes and their hierarchies, without references to external terms.
Mondo: Integrating Disease Terminology Across Communities
Mondo: Unifying diseases for the world, by the world
Mondo is used by the Monarch Initiative for disease annotations.
Mondo is used by the ClinGen for disease curations.
FBN1 is an autosomal dominant mutation in Marfan syndrome.
Mondo is used by the Kids First Data Resource Portal for disease annotations. Note, a login is needed to access the portal and view the Mondo-curated data.
Mondo is used by the Ancestory for some disease curations.
Some term names in ancestory.com are curated with Mondo, for ease of use.
Mondo is used by the Human Cell Atlas for some disease annotations.
Disease status specimen is normal, type 2 diabetes mellitus.
Standard terms for annotating mammalian phenotypic data.
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.
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
MGI annotates phenotypes of mouse models using the MP
Term browser page for embryonic lethality showing information about the term including definition, placement in the MP hierarchy, and link to mouse models annotated to this term or any of its decendants
RGD annotates phenotypes associated with rat genes and alleles using the MP
Term browser page for embryonic lethality showing information about the term including definition, placement in the MP hierarchy, and link to annotations to this term or any of its decendants
IMPC annotates abnormal phenotypes of mice carrying null alleles found following the application of a standardised set of physiological tests
All IMPC alleles that have been annotated to the MP term 'decreased memory-marker CD4-positive NK T cell number'.
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
MRO is used by the The Immune Epitope Database (IEDB) annotations
Epitope ID: 59611 based on reference 1003499
An ontology for major histocompatibility restriction
A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry.
The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.
An ontology of human and animal behaviours and behavioural phenotypes
Analyzing gene expression data in mice with the Neuro Behavior Ontology
An ontology representation of the NCBI organismal taxonomy
The Immune Epitope Database (IEDB) is funded by NIAID that catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation.
A specific assay curated in the IEDB using the NCBITaxon:520 Bordetella pertussis as the source organism.
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.
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
TaxonWorks is an integrated web-based workbench for taxonomists and biodiversity scientists.
A biomedical ontology in the domain of adverse events
OArCS is an ontology describing the Arthropod ciruclatory system.
Ontology of Arthropod Circulatory Systems
A collection of biological attributes (traits) covering all kingdoms of life.
The Ontology of Biological Attributes (OBA) - computational traits for the life sciences
OBA terms are used by the NHGRI-EBI GWAS Catalog for phenotypic trait annotation.
The NHGRI-EBI GWAS Catalog: standards for reusability, sustainability and diversity
OBA trait terms facilitate computational drug target identification via the Open Targets Platform.
The next-generation Open Targets Platform: reimagined, redesigned, rebuilt
The Encyclopedia of Life (EOL) TraitBank takes advantage of the well-axiomatised OBA terms to infer traits in biodiversity data and to improve their search functionality.
cell size http://purl.obolibrary.org/obo/OBA_0000055
TraitBank: Practical semantics for organism attribute data
OBA terms are used by the Functional Trait Resource for Environmental Studies (FuTRES) for the annotation of measurable traits in vertebrates.
A solution to the challenges of interdisciplinary aggregation and use of specimen-level trait data
A biomedical ontology in the domain of biological and clinical statistics.
Ontology of Biological and Clinical Statistics
The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines
In Methods, "Both OBCS and the Vaccine Ontology (VO) were used to ontologically model various components and relations ..."
An integrated ontology for the description of life-science and clinical investigations
A collection of important high-level terms and their relations from OBI and other ontologies
The Ontology for Biomedical Investigations
A specific assay curated in the IEDB using the OBI:1110180 '3H-thymidine assay measuring epitope specific proliferation of T cells' ('3H-thymidine')
ENCODE is a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.
A specific assay annotated in ENCODE using OBI:0000716 'ChiP-seq'
The NASA GeneLab data repository hosts space biology and space-related datasets funded by multiple space agencies around the world.
A specific assay annotated in NASA GeneLab using OBI:0001271 'RNA-seq assay'
The CFDE is providing a centralized metadata resource to allow search across data coordination centers from multiple Common Fund programs.
OBI is used in CFDE to captures types of experiments with assay terms such as OBI:0003094 'fluorescence in-situ hybridization assay'
NIF is a dynamic inventory of Web-based neuroscience resources, data, and tools accessible via any computer connected to the Internet.
A specific OBI term used to autocomplete in NIF search OBI:0100026 'organism'
An ontology built for annotation and modeling of biobank repository and biobanking administration
TURBO ontology supporting the PennTURBO project.
The Minimum Information About BIobank data Sharing (MIABIS) aims to standardize data elements used to describe biobanks, research on samples and associated data. General attributes to describe biobanks, sample collections and studies at an aggregated/metadata level are defined in MIABIS Core 2.0 (Merino-Martinez et al., 2016).
The National Cancer Institute Biorepositories and Biospecimen Research Branch (BBRB) is an international leader in research and policy activities related to biospecimen collection, processing, and storage, also known as biobanking.
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.
An ontology for representing treatment of disease and diagnosis and on carcinomas and other pathological entities
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
Ontology to establish data exchange standards and common data elements in the microRNA (miR) domain
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).
OMO is imported by multiple OBO ontologies for ontology term annotations.
An ontology of phenotypes covering microbes
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.
The ontology of medically related social entities: recent developments
Ontology for Modeling and Representation of Social Entities
OMRSE is used by the CAFÊ and TIPTOE projects
The project creates and maintains the Ontology of Organizational Structures of Trauma centers and Trauma systems or OOSTT, which reuses OMRSE terms
OMRSE is used by the Intervention Setting Ontology component of the Behavior Change Intervention Ontology
Several facility classes extend OMRSE's 'facility'
Development of an Intervention Setting Ontology for behaviour change: Specifying where interventions take place
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
nutrition, nutritional studies, nutrition professionals
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).
Equivalent to ontoavida.owl, in obo format
Ontology for the Avida digital evolution platform
OntoAvida: ontology for Avida digital evolution platform
An R package—avidaR—uses OntoAvida to perform complex queries on an RDF database—avidaDB—containing the genomes, transcriptomes, and phenotypes of more than a million digital organisms
avidaR: an R library to perform complex queries on an ontology-based database of digital organisms
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.
The full version of ONTONEO in OWL format
OntONeo: The Obstetric and Neonatal Ontology
Formal Ontologies in Knowledge Organization within the Obstetric and Neonatal Domain
The ReCOL research group uses OntONeo to model and structure biomedical information, particularly in obstetrics and neonatology.
The ontology has been applied in studies on data interoperability and semantic integration, improving access to structured medical information and enabling knowledge sharing between systems.
OntONeo serves as a knowledge representation framework to support clinical decision-making and data interoperability in healthcare. It is used in information retrieval applications, enabling structured queries over medical databases and facilitating access to critical obstetric and neonatal health information.
Demonstrates OntONeo’s application for enabling structured data access and semantic reasoning in clinical contexts.
An ontology built for representating the organizational components of trauma centers and trauma systems.
Ontology of Organizational Structures of Trauma centers and Trauma systems
OOSTT terms, such as OOSTT_00000017 'trauma program' and OOSTT_00000021 'trauma medical director role,' are used in the CAFE questionnaire to assess trauma centers and systems.
OOSTT terms, such as OOSTT_00000002 'trauma center' and OOSTT_00000066 'emergency medicine liaison role,' are used in the TIPTOE questionnaire to relate trauma center/system structure to patient outcomes.
Terms from OOSTT are imported and used by OMRSE.
A reference ontology for parasite life cycle stages.
The ontology for parasite lifecycle is used in the VEuPathDB (Eukaryotic Pathogen, Vector & Host Informatics Resources) for parasite life cycle annotation.
