Publications Related to the OBO Foundry
Citing the OBO Foundry
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies (2021).
Rebecca Jackson, Nicolas Matentzoglu, James A Overton, Randi Vita, James P Balhoff, Pier Luigi Buttigieg, Seth Carbon, Melanie Courtot, Alexander D Diehl, Damion M Dooley, William D Duncan, Nomi L Harris, Melissa A Haendel, Suzanna E Lewis, Darren A Natale, David Osumi-Sutherland, Alan Ruttenberg, Lynn M Schriml, Barry Smith, Christian J Stoeckert Jr., Nicole A Vasilevsky, Ramona L Walls, Jie Zheng, Christopher J Mungall, Bjoern Peters. Database, Volume 2021, baab069, https://doi.org/10.1093/database/baab069
Other papers about the OBO Foundry
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J Mungall, The OBI Consortium, Neocles Leontis, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H Scheuermann, Nigam Shah, Patricia L Whetzel, and Suzanna Lewis
Nature Biotechnology 25, 1251 - 1255 (2007)
Google Scholar list of papers citing The OBO Foundry
Some Ontology Project Publications (not a complete list)
- 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): Knowledge representation and data sharing to unlock crop variation for nutritional food security
- 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.
- Clinical measurement ontology (cmo): 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
- Human Disease Ontology (doid): 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 ontology (eco): ECO: the Evidence and Conclusion Ontology, an update for 2022.
- Evidence ontology (eco): ECO, the Evidence & Conclusion Ontology: community standard for evidence information.
- Evidence ontology (eco): 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
- Mouse Developmental Anatomy Ontology (emapa): EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update
- Mouse Developmental Anatomy Ontology (emapa): Mouse Anatomy Ontologies: Enhancements and Tools for Exploring and Integrating Biomedical Data
- Mouse Developmental Anatomy Ontology (emapa): 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
- Environment Ontology (envo): The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation
- VEuPathDB ontology (eupath): Malaria study data integration and information retrieval based on OBO Foundry ontologies.
- Drosophila gross anatomy (fbbt): The Drosophila anatomy ontology
- Drosophila gross anatomy (fbbt): A strategy for building neuroanatomy ontologies
- Drosophila gross anatomy (fbbt): The Virtual Fly Brain Browser and Query Interface
- Drosophila gross anatomy (fbbt): 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
- Food-Biomarker Ontology (fobi): 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
- Gene Ontology (go): 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.
- Measurement method ontology (mmo): 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
- Ontology for General Medical Science (ogms): 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 of Medically Related 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
- Phenotype And Trait Ontology (pato): 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.
- Plant Ontology (po): 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.
- Pathway ontology (pw): 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.
- Sequence types and features ontology (so): 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
- 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
- Symptom Ontology (symp): 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
- Pathogen Transmission Ontology (trans): 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
- Uberon multi-species anatomy ontology (uberon): 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
- Unified phenotype ontology (uPheno) (upheno): 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
- Vaccine Ontology (vo): 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.
- Xenopus Anatomy Ontology (xao): 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.
- Experimental condition ontology (xco): 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.
- Human Phenotype Ontology (hp): The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.
- Human Phenotype Ontology (hp): The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.
- Human Phenotype Ontology (hp): 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.
- Sickle Cell Disease Ontology (scdo): The Sickle Cell Disease Ontology: Enabling Collaborative Research and Co-Designing of New Planetary Health Applications.
- Sickle Cell Disease Ontology (scdo): 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 (vario): Variation ontology: annotator guide
- Variation Ontology (vario): Types and effects of protein variations
- 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
- Foundational Model of Anatomy Ontology (subset) (fma): The foundational model of anatomy in OWL: Experience and perspectives
- Foundational Model of Anatomy Ontology (subset) (fma): 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