Publications Related to the OBO Foundry

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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.
• Antibiotic Resistance Ontology (aro): CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance 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
• Ascomycete phenotype ontology (apo): New mutant phenotype data curation system in the Saccharomyces Genome Database
• BRENDA tissue / enzyme source (bto): The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources
• Biological Spatial Ontology (bspo): Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.
• 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.
• CHEBI Integrated Role Ontology (chiro): Extension of Roles in the ChEBI Ontology
• Cell Line Ontology (clo): CLO: The Cell Line Ontology
• Cell Ontology (cl): The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.
• 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
• Clinical measurement ontology (cmo): Three ontologies to define phenotype measurement data.
• 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
• 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
• Drosophila Phenotype Ontology (dpo): The Drosophila phenotype ontology.
• Drosophila gross anatomy (fbbt): The Drosophila anatomy ontology
• Environment Ontology (envo): The environment ontology: contextualising biological and biomedical entities
• Evidence ontology (eco): ECO, the Evidence & Conclusion Ontology: community standard for evidence information.
• Experimental condition ontology (xco): Three ontologies to define phenotype measurement data.
• Fission Yeast Phenotype Ontology (fypo): FYPO: The Fission Yeast Phenotype Ontology.
• Flora Phenotype Ontology (flopo): The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants
• Food Ontology (foodon): FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration
• Food-Biomarker Ontology (fobi): FOBI: an ontology to represent food intake data and associate it with metabolomic data
• Foundational Model of Anatomy Ontology (subset) (fma): Translating the Foundational Model of Anatomy into OWL
• Gene Ontology (go): Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
• Glycan Naming and Subsumption Ontology (GNOme) (gno): GNOme - Glycan Naming and Subsumption Ontology
• Human Ancestry Ontology (hancestro): A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog
• Human Disease Ontology (doid): Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data
• Human Phenotype Ontology (hp): The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease.
• Human developmental anatomy, abstract (ehdaa2): A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20).
• Hymenoptera Anatomy Ontology (hao): A gross anatomy ontology for hymenoptera
• Kinetic Simulation Algorithm Ontology (kisao): Controlled vocabularies and semantics in systems biology
• 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.
• Measurement method ontology (mmo): Three ontologies to define phenotype measurement data.
• Mondo Disease Ontology (mondo): Mondo: Unifying diseases for the world, by the world
• Neuro Behavior Ontology (nbo): Analyzing gene expression data in mice with the Neuro Behavior Ontology
• Ontology for Biomedical Investigations (obi): The Ontology for Biomedical Investigations
• Ontology for Nutritional Studies (ons): ONS: an ontology for a standardized description of interventions and observational studies in nutrition
• Ontology of Medically Related Social Entities (omrse): The ontology of medically related social entities: recent developments
• PRotein Ontology (PRO) (pr): Protein Ontology (PRO): enhancing and scaling up the representation of protein entities
• Pathogen Host Interaction Phenotype Ontology (phipo): PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions
• Pathogen Transmission Ontology (trans): GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database
• Pathway ontology (pw): The Rat Genome Database pathway portal.
• Phenotype And Trait Ontology (pato): The anatomy of phenotype ontologies: principles, properties and applications
• Plant Environment Ontology (eo): Ontologies as integrative tools for plant science.
• Plant Experimental Conditions Ontology (peco): The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.
• Plant Ontology (po): The plant ontology as a tool for comparative plant anatomy and genomic analyses.
• Plant Stress Ontology (pso): The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.
• Plant Trait Ontology (to): 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 modification (mod): The PSI-MOD community standard for representation of protein modification data
• 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.
• Sickle Cell Disease Ontology (scdo): The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation.
• Software ontology (swo): The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation
• Spider Ontology (spd): The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with Cross-Disciplinary Data
• Symptom Ontology (symp): GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database
• Taxonomic rank vocabulary (taxrank): The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes
• Teleost Anatomy Ontology (tao): The teleost anatomy ontology: anatomical representation for the genomics age
• Teleost taxonomy ontology (tto): The Teleost Taxonomy 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
• The Drug-Drug Interactions Ontology (dinto): DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug–Drug Interactions and Their Mechanisms.
• The Prescription of Drugs Ontology (pdro): The Prescription of Drug Ontology 2.0 (PDRO): More Than the Sum of Its Parts
• 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
• Unified phenotype ontology (uPheno) (upheno): Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species
• Unipathway (upa): UniPathway: a resource for the exploration and annotation of metabolic pathways
• Units of measurement ontology (uo): The Units Ontology: a tool for integrating units of measurement in science
• VEuPathDB ontology (eupath): Malaria study data integration and information retrieval based on OBO Foundry ontologies.
• Vaccine Ontology (vo): Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses
• Vertebrate Taxonomy Ontology (vto): The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes
• Xenopus Anatomy Ontology (xao): An ontology for Xenopus anatomy and development.
• 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.
• clinical LABoratory Ontology (labo): LABO: An Ontology for Laboratory Test Prescription and Reporting
• planaria-ontology (plana): Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms