ArticleDatabase : the journal of biological databases and curation2021
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.
Article in Database : the journal of biological databases and curation, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 133 papers, 3 of them syntheses that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
133 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Profiling of human lung and gut microbiomes in different conditions of chronic obstructive pulmonary disease using ontology-based evidence synthesis and reasoning.Frontiers in cellular and infection microbiology · 2026Pooled it
- Operational Ontology for Oncology (O3): A Professional Society-Based, Multistakeholder, Consensus-Driven Informatics Standard Supporting Clinical and Research Use of Real-World Data From Patients Treated for Cancer.International journal of radiation oncology, biology, physics · 2023Guideline
- Content and quality of physical activity ontologies: a systematic review.The international journal of behavioral nutrition and physical activity · 2023Pooled it
- Advancing FAIR data towards comparable, organized, predictive AI-ready data for community validation.Communications biology · 2026Review
- ACCELERATE-BASSO: early experiences and emerging best practices for ontology development in behavioral and social science research.Journal of biomedical semantics · 2026Article
- VO: The Vaccine Ontology.Scientific data · 2026Article
- Representing dental caries and dysbiosis within the oral microbiome in the Oral Health and Disease Ontology.Journal of biomedical semantics · 2026Article
- The Cell Ontology in the age of single-cell omics.Scientific data · 2026Article
- Representing dental restoration materials in the oral health and disease ontology.Journal of biomedical semantics · 2026Article
- Mondo: integrating disease terminology across communities.Genetics · 2026Article
- A stage and anatomy ontology for embryogenesis in indirect-developing echinoderms.Development (Cambridge, England) · 2026Article
- Advancing the bioassay ontology through integrated PK/PD and safety pharmacology representation.Journal of biomedical semantics · 2026Article
- Application of in vitro to in vivo extrapolation (IVIVE) to inform chemical health guidance value derivation-sample case studies comparing neuro-, hepato-, and developmental toxicities.Toxicological sciences : an official journal of the Society of Toxicology · 2026Article
- Lessons learned on stakeholder engagement in radiation protection, and communication and dissemination of results from the radonorm project.Radiation and environmental biophysics · 2026Article
- pyBiodatafuse: extending interoperability of data using modular queries across biomedical resources.Bioinformatics (Oxford, England) · 2026Article
- SPHN Connector - a scalable pipeline for generating validated knowledge graphs from federated and semantically enriched health data.BMC medical informatics and decision making · 2026Article
- Assessing the effectiveness of ontology-grounded AI term extraction using OntoGPT for environmental evidence synthesis.Environmental evidence · 2026Article
- LinkML: an open data modeling framework.GigaScience · 2026Article
- Improving annotation, access, and comparison of nutritional composition data for underutilized crops.Database : the journal of biological databases and curation · 2026Article
- The Ontology of Adverse Events in 2025.Scientific data · 2026Article
73 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
25 authors.
Funding
Abstract
Biological ontologies are used to organize, curate and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies (OBO) Foundry was created to address this by facilitating the development, harmonization, application and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here, we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology's compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable, federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data Findable, Accessible, Interoperable, and Reusable (FAIR). Database URL http://obofoundry.org/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.