The ontology for parasite lifecycle is used in the GeneDB for parasite life cycle annotation.
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
An application ontology designed to annotate next-generation sequencing experiments performed on RNA.
A biomedical ontology in the domain of vaccine adverse events.
An ontology of phenotypic qualities (properties, attributes or characteristics)
The anatomy of phenotype ontologies: principles, properties and applications
Using ontologies to describe mouse phenotypes
PATO is used by the Human Phenotype Ontology (HPO) for logical definitions of phenotypes that facilitate cross-species integration.
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources
An ontology for modeling and understanding of pharmacokinetics in biological systems.
Physiologically-Based Pharmacokinetic Ontology
PBPKO is used for annotation of kinetic model in SBML description format.
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.
An ontology about groups of interacting organisms such as populations and communities
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
A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments.
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.
PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions
Pathogen Host Interaction Phenotype Ontology
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
Planosphere's PAGE database uses PLANA to annotate gene expression locations
The user can get an overview of the genes expressed in the planarian epidermis
Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea.
The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.
The plant ontology as a tool for comparative plant anatomy and genomic analyses.
Planteome uses PO to describe location of tissue expression for genes in viridiplantae
Maize CELL genomics DB uses PO to annotate images
MaizeGDB uses PO for annotation of genes
Introduced in gene model set 5b in assembly version RefGen_v2.
Gramene uses PO for the annotation of plant genes
Gramene annotations to leaf from Arabidopsis
An ontology covering the anatomy of the taxon Porifera (sponges)
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.
An ontological representation of protein-related 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.
Protein Ontology (PRO): enhancing and scaling up the representation of protein entities
Colorado Richly Annotated Full-Text (CRAFT) Corpus; PRO is used for entity tagging and annotation
Cell Ontology is a structured controlled vocabulary for cell types in animals; PRO is used for cell type definitions
A B cell that is CD19-positive (uses the PRO term for non-species-specific CD19 molecule, PR:000001002)
PROCO covers process chemistry, the chemical field concerned with scaling up laboratory syntheses to commercially viable processes.
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.
Radiation Biology Ontology main release in OWL format
Radiation Biology Ontology additional release in OBO format
Radiation Biology Ontology additional release in OBOJSon format
Relationship types shared across multiple ontologies
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
RO is used for annotation extensions in the GO and GO Causal Activity Models.
A method for increasing expressivity of Gene Ontology annotations using a compositional approach
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
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.
A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases.
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)
The Sequence Ontology: a tool for the unification of genome annotations.
Evolution of the Sequence Ontology terms and relationships.
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
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.
Experiment design driven FAIRification of omics data matrices, an exemplar
Semantic concept schema of the linear mixed model of experimental observations
struct (Statistics in R using Class-based Templates), Struct integrates with the STATistics Ontology to ensure consistent reporting and maximizes semantic interoperability
struct: an R/Bioconductor-based framework for standardized metabolomics data analysis and beyond
Scientific Evidence Code System (SEVCO) on the FEvIR platform. The FEvIR Platform includes many Builder Tools to create FHIR Resources without requiring expertise in FHIR or JSON, and Converter Tools to convert structured data to FHIR Resources
Making science computable: Developing code systems for statistics, study design, and risk of bias
The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis
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.
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.
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.
EOSC Co-creation funded project 074: Delivery of a proof of concept for terms4FAIRskills: Technical report
Semaphora integrates terms4FAIRskills, allowing users to annotate training materials with the ontology.
FAIRassist is designed to offer personalised guidance to all stakeholders to enable the discovery of standards and repositories in FAIRsharing, which should be used to make data FAIR, as well as to signpost FAIR assessment resources.
FAIRsFAIR Competence Centre (project wp6) will provide a platform for training materials resulting from project training activities, annot
A vocabulary of taxonomic ranks (species, family, phylum, etc)
The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes
A controlled vocabulary to describe phenotypic traits in plants.
