Known Ontology Project Publications

Agronomy Ontology (agro)

• Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics.

Ascomycete phenotype ontology (apo)

• New mutant phenotype data curation system in the Saccharomyces Genome Database

Apollo Structured Vocabulary (apollo_sv)

• The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation

Antibiotic Resistance Ontology (aro)

• CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.

Biological Collections Ontology (bco)

• Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies

Biological Spatial Ontology (bspo)

• Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.

BRENDA tissue / enzyme source (bto)

• The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources

Comparative Data Analysis Ontology (cdao)

• Initial Implementation of a Comparative Data Analysis Ontology

Compositional Dietary Nutrition Ontology (cdno)

• Establishing a Common Nutritional Vocabulary - From Food Production to Diet

Chemical Entities of Biological Interest (chebi)

• ChEBI in 2016: Improved services and an expanding collection of metabolites.

Chemical Information Ontology (cheminf)

• The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web

CHEBI Integrated Role Ontology (chiro)

• Extension of Roles in the ChEBI Ontology

Coronavirus Infectious Disease Ontology (cido)

• A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology

Confidence Information Ontology (cio)

• The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations

Cell Ontology (cl)

• The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.

Cell Line Ontology (clo)

• CLO: The Cell Line Ontology

Clinical measurement ontology (cmo)

• Three ontologies to define phenotype measurement data.
• The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.

Dictyostelium discoideum anatomy (ddanat)

• An anatomy ontology to represent biological knowledge in Dictyostelium discoideum

Dictyostelium discoideum phenotype ontology (ddpheno)

• dictyBase and the Dicty Stock Center (version 2.0) - a progress report

Human Disease Ontology (doid)

• Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data
• The Human Disease Ontology 2022 update

Drosophila Phenotype Ontology (dpo)

• The Drosophila phenotype ontology.

The Drug Ontology (dron)

• Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request

Evidence and Conclusion Ontology (eco)

• 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)

Mouse Developmental Anatomy Ontology (emapa)

• 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)

Environment Ontology (envo)

• The environment ontology: contextualising biological and biomedical entities
• The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation

Drosophila gross anatomy (fbbt)

• The Drosophila anatomy ontology
• A strategy for building neuroanatomy ontologies
• The Virtual Fly Brain Browser and Query Interface
• FlyBase: anatomical data, images and queries

Flora Phenotype Ontology (flopo)

• The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants

Food-Biomarker Ontology (fobi)

• FOBI: an ontology to represent food intake data and associate it with metabolomic data
• The fobitools framework: the first steps towards food enrichment analysis

Food Ontology (foodon)

• FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration

Fission Yeast Phenotype Ontology (fypo)

• FYPO: The Fission Yeast Phenotype Ontology.

Glycan Naming and Subsumption Ontology (GNOme) (gno)

• GNOme - Glycan Naming and Subsumption Ontology

Gene Ontology (go)

• Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
• The Gene Ontology resource: enriching a GOld mine

Human Ancestry Ontology (hancestro)

• A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog

Hymenoptera Anatomy Ontology (hao)

• A gross anatomy ontology for hymenoptera

Homology Ontology (hom)

• An ontology to clarify homology-related concepts

Integrative and Conjugative Element Ontology (iceo)

• ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements

Infectious Disease Ontology (ido)

• The Infectious Disease Ontology in the age of COVID-19

Interaction Network Ontology (ino)

• Development and application of an Interaction Network Ontology for literature mining of vaccine-associated gene-gene interactions

clinical LABoratory Ontology (labo)

• LABO: An Ontology for Laboratory Test Prescription and Reporting

Model Card Report Ontology (mcro)

• Toward a standard formal semantic representation of the model card report

MIAPA Ontology (miapa)

• Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)

Measurement method ontology (mmo)

• Three ontologies to define phenotype measurement data.
• The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.

Protein modification (mod)

• The PSI-MOD community standard for representation of protein modification data

Mondo Disease Ontology (mondo)

• Mondo: Unifying diseases for the world, by the world

Mammalian Phenotype Ontology (mp)

• The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data

Mass spectrometry ontology (ms)

• The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.

Neuro Behavior Ontology (nbo)

• Analyzing gene expression data in mice with the Neuro Behavior Ontology

Ontology of Biological Attributes (oba)

• The Ontology of Biological Attributes (OBA) - computational traits for the life sciences

Ontology for Biomedical Investigations (obi)

• The Ontology for Biomedical Investigations

Ontology for General Medical Science (ogms)

• Toward an ontological treatment of disease and diagnosis
• Biomarkers in the Ontology for General Medical Science

Oral Health and Disease Ontology (ohd)

• Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology

Ontology of Host Pathogen Interactions (ohpi)

• Victors: a web-based knowledge base of virulence factors in human and animal pathogens

Ontology of Microbial Phenotypes (omp)

• An ontology for microbial phenotypes

Ontology for Modeling and Representation of Social Entities (omrse)

• The ontology of medically related social entities: recent developments

Ontology for Nutritional Studies (ons)

• ONS: an ontology for a standardized description of interventions and observational studies in nutrition

OntoAvida: ontology for Avida digital evolution platform (ontoavida)

• Ontology for the Avida digital evolution platform

Phenotype And Trait Ontology (pato)

• The anatomy of phenotype ontologies: principles, properties and applications
• Using ontologies to describe mouse phenotypes

The Prescription of Drugs Ontology (pdro)

• The Prescription of Drug Ontology 2.0 (PDRO): More Than the Sum of Its Parts

Plant Experimental Conditions Ontology (peco)

• The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.

Pathogen Host Interaction Phenotype Ontology (phipo)

• PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions

planaria-ontology (plana)

• Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms

Plant Ontology (po)

• The plant ontology as a tool for comparative plant anatomy and genomic analyses.
• The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.

Porifera Ontology (poro)

• The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology

PRotein Ontology (PRO) (pr)

• Protein Ontology (PRO): enhancing and scaling up the representation of protein entities

Plant Stress Ontology (pso)

• The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.

Pathway ontology (pw)

• The Rat Genome Database pathway portal.
• The pathway ontology - updates and applications.

Rat Strain Ontology (rs)

• Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD.

Sequence types and features ontology (so)

• The Sequence Ontology: a tool for the unification of genome annotations.
• Evolution of the Sequence Ontology terms and relationships.

Spider Ontology (spd)

• The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with Cross-Disciplinary Data

The Statistical Methods Ontology (stato)

• Experiment design driven FAIRification of omics data matrices, an exemplar
• Semantic concept schema of the linear mixed model of experimental observations

Software ontology (swo)

• The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation

Symptom Ontology (symp)

• GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database
• The Human Disease Ontology 2022 update

terms4FAIRskills (t4fs)

• EOSC Co-creation funded project 074: Delivery of a proof of concept for terms4FAIRskills: Technical report

Taxonomic rank vocabulary (taxrank)

• The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes

Plant Trait Ontology (to)

• The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.

Pathogen Transmission Ontology (trans)

• GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database
• The Human Disease Ontology 2022 update

Teleost taxonomy ontology (tto)

• The Teleost Taxonomy Ontology

Toxic Process Ontology (txpo)

• Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management

Uberon multi-species anatomy ontology (uberon)

• Uberon, an integrative multi-species anatomy ontology
• Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

Units of measurement ontology (uo)

• The Units Ontology: a tool for integrating units of measurement in science

Unified phenotype ontology (uPheno) (upheno)

• 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

Vaccine Ontology (vo)

• 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

Vertebrate Taxonomy Ontology (vto)

• The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes

C. elegans Gross Anatomy Ontology (wbbt)

• Building a cell and anatomy ontology of Caenorhabditis elegans

C. elegans development ontology (wbls)

• WormBase: a modern Model Organism Information Resource

C. elegans phenotype (wbphenotype)

• Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community.

Xenopus Anatomy Ontology (xao)

• 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.

Experimental condition ontology (xco)

• Three ontologies to define phenotype measurement data.
• The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.

Xenopus Phenotype Ontology (xpo)

• The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development.

Zebrafish anatomy and development ontology (zfa)

• The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio.

Human Phenotype Ontology (hp)

• 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.

Kinetic Simulation Algorithm Ontology (kisao)

• Controlled vocabularies and semantics in systems biology

Sickle Cell Disease Ontology (scdo)

• 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.

Variation Ontology (vario)

• Variation Ontology for annotation of variation effects and mechanisms
• Variation ontology: annotator guide
• Types and effects of protein variations

VEuPathDB ontology (eupath)

• Malaria study data integration and information retrieval based on OBO Foundry ontologies.

Human developmental anatomy, abstract (ehdaa2)

• A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20).

Foundational Model of Anatomy Ontology (subset) (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

Unipathway (upa)

• UniPathway: a resource for the exploration and annotation of metabolic pathways

The Drug-Drug Interactions Ontology (dinto)

• DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug–Drug Interactions and Their Mechanisms.

Plant Environment Ontology (eo)

• Ontologies as integrative tools for plant science.

Teleost Anatomy Ontology (tao)

• The teleost anatomy ontology: anatomical representation for the genomics age