Planteome uses TO to describe traits for genes and germplasm
Genes and proteins annotated to submergence tolerance, including SUB1
Gramene uses PO for the annotation of plant genes and QTLs
Gramene annotations to submergence tolerance
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.
Methods of transmission of human diseases in the DO
methods of transmission of human diseases
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
An integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies
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
Uberon, an integrative multi-species anatomy ontology
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon
Bgee is a database to retrieve and compare gene expression patterns between animal species. Bgee in using Uberon to annotate the site of expression, and Bgee curators one the major contributors to the ontology.
Uberon terms used to annotate expression of human hemoglobin subunit beta
The National Human Genome Research Institute (NHGRI) launched a public research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to identify all functional elements in the human genome sequence. The ENCODE DCC users Uberon to annotate samples
FANTOM5 samples annotated to telencephalon or its parts
GO Database is used for querying for functional annotations relevant to a tissue
GO annotations relevant to the uberon class for brain
The Phenoscape project is both a major driver of and contributor to Uberon, contibuting thousands of terms. The teleost (bony fishes) component of Uberon was derived from the Teleost Anatomy Ontology, developed by the Phenoscape group. Most of the high level design of the skeletal system comes from the Vertebrate Skeletal Anatomy Ontology (VSAO), also created by the Phenoscape group. Phenoscape curators continue to extend the ontology, covering a wide variety of tetrapod structures, with an emphasis on the appendicular system.
Searchable collection of neuroscience data and ontology for neuroscience
cooperative data platform to be used by diverse communities in making data more FAIR.
SCPortalen: human and mouse single-cell centric database
ChEMBL uses Uberon to describe organ/tissue information in assays
ChEMBL: towards direct deposition of bioassay data
Metrical units for use in conjunction with PATO
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.
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.
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 is used by the Monarch Initiative for cross-species inference.
Characteristic neurologic anomaly resulting form degeneration of dopamine-generating cells in the substantia nigra, a region of the midbrain, characterized clinically by shaking, rigidity, slowness of movement and difficulty with walking and gait.
Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names.
Vertebrate Breed Ontology main release in OWL format
Vertebrate Breed Ontology additional release in OBO format
Vertebrate Breed Ontology additional release in OBOJSon format
The Vertebrate Breed Ontology: Toward Effective Breed Data Standardization
VBO is used in the Online Mendelian Inheritance in Animals (OMIA) for breed annotations.
Urticaria pigmentosa affects the Sphynx (Cat) (VBO:0100230) breed.
VBO is used in Cellosaurus for breed/subspecies of origin of cell lines.
The cell line AG07906 derived from the Thoroughbred (VBO:0001083) breed of Equuus caballus (Horse).
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
VIOLIN uses VO to standardize vaccine information
VIOLIN using VO grouped all SARS-CoV-2 vaccines
A specific vaccine ‘Allogeneic Tumor Cell Vaccine’ curated in VO for VIOLIN vaccine record
Vaccine Adjuvant Compendium (VAC) uses Vaccine Ontology to standard vaccine adjuvants developed by NIH
A specific vaccine adjuvant, such as CaPNP (CaPtivant)(TM), in Vaccine Adjuvant Compendium, uses VO_0005295 ‘CaPNP (CaPtivant)(TM) vaccine adjuvant’
ImmPort uses Vaccine Ontology to standardize vaccine recorded collected in NIH funded ImmPort studies
ImmPort data used VO for annotation shown in its dataModel
Human Immunology Project Consortium (HIPC) uses VO to standardize vaccine records
Influenza Vaccine Live, Intranasal used VO_0000044
An ontology of traits covering vertebrates
The Animal Quantitative Trait Loci (QTL) Database (Animal QTLdb) annotates trait mapping data for livestock animals using the VTO
Links to cattle QTL associated with the VTO term gastrointestinal system morphology trait or its descendants
The Rat Genome Database (RGD) uses the VTO to annotate rat QTL
Annotations of rat QTL associated with the VTO term cholesterol amount or its descendants
The Mouse Phenome Database (MPD) uses the VTO to annotate mouse strain traits
Studies in the MPD database that have measurements related to the VTO term spleen size trait or its descendants
Comprehensive hierarchy of extinct and extant vertebrate taxa.
Phenoscape uses VTO to annotate systematics data
A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.
Building a cell and anatomy ontology of Caenorhabditis elegans
WormBase uses WBbt to curate anatomical expression patterns and anatomy function annotations, and to allow search and indexing on the WormBase site
Expression for gene daf-16 with WormBase ID WBGene00000912
WormBase: a modern Model Organism Information Resource
A structured controlled vocabulary of the development of Caenorhabditis elegans.
WormBase uses WBls to curate temporal expression patterns, and to allow search and indexing on the WormBase site
Expression for daf-16 gene with WormBase ID WBGene00000912.
A structured controlled vocabulary of Caenorhabditis elegans phenotypes
Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community.
WormBase uses WBPhenotype to curate worm phenotypes, and to allow search and indexing on the WormBase site
Monarch integrates phenotype annotations from sources such as WormBase, and allows for querying using the WBPhenotype ontology.
Egg long: The fertilized oocytes have a greater than standard length measured end to end compared to control.
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.
Xenbase uses XAO to annotate gene expression.
Xenopus genes expressed in the pronephric kidney.
Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.
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.
Experimental conditions applied to zebrafish, developed to facilitate experiment condition annotation at ZFIN
Zebrafish Experimental Conditions Ontology
A structured controlled vocabulary of the anatomy and development of the Zebrafish
The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio.
Zebrafish anatomy and development ontology
ZFIN uses ZFA to annotate gene expression and phenotype
zebrafish genes expressed in hindbrain and genotypes with hindbrain phenotype
The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism.
Monarch integrates phenotype annotations from sources such as ZFIIN, and allows for querying using the ZP ontology.
adaxial cell absent, abnormal: Abnormal(ly) absent (of) adaxial cell.
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
The Human Phenotype Ontology (HPO) is a structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease.
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
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.
HPO is used by the Monarch Initiative for phenotype annotations.
A classification of algorithms for simulating biology, their parameters, and their outputs
Controlled vocabularies and semantics in systems biology
The Simulation Experiment Description Markup Language (SED-ML) is a language for describing simulations and visualizations of their results.
Several examples of simulations encoded in SED-ML
BioSimulations is a repository of biosimulation projects.
Simulation of a synthetic oscillatory biochemical network
runBioSimulations is a web application for execution biological simulations.
BioSimulators is a registry of biosimulation tools.
tellurium is a software tool for kinetic simulation of biochemical networks
Terms commonly used in Systems Biology, and in particular in computational modeling.
An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease.
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.
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
An ontology is developed to support Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org).
Malaria study data integration and information retrieval based on OBO Foundry ontologies.
The VEuPathDB ontology is used in the VEuPathDB (Eukaryotic Pathogen, Vector & Host Informatics Resources) covers both functional genomics and population biology.
The VEuPathDB ontology is used in the clinical epidemiology resources.
The VEuPathDB ontology is used in the MicrobiomeDB, a systems biology platform for integrating, mining and analyzing microbiome experiments.
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 ontology of prokaryotic phenotypic and metabolic characters
Ontology of Prokaryotic Phenotypic and Metabolic Characters
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
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
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
Foundational Model of Anatomy Ontology (subset)
An application ontology to cover all aspects of malaria as well as the intervention attempts to control it.
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.
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.
An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species
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.
Planteome uses EO to describe traits for genes and germplasm
Genes and proteins annotated to cold temperature regiment
Gramene uses EO for the annotation of plant genes and QTLs
Gramene annotations to cold temperature regiment
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
An ontological version of MIABIS (Minimum Information About BIobank data Sharing)
For the description of covalent bonds in proteins.
SEP developers via the PSI and MSI mailing lists
A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments.
Sample processing and separation techniques
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